diff --git a/examples/output/README.md b/examples/output/README.md deleted file mode 100644 index 8eddbbfd..00000000 --- a/examples/output/README.md +++ /dev/null @@ -1,2611 +0,0 @@ -## SampleData-jgi_mg_data-in-tube -### Input -```yaml -jgi_mg_data: -- analysis_type: - - metagenomics - - metatranscriptomics - dna_concentration: 1.23 - dna_cont_type: tube - dna_container_id: xxx - dna_dnase: 'no' - dna_isolate_meth: xxx - dna_project_contact: xxx - dna_samp_id: xxx - dna_sample_format: DNAStable - dna_sample_name: xxx - dna_seq_project: xxx - dna_seq_project_name: xxx - dna_seq_project_pi: xxx - dna_volume: 111 - proposal_dna: xxx - samp_name: xxx - source_mat_id: x:1 - -``` -## SampleData-soil-data-minimal -### Input -```yaml -soil_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: 0 - 1 - elev: 123 - env_broad_scale: ______urban biome [ENVO:01000249] - env_local_scale: ________tunnel [ENVO:00000068] - env_medium: bare soil [ENVO:01001616] - env_package: soil - geo_loc_name: 'USA: Nowhere, Oklahoma' - growth_facil: greenhouse - lat_lon: 35.211445 -98.464612 - samp_name: b - samp_store_temp: -80 Celsius - store_cond: frozen - -``` -## SampleData-water-data-exhaustive-max-generic -### Input -```yaml -water_data: -- alkalinity: 100 units - alkalinity_method: xyz - alkyl_diethers: 100 units - aminopept_act: 100 units - ammonium: 100 units - analysis_type: - - metagenomics - - metatranscriptomics - atmospheric_data: xyz;100 units - bac_prod: 100 units - bac_resp: 100 units - bacteria_carb_prod: 100 units - biomass: xyz;100 units - bishomohopanol: 100 units - bromide: 100 units - calcium: 100 units - carb_nitro_ratio: 1.5 - chem_administration: xyz [XYZ:123];2111-11-11 - chloride: 100 units - chlorophyll: 100 units - collection_date: '2021-01-01' - conduc: 100 units - density: 100 units - depth: '1.5' - diether_lipids: xyz;100 units - diss_carb_dioxide: 100 units - diss_hydrogen: 100 units - diss_inorg_carb: 100 units - diss_inorg_nitro: 100 units - diss_inorg_phosp: 100 units - diss_org_carb: 100 units - diss_org_nitro: 100 units - diss_oxygen: 100 units - down_par: 100 units - ecosystem: xyz - ecosystem_category: xyz - ecosystem_subtype: xyz - ecosystem_type: xyz - elev: 1.5 - env_broad_scale: xyz xyz xyz [XYZ:123] - env_local_scale: xyz xyz xyz [XYZ:123] - env_medium: xyz xyz xyz [XYZ:123] - env_package: xyz - experimental_factor: xyz xyz xyz [XYZ:123] - fluor: 100 units - geo_loc_name: 'xyz: xyz, xyz' - glucosidase_act: 100 units - horizon_meth: xyz - lat_lon: 78 89 - light_intensity: 100 units - mean_frict_vel: 100 units - mean_peak_frict_vel: 100 units - misc_param: xyz;100 units - n_alkanes: xyz;100 units - nitrate: 100 units - nitrite: 100 units - nitro: 100 units - org_carb: 100 units - org_matter: 100 units - org_nitro: 100 units - organism_count: xyz;100 units;qPCR - oxy_stat_samp: anaerobic - part_org_carb: 100 units - part_org_nitro: 100 units - perturbation: xyz - petroleum_hydrocarb: 100 units - ph: 1.5 - ph_meth: xyz - phaeopigments: xyz;100 units - phosphate: 100 units - phosplipid_fatt_acid: xyz;100 units - potassium: 100 units - pressure: 100 units - primary_prod: 100 units - redox_potential: 100 units - salinity: 100 units - samp_collec_device: xyz - samp_collec_method: xyz - samp_mat_process: text [ONTO:000000000] - samp_name: xyz - samp_size: 100 units - samp_store_dur: xyz - samp_store_loc: xyz - samp_store_temp: 100 units - sample_link: z:99 - silicate: 100 units - size_frac: xyz - size_frac_low: 100 units - size_frac_up: 100 units - sodium: 100 units - soluble_react_phosp: 100 units - source_mat_id: x:1 - specific_ecosystem: xyz - sulfate: 100 units - sulfide: 100 units - suspend_part_matter: 100 units - temp: 100 units - tidal_stage: high tide - tot_depth_water_col: 100 units - tot_diss_nitro: 100 units - tot_inorg_nitro: 100 units - tot_nitro: 100 units - tot_part_carb: 100 units - turbidity: 100 units - water_current: 100 units - -``` -## SampleData-jgi_mt_data_exhaustive -### Input -```yaml -jgi_mt_data: -- analysis_type: - - metatranscriptomics - dnase_rna: 'no' - proposal_rna: '504000' - rna_absorb1: 2.02 - rna_absorb2: 1.4 - rna_concentration: 100.3 - rna_cont_type: plate - rna_cont_well: H7 - rna_container_id: cat_ht_1999 - rna_isolate_meth: phenol/cloroform extraction - rna_project_contact: Leslie Ann Levine - rna_samp_id: '123456' - rna_sample_format: MDA reaction buffer - rna_sample_name: JGI_lagoon_14343 - rna_seq_project: '123456789' - rna_seq_project_name: JGI Lagoon metatranscritpomics - rna_seq_project_pi: Patty Smith - rna_volume: 25.1 - samp_name: sample name - source_mat_id: MPI:012345 - -``` -## SampleData-jgi_mg_data-exhaustive -### Input -```yaml -jgi_mg_data: -- analysis_type: - - metagenomics - - metatranscriptomics - dna_absorb1: 1.23 - dna_absorb2: 1.23 - dna_concentration: 1.23 - dna_cont_type: plate - dna_cont_well: C3 - dna_container_id: xxx - dna_dnase: 'no' - dna_isolate_meth: xxx - dna_project_contact: xxx - dna_samp_id: xxx - dna_sample_format: DNAStable - dna_sample_name: xxx - dna_seq_project: xxx - dna_seq_project_name: xxx - dna_seq_project_pi: xxx - dna_volume: 33 - proposal_dna: xxx - samp_name: xxx - source_mat_id: x:1 - -``` -## SampleData-emsl_data-minimal -### Input -```yaml -emsl_data: -- analysis_type: - - metagenomics - - metatranscriptomics - emsl_store_temp: -80 - project_id: xxx - samp_name: xxx - sample_shipped: 100 units - sample_type: soil - -``` -## SampleData-plant-assoc-min -### Input -```yaml -plant_associated_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2021-01-01' - depth: '111' - elev: 111 - env_broad_scale: Code Generation [OP:8888] - env_local_scale: Code Generation [OP:8888] - env_medium: Code Generation [OP:8888] - env_package: plant-associated - geo_loc_name: 'USA: Philadelphia, Pennsylvania' - growth_facil: field - lat_lon: 77 88 - samp_name: our first houseplant is dying - samp_store_temp: 20 C - source_mat_id: example:plant_associated_data001 - -``` -## SampleData-water-data-exhaustive -### Input -```yaml -water_data: -- alkalinity: 50 milligram per liter - alkalinity_method: titration - alkyl_diethers: 0.005 mole per liter - aminopept_act: 0.269 mole per liter per hour - ammonium: 1.5 milligram per liter - analysis_type: - - metagenomics - - metatranscriptomics - atmospheric_data: wind speed;9 knots|rain;2.3 inches - bac_prod: 5 milligram per cubic meter per day - bac_resp: 300 micromole oxygen per liter per hour - bacteria_carb_prod: 2.53 microgram per liter per hour - biomass: total;20 gram|archeal;1 gram - bishomohopanol: 14 microgram per liter - bromide: 0.05 parts per million - calcium: 0.2 micromole per liter - carb_nitro_ratio: 1.5 - chem_administration: agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22 - chloride: 5000 milligram per liter - chlorophyll: 5 milligram per cubic meter - collection_date: '2021-01-01' - conduc: 10 milliSiemens per centimeter - density: 1000 kilogram per cubic meter - depth: '1.5' - diether_lipids: phosphatidylglycerol;1.5 parts per million|phosphatidylglycerylsulphate;1.5 - parts per million - diss_carb_dioxide: 5 milligram per liter - diss_hydrogen: 0.3 micromole per liter - diss_inorg_carb: 2059 micromole per liter - diss_inorg_nitro: 761 micromole per liter - diss_inorg_phosp: 56.5 micromole per liter - diss_org_carb: 205.9 micromole per liter - diss_org_nitro: 76.1 micromole per liter - diss_oxygen: 175 micromole per liter - down_par: 28.71 microEinstein per square meter per second - ecosystem: xyz - ecosystem_category: xyz - ecosystem_subtype: xyz - ecosystem_type: xyz - elev: 1.5 - env_broad_scale: oceanic epipelagic zone biome [ENVO:01000033] - env_local_scale: sand [ONTO:1234] - env_medium: sand [ONTO:1234] - env_package: xyz - experimental_factor: time series design [EFO:0001779] - fluor: 2.5 volts - geo_loc_name: 'USA: Maryland, Bethesda' - glucosidase_act: 5 mol per liter per hour - horizon_meth: xyz - lat_lon: 78 89 - light_intensity: 0.3 lux - mean_frict_vel: 0.5 meter per second - mean_peak_frict_vel: 1 meter per second - misc_param: Bicarbonate ion concentration;2075 micromole per kilogram|Perchlorate - ion concentration;1111 micromole per kilogram - n_alkanes: n-hexadecane;100 milligram per liter|n-octane;111 milligram per liter - nitrate: 65 micromole per liter - nitrite: 0.5 micromole per liter - nitro: 4.2 micromole per liter - org_carb: 1.5 microgram per liter - org_matter: 1.75 milligram per cubic meter - org_nitro: 4 micromole per liter - organism_count: total prokaryotes;3.5e7 cells per milliliter;qPCR|total prokaryotes;1e5 - CFU;MPN - oxy_stat_samp: anaerobic - part_org_carb: 1.92 micromole per liter - part_org_nitro: 0.3 micromole per liter - perturbation: xyz1|xyz2 - petroleum_hydrocarb: 0.05 micromole per liter - ph: 1.5 - ph_meth: xyz - phaeopigments: phaeopigment 1;1.5 parts per million|phaeopigment 2;1.5 parts per - million - phosphate: 0.7 micromole per liter - phosplipid_fatt_acid: Tuberculostearic acid;1.5 parts per million|Palmitoleic acid;1.5 - parts per million - photon_flux: 3.926 micromole photons per second per square meter - potassium: 463 milligram per liter - pressure: 50 atmosphere - primary_prod: 100 milligram per cubic meter per day - redox_potential: 300 millivolt - salinity: 25 practical salinity unit - samp_collec_device: xyz - samp_collec_method: xyz - samp_mat_process: text [ONTO:000000000] - samp_name: xyz - samp_size: 5 liter - samp_store_dur: xyz - samp_store_loc: xyz - samp_store_temp: -80 degree Celsius - sample_link: z:99 - silicate: 0.05 micromole per liter - size_frac: xyz - size_frac_low: 0.2 micrometer - size_frac_up: 20 micrometer - sodium: 10.5 milligram per liter - soluble_react_phosp: 0.1 milligram per liter - source_mat_id: x:1 - specific_ecosystem: xyz - sulfate: 5 micromole per liter - sulfide: 2 micromole per liter - suspend_part_matter: 0.5 milligram per liter - temp: 25 degree Celsius - tidal_stage: high tide - tot_depth_water_col: 500 meter - tot_diss_nitro: 40 microgram per liter - tot_inorg_nitro: 40 microgram per liter - tot_nitro: 50 micromole per liter - tot_part_carb: 35 micromole per liter - turbidity: 0.3 nephelometric turbidity units - water_current: 10 cubic meter per second - -``` -## SampleData-soil-data-exhaustive -### Input -```yaml -soil_data: -- air_temp_regm: xxx - al_sat_meth: xxx - analysis_type: - - metagenomics - - metatranscriptomics - annual_precpt: 111 units - annual_temp: 111 units - biotic_regm: xxx - biotic_relationship: free living - carb_nitro_ratio: 0.5 - chem_administration: agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22 - climate_environment: xxx - collection_date: '2022-01-15' - collection_date_inc: '2022-01-22' - collection_time: '11:11' - collection_time_inc: '11:11' - crop_rotation: xxx - cur_land_use: cities - cur_vegetation: xxx - cur_vegetation_meth: xxx - depth: 0 - 1 - drainage_class: well - ecosystem: Environmental - ecosystem_category: Terrestrial - ecosystem_subtype: Unclassified - ecosystem_type: Soil - elev: 123 - env_broad_scale: ______urban biome [ENVO:01000249] - env_local_scale: ________tunnel [ENVO:00000068] - env_medium: bare soil [ENVO:01001616] - env_package: soil - experimental_factor: xxx [ENVO:00000000] - experimental_factor_other: xxx - extreme_event: xxx - fao_class: Rankers - filter_method: xxx - fire: '2022-01-15' - flooding: xxx - gaseous_environment: xxx - geo_loc_name: 'USA: Maryland, Bethesda' - growth_facil: greenhouse - heavy_metals_meth: xxx - horizon_meth: xxx - humidity_regm: xxx - isotope_exposure: strontium 90 [ONTO:00000000]; 2010-10-31T08:45:15.432-0700 - lat_lon: 77 88 - light_regm: incandescant light;10 lux;450 nanometer - link_class_info: xxx - link_climate_info: xxx - local_class: xxx - local_class_meth: xxx - micro_biomass_c_meth: xxx - micro_biomass_meth: xxx - micro_biomass_n_meth: xxx - microbial_biomass: 111 units - microbial_biomass_c: 111 units - microbial_biomass_n: 111 units - non_microb_biomass: xxx;123.45 units - non_microb_biomass_method: xxx - org_matter: 111 units - org_nitro: 111 units - org_nitro_method: xxx - other_treatment: xxx - oxy_stat_samp: anaerobic - ph: 9 - ph_meth: xxx - phosphate: 111 units - prev_land_use_meth: xxx - previous_land_use: circus tent;+0530 - profile_position: summit - salinity: 111 units - salinity_meth: xxx - samp_collec_device: xxx - samp_collec_method: xxx - samp_mat_process: text [ONTO:000000000] - samp_name: a - samp_size: 111 units - samp_store_temp: -80 Celsius - sample_link: z:99 - season_precpt: 111 units - season_temp: 111 units - sieving: xxx - size_frac_low: 99 units - size_frac_up: 111 units - slope_aspect: 100 units - slope_gradient: 111 units - soil_horizon: O horizon - soil_text_measure: 111 units - soil_texture_meth: xxx - soil_type: xxx [ENVO:00000000] - soil_type_meth: xxx - source_mat_id: x:1 - specific_ecosystem: Unclassified - start_date_inc: '2022-02-15' - start_time_inc: '13:33:55' - store_cond: frozen - temp: 111 units - tillage: - - drill - - chisel - tot_carb: 111 units - tot_nitro_cont_meth: xxx - tot_nitro_content: 111 units - tot_org_c_meth: xxx - tot_org_carb: 111 units - tot_phosp: 111 units - water_cont_soil_meth: xxx - water_content: 111 units - watering_regm: xxx -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: 0 - 1 - ecosystem: Environmental - ecosystem_category: Terrestrial - ecosystem_subtype: Unclassified - ecosystem_type: Soil - elev: 123 - env_broad_scale: ______urban biome [ENVO:01000249] - env_local_scale: ________tunnel [ENVO:00000068] - env_medium: bare soil [ENVO:01001616] - env_package: soil - geo_loc_name: 'USA: Maryland, Bethesda' - growth_facil: greenhouse - lat_lon: 77 88 - samp_name: b - samp_store_temp: -80 Celsius - sample_link: z:99 - slope_aspect: 100 units - source_mat_id: x:2 - specific_ecosystem: Unclassified - store_cond: frozen - -``` -## SampleData-jgi_mt_data-minimal -### Input -```yaml -jgi_mt_data: -- analysis_type: - - metatranscriptomics - dnase_rna: 'no' - proposal_rna: '504000' - rna_concentration: 100.3 - rna_cont_type: plate - rna_cont_well: H7 - rna_container_id: cat_ht_1999 - rna_isolate_meth: phenol/cloroform extraction - rna_project_contact: Leslie Ann Levine - rna_samp_id: '123456' - rna_sample_format: MDA reaction buffer - rna_sample_name: JGI_lagoon_14343 - rna_seq_project: '123456789' - rna_seq_project_name: JGI Lagoon metatranscritpomics - rna_seq_project_pi: Patty Smith - rna_volume: 25.1 - samp_name: sample name - source_mat_id: MPI:012345 - -``` -## SampleData-soil-data-depth-formats -### Input -```yaml -soil_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: 10.4-45.9999 - elev: 123 - env_broad_scale: ______urban biome [ENVO:01000249] - env_local_scale: ________tunnel [ENVO:00000068] - env_medium: bare soil [ENVO:01001616] - env_package: soil - geo_loc_name: 'USA: Nowhere, Oklahoma' - growth_facil: greenhouse - lat_lon: 35.211445 -98.464612 - samp_name: b - samp_store_temp: -80 Celsius - source_mat_id: x:6 - store_cond: frozen -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: 10.4 - 45.9999 - elev: 123 - env_broad_scale: ______urban biome [ENVO:01000249] - env_local_scale: ________tunnel [ENVO:00000068] - env_medium: bare soil [ENVO:01001616] - env_package: soil - geo_loc_name: 'USA: Nowhere, Oklahoma' - growth_facil: greenhouse - lat_lon: 35.211445 -98.464612 - samp_name: b - samp_store_temp: -80 Celsius - source_mat_id: x:7 - store_cond: frozen -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: -10.4 - 45.9999 - elev: 123 - env_broad_scale: ______urban biome [ENVO:01000249] - env_local_scale: ________tunnel [ENVO:00000068] - env_medium: bare soil [ENVO:01001616] - env_package: soil - geo_loc_name: 'USA: Nowhere, Oklahoma' - growth_facil: greenhouse - lat_lon: 35.211445 -98.464612 - samp_name: b - samp_store_temp: -80 Celsius - source_mat_id: x:8 - store_cond: frozen -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: -5--6 - elev: 123 - env_broad_scale: ______urban biome [ENVO:01000249] - env_local_scale: ________tunnel [ENVO:00000068] - env_medium: bare soil [ENVO:01001616] - env_package: soil - geo_loc_name: 'USA: Nowhere, Oklahoma' - growth_facil: greenhouse - lat_lon: 35.211445 -98.464612 - samp_name: b - samp_store_temp: -80 Celsius - source_mat_id: x:9 - store_cond: frozen - -``` -## SampleData-water-data-0-dim-depth -### Input -```yaml -water_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: '1.5' - env_broad_scale: oceanic epipelagic zone biome [ENVO:01000033] - env_local_scale: sand [ONTO:1234] - env_medium: sand [ONTO:1234] - env_package: xyz - geo_loc_name: 'USA: Crater Lake' - samp_name: xyz - source_mat_id: x:1 - -``` -## SampleData-water-data-1-dim-depth -### Input -```yaml -water_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: 1.5 - 2.5 - env_broad_scale: oceanic epipelagic zone biome [ENVO:01000033] - env_local_scale: sand [ONTO:1234] - env_medium: sand [ONTO:1234] - env_package: xyz - geo_loc_name: 'USA: Crater Lake' - samp_name: xyz - source_mat_id: x:1 - -``` -## SampleData-jgi_mg_data-minimal -### Input -```yaml -jgi_mg_data: -- analysis_type: - - metagenomics - - metatranscriptomics - dna_concentration: 1.23 - dna_cont_type: plate - dna_cont_well: C3 - dna_container_id: xxx - dna_dnase: 'no' - dna_isolate_meth: xxx - dna_project_contact: xxx - dna_samp_id: xxx - dna_sample_format: DNAStable - dna_sample_name: xxx - dna_seq_project: xxx - dna_seq_project_name: xxx - dna_seq_project_pi: xxx - dna_volume: 33 - proposal_dna: xxx - samp_name: xxx - -``` -## SampleData-sediment-data-minimal -### Input -```yaml -sediment_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: 0-.1 - elev: 0 - env_broad_scale: ______urban biome [ENVO:01000249] - env_local_scale: ________tunnel [ENVO:00000068] - env_medium: bare soil [ENVO:01001616] - env_package: sediment - geo_loc_name: 'USA: Nowhere, Oklahoma' - lat_lon: 35.211445 -98.464612 - samp_name: a - samp_store_temp: -80 Celsius - -``` -## SampleData-water-data-minimal -### Input -```yaml -water_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: '111' - env_broad_scale: oceanic epipelagic zone biome [ENVO:01000033] - env_local_scale: sand [ONTO:1234] - env_medium: sand [ONTO:1234] - env_package: xyz - geo_loc_name: 'USA: Crater Lake' - samp_mat_process: text [ONTO:000000000] - samp_name: xyz - -``` -## SampleData-jgi_mt_data-in-plate-valid-well-val -### Input -```yaml -jgi_mt_data: -- analysis_type: - - metagenomics - - metatranscriptomics - dnase_rna: 'no' - proposal_rna: xxx - rna_concentration: 1.23 - rna_cont_type: plate - rna_cont_well: B2 - rna_container_id: xxx - rna_isolate_meth: xxx - rna_project_contact: xxx - rna_samp_id: xxx - rna_sample_format: DNAStable - rna_sample_name: xxx - rna_seq_project: xxx - rna_seq_project_name: xxx - rna_seq_project_pi: xxx - rna_volume: 111 - samp_name: xxx - source_mat_id: x:1 - -``` -## SampleData-soil-data-water-content -### Input -```yaml -soil_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: 0 - 1 - elev: 123 - env_broad_scale: ______urban biome [ENVO:01000249] - env_local_scale: ________tunnel [ENVO:00000068] - env_medium: bare soil [ENVO:01001616] - env_package: soil - geo_loc_name: 'USA: Nowhere, Oklahoma' - growth_facil: greenhouse - lat_lon: 35.211445 -98.464612 - samp_name: b - samp_store_temp: -80 Celsius - store_cond: frozen - water_content: 75% dry weight -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: 0 - 1 - elev: 123 - env_broad_scale: ______urban biome [ENVO:01000249] - env_local_scale: ________tunnel [ENVO:00000068] - env_medium: bare soil [ENVO:01001616] - env_package: soil - geo_loc_name: 'USA: Nowhere, Oklahoma' - growth_facil: greenhouse - lat_lon: 35.211445 -98.464612 - samp_name: c - samp_store_temp: -80 Celsius - store_cond: frozen - water_content: 5 g water / g dry soil -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: 0 - 1 - elev: 123 - env_broad_scale: ______urban biome [ENVO:01000249] - env_local_scale: ________tunnel [ENVO:00000068] - env_medium: bare soil [ENVO:01001616] - env_package: soil - geo_loc_name: 'USA: Nowhere, Oklahoma' - growth_facil: greenhouse - lat_lon: 35.211445 -98.464612 - samp_name: d - samp_store_temp: -80 Celsius - store_cond: frozen - water_content: .75 g water per g soil WHC - -``` -## SampleData-water-data-depth-formats -### Input -```yaml -water_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: '111' - env_broad_scale: oceanic epipelagic zone biome [ENVO:01000033] - env_local_scale: sand [ONTO:1234] - env_medium: sand [ONTO:1234] - env_package: xyz - geo_loc_name: 'USA: Crater Lake' - samp_mat_process: text [ONTO:000000000] - samp_name: xyz - source_mat_id: x:1 -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: '0' - env_broad_scale: oceanic epipelagic zone biome [ENVO:01000033] - env_local_scale: sand [ONTO:1234] - env_medium: sand [ONTO:1234] - env_package: xyz - geo_loc_name: 'USA: Crater Lake' - samp_mat_process: text [ONTO:000000000] - samp_name: xyz - source_mat_id: x:1 -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: '-3.333' - env_broad_scale: oceanic epipelagic zone biome [ENVO:01000033] - env_local_scale: sand [ONTO:1234] - env_medium: sand [ONTO:1234] - env_package: xyz - geo_loc_name: 'USA: Crater Lake' - samp_mat_process: text [ONTO:000000000] - samp_name: xyz - source_mat_id: x:1 -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: 13.4-16.99 - env_broad_scale: oceanic epipelagic zone biome [ENVO:01000033] - env_local_scale: sand [ONTO:1234] - env_medium: sand [ONTO:1234] - env_package: xyz - geo_loc_name: 'USA: Crater Lake' - samp_mat_process: text [ONTO:000000000] - samp_name: xyz - source_mat_id: x:1 -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: -99.99 - 38 - env_broad_scale: oceanic epipelagic zone biome [ENVO:01000033] - env_local_scale: sand [ONTO:1234] - env_medium: sand [ONTO:1234] - env_package: xyz - geo_loc_name: 'USA: Crater Lake' - samp_mat_process: text [ONTO:000000000] - samp_name: xyz - source_mat_id: x:1 -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: -3--4 - env_broad_scale: oceanic epipelagic zone biome [ENVO:01000033] - env_local_scale: sand [ONTO:1234] - env_medium: sand [ONTO:1234] - env_package: xyz - geo_loc_name: 'USA: Crater Lake' - samp_mat_process: text [ONTO:000000000] - samp_name: xyz - source_mat_id: x:1 - -``` -## SampleData-jgi_mt_data-in-tube -### Input -```yaml -jgi_mt_data: -- analysis_type: - - metagenomics - - metatranscriptomics - dnase_rna: 'no' - proposal_rna: xxx - rna_concentration: 1.23 - rna_cont_type: tube - rna_container_id: xxx - rna_isolate_meth: xxx - rna_project_contact: xxx - rna_samp_id: xxx - rna_sample_format: DNAStable - rna_sample_name: xxx - rna_seq_project: xxx - rna_seq_project_name: xxx - rna_seq_project_pi: xxx - rna_volume: 111 - samp_name: xxx - source_mat_id: x:1 - -``` -## SampleData-sediment-data-depth-formats -### Input -```yaml -sediment_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: 0-.1 - elev: 0 - env_broad_scale: ______urban biome [ENVO:01000249] - env_local_scale: ________tunnel [ENVO:00000068] - env_medium: bare soil [ENVO:01001616] - env_package: sediment - geo_loc_name: 'USA: Nowhere, Oklahoma' - lat_lon: 35.211445 -98.464612 - samp_name: a - samp_store_temp: -80 Celsius - source_mat_id: x:1 -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: -2 - -3 - elev: 0 - env_broad_scale: ______urban biome [ENVO:01000249] - env_local_scale: ________tunnel [ENVO:00000068] - env_medium: bare soil [ENVO:01001616] - env_package: sediment - geo_loc_name: 'USA: Nowhere, Oklahoma' - lat_lon: 35.211445 -98.464612 - samp_name: a - samp_store_temp: -80 Celsius - source_mat_id: x:1 -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: 0.5 - 10.3333 - elev: 0 - env_broad_scale: ______urban biome [ENVO:01000249] - env_local_scale: ________tunnel [ENVO:00000068] - env_medium: bare soil [ENVO:01001616] - env_package: sediment - geo_loc_name: 'USA: Nowhere, Oklahoma' - lat_lon: 35.211445 -98.464612 - samp_name: a - samp_store_temp: -80 Celsius - source_mat_id: x:1 - -``` -## SampleData-emsl_data-exhasutive -### Input -```yaml -emsl_data: -- analysis_type: - - metagenomics - - metatranscriptomics - emsl_store_temp: -80 - project_id: xxx - replicate_number: 2 - samp_name: xxx - sample_shipped: 100 units - sample_type: soil - source_mat_id: x:1 - technical_reps: 3 - -``` -## SampleData-jgi_mg_data-in-plate-valid-well-val -### Input -```yaml -jgi_mg_data: -- analysis_type: - - metagenomics - - metatranscriptomics - dna_concentration: 1.23 - dna_cont_type: plate - dna_cont_well: B2 - dna_container_id: xxx - dna_dnase: 'no' - dna_isolate_meth: xxx - dna_project_contact: xxx - dna_samp_id: xxx - dna_sample_format: DNAStable - dna_sample_name: xxx - dna_seq_project: xxx - dna_seq_project_name: xxx - dna_seq_project_pi: xxx - dna_volume: 111 - proposal_dna: xxx - samp_name: xxx - source_mat_id: x:1 - -``` -## SampleData-jgi_mt_data-illegal-string-rna_volume -### Input -```yaml -jgi_mt_data: -- analysis_type: - - metatranscriptomics - dnase_rna: 'no' - proposal_rna: '504000' - rna_concentration: 100.3 - rna_cont_type: plate - rna_cont_well: H7 - rna_container_id: cat_ht_1999 - rna_isolate_meth: phenol/cloroform extraction - rna_project_contact: Leslie Ann Levine - rna_samp_id: '123456' - rna_sample_format: MDA reaction buffer - rna_sample_name: JGI_lagoon_14343 - rna_seq_project: '123456789' - rna_seq_project_name: JGI Lagoon metatranscritpomics - rna_seq_project_pi: Patty Smith - rna_volume: Four hundred uL - samp_name: sample name - source_mat_id: MPI:012345 - -``` -## SampleData-jgi_mt_data-string-dnase_rna -### Input -```yaml -jgi_mt_data: -- analysis_type: - - metatranscriptomics - dnase_rna: Not Applicable - proposal_rna: '504000' - rna_concentration: 100.3 - rna_cont_type: tube - rna_cont_well: H7 - rna_container_id: cat_ht_1999 - rna_isolate_meth: phenol/cloroform extraction - rna_project_contact: Leslie Ann Levine - rna_samp_id: '123456' - rna_sample_format: MDA reaction buffer - rna_sample_name: JGI_lagoon_14343 - rna_seq_project: '123456789' - rna_seq_project_name: JGI Lagoon metatranscritpomics - rna_seq_project_pi: Patty Smith - rna_volume: 25.1 - samp_name: sample name - source_mat_id: MPI:012345 - -``` -## SampleData-jgi_mg_data-bad-dna_cont_well -### Input -```yaml -jgi_mg_data: -- analysis_type: - - metagenomics - - metatranscriptomics - dna_concentration: 1.23 - dna_cont_type: plate - dna_cont_well: Z99 - dna_container_id: xxx - dna_dnase: 'no' - dna_isolate_meth: xxx - dna_project_contact: xxx - dna_samp_id: xxx - dna_sample_format: DNAStable - dna_sample_name: xxx - dna_seq_project: xxx - dna_seq_project_name: xxx - dna_seq_project_pi: xxx - dna_volume: 1.23 - proposal_dna: xxx - samp_name: xxx - -``` -## SampleData-jgi_mt_data-in-bucket -### Input -```yaml -jgi_mt_data: -- analysis_type: - - metagenomics - - metatranscriptomics - dnase_rna: 'no' - proposal_rna: xxx - rna_concentration: 1.23 - rna_cont_type: bucket - rna_container_id: xxx - rna_isolate_meth: xxx - rna_project_contact: xxx - rna_samp_id: xxx - rna_sample_format: DNAStable - rna_sample_name: xxx - rna_seq_project: xxx - rna_seq_project_name: xxx - rna_seq_project_pi: xxx - rna_volume: 999 - samp_name: xxx - source_mat_id: x:1 - -``` -## SampleData-jgi_mg_data-high-dna_concentration -### Input -```yaml -jgi_mg_data: -- analysis_type: - - metagenomics - - metatranscriptomics - dna_concentration: 2001 - dna_cont_type: plate - dna_cont_well: C3 - dna_container_id: xxx - dna_dnase: 'no' - dna_isolate_meth: xxx - dna_project_contact: xxx - dna_samp_id: xxx - dna_sample_format: DNAStable - dna_sample_name: xxx - dna_seq_project: xxx - dna_seq_project_name: xxx - dna_seq_project_pi: xxx - dna_volume: 0 - proposal_dna: xxx - samp_name: xxx - -``` -## SampleData-emsl_data-bad-emsl_store_temp -### Input -```yaml -emsl_data: -- analysis_type: - - metagenomics - - metatranscriptomics - emsl_store_temp: ice cold - project_id: xxx - samp_name: xxx - sample_shipped: 100 units - sample_type: soil - -``` -## SampleData-water-data-invalid-rel_to_oxygen -### Input -```yaml -water_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: '111' - ecosystem: Environmental - ecosystem_category: Terrestrial - ecosystem_subtype: Unclassified - ecosystem_type: Soil - env_broad_scale: oceanic epipelagic zone biome [ENVO:01000033] - env_local_scale: sand [ONTO:1234] - env_medium: sand [ONTO:1234] - env_package: xyz - geo_loc_name: 'USA: Crater Lake' - rel_to_oxygen: xyz - samp_name: xyz - specific_ecosystem: Unclassified - -``` -## SampleData-jgi_mt_data-illegal-string-rna_concentration -### Input -```yaml -jgi_mt_data: -- analysis_type: - - metatranscriptomics - dnase_rna: false - proposal_rna: '504000' - rna_concentration: one hundred - rna_cont_type: tube - rna_cont_well: H7 - rna_container_id: cat_ht_1999 - rna_isolate_meth: phenol/cloroform extraction - rna_project_contact: Leslie Ann Levine - rna_samp_id: '123456' - rna_sample_format: MDA reaction buffer - rna_sample_name: JGI_lagoon_14343 - rna_seq_project: '123456789' - rna_seq_project_name: JGI Lagoon metatranscritpomics - rna_seq_project_pi: Patty Smith - rna_volume: 25.1 - samp_name: sample name - source_mat_id: MPI:012345 - -``` -## SampleData-jgi_mt_data-illegal-rna_sample_format -### Input -```yaml -jgi_mt_data: -- analysis_type: - - metatranscriptomics - dnase_rna: false - proposal_rna: '504000' - rna_concentration: 100.3 - rna_cont_type: plate - rna_cont_well: H7 - rna_container_id: cat_ht_1999 - rna_isolate_meth: phenol/cloroform extraction - rna_project_contact: Leslie Ann Levine - rna_samp_id: '123456' - rna_sample_format: Phosphate Buffered Saline - rna_sample_name: JGI_lagoon_14343 - rna_seq_project: '123456789' - rna_seq_project_name: JGI Lagoon metatranscritpomics - rna_seq_project_pi: Patty Smith - rna_volume: 25.1 - samp_name: sample name - source_mat_id: MPI:012345 - -``` -## SampleData-jgi_mg_data-illegal-string-dna_absorb1 -### Input -```yaml -jgi_mg_data: -- analysis_type: - - metagenomics - - metatranscriptomics - dna_absorb1: seven - dna_concentration: 1.23 - dna_cont_type: plate - dna_cont_well: C3 - dna_container_id: xxx - dna_dnase: 'no' - dna_isolate_meth: xxx - dna_project_contact: xxx - dna_samp_id: xxx - dna_sample_format: DNAStable - dna_sample_name: xxx - dna_seq_project: xxx - dna_seq_project_name: xxx - dna_seq_project_pi: xxx - dna_volume: 0 - proposal_dna: xxx - samp_name: xxx - -``` -## SampleData-jgi_mt_data-illlegal-string-rna_absorb1 -### Input -```yaml -jgi_mt_data: -- analysis_type: - - metatranscriptomics - dnase_rna: 'no' - proposal_rna: '504000' - rna_absorb1: one - rna_concentration: 100.3 - rna_cont_type: plate - rna_cont_well: H7 - rna_container_id: cat_ht_1999 - rna_isolate_meth: phenol/cloroform extraction - rna_project_contact: Leslie Ann Levine - rna_samp_id: '123456' - rna_sample_format: MDA reaction buffer - rna_sample_name: JGI_lagoon_14343 - rna_seq_project: '123456789' - rna_seq_project_name: JGI Lagoon metatranscritpomics - rna_seq_project_pi: Patty Smith - rna_volume: 25.1 - samp_name: sample name - source_mat_id: MPI:012345 - -``` -## SampleData-water-data-missing-broad -### Input -```yaml -water_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: '111' - ecosystem: Environmental - ecosystem_category: Terrestrial - ecosystem_subtype: Unclassified - ecosystem_type: Soil - env_local_scale: sand [ONTO:1234] - env_medium: sand [ONTO:1234] - env_package: xyz - geo_loc_name: 'USA: Crater Lake' - samp_name: xyz - specific_ecosystem: Unclassified - -``` -## SampleData-jgi_mg_data-in-bucket -### Input -```yaml -jgi_mg_data: -- analysis_type: - - metagenomics - - metatranscriptomics - dna_concentration: 1.23 - dna_cont_type: bucket - dna_container_id: xxx - dna_dnase: 'no' - dna_isolate_meth: xxx - dna_project_contact: xxx - dna_samp_id: xxx - dna_sample_format: DNAStable - dna_sample_name: xxx - dna_seq_project: xxx - dna_seq_project_name: xxx - dna_seq_project_pi: xxx - dna_volume: 999 - proposal_dna: xxx - samp_name: xxx - -``` -## SampleData-soil-data-bad-geo_loc_name -### Input -```yaml -soil_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: 0 - 1 - elev: 123 - env_broad_scale: ______urban biome [ENVO:01000249] - env_local_scale: ________tunnel [ENVO:00000068] - env_medium: bare soil [ENVO:01001616] - env_package: soil - geo_loc_name: 'USA: Brooklyn Bridge' - growth_facil: greenhouse - lat_lon: 35.211445 -98.464612 - samp_name: b - samp_store_temp: -80 Celsius - store_cond: frozen - -``` -## SampleData-water-data-broad-label-only -### Input -```yaml -water_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: '111' - ecosystem: Environmental - ecosystem_category: Terrestrial - ecosystem_subtype: Unclassified - ecosystem_type: Soil - env_broad_scale: oceanic epipelagic zone biome - env_local_scale: sand [ONTO:1234] - env_medium: sand [ONTO:1234] - env_package: xyz - geo_loc_name: 'USA: Crater Lake' - samp_name: xyz - specific_ecosystem: Unclassified - -``` -## SampleData-jgi_mg_data-bad-dna_dnase -### Input -```yaml -jgi_mg_data: -- analysis_type: - - metagenomics - - metatranscriptomics - dna_concentration: 1.23 - dna_cont_type: plate - dna_cont_well: C3 - dna_container_id: xxx - dna_dnase: false - dna_isolate_meth: xxx - dna_project_contact: xxx - dna_samp_id: xxx - dna_sample_format: DNAStable - dna_sample_name: xxx - dna_seq_project: xxx - dna_seq_project_name: xxx - dna_seq_project_pi: xxx - dna_volume: 1.23 - proposal_dna: xxx - samp_name: xxx - -``` -## SampleData-soil-data-depth-format-004 -### Input -```yaml -soil_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: '55.22' - elev: 123 - env_broad_scale: ______urban biome [ENVO:01000249] - env_local_scale: ________tunnel [ENVO:00000068] - env_medium: bare soil [ENVO:01001616] - env_package: soil - geo_loc_name: 'USA: Nowhere, Oklahoma' - growth_facil: greenhouse - lat_lon: 35.211445 -98.464612 - samp_name: b - samp_store_temp: -80 Celsius - store_cond: frozen - -``` -## SampleData-water-data-incomplete-organsim_count -### Input -```yaml -water_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: '111' - ecosystem: Environmental - ecosystem_category: Terrestrial - ecosystem_subtype: Unclassified - ecosystem_type: Soil - env_broad_scale: oceanic epipelagic zone biome [ENVO:01000033] - env_local_scale: sand [ONTO:1234] - env_medium: sand [ONTO:1234] - env_package: xyz - geo_loc_name: 'USA: Crater Lake' - organism_count: xyz;100 units - samp_name: xyz - specific_ecosystem: Unclassified - -``` -## SampleData-jgi_mg_data-dna_organisms -### Input -```yaml -jgi_mg_data: -- analysis_type: - - metagenomics - - metatranscriptomics - dna_concentration: 1.23 - dna_cont_type: plate - dna_cont_well: C3 - dna_container_id: xxx - dna_dnase: 'no' - dna_isolate_meth: xxx - dna_organisms: xxx - dna_project_contact: xxx - dna_samp_id: xxx - dna_sample_format: DNAStable - dna_sample_name: xxx - dna_seq_project: xxx - dna_seq_project_name: xxx - dna_seq_project_pi: xxx - dna_volume: 999 - proposal_dna: xxx - samp_name: xxx - -``` -## SampleData-emsl_data-capital-sample_type -### Input -```yaml -emsl_data: -- analysis_type: - - metagenomics - - metatranscriptomics - emsl_store_temp: -80 - project_id: xxx - replicate_number: 5 - samp_name: xxx - sample_shipped: 100 units - sample_type: Water_extract_soil - -``` -## SampleData-jgi_mg_data-missing-dna_cont_type -### Input -```yaml -jgi_mg_data: -- analysis_type: - - metagenomics - - metatranscriptomics - dna_concentration: 1.23 - dna_container_id: xxx - dna_dnase: 'no' - dna_isolate_meth: xxx - dna_project_contact: xxx - dna_samp_id: xxx - dna_sample_format: DNAStable - dna_sample_name: xxx - dna_seq_project: xxx - dna_seq_project_name: xxx - dna_seq_project_pi: xxx - dna_volume: 0 - proposal_dna: xxx - samp_name: xxx - source_mat_id: x:1 - -``` -## SampleData-jgi_mt_data-capitalized-dnase_rna -### Input -```yaml -jgi_mt_data: -- analysis_type: - - metatranscriptomics - dnase_rna: true - proposal_rna: '504000' - rna_concentration: 100.3 - rna_cont_type: tube - rna_cont_well: H7 - rna_container_id: cat_ht_1999 - rna_isolate_meth: phenol/cloroform extraction - rna_project_contact: Leslie Ann Levine - rna_samp_id: '123456' - rna_sample_format: MDA reaction buffer - rna_sample_name: JGI_lagoon_14343 - rna_seq_project: '123456789' - rna_seq_project_name: JGI Lagoon metatranscritpomics - rna_seq_project_pi: Patty Smith - rna_volume: 25.1 - samp_name: sample name - source_mat_id: MPI:012345 - -``` -## SampleData-jgi_mg_data-negative-dna_concenctration -### Input -```yaml -jgi_mg_data: -- analysis_type: - - metagenomics - - metatranscriptomics - dna_concentration: -1.23 - dna_cont_type: plate - dna_cont_well: C3 - dna_container_id: xxx - dna_dnase: 'no' - dna_isolate_meth: xxx - dna_project_contact: xxx - dna_samp_id: xxx - dna_sample_format: DNAStable - dna_sample_name: xxx - dna_seq_project: xxx - dna_seq_project_name: xxx - dna_seq_project_pi: xxx - dna_volume: 0 - proposal_dna: xxx - samp_name: xxx - -``` -## SampleData-soil-data-depth-format-003 -### Input -```yaml -soil_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: '-5' - elev: 123 - env_broad_scale: ______urban biome [ENVO:01000249] - env_local_scale: ________tunnel [ENVO:00000068] - env_medium: bare soil [ENVO:01001616] - env_package: soil - geo_loc_name: 'USA: Nowhere, Oklahoma' - growth_facil: greenhouse - lat_lon: 35.211445 -98.464612 - samp_name: b - samp_store_temp: -80 Celsius - store_cond: frozen - -``` -## SampleData-jgi_mg_data-illegal-string-dna_concentration -### Input -```yaml -jgi_mg_data: -- analysis_type: - - metagenomics - - metatranscriptomics - dna_concentration: five hundred - dna_cont_type: plate - dna_cont_well: C3 - dna_container_id: xxx - dna_dnase: 'no' - dna_isolate_meth: xxx - dna_project_contact: xxx - dna_samp_id: xxx - dna_sample_format: DNAStable - dna_sample_name: xxx - dna_seq_project: xxx - dna_seq_project_name: xxx - dna_seq_project_pi: xxx - dna_volume: 0 - proposal_dna: xxx - samp_name: xxx - -``` -## SampleData-jgi_mg_data-bad-dna_sample_format -### Input -```yaml -jgi_mg_data: -- analysis_type: - - metagenomics - - metatranscriptomics - dna_concentration: 1.23 - dna_cont_type: plate - dna_cont_well: C3 - dna_container_id: xxx - dna_dnase: 'no' - dna_isolate_meth: xxx - dna_project_contact: xxx - dna_samp_id: xxx - dna_sample_format: red red wine - dna_sample_name: xxx - dna_seq_project: xxx - dna_seq_project_name: xxx - dna_seq_project_pi: xxx - dna_volume: 1.23 - proposal_dna: xxx - samp_name: xxx - -``` -## SampleData-sediment-data-depth-format-002 -### Input -```yaml -sediment_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: '0' - elev: 0 - env_broad_scale: ______urban biome [ENVO:01000249] - env_local_scale: ________tunnel [ENVO:00000068] - env_medium: bare soil [ENVO:01001616] - env_package: sediment - geo_loc_name: 'USA: Nowhere, Oklahoma' - lat_lon: 35.211445 -98.464612 - samp_name: a - samp_store_temp: -80 Celsius - -``` -## SampleData-soil-data-water-content-001 -### Input -```yaml -soil_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: 0 - 1 - elev: 123 - env_broad_scale: ______urban biome [ENVO:01000249] - env_local_scale: ________tunnel [ENVO:00000068] - env_medium: bare soil [ENVO:01001616] - env_package: soil - geo_loc_name: 'USA: Nowhere, Oklahoma' - growth_facil: greenhouse - lat_lon: 35.211445 -98.464612 - samp_name: b - samp_store_temp: -80 Celsius - store_cond: frozen - water_content: 3 - -``` -## SampleData-water-data-string-alkalinity -### Input -```yaml -water_data: -- alkalinity: really high - analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: '111' - ecosystem: Environmental - ecosystem_category: Terrestrial - ecosystem_subtype: Unclassified - ecosystem_type: Soil - env_broad_scale: oceanic epipelagic zone biome [ENVO:01000033] - env_local_scale: sand [ONTO:1234] - env_medium: sand [ONTO:1234] - env_package: xyz - geo_loc_name: 'USA: Crater Lake' - samp_name: xyz - specific_ecosystem: Unclassified - -``` -## SampleData-jgi_mt_data-illegal-string-rna_cont_well -### Input -```yaml -jgi_mt_data: -- analysis_type: - - metatranscriptomics - dnase_rna: false - proposal_rna: '504000' - rna_concentration: 100.3 - rna_cont_type: plate - rna_cont_well: A2-A11 - rna_container_id: cat_ht_1999 - rna_isolate_meth: phenol/cloroform extraction - rna_project_contact: Leslie Ann Levine - rna_samp_id: '123456' - rna_sample_format: MDA reaction buffer - rna_sample_name: JGI_lagoon_14343 - rna_seq_project: '123456789' - rna_seq_project_name: JGI Lagoon metatranscritpomics - rna_seq_project_pi: Patty Smith - rna_volume: 25.1 - samp_name: sample name - source_mat_id: MPI:012345 - -``` -## SampleData-emsl_data-string-replicate_number -### Input -```yaml -emsl_data: -- analysis_type: - - metagenomics - - metatranscriptomics - emsl_store_temp: -80 - project_id: xxx - replicate_number: hello - samp_name: xxx - sample_shipped: 100 units - sample_type: soil - -``` -## SampleData-water-data-broad-term-only -### Input -```yaml -water_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: '111' - ecosystem: Environmental - ecosystem_category: Terrestrial - ecosystem_subtype: Unclassified - ecosystem_type: Soil - env_local_scale: - - ONTO:1234 - env_medium: sand [ONTO:1234] - env_package: xyz - geo_loc_name: 'USA: Crater Lake' - samp_name: xyz - specific_ecosystem: Unclassified - -``` -## SampleData-water-data-scalar-analysis-type -### Input -```yaml -water_data: -- analysis_type: metatranscriptomics - collection_date: '2022-01-15' - depth: '111' - ecosystem: Environmental - ecosystem_category: Terrestrial - ecosystem_subtype: Unclassified - ecosystem_type: Soil - env_broad_scale: oceanic epipelagic zone biome [ENVO:01000033] - env_local_scale: sand [ONTO:1234] - env_medium: sand [ONTO:1234] - env_package: xyz - geo_loc_name: 'USA: Crater Lake' - samp_name: xyz - specific_ecosystem: Unclassified - -``` -## SampleData-jgi_mt_data-exceeds-char-limit-rna_container_id -### Input -```yaml -jgi_mt_data: -- analysis_type: - - metatranscriptomics - dnase_rna: 'no' - proposal_rna: '504000' - rna_concentration: 100.3 - rna_cont_type: plate - rna_cont_well: H7 - rna_container_id: Columbia_River_Watershed_MT_052292 - rna_isolate_meth: phenol/cloroform extraction - rna_project_contact: Leslie Ann Levine - rna_samp_id: '123456' - rna_sample_format: MDA reaction buffer - rna_sample_name: JGI_lagoon_14343 - rna_seq_project: '123456789' - rna_seq_project_name: JGI Lagoon metatranscritpomics - rna_seq_project_pi: Patty Smith - rna_volume: 25.1 - samp_name: sample name - source_mat_id: MPI:012345 - -``` -## SampleData-jgi_mt_data-capital-rna_cont_type -### Input -```yaml -jgi_mt_data: -- analysis_type: - - metatranscriptomics - dnase_rna: false - proposal_rna: '504000' - rna_concentration: 100.3 - rna_cont_type: Tube - rna_cont_well: H7 - rna_container_id: cat_ht_1999 - rna_isolate_meth: phenol/cloroform extraction - rna_project_contact: Leslie Ann Levine - rna_samp_id: '123456' - rna_sample_format: MDA reaction buffer - rna_sample_name: JGI_lagoon_14343 - rna_seq_project: '123456789' - rna_seq_project_name: JGI Lagoon metatranscritpomics - rna_seq_project_pi: Patty Smith - rna_volume: 25.1 - samp_name: sample name - source_mat_id: MPI:012345 - -``` -## SampleData-plant-associated-illegally-high-lat -### Input -```yaml -plant_associated_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: 2021-01-01 - depth: '111' - elev: 111 - env_broad_scale: Code Generation [OP:8888] - env_local_scale: Code Generation [OP:8888] - env_medium: Code Generation [OP:8888] - env_package: plant-associated - geo_loc_name: our first houseplant is dying - growth_facil: field - lat_lon: 111 88 - samp_name: our first houseplant is dying - samp_store_temp: 20 C - source_mat_id: example:plant_associated_data001 - -``` -## SampleData-emsl_data-bad-sample_type -### Input -```yaml -emsl_data: -- analysis_type: - - metagenomics - - metatranscriptomics - emsl_store_temp: -80 - project_id: xxx - samp_name: xxx - sample_shipped: 100 units - sample_type: sandwich - -``` -## SampleData-jgi_mg_data-capital-dna_dnase -### Input -```yaml -jgi_mg_data: -- analysis_type: - - metagenomics - - metatranscriptomics - dna_concentration: 1.23 - dna_cont_type: plate - dna_cont_well: C3 - dna_container_id: xxx - dna_dnase: 'No' - dna_isolate_meth: xxx - dna_project_contact: xxx - dna_samp_id: xxx - dna_sample_format: DNAStable - dna_sample_name: xxx - dna_seq_project: xxx - dna_seq_project_name: xxx - dna_seq_project_pi: xxx - dna_volume: 0 - proposal_dna: xxx - samp_name: xxx - -``` -## SampleData-emsl_data-bad-source_mat_id -### Input -```yaml -emsl_data: -- analysis_type: - - metagenomics - - metatranscriptomics - emsl_store_temp: -80 - project_id: xxx - samp_name: xxx - sample_shipped: 100 units - sample_type: soil - source_mat_id: no_colon - -``` -## SampleData-water-data-depth-invalid-range -### Input -```yaml -water_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: 1.5 to 2.5 - ecosystem: Environmental - ecosystem_category: Terrestrial - ecosystem_subtype: Unclassified - ecosystem_type: Soil - env_broad_scale: oceanic epipelagic zone biome [ENVO:01000033] - env_local_scale: sand [ONTO:1234] - env_medium: sand [ONTO:1234] - env_package: xyz - geo_loc_name: 'USA: Crater Lake' - samp_name: xyz - specific_ecosystem: Unclassified - -``` -## SampleData-emsl_data-bad-sample_shipped -### Input -```yaml -emsl_data: -- analysis_type: - - metagenomics - - metatranscriptomics - emsl_store_temp: -80 - project_id: xxx - samp_name: xxx - sample_shipped: three buckets - sample_type: soil - -``` -## SampleData-soil-data-depth-format-002 -### Input -```yaml -soil_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: '0' - elev: 123 - env_broad_scale: ______urban biome [ENVO:01000249] - env_local_scale: ________tunnel [ENVO:00000068] - env_medium: bare soil [ENVO:01001616] - env_package: soil - geo_loc_name: 'USA: Nowhere, Oklahoma' - growth_facil: greenhouse - lat_lon: 35.211445 -98.464612 - samp_name: b - samp_store_temp: -80 Celsius - store_cond: frozen - -``` -## SampleData-water-data-depth-format -### Input -```yaml -water_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: really deep - env_broad_scale: oceanic epipelagic zone biome [ENVO:01000033] - env_local_scale: sand [ONTO:1234] - env_medium: sand [ONTO:1234] - env_package: xyz - geo_loc_name: 'USA: Crater Lake' - samp_mat_process: text [ONTO:000000000] - samp_name: xyz - -``` -## SampleData-soil-data-water-content-003 -### Input -```yaml -soil_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: 0 - 1 - elev: 123 - env_broad_scale: ______urban biome [ENVO:01000249] - env_local_scale: ________tunnel [ENVO:00000068] - env_medium: bare soil [ENVO:01001616] - env_package: soil - geo_loc_name: 'USA: Nowhere, Oklahoma' - growth_facil: greenhouse - lat_lon: 35.211445 -98.464612 - samp_name: b - samp_store_temp: -80 Celsius - store_cond: frozen - water_content: just some water - -``` -## SampleData-jgi_mt_data-illegal-string-rna_absorb2 -### Input -```yaml -jgi_mt_data: -- analysis_type: - - metatranscriptomics - dnase_rna: 'no' - proposal_rna: '504000' - rna_absorb1: 2.02 - rna_absorb2: two and a half - rna_concentration: 100.3 - rna_cont_type: plate - rna_cont_well: H7 - rna_container_id: cat_ht_1999 - rna_isolate_meth: phenol/cloroform extraction - rna_project_contact: Leslie Ann Levine - rna_samp_id: '123456' - rna_sample_format: MDA reaction buffer - rna_sample_name: JGI_lagoon_14343 - rna_seq_project: '123456789' - rna_seq_project_name: JGI Lagoon metatranscritpomics - rna_seq_project_pi: Patty Smith - rna_volume: 25.1 - samp_name: sample name - source_mat_id: MPI:012345 - -``` -## SampleData-water-data-string-depth -### Input -```yaml -water_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: meters - ecosystem: Environmental - ecosystem_category: Terrestrial - ecosystem_subtype: Unclassified - ecosystem_type: Soil - env_broad_scale: oceanic epipelagic zone biome [ENVO:01000033] - env_local_scale: sand [ONTO:1234] - env_medium: sand [ONTO:1234] - env_package: xyz - geo_loc_name: 'USA: Crater Lake' - samp_name: xyz - specific_ecosystem: Unclassified - -``` -## SampleData-soil-data-depth-format-001 -### Input -```yaml -soil_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: 0 to 1 - elev: 123 - env_broad_scale: ______urban biome [ENVO:01000249] - env_local_scale: ________tunnel [ENVO:00000068] - env_medium: bare soil [ENVO:01001616] - env_package: soil - geo_loc_name: 'USA: Nowhere, Oklahoma' - growth_facil: greenhouse - lat_lon: 35.211445 -98.464612 - samp_name: b - samp_store_temp: -80 Celsius - store_cond: frozen - -``` -## SampleData-water-data-string-c-n-ratio -### Input -```yaml -water_data: -- analysis_type: - - metagenomics - - metatranscriptomics - carb_nitro_ratio: really high - collection_date: '2022-01-15' - depth: '111' - ecosystem: Environmental - ecosystem_category: Terrestrial - ecosystem_subtype: Unclassified - ecosystem_type: Soil - env_broad_scale: oceanic epipelagic zone biome [ENVO:01000033] - env_local_scale: sand [ONTO:1234] - env_medium: sand [ONTO:1234] - env_package: xyz - geo_loc_name: 'USA: Crater Lake' - samp_name: xyz - specific_ecosystem: Unclassified - -``` -## SampleData-jgi_mt_data-missing-colon-source_mat_id -### Input -```yaml -jgi_mt_data: -- analysis_type: - - metatranscriptomics - dnase_rna: false - proposal_rna: '504000' - rna_concentration: 100.3 - rna_cont_type: tube - rna_cont_well: H7 - rna_container_id: cat_ht_1999 - rna_isolate_meth: phenol/cloroform extraction - rna_project_contact: Leslie Ann Levine - rna_samp_id: '123456' - rna_sample_format: MDA reaction buffer - rna_sample_name: JGI_lagoon_14343 - rna_seq_project: '123456789' - rna_seq_project_name: JGI Lagoon metatranscritpomics - rna_seq_project_pi: Patty Smith - rna_volume: 25.1 - samp_name: Sample Name - source_mat_id: MPI012345 - -``` -## SampleData-jgi_mg_data-string-dna_absorb2 -### Input -```yaml -jgi_mg_data: -- analysis_type: - - metagenomics - - metatranscriptomics - dna_absorb2: four - dna_concentration: 1.23 - dna_cont_type: plate - dna_cont_well: C3 - dna_container_id: xxx - dna_dnase: 'no' - dna_isolate_meth: xxx - dna_project_contact: xxx - dna_samp_id: xxx - dna_sample_format: DNAStable - dna_sample_name: xxx - dna_seq_project: xxx - dna_seq_project_name: xxx - dna_seq_project_pi: xxx - dna_volume: 0 - proposal_dna: xxx - samp_name: xxx - -``` -## SampleData-jgi_mt_data-corner-well-rna_cont_well -### Input -```yaml -jgi_mt_data: -- analysis_type: - - metatranscriptomics - dnase_rna: false - proposal_rna: '504000' - rna_concentration: 100.3 - rna_cont_type: plate - rna_cont_well: A1 - rna_container_id: cat_ht_1999 - rna_isolate_meth: phenol/cloroform extraction - rna_project_contact: Leslie Ann Levine - rna_samp_id: '123456' - rna_sample_format: MDA reaction buffer - rna_sample_name: JGI_lagoon_14343 - rna_seq_project: '123456789' - rna_seq_project_name: JGI Lagoon metatranscritpomics - rna_seq_project_pi: Patty Smith - rna_volume: 25.1 - samp_name: sample name - source_mat_id: MPI:012345 - -``` -## SampleData-jgi_mg_data-bad-dna_volume -### Input -```yaml -jgi_mg_data: -- analysis_type: - - metagenomics - - metatranscriptomics - dna_concentration: 1.23 - dna_cont_type: plate - dna_cont_well: C3 - dna_container_id: xxx - dna_dnase: 'no' - dna_isolate_meth: xxx - dna_project_contact: xxx - dna_samp_id: xxx - dna_sample_format: DNAStable - dna_sample_name: xxx - dna_seq_project: xxx - dna_seq_project_name: xxx - dna_seq_project_pi: xxx - dna_volume: 1.23 liters - proposal_dna: xxx - samp_name: xxx - -``` -## SampleData-water-data-numeric-depth -### Input -```yaml -water_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: 1.5 - ecosystem: Environmental - ecosystem_category: Terrestrial - ecosystem_subtype: Unclassified - ecosystem_type: Soil - env_broad_scale: oceanic epipelagic zone biome [ENVO:01000033] - env_local_scale: sand [ONTO:1234] - env_medium: sand [ONTO:1234] - env_package: xyz - geo_loc_name: 'USA: Crater Lake' - samp_name: xyz - specific_ecosystem: Unclassified - -``` -## SampleData-water-data-invalid-tidal_stage -### Input -```yaml -water_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: '111' - ecosystem: Environmental - ecosystem_category: Terrestrial - ecosystem_subtype: Unclassified - ecosystem_type: Soil - env_broad_scale: oceanic epipelagic zone biome [ENVO:01000033] - env_local_scale: sand [ONTO:1234] - env_medium: sand [ONTO:1234] - env_package: xyz - geo_loc_name: 'USA: Crater Lake' - samp_name: xyz - specific_ecosystem: Unclassified - tidal_stage: xyz - -``` -## SampleData-soil-data-missing-elev -### Input -```yaml -soil_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: 111 - 222 - ecosystem: Environmental - ecosystem_category: Terrestrial - ecosystem_subtype: Unclassified - ecosystem_type: Soil - env_broad_scale: ______urban biome [ENVO:01000249] - env_local_scale: ________tunnel [ENVO:00000068] - env_medium: bare soil [ENVO:01001616] - env_package: soil - geo_loc_name: 'USA: Nowhere, Oklahoma' - growth_facil: greenhouse - lat_lon: 35.211445 -98.464612 - samp_name: b - samp_store_temp: -80 Celsius - specific_ecosystem: Unclassified - store_cond: frozen - -``` -## SampleData-water-data-organsim_count-invalid-method -### Input -```yaml -water_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: '111' - ecosystem: Environmental - ecosystem_category: Terrestrial - ecosystem_subtype: Unclassified - ecosystem_type: Soil - env_broad_scale: oceanic epipelagic zone biome [ENVO:01000033] - env_local_scale: sand [ONTO:1234] - env_medium: sand [ONTO:1234] - env_package: xyz - geo_loc_name: 'USA: Crater Lake' - organism_count: xyz;100 units;xyz - samp_name: xyz - specific_ecosystem: Unclassified - -``` -## SampleData-sediment-data-depth-format-001 -### Input -```yaml -sediment_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: '-5' - elev: 0 - env_broad_scale: ______urban biome [ENVO:01000249] - env_local_scale: ________tunnel [ENVO:00000068] - env_medium: bare soil [ENVO:01001616] - env_package: sediment - geo_loc_name: 'USA: Nowhere, Oklahoma' - lat_lon: 35.211445 -98.464612 - samp_name: a - samp_store_temp: -80 Celsius - -``` -## SampleData-soil-data-water-content-002 -### Input -```yaml -soil_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: 0 - 1 - elev: 123 - env_broad_scale: ______urban biome [ENVO:01000249] - env_local_scale: ________tunnel [ENVO:00000068] - env_medium: bare soil [ENVO:01001616] - env_package: soil - geo_loc_name: 'USA: Nowhere, Oklahoma' - growth_facil: greenhouse - lat_lon: 35.211445 -98.464612 - samp_name: b - samp_store_temp: -80 Celsius - store_cond: frozen - water_content: 3% - -``` -## SampleData-jgi_mt_data-rna-capital-rna_sample_format -### Input -```yaml -jgi_mt_data: -- analysis_type: - - metatranscriptomics - dnase_rna: false - proposal_rna: '504000' - rna_concentration: 100.3 - rna_cont_type: plate - rna_cont_well: H7 - rna_container_id: cat_ht_1999 - rna_isolate_meth: phenol/cloroform extraction - rna_project_contact: Leslie Ann Levine - rna_samp_id: '123456' - rna_sample_format: MDA Reaction Buffer - rna_sample_name: JGI_lagoon_14343 - rna_seq_project: '123456789' - rna_seq_project_name: JGI Lagoon metatranscritpomics - rna_seq_project_pi: Patty Smith - rna_volume: 25.1 - samp_name: sample name - source_mat_id: MPI:012345 - -``` -## SampleData-jgi_mt_data-illegal-string-rna_cont_type -### Input -```yaml -jgi_mt_data: -- analysis_type: - - metatranscriptomics - dnase_rna: false - proposal_rna: '504000' - rna_concentration: 100.3 - rna_cont_type: none - rna_cont_well: H7 - rna_container_id: cat_ht_1999 - rna_isolate_meth: phenol/cloroform extraction - rna_project_contact: Leslie Ann Levine - rna_samp_id: '123456' - rna_sample_format: MDA reaction buffer - rna_sample_name: JGI_lagoon_14343 - rna_seq_project: '123456789' - rna_seq_project_name: JGI Lagoon metatranscritpomics - rna_seq_project_pi: Patty Smith - rna_volume: 25.1 - samp_name: sample name - source_mat_id: MPI:012345 - -``` -## SampleData-jgi_mt_data-captilized-analysis_type -### Input -```yaml -jgi_mt_data: -- analysis_type: - - Metatranscriptomics - dnase_rna: 'no' - proposal_rna: '504000' - rna_concentration: 100.3 - rna_cont_type: plate - rna_cont_well: H7 - rna_container_id: cat_ht_1999 - rna_isolate_meth: phenol/cloroform extraction - rna_project_contact: Leslie Ann Levine - rna_samp_id: '123456' - rna_sample_format: MDA reaction buffer - rna_sample_name: JGI_lagoon_14343 - rna_seq_project: '123456789' - rna_seq_project_name: JGI Lagoon metatranscritpomics - rna_seq_project_pi: Patty Smith - rna_volume: 25.1 - samp_name: sample name - source_mat_id: MPI:012345 - -``` -## SampleData-plant-assoc--with-flavor -### Input -```yaml -plant_associated_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: 2021-01-01 - depth: '111' - elev: 111 - env_broad_scale: Code Generation [OP:8888] - env_local_scale: Code Generation [OP:8888] - env_medium: Code Generation [OP:8888] - env_package: plant-associated - flavor: grape - geo_loc_name: our first houseplant is dying - growth_facil: field - lat_lon: 77 88 - samp_name: our first houseplant is dying - samp_store_temp: 20 C - source_mat_id: example:plant_associated_data001 - -``` -## SampleData-jgi_mg_data-long-dna_container_id -### Input -```yaml -jgi_mg_data: -- analysis_type: - - metagenomics - - metatranscriptomics - dna_concentration: 1.23 - dna_cont_type: plate - dna_cont_well: C3 - dna_container_id: mount_mordor_012356789 - dna_dnase: 'no' - dna_isolate_meth: xxx - dna_project_contact: xxx - dna_samp_id: xxx - dna_sample_format: DNAStable - dna_sample_name: xxx - dna_seq_project: xxx - dna_seq_project_name: xxx - dna_seq_project_pi: xxx - dna_volume: 0 - proposal_dna: xxx - samp_name: xxx - -``` -## SampleData-water-data-numeric-alkalinity -### Input -```yaml -water_data: -- alkalinity: 999 - analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: '111' - ecosystem: Environmental - ecosystem_category: Terrestrial - ecosystem_subtype: Unclassified - ecosystem_type: Soil - env_broad_scale: oceanic epipelagic zone biome [ENVO:01000033] - env_local_scale: sand [ONTO:1234] - env_medium: sand [ONTO:1234] - env_package: xyz - geo_loc_name: 'USA: Crater Lake' - samp_name: xyz - specific_ecosystem: Unclassified - -``` -## SampleData-water-data-alkalinity-list -### Input -```yaml -water_data: -- alkalinity: - - 50 milligram per liter - - 100 spoons per bucket - analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: '111' - ecosystem: Environmental - ecosystem_category: Terrestrial - ecosystem_subtype: Unclassified - ecosystem_type: Soil - env_broad_scale: oceanic epipelagic zone biome [ENVO:01000033] - env_local_scale: sand [ONTO:1234] - env_medium: sand [ONTO:1234] - env_package: xyz - geo_loc_name: 'USA: Crater Lake' - samp_mat_process: text [ONTO:000000000] - samp_name: xyz - specific_ecosystem: Unclassified - -``` -## SampleData-jgi_mt_data-illegal-string-anlaysis_type -### Input -```yaml -jgi_mt_data: -- analysis_type: - - transcriptomics - dnase_rna: 'no' - proposal_rna: '504000' - rna_concentration: 100.3 - rna_cont_type: plate - rna_cont_well: H7 - rna_container_id: cat_ht_1999 - rna_isolate_meth: phenol/cloroform extraction - rna_project_contact: Leslie Ann Levine - rna_samp_id: '123456' - rna_sample_format: MDA reaction buffer - rna_sample_name: JGI_lagoon_14343 - rna_seq_project: '123456789' - rna_seq_project_name: JGI Lagoon metatranscritpomics - rna_seq_project_pi: Patty Smith - rna_volume: 25.1 - samp_name: sample name - source_mat_id: MPI:012345 - -``` -## SampleData-jgi_mg_data-dna_collect_site -### Input -```yaml -jgi_mg_data: -- analysis_type: - - metagenomics - - metatranscriptomics - dna_collect_site: xxx - dna_concentration: 1.23 - dna_cont_type: plate - dna_cont_well: C3 - dna_container_id: xxx - dna_dnase: 'no' - dna_isolate_meth: xxx - dna_project_contact: xxx - dna_samp_id: xxx - dna_sample_format: DNAStable - dna_sample_name: xxx - dna_seq_project: xxx - dna_seq_project_name: xxx - dna_seq_project_pi: xxx - dna_volume: 999 - proposal_dna: xxx - samp_name: xxx - -``` -## SampleData-water-data-invalid-analysis-type -### Input -```yaml -water_data: -- analysis_type: - - metagenomics - - invalid - collection_date: '2022-01-15' - depth: '111' - ecosystem: Environmental - ecosystem_category: Terrestrial - ecosystem_subtype: Unclassified - ecosystem_type: Soil - env_broad_scale: oceanic epipelagic zone biome [ENVO:01000033] - env_local_scale: sand [ONTO:1234] - env_medium: sand [ONTO:1234] - env_package: xyz - geo_loc_name: 'USA: Crater Lake' - samp_name: xyz - specific_ecosystem: Unclassified - -``` -## SampleData-jgi_mg_data-bad-dna_cont_type -### Input -```yaml -jgi_mg_data: -- analysis_type: - - metagenomics - - metatranscriptomics - dna_concentration: 1.23 - dna_cont_type: bucket - dna_cont_well: H3 - dna_container_id: xxx - dna_dnase: 'no' - dna_isolate_meth: xxx - dna_project_contact: xxx - dna_samp_id: xxx - dna_sample_format: DNAStable - dna_sample_name: xxx - dna_seq_project: xxx - dna_seq_project_name: xxx - dna_seq_project_pi: xxx - dna_volume: 1.23 - proposal_dna: xxx - samp_name: xxx - -``` -## SampleData-water-data-no-samp_name -### Input -```yaml -water_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: '111' - ecosystem: Environmental - ecosystem_category: Terrestrial - ecosystem_subtype: Unclassified - ecosystem_type: Soil - env_broad_scale: oceanic epipelagic zone biome [ENVO:01000033] - env_local_scale: sand [ONTO:1234] - env_medium: sand [ONTO:1234] - env_package: xyz - geo_loc_name: 'USA: Crater Lake' - specific_ecosystem: Unclassified - -``` -## SampleData-emsl_data-string-technical_reps -### Input -```yaml -emsl_data: -- analysis_type: - - metagenomics - - metatranscriptomics - emsl_store_temp: -80 - project_id: xxx - replicate_number: 5 - samp_name: xxx - sample_shipped: 100 units - sample_type: water_extract_soil - technical_reps: turkey_sub - -``` diff --git a/examples/output/SampleData-emsl_data-exhasutive.json b/examples/output/SampleData-emsl_data-exhasutive.json deleted file mode 100644 index 16b20abf..00000000 --- a/examples/output/SampleData-emsl_data-exhasutive.json +++ /dev/null @@ -1,19 +0,0 @@ -{ - "emsl_data": [ - { - "emsl_store_temp": "-80.0", - "project_id": "xxx", - "sample_shipped": "100 units", - "sample_type": "soil", - "analysis_type": [ - "metagenomics", - "metatranscriptomics" - ], - "replicate_number": "2", - "technical_reps": "3", - "samp_name": "xxx", - "source_mat_id": "x:1" - } - ], - "@type": "SampleData" -} \ No newline at end of file diff --git a/examples/output/SampleData-emsl_data-exhasutive.yaml b/examples/output/SampleData-emsl_data-exhasutive.yaml deleted file mode 100644 index 9d52dbf0..00000000 --- a/examples/output/SampleData-emsl_data-exhasutive.yaml +++ /dev/null @@ -1,12 +0,0 @@ -emsl_data: -- emsl_store_temp: '-80.0' - project_id: xxx - sample_shipped: 100 units - sample_type: soil - analysis_type: - - metagenomics - - metatranscriptomics - replicate_number: '2' - technical_reps: '3' - samp_name: xxx - source_mat_id: x:1 diff --git a/examples/output/SampleData-emsl_data-minimal.json b/examples/output/SampleData-emsl_data-minimal.json deleted file mode 100644 index a8be23be..00000000 --- a/examples/output/SampleData-emsl_data-minimal.json +++ /dev/null @@ -1,16 +0,0 @@ -{ - "emsl_data": [ - { - "emsl_store_temp": "-80.0", - "project_id": "xxx", - "sample_shipped": "100 units", - "sample_type": "soil", - "analysis_type": [ - "metagenomics", - "metatranscriptomics" - ], - "samp_name": "xxx" - } - ], - "@type": "SampleData" -} \ No newline at end of file diff --git a/examples/output/SampleData-emsl_data-minimal.yaml b/examples/output/SampleData-emsl_data-minimal.yaml deleted file mode 100644 index 3dc71443..00000000 --- a/examples/output/SampleData-emsl_data-minimal.yaml +++ /dev/null @@ -1,9 +0,0 @@ -emsl_data: -- emsl_store_temp: '-80.0' - project_id: xxx - sample_shipped: 100 units - sample_type: soil - analysis_type: - - metagenomics - - metatranscriptomics - samp_name: xxx diff --git a/examples/output/SampleData-jgi_mg_data-exhaustive.json b/examples/output/SampleData-jgi_mg_data-exhaustive.json deleted file mode 100644 index a666d715..00000000 --- a/examples/output/SampleData-jgi_mg_data-exhaustive.json +++ /dev/null @@ -1,30 +0,0 @@ -{ - "jgi_mg_data": [ - { - "dna_concentration": 1.23, - "dna_cont_type": "plate", - "dna_container_id": "xxx", - "dna_dnase": "no", - "dna_isolate_meth": "xxx", - "dna_project_contact": "xxx", - "dna_samp_id": "xxx", - "dna_sample_format": "DNAStable", - "dna_sample_name": "xxx", - "dna_seq_project": "xxx", - "dna_seq_project_name": "xxx", - "dna_seq_project_pi": "xxx", - "dna_volume": 33.0, - "proposal_dna": "xxx", - "analysis_type": [ - "metagenomics", - "metatranscriptomics" - ], - "dna_absorb1": 1.23, - "dna_absorb2": 1.23, - "dna_cont_well": "C3", - "samp_name": "xxx", - "source_mat_id": "x:1" - } - ], - "@type": "SampleData" -} \ No newline at end of file diff --git a/examples/output/SampleData-jgi_mg_data-exhaustive.yaml b/examples/output/SampleData-jgi_mg_data-exhaustive.yaml deleted file mode 100644 index 15989bf1..00000000 --- a/examples/output/SampleData-jgi_mg_data-exhaustive.yaml +++ /dev/null @@ -1,23 +0,0 @@ -jgi_mg_data: -- dna_concentration: 1.23 - dna_cont_type: plate - dna_container_id: xxx - dna_dnase: 'no' - dna_isolate_meth: xxx - dna_project_contact: xxx - dna_samp_id: xxx - dna_sample_format: DNAStable - dna_sample_name: xxx - dna_seq_project: xxx - dna_seq_project_name: xxx - dna_seq_project_pi: xxx - dna_volume: 33.0 - proposal_dna: xxx - analysis_type: - - metagenomics - - metatranscriptomics - dna_absorb1: 1.23 - dna_absorb2: 1.23 - dna_cont_well: C3 - samp_name: xxx - source_mat_id: x:1 diff --git a/examples/output/SampleData-jgi_mg_data-in-plate-valid-well-val.json b/examples/output/SampleData-jgi_mg_data-in-plate-valid-well-val.json deleted file mode 100644 index 8ccfa9bb..00000000 --- a/examples/output/SampleData-jgi_mg_data-in-plate-valid-well-val.json +++ /dev/null @@ -1,28 +0,0 @@ -{ - "jgi_mg_data": [ - { - "dna_concentration": 1.23, - "dna_cont_type": "plate", - "dna_container_id": "xxx", - "dna_dnase": "no", - "dna_isolate_meth": "xxx", - "dna_project_contact": "xxx", - "dna_samp_id": "xxx", - "dna_sample_format": "DNAStable", - "dna_sample_name": "xxx", - "dna_seq_project": "xxx", - "dna_seq_project_name": "xxx", - "dna_seq_project_pi": "xxx", - "dna_volume": 111.0, - "proposal_dna": "xxx", - "analysis_type": [ - "metagenomics", - "metatranscriptomics" - ], - "dna_cont_well": "B2", - "samp_name": "xxx", - "source_mat_id": "x:1" - } - ], - "@type": "SampleData" -} \ No newline at end of file diff --git a/examples/output/SampleData-jgi_mg_data-in-plate-valid-well-val.yaml b/examples/output/SampleData-jgi_mg_data-in-plate-valid-well-val.yaml deleted file mode 100644 index aed2cb53..00000000 --- a/examples/output/SampleData-jgi_mg_data-in-plate-valid-well-val.yaml +++ /dev/null @@ -1,21 +0,0 @@ -jgi_mg_data: -- dna_concentration: 1.23 - dna_cont_type: plate - dna_container_id: xxx - dna_dnase: 'no' - dna_isolate_meth: xxx - dna_project_contact: xxx - dna_samp_id: xxx - dna_sample_format: DNAStable - dna_sample_name: xxx - dna_seq_project: xxx - dna_seq_project_name: xxx - dna_seq_project_pi: xxx - dna_volume: 111.0 - proposal_dna: xxx - analysis_type: - - metagenomics - - metatranscriptomics - dna_cont_well: B2 - samp_name: xxx - source_mat_id: x:1 diff --git a/examples/output/SampleData-jgi_mg_data-in-tube.json b/examples/output/SampleData-jgi_mg_data-in-tube.json deleted file mode 100644 index d66c512b..00000000 --- a/examples/output/SampleData-jgi_mg_data-in-tube.json +++ /dev/null @@ -1,27 +0,0 @@ -{ - "jgi_mg_data": [ - { - "dna_concentration": 1.23, - "dna_cont_type": "tube", - "dna_container_id": "xxx", - "dna_dnase": "no", - "dna_isolate_meth": "xxx", - "dna_project_contact": "xxx", - "dna_samp_id": "xxx", - "dna_sample_format": "DNAStable", - "dna_sample_name": "xxx", - "dna_seq_project": "xxx", - "dna_seq_project_name": "xxx", - "dna_seq_project_pi": "xxx", - "dna_volume": 111.0, - "proposal_dna": "xxx", - "analysis_type": [ - "metagenomics", - "metatranscriptomics" - ], - "samp_name": "xxx", - "source_mat_id": "x:1" - } - ], - "@type": "SampleData" -} \ No newline at end of file diff --git a/examples/output/SampleData-jgi_mg_data-in-tube.yaml b/examples/output/SampleData-jgi_mg_data-in-tube.yaml deleted file mode 100644 index 3a760032..00000000 --- a/examples/output/SampleData-jgi_mg_data-in-tube.yaml +++ /dev/null @@ -1,20 +0,0 @@ -jgi_mg_data: -- dna_concentration: 1.23 - dna_cont_type: tube - dna_container_id: xxx - dna_dnase: 'no' - dna_isolate_meth: xxx - dna_project_contact: xxx - dna_samp_id: xxx - dna_sample_format: DNAStable - dna_sample_name: xxx - dna_seq_project: xxx - dna_seq_project_name: xxx - dna_seq_project_pi: xxx - dna_volume: 111.0 - proposal_dna: xxx - analysis_type: - - metagenomics - - metatranscriptomics - samp_name: xxx - source_mat_id: x:1 diff --git a/examples/output/SampleData-jgi_mg_data-minimal.json b/examples/output/SampleData-jgi_mg_data-minimal.json deleted file mode 100644 index 661fef87..00000000 --- a/examples/output/SampleData-jgi_mg_data-minimal.json +++ /dev/null @@ -1,27 +0,0 @@ -{ - "jgi_mg_data": [ - { - "dna_concentration": 1.23, - "dna_cont_type": "plate", - "dna_container_id": "xxx", - "dna_dnase": "no", - "dna_isolate_meth": "xxx", - "dna_project_contact": "xxx", - "dna_samp_id": "xxx", - "dna_sample_format": "DNAStable", - "dna_sample_name": "xxx", - "dna_seq_project": "xxx", - "dna_seq_project_name": "xxx", - "dna_seq_project_pi": "xxx", - "dna_volume": 33.0, - "proposal_dna": "xxx", - "analysis_type": [ - "metagenomics", - "metatranscriptomics" - ], - "dna_cont_well": "C3", - "samp_name": "xxx" - } - ], - "@type": "SampleData" -} \ No newline at end of file diff --git a/examples/output/SampleData-jgi_mg_data-minimal.yaml b/examples/output/SampleData-jgi_mg_data-minimal.yaml deleted file mode 100644 index 66f63143..00000000 --- a/examples/output/SampleData-jgi_mg_data-minimal.yaml +++ /dev/null @@ -1,20 +0,0 @@ -jgi_mg_data: -- dna_concentration: 1.23 - dna_cont_type: plate - dna_container_id: xxx - dna_dnase: 'no' - dna_isolate_meth: xxx - dna_project_contact: xxx - dna_samp_id: xxx - dna_sample_format: DNAStable - dna_sample_name: xxx - dna_seq_project: xxx - dna_seq_project_name: xxx - dna_seq_project_pi: xxx - dna_volume: 33.0 - proposal_dna: xxx - analysis_type: - - metagenomics - - metatranscriptomics - dna_cont_well: C3 - samp_name: xxx diff --git a/examples/output/SampleData-jgi_mt_data-in-plate-valid-well-val.json b/examples/output/SampleData-jgi_mt_data-in-plate-valid-well-val.json deleted file mode 100644 index 4e2f8c2a..00000000 --- a/examples/output/SampleData-jgi_mt_data-in-plate-valid-well-val.json +++ /dev/null @@ -1,28 +0,0 @@ -{ - "jgi_mt_data": [ - { - "dnase_rna": "no", - "proposal_rna": "xxx", - "rna_concentration": 1.23, - "rna_cont_type": "plate", - "rna_container_id": "xxx", - "rna_isolate_meth": "xxx", - "rna_project_contact": "xxx", - "rna_samp_id": "xxx", - "rna_sample_format": "DNAStable", - "rna_sample_name": "xxx", - "rna_seq_project": "xxx", - "rna_seq_project_name": "xxx", - "rna_seq_project_pi": "xxx", - "rna_volume": 111.0, - "analysis_type": [ - "metagenomics", - "metatranscriptomics" - ], - "rna_cont_well": "B2", - "samp_name": "xxx", - "source_mat_id": "x:1" - } - ], - "@type": "SampleData" -} \ No newline at end of file diff --git a/examples/output/SampleData-jgi_mt_data-in-plate-valid-well-val.yaml b/examples/output/SampleData-jgi_mt_data-in-plate-valid-well-val.yaml deleted file mode 100644 index 0f0117a0..00000000 --- a/examples/output/SampleData-jgi_mt_data-in-plate-valid-well-val.yaml +++ /dev/null @@ -1,21 +0,0 @@ -jgi_mt_data: -- dnase_rna: 'no' - proposal_rna: xxx - rna_concentration: 1.23 - rna_cont_type: plate - rna_container_id: xxx - rna_isolate_meth: xxx - rna_project_contact: xxx - rna_samp_id: xxx - rna_sample_format: DNAStable - rna_sample_name: xxx - rna_seq_project: xxx - rna_seq_project_name: xxx - rna_seq_project_pi: xxx - rna_volume: 111.0 - analysis_type: - - metagenomics - - metatranscriptomics - rna_cont_well: B2 - samp_name: xxx - source_mat_id: x:1 diff --git a/examples/output/SampleData-jgi_mt_data-in-tube.json b/examples/output/SampleData-jgi_mt_data-in-tube.json deleted file mode 100644 index 21d72a19..00000000 --- a/examples/output/SampleData-jgi_mt_data-in-tube.json +++ /dev/null @@ -1,27 +0,0 @@ -{ - "jgi_mt_data": [ - { - "dnase_rna": "no", - "proposal_rna": "xxx", - "rna_concentration": 1.23, - "rna_cont_type": "tube", - "rna_container_id": "xxx", - "rna_isolate_meth": "xxx", - "rna_project_contact": "xxx", - "rna_samp_id": "xxx", - "rna_sample_format": "DNAStable", - "rna_sample_name": "xxx", - "rna_seq_project": "xxx", - "rna_seq_project_name": "xxx", - "rna_seq_project_pi": "xxx", - "rna_volume": 111.0, - "analysis_type": [ - "metagenomics", - "metatranscriptomics" - ], - "samp_name": "xxx", - "source_mat_id": "x:1" - } - ], - "@type": "SampleData" -} \ No newline at end of file diff --git a/examples/output/SampleData-jgi_mt_data-in-tube.yaml b/examples/output/SampleData-jgi_mt_data-in-tube.yaml deleted file mode 100644 index e1b06ffd..00000000 --- a/examples/output/SampleData-jgi_mt_data-in-tube.yaml +++ /dev/null @@ -1,20 +0,0 @@ -jgi_mt_data: -- dnase_rna: 'no' - proposal_rna: xxx - rna_concentration: 1.23 - rna_cont_type: tube - rna_container_id: xxx - rna_isolate_meth: xxx - rna_project_contact: xxx - rna_samp_id: xxx - rna_sample_format: DNAStable - rna_sample_name: xxx - rna_seq_project: xxx - rna_seq_project_name: xxx - rna_seq_project_pi: xxx - rna_volume: 111.0 - analysis_type: - - metagenomics - - metatranscriptomics - samp_name: xxx - source_mat_id: x:1 diff --git a/examples/output/SampleData-jgi_mt_data-minimal.json b/examples/output/SampleData-jgi_mt_data-minimal.json deleted file mode 100644 index 6a6850ad..00000000 --- a/examples/output/SampleData-jgi_mt_data-minimal.json +++ /dev/null @@ -1,27 +0,0 @@ -{ - "jgi_mt_data": [ - { - "dnase_rna": "no", - "proposal_rna": "504000", - "rna_concentration": 100.3, - "rna_cont_type": "plate", - "rna_container_id": "cat_ht_1999", - "rna_isolate_meth": "phenol/cloroform extraction", - "rna_project_contact": "Leslie Ann Levine", - "rna_samp_id": "123456", - "rna_sample_format": "MDA reaction buffer", - "rna_sample_name": "JGI_lagoon_14343", - "rna_seq_project": "123456789", - "rna_seq_project_name": "JGI Lagoon metatranscritpomics", - "rna_seq_project_pi": "Patty Smith", - "rna_volume": 25.1, - "analysis_type": [ - "metatranscriptomics" - ], - "rna_cont_well": "H7", - "samp_name": "sample name", - "source_mat_id": "MPI:012345" - } - ], - "@type": "SampleData" -} \ No newline at end of file diff --git a/examples/output/SampleData-jgi_mt_data-minimal.yaml b/examples/output/SampleData-jgi_mt_data-minimal.yaml deleted file mode 100644 index 5d408a44..00000000 --- a/examples/output/SampleData-jgi_mt_data-minimal.yaml +++ /dev/null @@ -1,20 +0,0 @@ -jgi_mt_data: -- dnase_rna: 'no' - proposal_rna: '504000' - rna_concentration: 100.3 - rna_cont_type: plate - rna_container_id: cat_ht_1999 - rna_isolate_meth: phenol/cloroform extraction - rna_project_contact: Leslie Ann Levine - rna_samp_id: '123456' - rna_sample_format: MDA reaction buffer - rna_sample_name: JGI_lagoon_14343 - rna_seq_project: '123456789' - rna_seq_project_name: JGI Lagoon metatranscritpomics - rna_seq_project_pi: Patty Smith - rna_volume: 25.1 - analysis_type: - - metatranscriptomics - rna_cont_well: H7 - samp_name: sample name - source_mat_id: MPI:012345 diff --git a/examples/output/SampleData-jgi_mt_data_exhaustive.json b/examples/output/SampleData-jgi_mt_data_exhaustive.json deleted file mode 100644 index 81f492c4..00000000 --- a/examples/output/SampleData-jgi_mt_data_exhaustive.json +++ /dev/null @@ -1,29 +0,0 @@ -{ - "jgi_mt_data": [ - { - "dnase_rna": "no", - "proposal_rna": "504000", - "rna_concentration": 100.3, - "rna_cont_type": "plate", - "rna_container_id": "cat_ht_1999", - "rna_isolate_meth": "phenol/cloroform extraction", - "rna_project_contact": "Leslie Ann Levine", - "rna_samp_id": "123456", - "rna_sample_format": "MDA reaction buffer", - "rna_sample_name": "JGI_lagoon_14343", - "rna_seq_project": "123456789", - "rna_seq_project_name": "JGI Lagoon metatranscritpomics", - "rna_seq_project_pi": "Patty Smith", - "rna_volume": 25.1, - "analysis_type": [ - "metatranscriptomics" - ], - "rna_absorb1": 2.02, - "rna_absorb2": 1.4, - "rna_cont_well": "H7", - "samp_name": "sample name", - "source_mat_id": "MPI:012345" - } - ], - "@type": "SampleData" -} \ No newline at end of file diff --git a/examples/output/SampleData-jgi_mt_data_exhaustive.yaml b/examples/output/SampleData-jgi_mt_data_exhaustive.yaml deleted file mode 100644 index 3c33d658..00000000 --- a/examples/output/SampleData-jgi_mt_data_exhaustive.yaml +++ /dev/null @@ -1,22 +0,0 @@ -jgi_mt_data: -- dnase_rna: 'no' - proposal_rna: '504000' - rna_concentration: 100.3 - rna_cont_type: plate - rna_container_id: cat_ht_1999 - rna_isolate_meth: phenol/cloroform extraction - rna_project_contact: Leslie Ann Levine - rna_samp_id: '123456' - rna_sample_format: MDA reaction buffer - rna_sample_name: JGI_lagoon_14343 - rna_seq_project: '123456789' - rna_seq_project_name: JGI Lagoon metatranscritpomics - rna_seq_project_pi: Patty Smith - rna_volume: 25.1 - analysis_type: - - metatranscriptomics - rna_absorb1: 2.02 - rna_absorb2: 1.4 - rna_cont_well: H7 - samp_name: sample name - source_mat_id: MPI:012345 diff --git a/examples/output/SampleData-plant-assoc-min.json b/examples/output/SampleData-plant-assoc-min.json deleted file mode 100644 index 279aae29..00000000 --- a/examples/output/SampleData-plant-assoc-min.json +++ /dev/null @@ -1,24 +0,0 @@ -{ - "plant_associated_data": [ - { - "analysis_type": [ - "metagenomics", - "metatranscriptomics" - ], - "collection_date": "2021-01-01", - "depth": "111", - "elev": "111.0", - "env_broad_scale": "Code Generation [OP:8888]", - "env_local_scale": "Code Generation [OP:8888]", - "env_medium": "Code Generation [OP:8888]", - "env_package": "plant-associated", - "geo_loc_name": "USA: Philadelphia, Pennsylvania", - "growth_facil": "field", - "lat_lon": "77 88", - "samp_store_temp": "20 C", - "samp_name": "our first houseplant is dying", - "source_mat_id": "example:plant_associated_data001" - } - ], - "@type": "SampleData" -} \ No newline at end of file diff --git a/examples/output/SampleData-plant-assoc-min.yaml b/examples/output/SampleData-plant-assoc-min.yaml deleted file mode 100644 index 9c4ff2d0..00000000 --- a/examples/output/SampleData-plant-assoc-min.yaml +++ /dev/null @@ -1,17 +0,0 @@ -plant_associated_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2021-01-01' - depth: '111' - elev: '111.0' - env_broad_scale: Code Generation [OP:8888] - env_local_scale: Code Generation [OP:8888] - env_medium: Code Generation [OP:8888] - env_package: plant-associated - geo_loc_name: 'USA: Philadelphia, Pennsylvania' - growth_facil: field - lat_lon: 77 88 - samp_store_temp: 20 C - samp_name: our first houseplant is dying - source_mat_id: example:plant_associated_data001 diff --git a/examples/output/SampleData-sediment-data-depth-formats.json b/examples/output/SampleData-sediment-data-depth-formats.json deleted file mode 100644 index 2dceff2f..00000000 --- a/examples/output/SampleData-sediment-data-depth-formats.json +++ /dev/null @@ -1,59 +0,0 @@ -{ - "sediment_data": [ - { - "analysis_type": [ - "metagenomics", - "metatranscriptomics" - ], - "collection_date": "2022-01-15", - "depth": "0-.1", - "elev": "0.0", - "env_broad_scale": "______urban biome [ENVO:01000249]", - "env_local_scale": "________tunnel [ENVO:00000068]", - "env_medium": "bare soil [ENVO:01001616]", - "env_package": "sediment", - "geo_loc_name": "USA: Nowhere, Oklahoma", - "lat_lon": "35.211445 -98.464612", - "samp_store_temp": "-80 Celsius", - "samp_name": "a", - "source_mat_id": "x:1" - }, - { - "analysis_type": [ - "metagenomics", - "metatranscriptomics" - ], - "collection_date": "2022-01-15", - "depth": "-2 - -3", - "elev": "0.0", - "env_broad_scale": "______urban biome [ENVO:01000249]", - "env_local_scale": "________tunnel [ENVO:00000068]", - "env_medium": "bare soil [ENVO:01001616]", - "env_package": "sediment", - "geo_loc_name": "USA: Nowhere, Oklahoma", - "lat_lon": "35.211445 -98.464612", - "samp_store_temp": "-80 Celsius", - "samp_name": "a", - "source_mat_id": "x:1" - }, - { - "analysis_type": [ - "metagenomics", - "metatranscriptomics" - ], - "collection_date": "2022-01-15", - "depth": "0.5 - 10.3333", - "elev": "0.0", - "env_broad_scale": "______urban biome [ENVO:01000249]", - "env_local_scale": "________tunnel [ENVO:00000068]", - "env_medium": "bare soil [ENVO:01001616]", - "env_package": "sediment", - "geo_loc_name": "USA: Nowhere, Oklahoma", - "lat_lon": "35.211445 -98.464612", - "samp_store_temp": "-80 Celsius", - "samp_name": "a", - "source_mat_id": "x:1" - } - ], - "@type": "SampleData" -} \ No newline at end of file diff --git a/examples/output/SampleData-sediment-data-depth-formats.yaml b/examples/output/SampleData-sediment-data-depth-formats.yaml deleted file mode 100644 index f0b6c876..00000000 --- a/examples/output/SampleData-sediment-data-depth-formats.yaml +++ /dev/null @@ -1,46 +0,0 @@ -sediment_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: 0-.1 - elev: '0.0' - env_broad_scale: ______urban biome [ENVO:01000249] - env_local_scale: ________tunnel [ENVO:00000068] - env_medium: bare soil [ENVO:01001616] - env_package: sediment - geo_loc_name: 'USA: Nowhere, Oklahoma' - lat_lon: 35.211445 -98.464612 - samp_store_temp: -80 Celsius - samp_name: a - source_mat_id: x:1 -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: -2 - -3 - elev: '0.0' - env_broad_scale: ______urban biome [ENVO:01000249] - env_local_scale: ________tunnel [ENVO:00000068] - env_medium: bare soil [ENVO:01001616] - env_package: sediment - geo_loc_name: 'USA: Nowhere, Oklahoma' - lat_lon: 35.211445 -98.464612 - samp_store_temp: -80 Celsius - samp_name: a - source_mat_id: x:1 -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: 0.5 - 10.3333 - elev: '0.0' - env_broad_scale: ______urban biome [ENVO:01000249] - env_local_scale: ________tunnel [ENVO:00000068] - env_medium: bare soil [ENVO:01001616] - env_package: sediment - geo_loc_name: 'USA: Nowhere, Oklahoma' - lat_lon: 35.211445 -98.464612 - samp_store_temp: -80 Celsius - samp_name: a - source_mat_id: x:1 diff --git a/examples/output/SampleData-sediment-data-minimal.json b/examples/output/SampleData-sediment-data-minimal.json deleted file mode 100644 index c5932b63..00000000 --- a/examples/output/SampleData-sediment-data-minimal.json +++ /dev/null @@ -1,22 +0,0 @@ -{ - "sediment_data": [ - { - "analysis_type": [ - "metagenomics", - "metatranscriptomics" - ], - "collection_date": "2022-01-15", - "depth": "0-.1", - "elev": "0.0", - "env_broad_scale": "______urban biome [ENVO:01000249]", - "env_local_scale": "________tunnel [ENVO:00000068]", - "env_medium": "bare soil [ENVO:01001616]", - "env_package": "sediment", - "geo_loc_name": "USA: Nowhere, Oklahoma", - "lat_lon": "35.211445 -98.464612", - "samp_store_temp": "-80 Celsius", - "samp_name": "a" - } - ], - "@type": "SampleData" -} \ No newline at end of file diff --git a/examples/output/SampleData-sediment-data-minimal.yaml b/examples/output/SampleData-sediment-data-minimal.yaml deleted file mode 100644 index 445b7873..00000000 --- a/examples/output/SampleData-sediment-data-minimal.yaml +++ /dev/null @@ -1,15 +0,0 @@ -sediment_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: 0-.1 - elev: '0.0' - env_broad_scale: ______urban biome [ENVO:01000249] - env_local_scale: ________tunnel [ENVO:00000068] - env_medium: bare soil [ENVO:01001616] - env_package: sediment - geo_loc_name: 'USA: Nowhere, Oklahoma' - lat_lon: 35.211445 -98.464612 - samp_store_temp: -80 Celsius - samp_name: a diff --git a/examples/output/SampleData-soil-data-depth-formats.json b/examples/output/SampleData-soil-data-depth-formats.json deleted file mode 100644 index 9a96aa99..00000000 --- a/examples/output/SampleData-soil-data-depth-formats.json +++ /dev/null @@ -1,85 +0,0 @@ -{ - "soil_data": [ - { - "analysis_type": [ - "metagenomics", - "metatranscriptomics" - ], - "collection_date": "2022-01-15", - "depth": "10.4-45.9999", - "elev": "123.0", - "env_broad_scale": "______urban biome [ENVO:01000249]", - "env_local_scale": "________tunnel [ENVO:00000068]", - "env_medium": "bare soil [ENVO:01001616]", - "env_package": "soil", - "geo_loc_name": "USA: Nowhere, Oklahoma", - "growth_facil": "greenhouse", - "lat_lon": "35.211445 -98.464612", - "samp_store_temp": "-80 Celsius", - "store_cond": "frozen", - "samp_name": "b", - "source_mat_id": "x:6" - }, - { - "analysis_type": [ - "metagenomics", - "metatranscriptomics" - ], - "collection_date": "2022-01-15", - "depth": "10.4 - 45.9999", - "elev": "123.0", - "env_broad_scale": "______urban biome [ENVO:01000249]", - "env_local_scale": "________tunnel [ENVO:00000068]", - "env_medium": "bare soil [ENVO:01001616]", - "env_package": "soil", - "geo_loc_name": "USA: Nowhere, Oklahoma", - "growth_facil": "greenhouse", - "lat_lon": "35.211445 -98.464612", - "samp_store_temp": "-80 Celsius", - "store_cond": "frozen", - "samp_name": "b", - "source_mat_id": "x:7" - }, - { - "analysis_type": [ - "metagenomics", - "metatranscriptomics" - ], - "collection_date": "2022-01-15", - "depth": "-10.4 - 45.9999", - "elev": "123.0", - "env_broad_scale": "______urban biome [ENVO:01000249]", - "env_local_scale": "________tunnel [ENVO:00000068]", - "env_medium": "bare soil [ENVO:01001616]", - "env_package": "soil", - "geo_loc_name": "USA: Nowhere, Oklahoma", - "growth_facil": "greenhouse", - "lat_lon": "35.211445 -98.464612", - "samp_store_temp": "-80 Celsius", - "store_cond": "frozen", - "samp_name": "b", - "source_mat_id": "x:8" - }, - { - "analysis_type": [ - "metagenomics", - "metatranscriptomics" - ], - "collection_date": "2022-01-15", - "depth": "-5--6", - "elev": "123.0", - "env_broad_scale": "______urban biome [ENVO:01000249]", - "env_local_scale": "________tunnel [ENVO:00000068]", - "env_medium": "bare soil [ENVO:01001616]", - "env_package": "soil", - "geo_loc_name": "USA: Nowhere, Oklahoma", - "growth_facil": "greenhouse", - "lat_lon": "35.211445 -98.464612", - "samp_store_temp": "-80 Celsius", - "store_cond": "frozen", - "samp_name": "b", - "source_mat_id": "x:9" - } - ], - "@type": "SampleData" -} \ No newline at end of file diff --git a/examples/output/SampleData-soil-data-depth-formats.yaml b/examples/output/SampleData-soil-data-depth-formats.yaml deleted file mode 100644 index 8be27ece..00000000 --- a/examples/output/SampleData-soil-data-depth-formats.yaml +++ /dev/null @@ -1,69 +0,0 @@ -soil_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: 10.4-45.9999 - elev: '123.0' - env_broad_scale: ______urban biome [ENVO:01000249] - env_local_scale: ________tunnel [ENVO:00000068] - env_medium: bare soil [ENVO:01001616] - env_package: soil - geo_loc_name: 'USA: Nowhere, Oklahoma' - growth_facil: greenhouse - lat_lon: 35.211445 -98.464612 - samp_store_temp: -80 Celsius - store_cond: frozen - samp_name: b - source_mat_id: x:6 -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: 10.4 - 45.9999 - elev: '123.0' - env_broad_scale: ______urban biome [ENVO:01000249] - env_local_scale: ________tunnel [ENVO:00000068] - env_medium: bare soil [ENVO:01001616] - env_package: soil - geo_loc_name: 'USA: Nowhere, Oklahoma' - growth_facil: greenhouse - lat_lon: 35.211445 -98.464612 - samp_store_temp: -80 Celsius - store_cond: frozen - samp_name: b - source_mat_id: x:7 -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: -10.4 - 45.9999 - elev: '123.0' - env_broad_scale: ______urban biome [ENVO:01000249] - env_local_scale: ________tunnel [ENVO:00000068] - env_medium: bare soil [ENVO:01001616] - env_package: soil - geo_loc_name: 'USA: Nowhere, Oklahoma' - growth_facil: greenhouse - lat_lon: 35.211445 -98.464612 - samp_store_temp: -80 Celsius - store_cond: frozen - samp_name: b - source_mat_id: x:8 -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: -5--6 - elev: '123.0' - env_broad_scale: ______urban biome [ENVO:01000249] - env_local_scale: ________tunnel [ENVO:00000068] - env_medium: bare soil [ENVO:01001616] - env_package: soil - geo_loc_name: 'USA: Nowhere, Oklahoma' - growth_facil: greenhouse - lat_lon: 35.211445 -98.464612 - samp_store_temp: -80 Celsius - store_cond: frozen - samp_name: b - source_mat_id: x:9 diff --git a/examples/output/SampleData-soil-data-exhaustive.json b/examples/output/SampleData-soil-data-exhaustive.json deleted file mode 100644 index e2a3f06d..00000000 --- a/examples/output/SampleData-soil-data-exhaustive.json +++ /dev/null @@ -1,145 +0,0 @@ -{ - "soil_data": [ - { - "analysis_type": [ - "metagenomics", - "metatranscriptomics" - ], - "air_temp_regm": "xxx", - "al_sat_meth": "xxx", - "annual_precpt": "111 units", - "annual_temp": "111 units", - "biotic_regm": "xxx", - "biotic_relationship": "free living", - "carb_nitro_ratio": 0.5, - "chem_administration": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22", - "climate_environment": "xxx", - "collection_date": "2022-01-15", - "collection_date_inc": "2022-01-22", - "collection_time": "11:11", - "collection_time_inc": "11:11", - "crop_rotation": "xxx", - "cur_land_use": "cities", - "cur_vegetation": "xxx", - "cur_vegetation_meth": "xxx", - "depth": "0 - 1", - "drainage_class": "well", - "ecosystem": "Environmental", - "ecosystem_category": "Terrestrial", - "ecosystem_subtype": "Unclassified", - "ecosystem_type": "Soil", - "elev": "123.0", - "env_broad_scale": "______urban biome [ENVO:01000249]", - "env_local_scale": "________tunnel [ENVO:00000068]", - "env_medium": "bare soil [ENVO:01001616]", - "env_package": "soil", - "experimental_factor": "xxx [ENVO:00000000]", - "experimental_factor_other": "xxx", - "extreme_event": "xxx", - "fao_class": "Rankers", - "filter_method": "xxx", - "fire": "2022-01-15", - "flooding": "xxx", - "gaseous_environment": "xxx", - "geo_loc_name": "USA: Maryland, Bethesda", - "growth_facil": "greenhouse", - "heavy_metals_meth": "xxx", - "horizon_meth": "xxx", - "humidity_regm": "xxx", - "isotope_exposure": "strontium 90 [ONTO:00000000]; 2010-10-31T08:45:15.432-0700", - "lat_lon": "77 88", - "light_regm": "incandescant light;10 lux;450 nanometer", - "link_class_info": "xxx", - "link_climate_info": "xxx", - "local_class": "xxx", - "local_class_meth": "xxx", - "micro_biomass_c_meth": "xxx", - "micro_biomass_meth": "xxx", - "micro_biomass_n_meth": "xxx", - "microbial_biomass": "111 units", - "microbial_biomass_c": "111 units", - "microbial_biomass_n": "111 units", - "non_microb_biomass": "xxx;123.45 units", - "non_microb_biomass_method": "xxx", - "org_matter": "111 units", - "org_nitro": "111 units", - "org_nitro_method": "xxx", - "other_treatment": "xxx", - "oxy_stat_samp": "anaerobic", - "ph": 9.0, - "ph_meth": "xxx", - "phosphate": "111 units", - "prev_land_use_meth": "xxx", - "previous_land_use": "circus tent;+0530", - "profile_position": "summit", - "salinity": "111 units", - "salinity_meth": "xxx", - "samp_collec_device": "xxx", - "samp_collec_method": "xxx", - "samp_mat_process": "text [ONTO:000000000]", - "samp_size": "111 units", - "samp_store_temp": "-80 Celsius", - "sample_link": "z:99", - "season_precpt": "111 units", - "season_temp": "111 units", - "sieving": "xxx", - "size_frac_low": "99 units", - "size_frac_up": "111 units", - "slope_aspect": "100 units", - "slope_gradient": "111 units", - "soil_horizon": "O horizon", - "soil_text_measure": "111 units", - "soil_texture_meth": "xxx", - "soil_type": "xxx [ENVO:00000000]", - "soil_type_meth": "xxx", - "specific_ecosystem": "Unclassified", - "start_date_inc": "2022-02-15", - "start_time_inc": "13:33:55", - "store_cond": "frozen", - "temp": "111 units", - "tillage": [ - "drill", - "chisel" - ], - "tot_carb": "111 units", - "tot_nitro_cont_meth": "xxx", - "tot_nitro_content": "111 units", - "tot_org_c_meth": "xxx", - "tot_org_carb": "111 units", - "tot_phosp": "111 units", - "water_cont_soil_meth": "xxx", - "water_content": "111 units", - "watering_regm": "xxx", - "samp_name": "a", - "source_mat_id": "x:1" - }, - { - "analysis_type": [ - "metagenomics", - "metatranscriptomics" - ], - "collection_date": "2022-01-15", - "depth": "0 - 1", - "ecosystem": "Environmental", - "ecosystem_category": "Terrestrial", - "ecosystem_subtype": "Unclassified", - "ecosystem_type": "Soil", - "elev": "123.0", - "env_broad_scale": "______urban biome [ENVO:01000249]", - "env_local_scale": "________tunnel [ENVO:00000068]", - "env_medium": "bare soil [ENVO:01001616]", - "env_package": "soil", - "geo_loc_name": "USA: Maryland, Bethesda", - "growth_facil": "greenhouse", - "lat_lon": "77 88", - "samp_store_temp": "-80 Celsius", - "sample_link": "z:99", - "slope_aspect": "100 units", - "specific_ecosystem": "Unclassified", - "store_cond": "frozen", - "samp_name": "b", - "source_mat_id": "x:2" - } - ], - "@type": "SampleData" -} \ No newline at end of file diff --git a/examples/output/SampleData-soil-data-exhaustive.yaml b/examples/output/SampleData-soil-data-exhaustive.yaml deleted file mode 100644 index c8f6486e..00000000 --- a/examples/output/SampleData-soil-data-exhaustive.yaml +++ /dev/null @@ -1,134 +0,0 @@ -soil_data: -- analysis_type: - - metagenomics - - metatranscriptomics - air_temp_regm: xxx - al_sat_meth: xxx - annual_precpt: 111 units - annual_temp: 111 units - biotic_regm: xxx - biotic_relationship: free living - carb_nitro_ratio: 0.5 - chem_administration: agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22 - climate_environment: xxx - collection_date: '2022-01-15' - collection_date_inc: '2022-01-22' - collection_time: '11:11' - collection_time_inc: '11:11' - crop_rotation: xxx - cur_land_use: cities - cur_vegetation: xxx - cur_vegetation_meth: xxx - depth: 0 - 1 - drainage_class: well - ecosystem: Environmental - ecosystem_category: Terrestrial - ecosystem_subtype: Unclassified - ecosystem_type: Soil - elev: '123.0' - env_broad_scale: ______urban biome [ENVO:01000249] - env_local_scale: ________tunnel [ENVO:00000068] - env_medium: bare soil [ENVO:01001616] - env_package: soil - experimental_factor: xxx [ENVO:00000000] - experimental_factor_other: xxx - extreme_event: xxx - fao_class: Rankers - filter_method: xxx - fire: '2022-01-15' - flooding: xxx - gaseous_environment: xxx - geo_loc_name: 'USA: Maryland, Bethesda' - growth_facil: greenhouse - heavy_metals_meth: xxx - horizon_meth: xxx - humidity_regm: xxx - isotope_exposure: strontium 90 [ONTO:00000000]; 2010-10-31T08:45:15.432-0700 - lat_lon: 77 88 - light_regm: incandescant light;10 lux;450 nanometer - link_class_info: xxx - link_climate_info: xxx - local_class: xxx - local_class_meth: xxx - micro_biomass_c_meth: xxx - micro_biomass_meth: xxx - micro_biomass_n_meth: xxx - microbial_biomass: 111 units - microbial_biomass_c: 111 units - microbial_biomass_n: 111 units - non_microb_biomass: xxx;123.45 units - non_microb_biomass_method: xxx - org_matter: 111 units - org_nitro: 111 units - org_nitro_method: xxx - other_treatment: xxx - oxy_stat_samp: anaerobic - ph: 9.0 - ph_meth: xxx - phosphate: 111 units - prev_land_use_meth: xxx - previous_land_use: circus tent;+0530 - profile_position: summit - salinity: 111 units - salinity_meth: xxx - samp_collec_device: xxx - samp_collec_method: xxx - samp_mat_process: text [ONTO:000000000] - samp_size: 111 units - samp_store_temp: -80 Celsius - sample_link: z:99 - season_precpt: 111 units - season_temp: 111 units - sieving: xxx - size_frac_low: 99 units - size_frac_up: 111 units - slope_aspect: 100 units - slope_gradient: 111 units - soil_horizon: O horizon - soil_text_measure: 111 units - soil_texture_meth: xxx - soil_type: xxx [ENVO:00000000] - soil_type_meth: xxx - specific_ecosystem: Unclassified - start_date_inc: '2022-02-15' - start_time_inc: '13:33:55' - store_cond: frozen - temp: 111 units - tillage: - - drill - - chisel - tot_carb: 111 units - tot_nitro_cont_meth: xxx - tot_nitro_content: 111 units - tot_org_c_meth: xxx - tot_org_carb: 111 units - tot_phosp: 111 units - water_cont_soil_meth: xxx - water_content: 111 units - watering_regm: xxx - samp_name: a - source_mat_id: x:1 -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: 0 - 1 - ecosystem: Environmental - ecosystem_category: Terrestrial - ecosystem_subtype: Unclassified - ecosystem_type: Soil - elev: '123.0' - env_broad_scale: ______urban biome [ENVO:01000249] - env_local_scale: ________tunnel [ENVO:00000068] - env_medium: bare soil [ENVO:01001616] - env_package: soil - geo_loc_name: 'USA: Maryland, Bethesda' - growth_facil: greenhouse - lat_lon: 77 88 - samp_store_temp: -80 Celsius - sample_link: z:99 - slope_aspect: 100 units - specific_ecosystem: Unclassified - store_cond: frozen - samp_name: b - source_mat_id: x:2 diff --git a/examples/output/SampleData-soil-data-minimal.json b/examples/output/SampleData-soil-data-minimal.json deleted file mode 100644 index 64e335a5..00000000 --- a/examples/output/SampleData-soil-data-minimal.json +++ /dev/null @@ -1,24 +0,0 @@ -{ - "soil_data": [ - { - "analysis_type": [ - "metagenomics", - "metatranscriptomics" - ], - "collection_date": "2022-01-15", - "depth": "0 - 1", - "elev": "123.0", - "env_broad_scale": "______urban biome [ENVO:01000249]", - "env_local_scale": "________tunnel [ENVO:00000068]", - "env_medium": "bare soil [ENVO:01001616]", - "env_package": "soil", - "geo_loc_name": "USA: Nowhere, Oklahoma", - "growth_facil": "greenhouse", - "lat_lon": "35.211445 -98.464612", - "samp_store_temp": "-80 Celsius", - "store_cond": "frozen", - "samp_name": "b" - } - ], - "@type": "SampleData" -} \ No newline at end of file diff --git a/examples/output/SampleData-soil-data-minimal.yaml b/examples/output/SampleData-soil-data-minimal.yaml deleted file mode 100644 index eed9a8bf..00000000 --- a/examples/output/SampleData-soil-data-minimal.yaml +++ /dev/null @@ -1,17 +0,0 @@ -soil_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: 0 - 1 - elev: '123.0' - env_broad_scale: ______urban biome [ENVO:01000249] - env_local_scale: ________tunnel [ENVO:00000068] - env_medium: bare soil [ENVO:01001616] - env_package: soil - geo_loc_name: 'USA: Nowhere, Oklahoma' - growth_facil: greenhouse - lat_lon: 35.211445 -98.464612 - samp_store_temp: -80 Celsius - store_cond: frozen - samp_name: b diff --git a/examples/output/SampleData-soil-data-water-content.json b/examples/output/SampleData-soil-data-water-content.json deleted file mode 100644 index e884fbaf..00000000 --- a/examples/output/SampleData-soil-data-water-content.json +++ /dev/null @@ -1,65 +0,0 @@ -{ - "soil_data": [ - { - "analysis_type": [ - "metagenomics", - "metatranscriptomics" - ], - "collection_date": "2022-01-15", - "depth": "0 - 1", - "elev": "123.0", - "env_broad_scale": "______urban biome [ENVO:01000249]", - "env_local_scale": "________tunnel [ENVO:00000068]", - "env_medium": "bare soil [ENVO:01001616]", - "env_package": "soil", - "geo_loc_name": "USA: Nowhere, Oklahoma", - "growth_facil": "greenhouse", - "lat_lon": "35.211445 -98.464612", - "samp_store_temp": "-80 Celsius", - "store_cond": "frozen", - "water_content": "75% dry weight", - "samp_name": "b" - }, - { - "analysis_type": [ - "metagenomics", - "metatranscriptomics" - ], - "collection_date": "2022-01-15", - "depth": "0 - 1", - "elev": "123.0", - "env_broad_scale": "______urban biome [ENVO:01000249]", - "env_local_scale": "________tunnel [ENVO:00000068]", - "env_medium": "bare soil [ENVO:01001616]", - "env_package": "soil", - "geo_loc_name": "USA: Nowhere, Oklahoma", - "growth_facil": "greenhouse", - "lat_lon": "35.211445 -98.464612", - "samp_store_temp": "-80 Celsius", - "store_cond": "frozen", - "water_content": "5 g water / g dry soil", - "samp_name": "c" - }, - { - "analysis_type": [ - "metagenomics", - "metatranscriptomics" - ], - "collection_date": "2022-01-15", - "depth": "0 - 1", - "elev": "123.0", - "env_broad_scale": "______urban biome [ENVO:01000249]", - "env_local_scale": "________tunnel [ENVO:00000068]", - "env_medium": "bare soil [ENVO:01001616]", - "env_package": "soil", - "geo_loc_name": "USA: Nowhere, Oklahoma", - "growth_facil": "greenhouse", - "lat_lon": "35.211445 -98.464612", - "samp_store_temp": "-80 Celsius", - "store_cond": "frozen", - "water_content": ".75 g water per g soil WHC", - "samp_name": "d" - } - ], - "@type": "SampleData" -} \ No newline at end of file diff --git a/examples/output/SampleData-soil-data-water-content.yaml b/examples/output/SampleData-soil-data-water-content.yaml deleted file mode 100644 index 4179c98d..00000000 --- a/examples/output/SampleData-soil-data-water-content.yaml +++ /dev/null @@ -1,52 +0,0 @@ -soil_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: 0 - 1 - elev: '123.0' - env_broad_scale: ______urban biome [ENVO:01000249] - env_local_scale: ________tunnel [ENVO:00000068] - env_medium: bare soil [ENVO:01001616] - env_package: soil - geo_loc_name: 'USA: Nowhere, Oklahoma' - growth_facil: greenhouse - lat_lon: 35.211445 -98.464612 - samp_store_temp: -80 Celsius - store_cond: frozen - water_content: 75% dry weight - samp_name: b -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: 0 - 1 - elev: '123.0' - env_broad_scale: ______urban biome [ENVO:01000249] - env_local_scale: ________tunnel [ENVO:00000068] - env_medium: bare soil [ENVO:01001616] - env_package: soil - geo_loc_name: 'USA: Nowhere, Oklahoma' - growth_facil: greenhouse - lat_lon: 35.211445 -98.464612 - samp_store_temp: -80 Celsius - store_cond: frozen - water_content: 5 g water / g dry soil - samp_name: c -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: 0 - 1 - elev: '123.0' - env_broad_scale: ______urban biome [ENVO:01000249] - env_local_scale: ________tunnel [ENVO:00000068] - env_medium: bare soil [ENVO:01001616] - env_package: soil - geo_loc_name: 'USA: Nowhere, Oklahoma' - growth_facil: greenhouse - lat_lon: 35.211445 -98.464612 - samp_store_temp: -80 Celsius - store_cond: frozen - water_content: .75 g water per g soil WHC - samp_name: d diff --git a/examples/output/SampleData-water-data-0-dim-depth.json b/examples/output/SampleData-water-data-0-dim-depth.json deleted file mode 100644 index f5694110..00000000 --- a/examples/output/SampleData-water-data-0-dim-depth.json +++ /dev/null @@ -1,20 +0,0 @@ -{ - "water_data": [ - { - "analysis_type": [ - "metagenomics", - "metatranscriptomics" - ], - "collection_date": "2022-01-15", - "depth": "1.5", - "env_broad_scale": "oceanic epipelagic zone biome [ENVO:01000033]", - "env_local_scale": "sand [ONTO:1234]", - "env_medium": "sand [ONTO:1234]", - "env_package": "xyz", - "geo_loc_name": "USA: Crater Lake", - "samp_name": "xyz", - "source_mat_id": "x:1" - } - ], - "@type": "SampleData" -} \ No newline at end of file diff --git a/examples/output/SampleData-water-data-0-dim-depth.yaml b/examples/output/SampleData-water-data-0-dim-depth.yaml deleted file mode 100644 index fb159ea8..00000000 --- a/examples/output/SampleData-water-data-0-dim-depth.yaml +++ /dev/null @@ -1,13 +0,0 @@ -water_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: '1.5' - env_broad_scale: oceanic epipelagic zone biome [ENVO:01000033] - env_local_scale: sand [ONTO:1234] - env_medium: sand [ONTO:1234] - env_package: xyz - geo_loc_name: 'USA: Crater Lake' - samp_name: xyz - source_mat_id: x:1 diff --git a/examples/output/SampleData-water-data-1-dim-depth.json b/examples/output/SampleData-water-data-1-dim-depth.json deleted file mode 100644 index 08101da2..00000000 --- a/examples/output/SampleData-water-data-1-dim-depth.json +++ /dev/null @@ -1,20 +0,0 @@ -{ - "water_data": [ - { - "analysis_type": [ - "metagenomics", - "metatranscriptomics" - ], - "collection_date": "2022-01-15", - "depth": "1.5 - 2.5", - "env_broad_scale": "oceanic epipelagic zone biome [ENVO:01000033]", - "env_local_scale": "sand [ONTO:1234]", - "env_medium": "sand [ONTO:1234]", - "env_package": "xyz", - "geo_loc_name": "USA: Crater Lake", - "samp_name": "xyz", - "source_mat_id": "x:1" - } - ], - "@type": "SampleData" -} \ No newline at end of file diff --git a/examples/output/SampleData-water-data-1-dim-depth.yaml b/examples/output/SampleData-water-data-1-dim-depth.yaml deleted file mode 100644 index fea324f0..00000000 --- a/examples/output/SampleData-water-data-1-dim-depth.yaml +++ /dev/null @@ -1,13 +0,0 @@ -water_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: 1.5 - 2.5 - env_broad_scale: oceanic epipelagic zone biome [ENVO:01000033] - env_local_scale: sand [ONTO:1234] - env_medium: sand [ONTO:1234] - env_package: xyz - geo_loc_name: 'USA: Crater Lake' - samp_name: xyz - source_mat_id: x:1 diff --git a/examples/output/SampleData-water-data-depth-formats.json b/examples/output/SampleData-water-data-depth-formats.json deleted file mode 100644 index b2cc0e3d..00000000 --- a/examples/output/SampleData-water-data-depth-formats.json +++ /dev/null @@ -1,101 +0,0 @@ -{ - "water_data": [ - { - "analysis_type": [ - "metagenomics", - "metatranscriptomics" - ], - "collection_date": "2022-01-15", - "depth": "111", - "env_broad_scale": "oceanic epipelagic zone biome [ENVO:01000033]", - "env_local_scale": "sand [ONTO:1234]", - "env_medium": "sand [ONTO:1234]", - "env_package": "xyz", - "geo_loc_name": "USA: Crater Lake", - "samp_mat_process": "text [ONTO:000000000]", - "samp_name": "xyz", - "source_mat_id": "x:1" - }, - { - "analysis_type": [ - "metagenomics", - "metatranscriptomics" - ], - "collection_date": "2022-01-15", - "depth": "0", - "env_broad_scale": "oceanic epipelagic zone biome [ENVO:01000033]", - "env_local_scale": "sand [ONTO:1234]", - "env_medium": "sand [ONTO:1234]", - "env_package": "xyz", - "geo_loc_name": "USA: Crater Lake", - "samp_mat_process": "text [ONTO:000000000]", - "samp_name": "xyz", - "source_mat_id": "x:1" - }, - { - "analysis_type": [ - "metagenomics", - "metatranscriptomics" - ], - "collection_date": "2022-01-15", - "depth": "-3.333", - "env_broad_scale": "oceanic epipelagic zone biome [ENVO:01000033]", - "env_local_scale": "sand [ONTO:1234]", - "env_medium": "sand [ONTO:1234]", - "env_package": "xyz", - "geo_loc_name": "USA: Crater Lake", - "samp_mat_process": "text [ONTO:000000000]", - "samp_name": "xyz", - "source_mat_id": "x:1" - }, - { - "analysis_type": [ - "metagenomics", - "metatranscriptomics" - ], - "collection_date": "2022-01-15", - "depth": "13.4-16.99", - "env_broad_scale": "oceanic epipelagic zone biome [ENVO:01000033]", - "env_local_scale": "sand [ONTO:1234]", - "env_medium": "sand [ONTO:1234]", - "env_package": "xyz", - "geo_loc_name": "USA: Crater Lake", - "samp_mat_process": "text [ONTO:000000000]", - "samp_name": "xyz", - "source_mat_id": "x:1" - }, - { - "analysis_type": [ - "metagenomics", - "metatranscriptomics" - ], - "collection_date": "2022-01-15", - "depth": "-99.99 - 38", - "env_broad_scale": "oceanic epipelagic zone biome [ENVO:01000033]", - "env_local_scale": "sand [ONTO:1234]", - "env_medium": "sand [ONTO:1234]", - "env_package": "xyz", - "geo_loc_name": "USA: Crater Lake", - "samp_mat_process": "text [ONTO:000000000]", - "samp_name": "xyz", - "source_mat_id": "x:1" - }, - { - "analysis_type": [ - "metagenomics", - "metatranscriptomics" - ], - "collection_date": "2022-01-15", - "depth": "-3--4", - "env_broad_scale": "oceanic epipelagic zone biome [ENVO:01000033]", - "env_local_scale": "sand [ONTO:1234]", - "env_medium": "sand [ONTO:1234]", - "env_package": "xyz", - "geo_loc_name": "USA: Crater Lake", - "samp_mat_process": "text [ONTO:000000000]", - "samp_name": "xyz", - "source_mat_id": "x:1" - } - ], - "@type": "SampleData" -} \ No newline at end of file diff --git a/examples/output/SampleData-water-data-depth-formats.yaml b/examples/output/SampleData-water-data-depth-formats.yaml deleted file mode 100644 index 9bfcd24e..00000000 --- a/examples/output/SampleData-water-data-depth-formats.yaml +++ /dev/null @@ -1,79 +0,0 @@ -water_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: '111' - env_broad_scale: oceanic epipelagic zone biome [ENVO:01000033] - env_local_scale: sand [ONTO:1234] - env_medium: sand [ONTO:1234] - env_package: xyz - geo_loc_name: 'USA: Crater Lake' - samp_mat_process: text [ONTO:000000000] - samp_name: xyz - source_mat_id: x:1 -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: '0' - env_broad_scale: oceanic epipelagic zone biome [ENVO:01000033] - env_local_scale: sand [ONTO:1234] - env_medium: sand [ONTO:1234] - env_package: xyz - geo_loc_name: 'USA: Crater Lake' - samp_mat_process: text [ONTO:000000000] - samp_name: xyz - source_mat_id: x:1 -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: '-3.333' - env_broad_scale: oceanic epipelagic zone biome [ENVO:01000033] - env_local_scale: sand [ONTO:1234] - env_medium: sand [ONTO:1234] - env_package: xyz - geo_loc_name: 'USA: Crater Lake' - samp_mat_process: text [ONTO:000000000] - samp_name: xyz - source_mat_id: x:1 -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: 13.4-16.99 - env_broad_scale: oceanic epipelagic zone biome [ENVO:01000033] - env_local_scale: sand [ONTO:1234] - env_medium: sand [ONTO:1234] - env_package: xyz - geo_loc_name: 'USA: Crater Lake' - samp_mat_process: text [ONTO:000000000] - samp_name: xyz - source_mat_id: x:1 -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: -99.99 - 38 - env_broad_scale: oceanic epipelagic zone biome [ENVO:01000033] - env_local_scale: sand [ONTO:1234] - env_medium: sand [ONTO:1234] - env_package: xyz - geo_loc_name: 'USA: Crater Lake' - samp_mat_process: text [ONTO:000000000] - samp_name: xyz - source_mat_id: x:1 -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: -3--4 - env_broad_scale: oceanic epipelagic zone biome [ENVO:01000033] - env_local_scale: sand [ONTO:1234] - env_medium: sand [ONTO:1234] - env_package: xyz - geo_loc_name: 'USA: Crater Lake' - samp_mat_process: text [ONTO:000000000] - samp_name: xyz - source_mat_id: x:1 diff --git a/examples/output/SampleData-water-data-exhaustive-max-generic.json b/examples/output/SampleData-water-data-exhaustive-max-generic.json deleted file mode 100644 index 2984106c..00000000 --- a/examples/output/SampleData-water-data-exhaustive-max-generic.json +++ /dev/null @@ -1,113 +0,0 @@ -{ - "water_data": [ - { - "analysis_type": [ - "metagenomics", - "metatranscriptomics" - ], - "alkalinity": "100 units", - "alkalinity_method": "xyz", - "alkyl_diethers": "100 units", - "aminopept_act": "100 units", - "ammonium": "100 units", - "atmospheric_data": "xyz;100 units", - "bac_prod": "100 units", - "bac_resp": "100 units", - "bacteria_carb_prod": "100 units", - "biomass": "xyz;100 units", - "bishomohopanol": "100 units", - "bromide": "100 units", - "calcium": "100 units", - "carb_nitro_ratio": 1.5, - "chem_administration": "xyz [XYZ:123];2111-11-11", - "chloride": "100 units", - "chlorophyll": "100 units", - "collection_date": "2021-01-01", - "conduc": "100 units", - "density": "100 units", - "depth": "1.5", - "diether_lipids": "xyz;100 units", - "diss_carb_dioxide": "100 units", - "diss_hydrogen": "100 units", - "diss_inorg_carb": "100 units", - "diss_inorg_nitro": "100 units", - "diss_inorg_phosp": "100 units", - "diss_org_carb": "100 units", - "diss_org_nitro": "100 units", - "diss_oxygen": "100 units", - "down_par": "100 units", - "ecosystem": "xyz", - "ecosystem_category": "xyz", - "ecosystem_subtype": "xyz", - "ecosystem_type": "xyz", - "elev": 1.5, - "env_broad_scale": "xyz xyz xyz [XYZ:123]", - "env_local_scale": "xyz xyz xyz [XYZ:123]", - "env_medium": "xyz xyz xyz [XYZ:123]", - "env_package": "xyz", - "experimental_factor": "xyz xyz xyz [XYZ:123]", - "fluor": "100 units", - "geo_loc_name": "xyz: xyz, xyz", - "glucosidase_act": "100 units", - "horizon_meth": "xyz", - "lat_lon": "78 89", - "light_intensity": "100 units", - "mean_frict_vel": "100 units", - "mean_peak_frict_vel": "100 units", - "misc_param": "xyz;100 units", - "n_alkanes": "xyz;100 units", - "nitrate": "100 units", - "nitrite": "100 units", - "nitro": "100 units", - "org_carb": "100 units", - "org_matter": "100 units", - "org_nitro": "100 units", - "organism_count": "xyz;100 units;qPCR", - "oxy_stat_samp": "anaerobic", - "part_org_carb": "100 units", - "part_org_nitro": "100 units", - "perturbation": "xyz", - "petroleum_hydrocarb": "100 units", - "ph": 1.5, - "ph_meth": "xyz", - "phaeopigments": "xyz;100 units", - "phosphate": "100 units", - "phosplipid_fatt_acid": "xyz;100 units", - "potassium": "100 units", - "pressure": "100 units", - "primary_prod": "100 units", - "redox_potential": "100 units", - "salinity": "100 units", - "samp_collec_device": "xyz", - "samp_collec_method": "xyz", - "samp_mat_process": "text [ONTO:000000000]", - "samp_size": "100 units", - "samp_store_dur": "xyz", - "samp_store_loc": "xyz", - "samp_store_temp": "100 units", - "sample_link": "z:99", - "silicate": "100 units", - "size_frac": "xyz", - "size_frac_low": "100 units", - "size_frac_up": "100 units", - "sodium": "100 units", - "soluble_react_phosp": "100 units", - "specific_ecosystem": "xyz", - "sulfate": "100 units", - "sulfide": "100 units", - "suspend_part_matter": "100 units", - "temp": "100 units", - "tidal_stage": "high tide", - "tot_depth_water_col": "100 units", - "tot_diss_nitro": "100 units", - "tot_inorg_nitro": "100 units", - "tot_nitro": "100 units", - "tot_part_carb": "100 units", - "turbidity": "100 units", - "water_current": "100 units", - "samp_name": "xyz", - "source_mat_id": "x:1" - } - ], - "@type": "SampleData" -} \ No newline at end of file diff --git a/examples/output/SampleData-water-data-exhaustive-max-generic.yaml b/examples/output/SampleData-water-data-exhaustive-max-generic.yaml deleted file mode 100644 index 491321a5..00000000 --- a/examples/output/SampleData-water-data-exhaustive-max-generic.yaml +++ /dev/null @@ -1,106 +0,0 @@ -water_data: -- analysis_type: - - metagenomics - - metatranscriptomics - alkalinity: 100 units - alkalinity_method: xyz - alkyl_diethers: 100 units - aminopept_act: 100 units - ammonium: 100 units - atmospheric_data: xyz;100 units - bac_prod: 100 units - bac_resp: 100 units - bacteria_carb_prod: 100 units - biomass: xyz;100 units - bishomohopanol: 100 units - bromide: 100 units - calcium: 100 units - carb_nitro_ratio: 1.5 - chem_administration: xyz [XYZ:123];2111-11-11 - chloride: 100 units - chlorophyll: 100 units - collection_date: '2021-01-01' - conduc: 100 units - density: 100 units - depth: '1.5' - diether_lipids: xyz;100 units - diss_carb_dioxide: 100 units - diss_hydrogen: 100 units - diss_inorg_carb: 100 units - diss_inorg_nitro: 100 units - diss_inorg_phosp: 100 units - diss_org_carb: 100 units - diss_org_nitro: 100 units - diss_oxygen: 100 units - down_par: 100 units - ecosystem: xyz - ecosystem_category: xyz - ecosystem_subtype: xyz - ecosystem_type: xyz - elev: 1.5 - env_broad_scale: xyz xyz xyz [XYZ:123] - env_local_scale: xyz xyz xyz [XYZ:123] - env_medium: xyz xyz xyz [XYZ:123] - env_package: xyz - experimental_factor: xyz xyz xyz [XYZ:123] - fluor: 100 units - geo_loc_name: 'xyz: xyz, xyz' - glucosidase_act: 100 units - horizon_meth: xyz - lat_lon: 78 89 - light_intensity: 100 units - mean_frict_vel: 100 units - mean_peak_frict_vel: 100 units - misc_param: xyz;100 units - n_alkanes: xyz;100 units - nitrate: 100 units - nitrite: 100 units - nitro: 100 units - org_carb: 100 units - org_matter: 100 units - org_nitro: 100 units - organism_count: xyz;100 units;qPCR - oxy_stat_samp: anaerobic - part_org_carb: 100 units - part_org_nitro: 100 units - perturbation: xyz - petroleum_hydrocarb: 100 units - ph: 1.5 - ph_meth: xyz - phaeopigments: xyz;100 units - phosphate: 100 units - phosplipid_fatt_acid: xyz;100 units - potassium: 100 units - pressure: 100 units - primary_prod: 100 units - redox_potential: 100 units - salinity: 100 units - samp_collec_device: xyz - samp_collec_method: xyz - samp_mat_process: text [ONTO:000000000] - samp_size: 100 units - samp_store_dur: xyz - samp_store_loc: xyz - samp_store_temp: 100 units - sample_link: z:99 - silicate: 100 units - size_frac: xyz - size_frac_low: 100 units - size_frac_up: 100 units - sodium: 100 units - soluble_react_phosp: 100 units - specific_ecosystem: xyz - sulfate: 100 units - sulfide: 100 units - suspend_part_matter: 100 units - temp: 100 units - tidal_stage: high tide - tot_depth_water_col: 100 units - tot_diss_nitro: 100 units - tot_inorg_nitro: 100 units - tot_nitro: 100 units - tot_part_carb: 100 units - turbidity: 100 units - water_current: 100 units - samp_name: xyz - source_mat_id: x:1 diff --git a/examples/output/SampleData-water-data-exhaustive.json b/examples/output/SampleData-water-data-exhaustive.json deleted file mode 100644 index 5be454ef..00000000 --- a/examples/output/SampleData-water-data-exhaustive.json +++ /dev/null @@ -1,114 +0,0 @@ -{ - "water_data": [ - { - "analysis_type": [ - "metagenomics", - "metatranscriptomics" - ], - "alkalinity": "50 milligram per liter", - "alkalinity_method": "titration", - "alkyl_diethers": "0.005 mole per liter", - "aminopept_act": "0.269 mole per liter per hour", - "ammonium": "1.5 milligram per liter", - "atmospheric_data": "wind speed;9 knots|rain;2.3 inches", - "bac_prod": "5 milligram per cubic meter per day", - "bac_resp": "300 micromole oxygen per liter per hour", - "bacteria_carb_prod": "2.53 microgram per liter per hour", - "biomass": "total;20 gram|archeal;1 gram", - "bishomohopanol": "14 microgram per liter", - "bromide": "0.05 parts per million", - "calcium": "0.2 micromole per liter", - "carb_nitro_ratio": 1.5, - "chem_administration": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22", - "chloride": "5000 milligram per liter", - "chlorophyll": "5 milligram per cubic meter", - "collection_date": "2021-01-01", - "conduc": "10 milliSiemens per centimeter", - "density": "1000 kilogram per cubic meter", - "depth": "1.5", - "diether_lipids": "phosphatidylglycerol;1.5 parts per million|phosphatidylglycerylsulphate;1.5 parts per million", - "diss_carb_dioxide": "5 milligram per liter", - "diss_hydrogen": "0.3 micromole per liter", - "diss_inorg_carb": "2059 micromole per liter", - "diss_inorg_nitro": "761 micromole per liter", - "diss_inorg_phosp": "56.5 micromole per liter", - "diss_org_carb": "205.9 micromole per liter", - "diss_org_nitro": "76.1 micromole per liter", - "diss_oxygen": "175 micromole per liter", - "down_par": "28.71 microEinstein per square meter per second", - "ecosystem": "xyz", - "ecosystem_category": "xyz", - "ecosystem_subtype": "xyz", - "ecosystem_type": "xyz", - "elev": 1.5, - "env_broad_scale": "oceanic epipelagic zone biome [ENVO:01000033]", - "env_local_scale": "sand [ONTO:1234]", - "env_medium": "sand [ONTO:1234]", - "env_package": "xyz", - "experimental_factor": "time series design [EFO:0001779]", - "fluor": "2.5 volts", - "geo_loc_name": "USA: Maryland, Bethesda", - "glucosidase_act": "5 mol per liter per hour", - "horizon_meth": "xyz", - "lat_lon": "78 89", - "light_intensity": "0.3 lux", - "mean_frict_vel": "0.5 meter per second", - "mean_peak_frict_vel": "1 meter per second", - "misc_param": "Bicarbonate ion concentration;2075 micromole per kilogram|Perchlorate ion concentration;1111 micromole per kilogram", - "n_alkanes": "n-hexadecane;100 milligram per liter|n-octane;111 milligram per liter", - "nitrate": "65 micromole per liter", - "nitrite": "0.5 micromole per liter", - "nitro": "4.2 micromole per liter", - "org_carb": "1.5 microgram per liter", - "org_matter": "1.75 milligram per cubic meter", - "org_nitro": "4 micromole per liter", - "organism_count": "total prokaryotes;3.5e7 cells per milliliter;qPCR|total prokaryotes;1e5 CFU;MPN", - "oxy_stat_samp": "anaerobic", - "part_org_carb": "1.92 micromole per liter", - "part_org_nitro": "0.3 micromole per liter", - "perturbation": "xyz1|xyz2", - "petroleum_hydrocarb": "0.05 micromole per liter", - "ph": 1.5, - "ph_meth": "xyz", - "phaeopigments": "phaeopigment 1;1.5 parts per million|phaeopigment 2;1.5 parts per million", - "phosphate": "0.7 micromole per liter", - "phosplipid_fatt_acid": "Tuberculostearic acid;1.5 parts per million|Palmitoleic acid;1.5 parts per million", - "photon_flux": "3.926 micromole photons per second per square meter", - "potassium": "463 milligram per liter", - "pressure": "50 atmosphere", - "primary_prod": "100 milligram per cubic meter per day", - "redox_potential": "300 millivolt", - "salinity": "25 practical salinity unit", - "samp_collec_device": "xyz", - "samp_collec_method": "xyz", - "samp_mat_process": "text [ONTO:000000000]", - "samp_size": "5 liter", - "samp_store_dur": "xyz", - "samp_store_loc": "xyz", - "samp_store_temp": "-80 degree Celsius", - "sample_link": "z:99", - "silicate": "0.05 micromole per liter", - "size_frac": "xyz", - "size_frac_low": "0.2 micrometer", - "size_frac_up": "20 micrometer", - "sodium": "10.5 milligram per liter", - "soluble_react_phosp": "0.1 milligram per liter", - "specific_ecosystem": "xyz", - "sulfate": "5 micromole per liter", - "sulfide": "2 micromole per liter", - "suspend_part_matter": "0.5 milligram per liter", - "temp": "25 degree Celsius", - "tidal_stage": "high tide", - "tot_depth_water_col": "500 meter", - "tot_diss_nitro": "40 microgram per liter", - "tot_inorg_nitro": "40 microgram per liter", - "tot_nitro": "50 micromole per liter", - "tot_part_carb": "35 micromole per liter", - "turbidity": "0.3 nephelometric turbidity units", - "water_current": "10 cubic meter per second", - "samp_name": "xyz", - "source_mat_id": "x:1" - } - ], - "@type": "SampleData" -} \ No newline at end of file diff --git a/examples/output/SampleData-water-data-exhaustive.yaml b/examples/output/SampleData-water-data-exhaustive.yaml deleted file mode 100644 index 4b92ca17..00000000 --- a/examples/output/SampleData-water-data-exhaustive.yaml +++ /dev/null @@ -1,112 +0,0 @@ -water_data: -- analysis_type: - - metagenomics - - metatranscriptomics - alkalinity: 50 milligram per liter - alkalinity_method: titration - alkyl_diethers: 0.005 mole per liter - aminopept_act: 0.269 mole per liter per hour - ammonium: 1.5 milligram per liter - atmospheric_data: wind speed;9 knots|rain;2.3 inches - bac_prod: 5 milligram per cubic meter per day - bac_resp: 300 micromole oxygen per liter per hour - bacteria_carb_prod: 2.53 microgram per liter per hour - biomass: total;20 gram|archeal;1 gram - bishomohopanol: 14 microgram per liter - bromide: 0.05 parts per million - calcium: 0.2 micromole per liter - carb_nitro_ratio: 1.5 - chem_administration: agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22 - chloride: 5000 milligram per liter - chlorophyll: 5 milligram per cubic meter - collection_date: '2021-01-01' - conduc: 10 milliSiemens per centimeter - density: 1000 kilogram per cubic meter - depth: '1.5' - diether_lipids: phosphatidylglycerol;1.5 parts per million|phosphatidylglycerylsulphate;1.5 - parts per million - diss_carb_dioxide: 5 milligram per liter - diss_hydrogen: 0.3 micromole per liter - diss_inorg_carb: 2059 micromole per liter - diss_inorg_nitro: 761 micromole per liter - diss_inorg_phosp: 56.5 micromole per liter - diss_org_carb: 205.9 micromole per liter - diss_org_nitro: 76.1 micromole per liter - diss_oxygen: 175 micromole per liter - down_par: 28.71 microEinstein per square meter per second - ecosystem: xyz - ecosystem_category: xyz - ecosystem_subtype: xyz - ecosystem_type: xyz - elev: 1.5 - env_broad_scale: oceanic epipelagic zone biome [ENVO:01000033] - env_local_scale: sand [ONTO:1234] - env_medium: sand [ONTO:1234] - env_package: xyz - experimental_factor: time series design [EFO:0001779] - fluor: 2.5 volts - geo_loc_name: 'USA: Maryland, Bethesda' - glucosidase_act: 5 mol per liter per hour - horizon_meth: xyz - lat_lon: 78 89 - light_intensity: 0.3 lux - mean_frict_vel: 0.5 meter per second - mean_peak_frict_vel: 1 meter per second - misc_param: Bicarbonate ion concentration;2075 micromole per kilogram|Perchlorate - ion concentration;1111 micromole per kilogram - n_alkanes: n-hexadecane;100 milligram per liter|n-octane;111 milligram per liter - nitrate: 65 micromole per liter - nitrite: 0.5 micromole per liter - nitro: 4.2 micromole per liter - org_carb: 1.5 microgram per liter - org_matter: 1.75 milligram per cubic meter - org_nitro: 4 micromole per liter - organism_count: total prokaryotes;3.5e7 cells per milliliter;qPCR|total prokaryotes;1e5 - CFU;MPN - oxy_stat_samp: anaerobic - part_org_carb: 1.92 micromole per liter - part_org_nitro: 0.3 micromole per liter - perturbation: xyz1|xyz2 - petroleum_hydrocarb: 0.05 micromole per liter - ph: 1.5 - ph_meth: xyz - phaeopigments: phaeopigment 1;1.5 parts per million|phaeopigment 2;1.5 parts per - million - phosphate: 0.7 micromole per liter - phosplipid_fatt_acid: Tuberculostearic acid;1.5 parts per million|Palmitoleic acid;1.5 - parts per million - photon_flux: 3.926 micromole photons per second per square meter - potassium: 463 milligram per liter - pressure: 50 atmosphere - primary_prod: 100 milligram per cubic meter per day - redox_potential: 300 millivolt - salinity: 25 practical salinity unit - samp_collec_device: xyz - samp_collec_method: xyz - samp_mat_process: text [ONTO:000000000] - samp_size: 5 liter - samp_store_dur: xyz - samp_store_loc: xyz - samp_store_temp: -80 degree Celsius - sample_link: z:99 - silicate: 0.05 micromole per liter - size_frac: xyz - size_frac_low: 0.2 micrometer - size_frac_up: 20 micrometer - sodium: 10.5 milligram per liter - soluble_react_phosp: 0.1 milligram per liter - specific_ecosystem: xyz - sulfate: 5 micromole per liter - sulfide: 2 micromole per liter - suspend_part_matter: 0.5 milligram per liter - temp: 25 degree Celsius - tidal_stage: high tide - tot_depth_water_col: 500 meter - tot_diss_nitro: 40 microgram per liter - tot_inorg_nitro: 40 microgram per liter - tot_nitro: 50 micromole per liter - tot_part_carb: 35 micromole per liter - turbidity: 0.3 nephelometric turbidity units - water_current: 10 cubic meter per second - samp_name: xyz - source_mat_id: x:1 diff --git a/examples/output/SampleData-water-data-minimal.json b/examples/output/SampleData-water-data-minimal.json deleted file mode 100644 index dfc8491b..00000000 --- a/examples/output/SampleData-water-data-minimal.json +++ /dev/null @@ -1,20 +0,0 @@ -{ - "water_data": [ - { - "analysis_type": [ - "metagenomics", - "metatranscriptomics" - ], - "collection_date": "2022-01-15", - "depth": "111", - "env_broad_scale": "oceanic epipelagic zone biome [ENVO:01000033]", - "env_local_scale": "sand [ONTO:1234]", - "env_medium": "sand [ONTO:1234]", - "env_package": "xyz", - "geo_loc_name": "USA: Crater Lake", - "samp_mat_process": "text [ONTO:000000000]", - "samp_name": "xyz" - } - ], - "@type": "SampleData" -} \ No newline at end of file diff --git a/examples/output/SampleData-water-data-minimal.yaml b/examples/output/SampleData-water-data-minimal.yaml deleted file mode 100644 index eff7c68e..00000000 --- a/examples/output/SampleData-water-data-minimal.yaml +++ /dev/null @@ -1,13 +0,0 @@ -water_data: -- analysis_type: - - metagenomics - - metatranscriptomics - collection_date: '2022-01-15' - depth: '111' - env_broad_scale: oceanic epipelagic zone biome [ENVO:01000033] - env_local_scale: sand [ONTO:1234] - env_medium: sand [ONTO:1234] - env_package: xyz - geo_loc_name: 'USA: Crater Lake' - samp_mat_process: text [ONTO:000000000] - samp_name: xyz diff --git a/project/json/nmdc_submission_schema.json b/project/json/nmdc_submission_schema.json deleted file mode 100644 index 98983072..00000000 --- a/project/json/nmdc_submission_schema.json +++ /dev/null @@ -1,119253 +0,0 @@ -{ - "name": "nmdc_submission_schema", - "description": "Schema for creating Data Harmonizer interfaces for biosamples based on MIxS and other standards", - "id": "https://example.com/nmdc_submission_schema", - "version": "0.0.0", - "prefixes": { - "UO": { - "prefix_prefix": "UO", - "prefix_reference": "http://purl.obolibrary.org/obo/UO_" - }, - "qud": { - "prefix_prefix": "qud", - "prefix_reference": "http://qudt.org/1.1/schema/qudt#" - }, - "xsd": { - "prefix_prefix": "xsd", - "prefix_reference": "http://www.w3.org/2001/XMLSchema#" - }, - "nmdc_sub_schema": { - "prefix_prefix": "nmdc_sub_schema", - "prefix_reference": "https://example.com/nmdc_sub_schema/" - }, - "linkml": { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - "shex": { - "prefix_prefix": "shex", - "prefix_reference": "http://www.w3.org/ns/shex#" - }, - "schema": { - "prefix_prefix": "schema", - "prefix_reference": "http://schema.org/" - }, - "EFO": { - "prefix_prefix": "EFO", - "prefix_reference": "http://www.ebi.ac.uk/efo/" - }, - "ISA": { - "prefix_prefix": "ISA", - "prefix_reference": "http://example.com/isa/" - }, - "MetaNetX": { - "prefix_prefix": "MetaNetX", - "prefix_reference": "http://example.com/metanetx/" - }, - "RetroRules": { - "prefix_prefix": "RetroRules", - "prefix_reference": "http://example.com/retrorules/" - }, - "emsl.project": { - "prefix_prefix": "emsl.project", - "prefix_reference": "https://bioregistry.io/emsl.project:" - }, - "generic": { - "prefix_prefix": "generic", - "prefix_reference": "https://example.com/generic/" - }, - "gnps.task": { - "prefix_prefix": "gnps.task", - "prefix_reference": "https://bioregistry.io/gnps.task:" - }, - "gtpo": { - "prefix_prefix": "gtpo", - "prefix_reference": "http://example.com/gtpo/" - }, - "igsn": { - "prefix_prefix": "igsn", - "prefix_reference": "https://app.geosamples.org/sample/igsn/" - }, - "jgi.proposal": { - "prefix_prefix": "jgi.proposal", - "prefix_reference": "https://bioregistry.io/jgi.proposal:" - }, - "jgi": { - "prefix_prefix": "jgi", - "prefix_reference": "http://example.com/jgi/" - }, - "mgnify.proj": { - "prefix_prefix": "mgnify.proj", - "prefix_reference": "https://identifiers.org/mgnify.proj:" - }, - "neon.identifier": { - "prefix_prefix": "neon.identifier", - "prefix_reference": "http://example.org/neon/identifier/" - }, - "neon.schema": { - "prefix_prefix": "neon.schema", - "prefix_reference": "http://example.org/neon/schema/" - }, - "nmdc": { - "prefix_prefix": "nmdc", - "prefix_reference": "https://w3id.org/nmdc/" - }, - "skos": { - "prefix_prefix": "skos", - "prefix_reference": "http://www.w3.org/2004/02/skos/core#" - }, - "prov": { - "prefix_prefix": "prov", - "prefix_reference": "http://www.w3.org/ns/prov#" - }, - "rdf": { - "prefix_prefix": "rdf", - "prefix_reference": "http://www.w3.org/1999/02/22-rdf-syntax-ns#" - }, - "rdfs": { - "prefix_prefix": "rdfs", - "prefix_reference": "http://www.w3.org/2000/01/rdf-schema#" - }, - "emsl": { - "prefix_prefix": "emsl", - "prefix_reference": "http://example.org/emsl_in_mongodb/" - }, - "Contaminant": { - "prefix_prefix": "Contaminant", - "prefix_reference": "http://example.org/contaminant/" - }, - "KEGG.COMPOUND": { - "prefix_prefix": "KEGG.COMPOUND", - "prefix_reference": "http://identifiers.org/kegg.compound/" - }, - "dcterms": { - "prefix_prefix": "dcterms", - "prefix_reference": "http://purl.org/dc/terms/" - }, - "UniProtKB": { - "prefix_prefix": "UniProtKB", - "prefix_reference": "https://identifiers.org/uniprot/" - }, - "biolink": { - "prefix_prefix": "biolink", - "prefix_reference": "https://w3id.org/biolink/vocab/" - }, - "sio": { - "prefix_prefix": "sio", - "prefix_reference": "http://semanticscience.org/resource/SIO_" - }, - "wgs84": { - "prefix_prefix": "wgs84", - "prefix_reference": "http://www.w3.org/2003/01/geo/wgs84_pos#" - }, - "GOLD": { - "prefix_prefix": "GOLD", - "prefix_reference": "http://identifiers.org/gold/" - }, - "CHEBI": { - "prefix_prefix": "CHEBI", - "prefix_reference": "http://purl.obolibrary.org/obo/CHEBI_" - }, - "CHMO": { - "prefix_prefix": "CHMO", - "prefix_reference": "http://purl.obolibrary.org/obo/CHMO_" - }, - "OBI": { - "prefix_prefix": "OBI", - "prefix_reference": "http://purl.obolibrary.org/obo/OBI_" - }, - "MIXS": { - "prefix_prefix": "MIXS", - "prefix_reference": "https://w3id.org/mixs/" - }, - "MIXS_yaml": { - "prefix_prefix": "MIXS_yaml", - "prefix_reference": "https://raw.githubusercontent.com/microbiomedata/mixs/main/model/schema/" - }, - "COG": { - "prefix_prefix": "COG", - "prefix_reference": "https://bioregistry.io/cog:" - }, - "EC": { - "prefix_prefix": "EC", - "prefix_reference": "https://bioregistry.io/eccode:" - }, - "GO": { - "prefix_prefix": "GO", - "prefix_reference": "http://purl.obolibrary.org/obo/GO_" - }, - "KEGG.ORTHOLOGY": { - "prefix_prefix": "KEGG.ORTHOLOGY", - "prefix_reference": "http://identifiers.org/kegg.orthology/" - }, - "KEGG.REACTION": { - "prefix_prefix": "KEGG.REACTION", - "prefix_reference": "http://identifiers.org/kegg.reaction/" - }, - "KEGG_PATHWAY": { - "prefix_prefix": "KEGG_PATHWAY", - "prefix_reference": "http://identifiers.org/kegg.pathway/" - }, - "MetaCyc": { - "prefix_prefix": "MetaCyc", - "prefix_reference": "https://identifiers.org/metacyc.reaction/" - }, - "RHEA": { - "prefix_prefix": "RHEA", - "prefix_reference": "http://identifiers.org/rhea/" - }, - "SEED": { - "prefix_prefix": "SEED", - "prefix_reference": "http://identifiers.org/seed/" - } - }, - "default_prefix": "nmdc_sub_schema", - "default_range": "string", - "subsets": { - "sample subset": { - "name": "sample subset", - "description": "Subset consisting of entities linked to the processing of samples. Currently, this subset consists of study, omics process, and biosample.", - "from_schema": "https://example.com/nmdc_submission_schema" - }, - "data object subset": { - "name": "data object subset", - "description": "Subset consisting of the data objects that either inputs or outputs of processes or workflows.", - "from_schema": "https://example.com/nmdc_submission_schema" - }, - "workflow subset": { - "name": "workflow subset", - "description": "Subset consisting of just the workflow execution activities", - "from_schema": "https://example.com/nmdc_submission_schema" - }, - "environment": { - "name": "environment", - "from_schema": "https://example.com/nmdc_submission_schema" - }, - "investigation": { - "name": "investigation", - "from_schema": "https://example.com/nmdc_submission_schema" - }, - "nucleic acid sequence source": { - "name": "nucleic acid sequence source", - "from_schema": "https://example.com/nmdc_submission_schema" - }, - "sequencing": { - "name": "sequencing", - "from_schema": "https://example.com/nmdc_submission_schema" - }, - "mixs_environmental_triad": { - "name": "mixs_environmental_triad", - "title": "MIxS Environmental Triad", - "from_schema": "https://example.com/nmdc_submission_schema" - }, - "mixs extension": { - "name": "mixs extension", - "from_schema": "https://example.com/nmdc_submission_schema" - }, - "checklist": { - "name": "checklist", - "description": "A MIxS checklist. These can be combined with packages", - "from_schema": "https://example.com/nmdc_submission_schema" - }, - "package": { - "name": "package", - "description": "A MIxS package. These can be combined with checklists", - "from_schema": "https://example.com/nmdc_submission_schema" - }, - "checklist_package_combination": { - "name": "checklist_package_combination", - "description": "A combination of a checklist and a package", - "from_schema": "https://example.com/nmdc_submission_schema" - } - }, - "types": { - "unit": { - "name": "unit", - "description": "a string representation of a unit", - "notes": [ - "why isn't this picked up from the nmdc.yaml import?" - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "mappings": [ - "qud:Unit", - "UO:0000000" - ], - "base": "str", - "uri": "xsd:string" - }, - "decimal degree": { - "name": "decimal degree", - "description": "a float representation of a degree of rotation", - "from_schema": "https://example.com/nmdc_submission_schema", - "base": "float", - "uri": "xsd:decimal" - }, - "language code": { - "name": "language code", - "description": "a string representation of a language", - "from_schema": "https://example.com/nmdc_submission_schema", - "base": "str", - "uri": "xsd:language" - }, - "string": { - "name": "string", - "description": "A character string", - "from_schema": "https://example.com/nmdc_submission_schema", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "xsd:string" - }, - "integer": { - "name": "integer", - "description": "An integer", - "from_schema": "https://example.com/nmdc_submission_schema", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "xsd:integer" - }, - "boolean": { - "name": "boolean", - "description": "A binary (true or false) value", - "from_schema": "https://example.com/nmdc_submission_schema", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "xsd:boolean", - "repr": "bool" - }, - "float": { - "name": "float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://example.com/nmdc_submission_schema", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "xsd:float" - }, - "double": { - "name": "double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://example.com/nmdc_submission_schema", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "xsd:double" - }, - "decimal": { - "name": "decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://example.com/nmdc_submission_schema", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "xsd:decimal" - }, - "time": { - "name": "time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "xsd:dateTime", - "repr": "str" - }, - "date": { - "name": "date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "xsd:date", - "repr": "str" - }, - "datetime": { - "name": "datetime", - "description": "The combination of a date and time", - "from_schema": "https://example.com/nmdc_submission_schema", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "xsd:dateTime", - "repr": "str" - }, - "date_or_datetime": { - "name": "date_or_datetime", - "description": "Either a date or a datetime", - "from_schema": "https://example.com/nmdc_submission_schema", - "base": "str", - "uri": "linkml:DateOrDatetime", - "repr": "str" - }, - "uriorcurie": { - "name": "uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://example.com/nmdc_submission_schema", - "base": "URIorCURIE", - "uri": "xsd:anyURI", - "repr": "str" - }, - "curie": { - "name": "curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "base": "Curie", - "uri": "xsd:string", - "repr": "str" - }, - "uri": { - "name": "uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "xsd:anyURI", - "repr": "str" - }, - "ncname": { - "name": "ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://example.com/nmdc_submission_schema", - "base": "NCName", - "uri": "xsd:string", - "repr": "str" - }, - "objectidentifier": { - "name": "objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritence and type checking" - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "base": "ElementIdentifier", - "uri": "shex:iri", - "repr": "str" - }, - "nodeidentifier": { - "name": "nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://example.com/nmdc_submission_schema", - "base": "NodeIdentifier", - "uri": "shex:nonLiteral", - "repr": "str" - } - }, - "enums": { - "AnalysisTypeEnum": { - "name": "AnalysisTypeEnum", - "description": "placeholder enum descr", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "metabolomics": { - "text": "metabolomics", - "description": "placeholder PV descr" - }, - "metagenomics": { - "text": "metagenomics", - "description": "placeholder PV descr" - }, - "metaproteomics": { - "text": "metaproteomics", - "description": "placeholder PV descr" - }, - "metatranscriptomics": { - "text": "metatranscriptomics", - "description": "placeholder PV descr" - }, - "natural organic matter": { - "text": "natural organic matter", - "description": "placeholder PV descr" - } - } - }, - "BioticRelationshipEnum": { - "name": "BioticRelationshipEnum", - "description": "placeholder enum descr", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "commensalism": { - "text": "commensalism", - "description": "placeholder PV descr", - "annotations": { - "sntc_name": { - "tag": "sntc_name", - "value": "samp_biotic_relationship" - } - }, - "notes": [ - "biotic_relationship_enum: free living", - "parasitism", - "commensalism", - "symbiotic", - "mutualism" - ], - "see_also": [ - "https://genomicsstandardsconsortium.github.io/mixs/biotic_relationship_enum/" - ] - }, - "free living": { - "text": "free living", - "description": "placeholder PV descr" - }, - "mutualism": { - "text": "mutualism", - "description": "placeholder PV descr" - }, - "parasitism": { - "text": "parasitism", - "description": "placeholder PV descr" - }, - "symbiotic": { - "text": "symbiotic", - "description": "placeholder enum descr" - } - } - }, - "JgiContTypeEnum": { - "name": "JgiContTypeEnum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "plate": { - "text": "plate" - }, - "tube": { - "text": "tube" - } - } - }, - "DnaSampleFormatEnum": { - "name": "DnaSampleFormatEnum", - "description": "placeholder enum descr", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "10 mM Tris-HCl": { - "text": "10 mM Tris-HCl", - "description": "placeholder PV descr" - }, - "DNAStable": { - "text": "DNAStable", - "description": "placeholder PV descr" - }, - "Ethanol": { - "text": "Ethanol", - "description": "placeholder PV descr" - }, - "Low EDTA TE": { - "text": "Low EDTA TE", - "description": "placeholder PV descr" - }, - "MDA reaction buffer": { - "text": "MDA reaction buffer", - "description": "placeholder PV descr" - }, - "PBS": { - "text": "PBS", - "description": "placeholder PV descr" - }, - "Pellet": { - "text": "Pellet", - "description": "placeholder PV descr" - }, - "RNAStable": { - "text": "RNAStable", - "description": "placeholder PV descr" - }, - "TE": { - "text": "TE", - "description": "placeholder PV descr" - }, - "Water": { - "text": "Water", - "description": "placeholder PV descr" - } - } - }, - "EcosystemCategoryEnum": { - "name": "EcosystemCategoryEnum", - "description": "placeholder enum descr", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "Terrestrial": { - "text": "Terrestrial", - "description": "placeholder PV descr", - "see_also": [ - "https://github.com/microbiomedata/sheets_and_friends/issues/22" - ] - } - } - }, - "EcosystemEnum": { - "name": "EcosystemEnum", - "description": "placeholder enum descr", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "Environmental": { - "text": "Environmental", - "description": "placeholder PV descr" - } - } - }, - "EcosystemSubtypeEnum": { - "name": "EcosystemSubtypeEnum", - "description": "placeholder enum descr", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "Biocrust": { - "text": "Biocrust", - "description": "placeholder PV descr" - }, - "Biofilm": { - "text": "Biofilm", - "description": "placeholder PV descr" - }, - "Bulk soil": { - "text": "Bulk soil", - "description": "placeholder PV descr" - }, - "Clay": { - "text": "Clay", - "description": "placeholder PV descr" - }, - "Floodplain": { - "text": "Floodplain", - "description": "placeholder PV descr" - }, - "Fossil": { - "text": "Fossil", - "description": "placeholder PV descr" - }, - "Glacier": { - "text": "Glacier", - "description": "placeholder PV descr" - }, - "Loam": { - "text": "Loam", - "description": "placeholder PV descr" - }, - "Mineral horizon": { - "text": "Mineral horizon", - "description": "placeholder PV descr" - }, - "Nature reserve": { - "text": "Nature reserve", - "description": "placeholder PV descr" - }, - "Organic layer": { - "text": "Organic layer", - "description": "placeholder PV descr" - }, - "Paddy field/soil": { - "text": "Paddy field/soil", - "description": "placeholder PV descr" - }, - "Pasture": { - "text": "Pasture", - "description": "placeholder PV descr" - }, - "Peat": { - "text": "Peat", - "description": "placeholder PV descr" - }, - "Ranch": { - "text": "Ranch", - "description": "placeholder PV descr" - }, - "Sand": { - "text": "Sand", - "description": "placeholder PV descr" - }, - "Silt": { - "text": "Silt", - "description": "placeholder PV descr" - }, - "Soil crust": { - "text": "Soil crust", - "description": "placeholder PV descr" - }, - "Unclassified": { - "text": "Unclassified", - "description": "placeholder PV descr" - }, - "Watershed": { - "text": "Watershed", - "description": "placeholder PV descr" - }, - "Wetlands": { - "text": "Wetlands", - "description": "placeholder PV descr" - } - } - }, - "EcosystemTypeEnum": { - "name": "EcosystemTypeEnum", - "description": "placeholder enum descr", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "Soil": { - "text": "Soil", - "description": "placeholder PV descr" - } - } - }, - "EnvPackageEnum": { - "name": "EnvPackageEnum", - "description": "placeholder enum descr", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "soil": { - "text": "soil", - "description": "placeholder PV descr", - "notes": [ - "I don't think this is a MIxS term anymore, so it make sense to define it here" - ] - } - } - }, - "GrowthFacilEnum": { - "name": "GrowthFacilEnum", - "description": "placeholder enum descr", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "experimental_garden": { - "text": "experimental_garden", - "description": "placeholder PV descr", - "annotations": { - "sntc_name": { - "tag": "sntc_name", - "value": "growth_facility" - } - }, - "notes": [ - "string range according to MIxS" - ], - "see_also": [ - "https://genomicsstandardsconsortium.github.io/mixs/growth_facil/" - ] - }, - "field": { - "text": "field", - "description": "placeholder PV descr" - }, - "field_incubation": { - "text": "field_incubation", - "description": "placeholder PV descr" - }, - "glasshouse": { - "text": "glasshouse", - "description": "placeholder PV descr" - }, - "greenhouse": { - "text": "greenhouse", - "description": "placeholder PV descr" - }, - "growth_chamber": { - "text": "growth_chamber", - "description": "placeholder PV descr" - }, - "lab_incubation": { - "text": "lab_incubation", - "description": "placeholder PV descr" - }, - "open_top_chamber": { - "text": "open_top_chamber", - "description": "placeholder PV descr" - }, - "other": { - "text": "other", - "description": "placeholder PV descr" - } - } - }, - "RelToOxygenEnum": { - "name": "RelToOxygenEnum", - "description": "placeholder enum descr", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "aerobe": { - "text": "aerobe", - "description": "placeholder PV descr", - "annotations": { - "sntc_name": { - "tag": "sntc_name", - "value": "oxygen_relationship" - } - }, - "see_also": [ - "https://genomicsstandardsconsortium.github.io/mixs/rel_to_oxygen_enum/" - ] - }, - "anaerobe": { - "text": "anaerobe", - "description": "placeholder PV descr" - }, - "facultative": { - "text": "facultative", - "description": "placeholder PV descr" - }, - "microaerophilic": { - "text": "microaerophilic", - "description": "placeholder PV descr" - }, - "microanaerobe": { - "text": "microanaerobe", - "description": "placeholder PV descr" - }, - "obligate aerobe": { - "text": "obligate aerobe", - "description": "placeholder PV descr" - }, - "obligate anaerobe": { - "text": "obligate anaerobe", - "description": "placeholder PV descr" - } - } - }, - "RnaSampleFormatEnum": { - "name": "RnaSampleFormatEnum", - "description": "placeholder enum descr", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "10 mM Tris-HCl": { - "text": "10 mM Tris-HCl", - "description": "placeholder PV descr" - }, - "DNAStable": { - "text": "DNAStable", - "description": "placeholder PV descr" - }, - "Ethanol": { - "text": "Ethanol", - "description": "placeholder PV descr" - }, - "Low EDTA TE": { - "text": "Low EDTA TE", - "description": "placeholder PV descr" - }, - "MDA reaction buffer": { - "text": "MDA reaction buffer", - "description": "placeholder PV descr" - }, - "PBS": { - "text": "PBS", - "description": "placeholder PV descr" - }, - "Pellet": { - "text": "Pellet", - "description": "placeholder PV descr" - }, - "RNAStable": { - "text": "RNAStable", - "description": "placeholder PV descr" - }, - "TE": { - "text": "TE", - "description": "placeholder PV descr" - }, - "Water": { - "text": "Water", - "description": "placeholder PV descr" - } - } - }, - "SampleTypeEnum": { - "name": "SampleTypeEnum", - "description": "placeholder enum descr", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "soil": { - "text": "soil", - "description": "placeholder PV descr" - }, - "water_extract_soil": { - "text": "water_extract_soil", - "description": "placeholder PV descr" - } - } - }, - "SpecificEcosystemEnum": { - "name": "SpecificEcosystemEnum", - "description": "placeholder enum descr", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "Agricultural": { - "text": "Agricultural", - "description": "placeholder PV descr" - }, - "Agricultural land": { - "text": "Agricultural land", - "description": "placeholder PV descr" - }, - "Agricultural soil": { - "text": "Agricultural soil", - "description": "placeholder PV descr" - }, - "Alpine": { - "text": "Alpine", - "description": "placeholder PV descr" - }, - "Bog": { - "text": "Bog", - "description": "placeholder PV descr" - }, - "Boreal forest": { - "text": "Boreal forest", - "description": "placeholder PV descr" - }, - "Contaminated": { - "text": "Contaminated", - "description": "placeholder PV descr" - }, - "Desert": { - "text": "Desert", - "description": "placeholder PV descr" - }, - "Farm": { - "text": "Farm", - "description": "placeholder PV descr" - }, - "Forest soil": { - "text": "Forest soil", - "description": "placeholder PV descr" - }, - "Forest Soil": { - "text": "Forest Soil", - "description": "placeholder PV descr" - }, - "Grasslands": { - "text": "Grasslands", - "description": "placeholder PV descr" - }, - "Meadow": { - "text": "Meadow", - "description": "placeholder PV descr" - }, - "Mine": { - "text": "Mine", - "description": "placeholder PV descr" - }, - "Mine drainage": { - "text": "Mine drainage", - "description": "placeholder PV descr" - }, - "Oil-contaminated": { - "text": "Oil-contaminated", - "description": "placeholder PV descr" - }, - "Orchard soil": { - "text": "Orchard soil", - "description": "placeholder PV descr" - }, - "Permafrost": { - "text": "Permafrost", - "description": "placeholder PV descr" - }, - "Riparian soil": { - "text": "Riparian soil", - "description": "placeholder PV descr" - }, - "River": { - "text": "River", - "description": "placeholder PV descr" - }, - "Shrubland": { - "text": "Shrubland", - "description": "placeholder PV descr" - }, - "Tropical rainforest": { - "text": "Tropical rainforest", - "description": "placeholder PV descr" - }, - "Unclassified": { - "text": "Unclassified", - "description": "placeholder PV descr" - }, - "Uranium contaminated": { - "text": "Uranium contaminated", - "description": "placeholder PV descr" - } - } - }, - "StoreCondEnum": { - "name": "StoreCondEnum", - "description": "placeholder enum descr", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "fresh": { - "text": "fresh", - "description": "placeholder PV descr", - "annotations": { - "sntc_name": { - "tag": "sntc_name", - "value": "storage_condt" - } - }, - "notes": [ - "see samp_store_dur, samp_store_loc, samp_store_temp and store_cond (which takes a string range according to mixs-source)." - ] - }, - "frozen": { - "text": "frozen", - "description": "placeholder PV descr" - }, - "lyophilized": { - "text": "lyophilized", - "description": "placeholder PV descr" - }, - "other": { - "text": "other", - "description": "placeholder PV descr" - } - } - }, - "YesNoEnum": { - "name": "YesNoEnum", - "description": "replaces DnaDnaseEnum and DnaseRnaEnum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "no": { - "text": "no" - }, - "yes": { - "text": "yes" - } - } - }, - "EnvBroadScaleSoilEnum": { - "name": "EnvBroadScaleSoilEnum", - "description": "placeholder enum descr, DO NOT SORT", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "arid biome [ENVO:01001838]": { - "text": "arid biome [ENVO:01001838]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "subalpine biome [ENVO:01001837]": { - "text": "subalpine biome [ENVO:01001837]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "montane biome [ENVO:01001836]": { - "text": "montane biome [ENVO:01001836]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__montane savanna biome [ENVO:01000223]": { - "text": "__montane savanna biome [ENVO:01000223]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__montane shrubland biome [ENVO:01000216]": { - "text": "__montane shrubland biome [ENVO:01000216]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "alpine biome [ENVO:01001835]": { - "text": "alpine biome [ENVO:01001835]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__alpine tundra biome [ENVO:01001505]": { - "text": "__alpine tundra biome [ENVO:01001505]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "subpolar biome [ENVO:01001834]": { - "text": "subpolar biome [ENVO:01001834]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "subtropical biome [ENVO:01001832]": { - "text": "subtropical biome [ENVO:01001832]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__mediterranean biome [ENVO:01001833]": { - "text": "__mediterranean biome [ENVO:01001833]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "____mediterranean savanna biome [ENVO:01000229]": { - "text": "____mediterranean savanna biome [ENVO:01000229]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "____mediterranean shrubland biome [ENVO:01000217]": { - "text": "____mediterranean shrubland biome [ENVO:01000217]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "____mediterranean woodland biome [ENVO:01000208]": { - "text": "____mediterranean woodland biome [ENVO:01000208]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__subtropical woodland biome [ENVO:01000222]": { - "text": "__subtropical woodland biome [ENVO:01000222]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__subtropical shrubland biome [ENVO:01000213]": { - "text": "__subtropical shrubland biome [ENVO:01000213]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__subtropical savanna biome [ENVO:01000187]": { - "text": "__subtropical savanna biome [ENVO:01000187]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "temperate biome [ENVO:01001831]": { - "text": "temperate biome [ENVO:01001831]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__temperate woodland biome [ENVO:01000221]": { - "text": "__temperate woodland biome [ENVO:01000221]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__temperate shrubland biome [ENVO:01000215]": { - "text": "__temperate shrubland biome [ENVO:01000215]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__temperate savanna biome [ENVO:01000189]": { - "text": "__temperate savanna biome [ENVO:01000189]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "tropical biome [ENVO:01001830]": { - "text": "tropical biome [ENVO:01001830]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__tropical woodland biome [ENVO:01000220]": { - "text": "__tropical woodland biome [ENVO:01000220]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__tropical shrubland biome [ENVO:01000214]": { - "text": "__tropical shrubland biome [ENVO:01000214]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__tropical savanna biome [ENVO:01000188]": { - "text": "__tropical savanna biome [ENVO:01000188]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "polar biome [ENVO:01000339]": { - "text": "polar biome [ENVO:01000339]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "terrestrial biome [ENVO:00000446]": { - "text": "terrestrial biome [ENVO:00000446]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__anthropogenic terrestrial biome [ENVO:01000219]": { - "text": "__anthropogenic terrestrial biome [ENVO:01000219]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "____dense settlement biome [ENVO:01000248]": { - "text": "____dense settlement biome [ENVO:01000248]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "______urban biome [ENVO:01000249]": { - "text": "______urban biome [ENVO:01000249]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "____rangeland biome [ENVO:01000247]": { - "text": "____rangeland biome [ENVO:01000247]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "____village biome [ENVO:01000246]": { - "text": "____village biome [ENVO:01000246]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__mangrove biome [ENVO:01000181]": { - "text": "__mangrove biome [ENVO:01000181]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__tundra biome [ENVO:01000180]": { - "text": "__tundra biome [ENVO:01000180]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "____alpine tundra biome [ENVO:01001505]": { - "text": "____alpine tundra biome [ENVO:01001505]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__shrubland biome [ENVO:01000176]": { - "text": "__shrubland biome [ENVO:01000176]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "____tidal mangrove shrubland [ENVO:01001369]": { - "text": "____tidal mangrove shrubland [ENVO:01001369]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "____xeric shrubland biome [ENVO:01000218]": { - "text": "____xeric shrubland biome [ENVO:01000218]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "____montane shrubland biome [ENVO:01000216]": { - "text": "____montane shrubland biome [ENVO:01000216]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "____temperate shrubland biome [ENVO:01000215]": { - "text": "____temperate shrubland biome [ENVO:01000215]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "____tropical shrubland biome [ENVO:01000214]": { - "text": "____tropical shrubland biome [ENVO:01000214]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "____subtropical shrubland biome [ENVO:01000213]": { - "text": "____subtropical shrubland biome [ENVO:01000213]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "______mediterranean shrubland biome [ENVO:01000217]": { - "text": "______mediterranean shrubland biome [ENVO:01000217]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__woodland biome [ENVO:01000175]": { - "text": "__woodland biome [ENVO:01000175]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "____subtropical woodland biome [ENVO:01000222]": { - "text": "____subtropical woodland biome [ENVO:01000222]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "______mediterranean woodland biome [ENVO:01000208]": { - "text": "______mediterranean woodland biome [ENVO:01000208]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "____temperate woodland biome [ENVO:01000221]": { - "text": "____temperate woodland biome [ENVO:01000221]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "____tropical woodland biome [ENVO:01000220]": { - "text": "____tropical woodland biome [ENVO:01000220]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "____savanna biome [ENVO:01000178]": { - "text": "____savanna biome [ENVO:01000178]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "______montane savanna biome [ENVO:01000223]": { - "text": "______montane savanna biome [ENVO:01000223]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "______flooded savanna biome [ENVO:01000190]": { - "text": "______flooded savanna biome [ENVO:01000190]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "______temperate savanna biome [ENVO:01000189]": { - "text": "______temperate savanna biome [ENVO:01000189]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "______tropical savanna biome [ENVO:01000188]": { - "text": "______tropical savanna biome [ENVO:01000188]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "______subtropical savanna biome [ENVO:01000187]": { - "text": "______subtropical savanna biome [ENVO:01000187]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "________mediterranean savanna biome [ENVO:01000229]": { - "text": "________mediterranean savanna biome [ENVO:01000229]", - "description": "placeholder PV descr, DO NOT SORT" - } - } - }, - "EnvMediumSoilEnum": { - "name": "EnvMediumSoilEnum", - "description": "placeholder enum descr, DO NOT SORT", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "pathogen-suppressive soil [ENVO:03600036]": { - "text": "pathogen-suppressive soil [ENVO:03600036]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "mangrove biome soil [ENVO:02000138]": { - "text": "mangrove biome soil [ENVO:02000138]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "surface soil [ENVO:02000059]": { - "text": "surface soil [ENVO:02000059]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "frost-susceptible soil [ENVO:01001638]": { - "text": "frost-susceptible soil [ENVO:01001638]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "bare soil [ENVO:01001616]": { - "text": "bare soil [ENVO:01001616]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "frozen soil [ENVO:01001526]": { - "text": "frozen soil [ENVO:01001526]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__friable-frozen soil [ENVO:01001528]": { - "text": "__friable-frozen soil [ENVO:01001528]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__plastic-frozen soil [ENVO:01001527]": { - "text": "__plastic-frozen soil [ENVO:01001527]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__hard-frozen soil [ENVO:01001525]": { - "text": "__hard-frozen soil [ENVO:01001525]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__frozen compost soil [ENVO:00005765]": { - "text": "__frozen compost soil [ENVO:00005765]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__cryosol [ENVO:00002236]": { - "text": "__cryosol [ENVO:00002236]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "ultisol [ENVO:01001397]": { - "text": "ultisol [ENVO:01001397]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__acrisol [ENVO:00002234]": { - "text": "__acrisol [ENVO:00002234]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "acidic soil [ENVO:01001185]": { - "text": "acidic soil [ENVO:01001185]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "bulk soil [ENVO:00005802]": { - "text": "bulk soil [ENVO:00005802]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "red soil [ENVO:00005790]": { - "text": "red soil [ENVO:00005790]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "upland soil [ENVO:00005786]": { - "text": "upland soil [ENVO:00005786]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__mountain forest soil [ENVO:00005769]": { - "text": "__mountain forest soil [ENVO:00005769]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__dune soil [ENVO:00002260]": { - "text": "__dune soil [ENVO:00002260]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "ornithogenic soil [ENVO:00005782]": { - "text": "ornithogenic soil [ENVO:00005782]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "heat stressed soil [ENVO:00005781]": { - "text": "heat stressed soil [ENVO:00005781]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "greenhouse soil [ENVO:00005780]": { - "text": "greenhouse soil [ENVO:00005780]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "tropical soil [ENVO:00005778]": { - "text": "tropical soil [ENVO:00005778]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "pasture soil [ENVO:00005773]": { - "text": "pasture soil [ENVO:00005773]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "muddy soil [ENVO:00005771]": { - "text": "muddy soil [ENVO:00005771]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "orchid soil [ENVO:00005768]": { - "text": "orchid soil [ENVO:00005768]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "manured soil [ENVO:00005767]": { - "text": "manured soil [ENVO:00005767]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "limed soil [ENVO:00005766]": { - "text": "limed soil [ENVO:00005766]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "pond soil [ENVO:00005764]": { - "text": "pond soil [ENVO:00005764]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "meadow soil [ENVO:00005761]": { - "text": "meadow soil [ENVO:00005761]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "burned soil [ENVO:00005760]": { - "text": "burned soil [ENVO:00005760]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "lawn soil [ENVO:00005756]": { - "text": "lawn soil [ENVO:00005756]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "field soil [ENVO:00005755]": { - "text": "field soil [ENVO:00005755]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__paddy field soil [ENVO:00005740]": { - "text": "__paddy field soil [ENVO:00005740]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "____peaty paddy field soil [ENVO:00005776]": { - "text": "____peaty paddy field soil [ENVO:00005776]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "____alluvial paddy field soil [ENVO:00005759]": { - "text": "____alluvial paddy field soil [ENVO:00005759]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "fertilized soil [ENVO:00005754]": { - "text": "fertilized soil [ENVO:00005754]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "sawah soil [ENVO:00005752]": { - "text": "sawah soil [ENVO:00005752]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "jungle soil [ENVO:00005751]": { - "text": "jungle soil [ENVO:00005751]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "grassland soil [ENVO:00005750]": { - "text": "grassland soil [ENVO:00005750]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__steppe soil [ENVO:00005777]": { - "text": "__steppe soil [ENVO:00005777]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__savanna soil [ENVO:00005746]": { - "text": "__savanna soil [ENVO:00005746]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "farm soil [ENVO:00005749]": { - "text": "farm soil [ENVO:00005749]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__rubber plantation soil [ENVO:00005788]": { - "text": "__rubber plantation soil [ENVO:00005788]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__orchard soil [ENVO:00005772]": { - "text": "__orchard soil [ENVO:00005772]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "dry soil [ENVO:00005748]": { - "text": "dry soil [ENVO:00005748]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "compost soil [ENVO:00005747]": { - "text": "compost soil [ENVO:00005747]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "roadside soil [ENVO:00005743]": { - "text": "roadside soil [ENVO:00005743]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "arable soil [ENVO:00005742]": { - "text": "arable soil [ENVO:00005742]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "alpine soil [ENVO:00005741]": { - "text": "alpine soil [ENVO:00005741]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "alluvial soil [ENVO:00002871]": { - "text": "alluvial soil [ENVO:00002871]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__alluvial paddy field soil [ENVO:00005759]": { - "text": "__alluvial paddy field soil [ENVO:00005759]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__alluvial swamp soil [ENVO:00005758]": { - "text": "__alluvial swamp soil [ENVO:00005758]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "technosol [ENVO:00002275]": { - "text": "technosol [ENVO:00002275]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "stagnosol [ENVO:00002274]": { - "text": "stagnosol [ENVO:00002274]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "fluvisol [ENVO:00002273]": { - "text": "fluvisol [ENVO:00002273]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "garden soil [ENVO:00002263]": { - "text": "garden soil [ENVO:00002263]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__vegetable garden soil [ENVO:00005779]": { - "text": "__vegetable garden soil [ENVO:00005779]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__allotment garden soil [ENVO:00005744]": { - "text": "__allotment garden soil [ENVO:00005744]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "clay soil [ENVO:00002262]": { - "text": "clay soil [ENVO:00002262]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "forest soil [ENVO:00002261]": { - "text": "forest soil [ENVO:00002261]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__eucalyptus forest soil [ENVO:00005787]": { - "text": "__eucalyptus forest soil [ENVO:00005787]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__spruce forest soil [ENVO:00005784]": { - "text": "__spruce forest soil [ENVO:00005784]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__leafy wood soil [ENVO:00005783]": { - "text": "__leafy wood soil [ENVO:00005783]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__beech forest soil [ENVO:00005770]": { - "text": "__beech forest soil [ENVO:00005770]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "agricultural soil [ENVO:00002259]": { - "text": "agricultural soil [ENVO:00002259]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__bluegrass field soil [ENVO:00005789]": { - "text": "__bluegrass field soil [ENVO:00005789]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "loam [ENVO:00002258]": { - "text": "loam [ENVO:00002258]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__clay loam [ENVO:06105277]": { - "text": "__clay loam [ENVO:06105277]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "____silty clay loam [ENVO:06105278]": { - "text": "____silty clay loam [ENVO:06105278]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "____sandy clay loam [ENVO:06105276]": { - "text": "____sandy clay loam [ENVO:06105276]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__silty loam [ENVO:06105275]": { - "text": "__silty loam [ENVO:06105275]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__sandy loam [ENVO:06105274]": { - "text": "__sandy loam [ENVO:06105274]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "podzol [ENVO:00002257]": { - "text": "podzol [ENVO:00002257]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "regosol [ENVO:00002256]": { - "text": "regosol [ENVO:00002256]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "solonetz [ENVO:00002255]": { - "text": "solonetz [ENVO:00002255]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "vertisol [ENVO:00002254]": { - "text": "vertisol [ENVO:00002254]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "umbrisol [ENVO:00002253]": { - "text": "umbrisol [ENVO:00002253]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "solonchak [ENVO:00002252]": { - "text": "solonchak [ENVO:00002252]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "planosol [ENVO:00002251]": { - "text": "planosol [ENVO:00002251]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "plinthosol [ENVO:00002250]": { - "text": "plinthosol [ENVO:00002250]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "phaeozem [ENVO:00002249]": { - "text": "phaeozem [ENVO:00002249]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "luvisol [ENVO:00002248]": { - "text": "luvisol [ENVO:00002248]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "nitisol [ENVO:00002247]": { - "text": "nitisol [ENVO:00002247]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "ferralsol [ENVO:00002246]": { - "text": "ferralsol [ENVO:00002246]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "gypsisol [ENVO:00002245]": { - "text": "gypsisol [ENVO:00002245]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "gleysol [ENVO:00002244]": { - "text": "gleysol [ENVO:00002244]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "histosol [ENVO:00002243]": { - "text": "histosol [ENVO:00002243]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__peat soil [ENVO:00005774]": { - "text": "__peat soil [ENVO:00005774]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "lixisol [ENVO:00002242]": { - "text": "lixisol [ENVO:00002242]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "leptosol [ENVO:00002241]": { - "text": "leptosol [ENVO:00002241]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "kastanozem [ENVO:00002240]": { - "text": "kastanozem [ENVO:00002240]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "calcisol [ENVO:00002239]": { - "text": "calcisol [ENVO:00002239]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "durisol [ENVO:00002238]": { - "text": "durisol [ENVO:00002238]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "chernozem [ENVO:00002237]": { - "text": "chernozem [ENVO:00002237]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "cambisol [ENVO:00002235]": { - "text": "cambisol [ENVO:00002235]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "albeluvisol [ENVO:00002233]": { - "text": "albeluvisol [ENVO:00002233]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "andosol [ENVO:00002232]": { - "text": "andosol [ENVO:00002232]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__volcanic soil [ENVO:01001841]": { - "text": "__volcanic soil [ENVO:01001841]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "alisol [ENVO:00002231]": { - "text": "alisol [ENVO:00002231]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "anthrosol [ENVO:00002230]": { - "text": "anthrosol [ENVO:00002230]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "arenosol [ENVO:00002229]": { - "text": "arenosol [ENVO:00002229]", - "description": "placeholder PV descr, DO NOT SORT" - } - } - }, - "EnvLocalScaleSoilEnum": { - "name": "EnvLocalScaleSoilEnum", - "description": "placeholder enum descr, DO NOT SORT", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "astronomical body part [ENVO:01000813]": { - "text": "astronomical body part [ENVO:01000813]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__coast [ENVO:01000687]": { - "text": "__coast [ENVO:01000687]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__solid astronomical body part [ENVO:00000191]": { - "text": "__solid astronomical body part [ENVO:00000191]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "______landform [ENVO:01001886]": { - "text": "______landform [ENVO:01001886]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "______channel [ENVO:03000117]": { - "text": "______channel [ENVO:03000117]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "________tunnel [ENVO:00000068]": { - "text": "________tunnel [ENVO:00000068]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "______surface landform [ENVO:01001884]": { - "text": "______surface landform [ENVO:01001884]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "________desert [ENVO:01001357]": { - "text": "________desert [ENVO:01001357]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "________outcrop [ENVO:01000302]": { - "text": "________outcrop [ENVO:01000302]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "________boulder field [ENVO:00000537]": { - "text": "________boulder field [ENVO:00000537]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "________landfill [ENVO:00000533]": { - "text": "________landfill [ENVO:00000533]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "________hummock [ENVO:00000516]": { - "text": "________hummock [ENVO:00000516]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "________terrace [ENVO:00000508]": { - "text": "________terrace [ENVO:00000508]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "________peninsula [ENVO:00000305]": { - "text": "________peninsula [ENVO:00000305]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "________shore [ENVO:00000304]": { - "text": "________shore [ENVO:00000304]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__________lake shore [ENVO:00000382]": { - "text": "__________lake shore [ENVO:00000382]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "________dry lake [ENVO:00000277]": { - "text": "________dry lake [ENVO:00000277]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "________karst [ENVO:00000175]": { - "text": "________karst [ENVO:00000175]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "________isthmus [ENVO:00000174]": { - "text": "________isthmus [ENVO:00000174]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "________badland [ENVO:00000127]": { - "text": "________badland [ENVO:00000127]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "________volcanic feature [ENVO:00000094]": { - "text": "________volcanic feature [ENVO:00000094]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__________volcanic cone [ENVO:00000398]": { - "text": "__________volcanic cone [ENVO:00000398]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "____________tuff cone [ENVO:01000664]": { - "text": "____________tuff cone [ENVO:01000664]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "________beach [ENVO:00000091]": { - "text": "________beach [ENVO:00000091]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "________plain [ENVO:00000086]": { - "text": "________plain [ENVO:00000086]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "________cave [ENVO:00000067]": { - "text": "________cave [ENVO:00000067]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "________spring [ENVO:00000027]": { - "text": "________spring [ENVO:00000027]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "______slope [ENVO:00002000]": { - "text": "______slope [ENVO:00002000]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "________talus slope [ENVO:01000334]": { - "text": "________talus slope [ENVO:01000334]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "________hillside [ENVO:01000333]": { - "text": "________hillside [ENVO:01000333]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "________levee [ENVO:00000178]": { - "text": "________levee [ENVO:00000178]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "________bank [ENVO:00000141]": { - "text": "________bank [ENVO:00000141]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "________cliff [ENVO:00000087]": { - "text": "________cliff [ENVO:00000087]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "______peak [ENVO:00000480]": { - "text": "______peak [ENVO:00000480]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "______depressed landform [ENVO:00000309]": { - "text": "______depressed landform [ENVO:00000309]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "________geographic basin [ENVO:03000015]": { - "text": "________geographic basin [ENVO:03000015]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__________valley [ENVO:00000100]": { - "text": "__________valley [ENVO:00000100]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "____________canyon [ENVO:00000169]": { - "text": "____________canyon [ENVO:00000169]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "____________dry valley [ENVO:00000128]": { - "text": "____________dry valley [ENVO:00000128]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "____________glacial valley [ENVO:00000248]": { - "text": "____________glacial valley [ENVO:00000248]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "________pit [ENVO:01001871]": { - "text": "________pit [ENVO:01001871]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "________trench [ENVO:01000649]": { - "text": "________trench [ENVO:01000649]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "________swale [ENVO:00000543]": { - "text": "________swale [ENVO:00000543]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "________crater [ENVO:00000514]": { - "text": "________crater [ENVO:00000514]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__________impact crater [ENVO:01001071]": { - "text": "__________impact crater [ENVO:01001071]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__________volcanic crater [ENVO:00000246]": { - "text": "__________volcanic crater [ENVO:00000246]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__________caldera [ENVO:00000096]": { - "text": "__________caldera [ENVO:00000096]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "________channel of a watercourse [ENVO:00000395]": { - "text": "________channel of a watercourse [ENVO:00000395]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__________strait [ENVO:00000394]": { - "text": "__________strait [ENVO:00000394]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__________dry stream [ENVO:00000278]": { - "text": "__________dry stream [ENVO:00000278]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "____________dry river [ENVO:01000995]": { - "text": "____________dry river [ENVO:01000995]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__________artificial channel [ENVO:00000121]": { - "text": "__________artificial channel [ENVO:00000121]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "____________plumbing drain [ENVO:01000924]": { - "text": "____________plumbing drain [ENVO:01000924]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "____________ditch [ENVO:00000037]": { - "text": "____________ditch [ENVO:00000037]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "________sinkhole [ENVO:00000195]": { - "text": "________sinkhole [ENVO:00000195]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "______elevated landform [ENVO:00000176]": { - "text": "______elevated landform [ENVO:00000176]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "________flattened elevation [ENVO:01001491]": { - "text": "________flattened elevation [ENVO:01001491]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__________butte [ENVO:00000287]": { - "text": "__________butte [ENVO:00000287]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__________plateau [ENVO:00000182]": { - "text": "__________plateau [ENVO:00000182]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__________mesa [ENVO:00000179]": { - "text": "__________mesa [ENVO:00000179]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "________pinnacle [ENVO:00000481]": { - "text": "________pinnacle [ENVO:00000481]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "________mount [ENVO:00000477]": { - "text": "________mount [ENVO:00000477]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__________hill [ENVO:00000083]": { - "text": "__________hill [ENVO:00000083]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "____________dune [ENVO:00000170]": { - "text": "____________dune [ENVO:00000170]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__________mountain [ENVO:00000081]": { - "text": "__________mountain [ENVO:00000081]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "________ridge [ENVO:00000283]": { - "text": "________ridge [ENVO:00000283]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "____part of a landmass [ENVO:01001781]": { - "text": "____part of a landmass [ENVO:01001781]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "______peninsula [ENVO:00000305]": { - "text": "______peninsula [ENVO:00000305]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "____geological fracture [ENVO:01000667]": { - "text": "____geological fracture [ENVO:01000667]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "______vein [ENVO:01000670]": { - "text": "______vein [ENVO:01000670]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "______geological fault [ENVO:01000668]": { - "text": "______geological fault [ENVO:01000668]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "________active geological fault [ENVO:01000669]": { - "text": "________active geological fault [ENVO:01000669]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "______volcano [ENVO:00000247]": { - "text": "______volcano [ENVO:00000247]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__field [ENVO:01000352]": { - "text": "__field [ENVO:01000352]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "____lava field [ENVO:01000437]": { - "text": "____lava field [ENVO:01000437]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "____gravel field [ENVO:00000548]": { - "text": "____gravel field [ENVO:00000548]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "____woodland clearing [ENVO:00000444]": { - "text": "____woodland clearing [ENVO:00000444]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "____agricultural field [ENVO:00000114]": { - "text": "____agricultural field [ENVO:00000114]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "____snow field [ENVO:00000146]": { - "text": "____snow field [ENVO:00000146]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "__geographic feature [ENVO:00000000]": { - "text": "__geographic feature [ENVO:00000000]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "____hydrographic feature [ENVO:00000012]": { - "text": "____hydrographic feature [ENVO:00000012]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "______reef [ENVO:01001899]": { - "text": "______reef [ENVO:01001899]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "______inlet [ENVO:00000475]": { - "text": "______inlet [ENVO:00000475]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "______bar [ENVO:00000167]": { - "text": "______bar [ENVO:00000167]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "________tombolo [ENVO:00000420]": { - "text": "________tombolo [ENVO:00000420]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "____anthropogenic geographic feature [ENVO:00000002]": { - "text": "____anthropogenic geographic feature [ENVO:00000002]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "______yard [ENVO:03600053]": { - "text": "______yard [ENVO:03600053]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "________residential backyard [ENVO:03600033]": { - "text": "________residential backyard [ENVO:03600033]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "______market [ENVO:01000987]": { - "text": "______market [ENVO:01000987]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "______park [ENVO:00000562]": { - "text": "______park [ENVO:00000562]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "______well [ENVO:00000026]": { - "text": "______well [ENVO:00000026]", - "description": "placeholder PV descr, DO NOT SORT" - }, - "______garden [ENVO:00000011]": { - "text": "______garden [ENVO:00000011]", - "description": "placeholder PV descr, DO NOT SORT" - } - } - }, - "OxyStatSampEnum": { - "name": "OxyStatSampEnum", - "description": "placeholder enum descr, DO NOT SORT", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "aerobic": { - "text": "aerobic", - "description": "placeholder PV descr, DO NOT SORT" - }, - "anaerobic": { - "text": "anaerobic", - "description": "placeholder PV descr, DO NOT SORT" - }, - "other": { - "text": "other", - "description": "placeholder PV descr, DO NOT SORT" - } - } - }, - "heat_cool_type_enum": { - "name": "heat_cool_type_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "radiant system": { - "text": "radiant system" - }, - "heat pump": { - "text": "heat pump" - }, - "forced air system": { - "text": "forced air system" - }, - "steam forced heat": { - "text": "steam forced heat" - }, - "wood stove": { - "text": "wood stove" - } - } - }, - "weekday_enum": { - "name": "weekday_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "Monday": { - "text": "Monday" - }, - "Tuesday": { - "text": "Tuesday" - }, - "Wednesday": { - "text": "Wednesday" - }, - "Thursday": { - "text": "Thursday" - }, - "Friday": { - "text": "Friday" - }, - "Saturday": { - "text": "Saturday" - }, - "Sunday": { - "text": "Sunday" - } - } - }, - "window_loc_enum": { - "name": "window_loc_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "north": { - "text": "north" - }, - "south": { - "text": "south" - }, - "east": { - "text": "east" - }, - "west": { - "text": "west" - } - } - }, - "vis_media_enum": { - "name": "vis_media_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "photos": { - "text": "photos" - }, - "videos": { - "text": "videos" - }, - "commonly of the building": { - "text": "commonly of the building" - }, - "site context (adjacent buildings, vegetation, terrain, streets)": { - "text": "site context (adjacent buildings, vegetation, terrain, streets)" - }, - "interiors": { - "text": "interiors" - }, - "equipment": { - "text": "equipment" - }, - "3D scans": { - "text": "3D scans" - } - } - }, - "rel_samp_loc_enum": { - "name": "rel_samp_loc_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "edge of car": { - "text": "edge of car" - }, - "center of car": { - "text": "center of car" - }, - "under a seat": { - "text": "under a seat" - } - } - }, - "door_mat_enum": { - "name": "door_mat_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "aluminum": { - "text": "aluminum" - }, - "cellular PVC": { - "text": "cellular PVC" - }, - "engineered plastic": { - "text": "engineered plastic" - }, - "fiberboard": { - "text": "fiberboard" - }, - "fiberglass": { - "text": "fiberglass" - }, - "metal": { - "text": "metal" - }, - "thermoplastic alloy": { - "text": "thermoplastic alloy" - }, - "vinyl": { - "text": "vinyl" - }, - "wood": { - "text": "wood" - }, - "wood/plastic composite": { - "text": "wood/plastic composite" - } - } - }, - "ceil_cond_enum": { - "name": "ceil_cond_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "new": { - "text": "new" - }, - "visible wear": { - "text": "visible wear" - }, - "needs repair": { - "text": "needs repair" - }, - "damaged": { - "text": "damaged" - }, - "rupture": { - "text": "rupture" - } - } - }, - "occup_document_enum": { - "name": "occup_document_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "automated count": { - "text": "automated count" - }, - "estimate": { - "text": "estimate" - }, - "manual count": { - "text": "manual count" - }, - "videos": { - "text": "videos" - } - } - }, - "train_stat_loc_enum": { - "name": "train_stat_loc_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "south station above ground": { - "text": "south station above ground" - }, - "south station underground": { - "text": "south station underground" - }, - "south station amtrak": { - "text": "south station amtrak" - }, - "forest hills": { - "text": "forest hills" - }, - "riverside": { - "text": "riverside" - } - } - }, - "surf_material_enum": { - "name": "surf_material_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "adobe": { - "text": "adobe" - }, - "carpet": { - "text": "carpet" - }, - "cinder blocks": { - "text": "cinder blocks" - }, - "concrete": { - "text": "concrete" - }, - "hay bales": { - "text": "hay bales" - }, - "glass": { - "text": "glass" - }, - "metal": { - "text": "metal" - }, - "paint": { - "text": "paint" - }, - "plastic": { - "text": "plastic" - }, - "stainless steel": { - "text": "stainless steel" - }, - "stone": { - "text": "stone" - }, - "stucco": { - "text": "stucco" - }, - "tile": { - "text": "tile" - }, - "vinyl": { - "text": "vinyl" - }, - "wood": { - "text": "wood" - } - } - }, - "surf_air_cont_enum": { - "name": "surf_air_cont_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "dust": { - "text": "dust" - }, - "organic matter": { - "text": "organic matter" - }, - "particulate matter": { - "text": "particulate matter" - }, - "volatile organic compounds": { - "text": "volatile organic compounds" - }, - "biological contaminants": { - "text": "biological contaminants" - }, - "radon": { - "text": "radon" - }, - "nutrients": { - "text": "nutrients" - }, - "biocides": { - "text": "biocides" - } - } - }, - "door_type_wood_enum": { - "name": "door_type_wood_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "bettened and ledged": { - "text": "bettened and ledged" - }, - "battened": { - "text": "battened" - }, - "ledged and braced": { - "text": "ledged and braced" - }, - "ledged and framed": { - "text": "ledged and framed" - }, - "ledged, braced and frame": { - "text": "ledged, braced and frame" - }, - "framed and paneled": { - "text": "framed and paneled" - }, - "glashed or sash": { - "text": "glashed or sash" - }, - "flush": { - "text": "flush" - }, - "louvered": { - "text": "louvered" - }, - "wire gauged": { - "text": "wire gauged" - } - } - }, - "water_feat_type_enum": { - "name": "water_feat_type_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "fountain": { - "text": "fountain" - }, - "pool": { - "text": "pool" - }, - "standing feature": { - "text": "standing feature" - }, - "stream": { - "text": "stream" - }, - "waterfall": { - "text": "waterfall" - } - } - }, - "heat_deliv_loc_enum": { - "name": "heat_deliv_loc_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "north": { - "text": "north" - }, - "south": { - "text": "south" - }, - "east": { - "text": "east" - }, - "west": { - "text": "west" - } - } - }, - "room_connected_enum": { - "name": "room_connected_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "attic": { - "text": "attic" - }, - "bathroom": { - "text": "bathroom" - }, - "closet": { - "text": "closet" - }, - "conference room": { - "text": "conference room" - }, - "elevator": { - "text": "elevator" - }, - "examining room": { - "text": "examining room" - }, - "hallway": { - "text": "hallway" - }, - "kitchen": { - "text": "kitchen" - }, - "mail room": { - "text": "mail room" - }, - "office": { - "text": "office" - }, - "stairwell": { - "text": "stairwell" - } - } - }, - "room_samp_pos_enum": { - "name": "room_samp_pos_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "north corner": { - "text": "north corner" - }, - "south corner": { - "text": "south corner" - }, - "west corner": { - "text": "west corner" - }, - "east corner": { - "text": "east corner" - }, - "northeast corner": { - "text": "northeast corner" - }, - "northwest corner": { - "text": "northwest corner" - }, - "southeast corner": { - "text": "southeast corner" - }, - "southwest corner": { - "text": "southwest corner" - }, - "center": { - "text": "center" - } - } - }, - "handidness_enum": { - "name": "handidness_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "ambidexterity": { - "text": "ambidexterity" - }, - "left handedness": { - "text": "left handedness" - }, - "mixed-handedness": { - "text": "mixed-handedness" - }, - "right handedness": { - "text": "right handedness" - } - } - }, - "drawings_enum": { - "name": "drawings_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "operation": { - "text": "operation" - }, - "as built": { - "text": "as built" - }, - "construction": { - "text": "construction" - }, - "bid": { - "text": "bid" - }, - "design": { - "text": "design" - }, - "building navigation map": { - "text": "building navigation map" - }, - "diagram": { - "text": "diagram" - }, - "sketch": { - "text": "sketch" - } - } - }, - "room_loc_enum": { - "name": "room_loc_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "corner room": { - "text": "corner room" - }, - "interior room": { - "text": "interior room" - }, - "exterior wall": { - "text": "exterior wall" - } - } - }, - "ext_wall_orient_enum": { - "name": "ext_wall_orient_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "north": { - "text": "north" - }, - "south": { - "text": "south" - }, - "east": { - "text": "east" - }, - "west": { - "text": "west" - }, - "northeast": { - "text": "northeast" - }, - "southeast": { - "text": "southeast" - }, - "southwest": { - "text": "southwest" - }, - "northwest": { - "text": "northwest" - } - } - }, - "samp_weather_enum": { - "name": "samp_weather_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "clear sky": { - "text": "clear sky" - }, - "cloudy": { - "text": "cloudy" - }, - "foggy": { - "text": "foggy" - }, - "hail": { - "text": "hail" - }, - "rain": { - "text": "rain" - }, - "snow": { - "text": "snow" - }, - "sleet": { - "text": "sleet" - }, - "sunny": { - "text": "sunny" - }, - "windy": { - "text": "windy" - } - } - }, - "floor_struc_enum": { - "name": "floor_struc_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "balcony": { - "text": "balcony" - }, - "floating floor": { - "text": "floating floor" - }, - "glass floor": { - "text": "glass floor" - }, - "raised floor": { - "text": "raised floor" - }, - "sprung floor": { - "text": "sprung floor" - }, - "wood-framed": { - "text": "wood-framed" - }, - "concrete": { - "text": "concrete" - } - } - }, - "door_type_enum": { - "name": "door_type_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "composite": { - "text": "composite" - }, - "metal": { - "text": "metal" - }, - "wooden": { - "text": "wooden" - } - } - }, - "window_cond_enum": { - "name": "window_cond_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "damaged": { - "text": "damaged" - }, - "needs repair": { - "text": "needs repair" - }, - "new": { - "text": "new" - }, - "rupture": { - "text": "rupture" - }, - "visible wear": { - "text": "visible wear" - } - } - }, - "specific_enum": { - "name": "specific_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "operation": { - "text": "operation" - }, - "as built": { - "text": "as built" - }, - "construction": { - "text": "construction" - }, - "bid": { - "text": "bid" - }, - "design": { - "text": "design" - }, - "photos": { - "text": "photos" - } - } - }, - "wall_const_type_enum": { - "name": "wall_const_type_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "frame construction": { - "text": "frame construction" - }, - "joisted masonry": { - "text": "joisted masonry" - }, - "light noncombustible": { - "text": "light noncombustible" - }, - "masonry noncombustible": { - "text": "masonry noncombustible" - }, - "modified fire resistive": { - "text": "modified fire resistive" - }, - "fire resistive": { - "text": "fire resistive" - } - } - }, - "window_type_enum": { - "name": "window_type_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "single-hung sash window": { - "text": "single-hung sash window" - }, - "horizontal sash window": { - "text": "horizontal sash window" - }, - "fixed window": { - "text": "fixed window" - } - } - }, - "train_line_enum": { - "name": "train_line_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "red": { - "text": "red" - }, - "green": { - "text": "green" - }, - "orange": { - "text": "orange" - } - } - }, - "wall_loc_enum": { - "name": "wall_loc_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "north": { - "text": "north" - }, - "south": { - "text": "south" - }, - "east": { - "text": "east" - }, - "west": { - "text": "west" - } - } - }, - "door_cond_enum": { - "name": "door_cond_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "damaged": { - "text": "damaged" - }, - "needs repair": { - "text": "needs repair" - }, - "new": { - "text": "new" - }, - "rupture": { - "text": "rupture" - }, - "visible wear": { - "text": "visible wear" - } - } - }, - "light_type_enum": { - "name": "light_type_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "natural light": { - "text": "natural light" - }, - "electric light": { - "text": "electric light" - }, - "desk lamp": { - "text": "desk lamp" - }, - "flourescent lights": { - "text": "flourescent lights" - }, - "none": { - "text": "none" - } - } - }, - "room_type_enum": { - "name": "room_type_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "attic": { - "text": "attic" - }, - "bathroom": { - "text": "bathroom" - }, - "closet": { - "text": "closet" - }, - "conference room": { - "text": "conference room" - }, - "elevator": { - "text": "elevator" - }, - "examining room": { - "text": "examining room" - }, - "hallway": { - "text": "hallway" - }, - "kitchen": { - "text": "kitchen" - }, - "mail room": { - "text": "mail room" - }, - "private office": { - "text": "private office" - }, - "open office": { - "text": "open office" - }, - "stairwell": { - "text": "stairwell" - }, - ",restroom": { - "text": ",restroom" - }, - "lobby": { - "text": "lobby" - }, - "vestibule": { - "text": "vestibule" - }, - "mechanical or electrical room": { - "text": "mechanical or electrical room" - }, - "data center": { - "text": "data center" - }, - "laboratory_wet": { - "text": "laboratory_wet" - }, - "laboratory_dry": { - "text": "laboratory_dry" - }, - "gymnasium": { - "text": "gymnasium" - }, - "natatorium": { - "text": "natatorium" - }, - "auditorium": { - "text": "auditorium" - }, - "lockers": { - "text": "lockers" - }, - "cafe": { - "text": "cafe" - }, - "warehouse": { - "text": "warehouse" - } - } - }, - "window_cover_enum": { - "name": "window_cover_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "blinds": { - "text": "blinds" - }, - "curtains": { - "text": "curtains" - }, - "none": { - "text": "none" - } - } - }, - "door_move_enum": { - "name": "door_move_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "collapsible": { - "text": "collapsible" - }, - "folding": { - "text": "folding" - }, - "revolving": { - "text": "revolving" - }, - "rolling shutter": { - "text": "rolling shutter" - }, - "sliding": { - "text": "sliding" - }, - "swinging": { - "text": "swinging" - } - } - }, - "door_direct_enum": { - "name": "door_direct_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "inward": { - "text": "inward" - }, - "outward": { - "text": "outward" - }, - "sideways": { - "text": "sideways" - } - } - }, - "window_mat_enum": { - "name": "window_mat_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "clad": { - "text": "clad" - }, - "fiberglass": { - "text": "fiberglass" - }, - "metal": { - "text": "metal" - }, - "vinyl": { - "text": "vinyl" - }, - "wood": { - "text": "wood" - } - } - }, - "shading_device_cond_enum": { - "name": "shading_device_cond_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "damaged": { - "text": "damaged" - }, - "needs repair": { - "text": "needs repair" - }, - "new": { - "text": "new" - }, - "rupture": { - "text": "rupture" - }, - "visible wear": { - "text": "visible wear" - } - } - }, - "shading_device_type_enum": { - "name": "shading_device_type_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "bahama shutters": { - "text": "bahama shutters" - }, - "exterior roll blind": { - "text": "exterior roll blind" - }, - "gambrel awning": { - "text": "gambrel awning" - }, - "hood awning": { - "text": "hood awning" - }, - "porchroller awning": { - "text": "porchroller awning" - }, - "sarasota shutters": { - "text": "sarasota shutters" - }, - "slatted aluminum": { - "text": "slatted aluminum" - }, - "solid aluminum awning": { - "text": "solid aluminum awning" - }, - "sun screen": { - "text": "sun screen" - }, - "tree": { - "text": "tree" - }, - "trellis": { - "text": "trellis" - }, - "venetian awning": { - "text": "venetian awning" - } - } - }, - "int_wall_cond_enum": { - "name": "int_wall_cond_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "new": { - "text": "new" - }, - "visible wear": { - "text": "visible wear" - }, - "needs repair": { - "text": "needs repair" - }, - "damaged": { - "text": "damaged" - }, - "rupture": { - "text": "rupture" - } - } - }, - "door_type_metal_enum": { - "name": "door_type_metal_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "collapsible": { - "text": "collapsible" - }, - "corrugated steel": { - "text": "corrugated steel" - }, - "hollow": { - "text": "hollow" - }, - "rolling shutters": { - "text": "rolling shutters" - }, - "steel plate": { - "text": "steel plate" - } - } - }, - "wall_texture_enum": { - "name": "wall_texture_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "crows feet": { - "text": "crows feet" - }, - "crows-foot stomp": { - "text": "crows-foot stomp" - }, - "": { - "text": "" - }, - "double skip": { - "text": "double skip" - }, - "hawk and trowel": { - "text": "hawk and trowel" - }, - "knockdown": { - "text": "knockdown" - }, - "popcorn": { - "text": "popcorn" - }, - "orange peel": { - "text": "orange peel" - }, - "rosebud stomp": { - "text": "rosebud stomp" - }, - "Santa-Fe texture": { - "text": "Santa-Fe texture" - }, - "skip trowel": { - "text": "skip trowel" - }, - "smooth": { - "text": "smooth" - }, - "stomp knockdown": { - "text": "stomp knockdown" - }, - "swirl": { - "text": "swirl" - } - } - }, - "build_docs_enum": { - "name": "build_docs_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "building information model": { - "text": "building information model" - }, - "commissioning report": { - "text": "commissioning report" - }, - "complaint logs": { - "text": "complaint logs" - }, - "contract administration": { - "text": "contract administration" - }, - "cost estimate": { - "text": "cost estimate" - }, - "janitorial schedules or logs": { - "text": "janitorial schedules or logs" - }, - "maintenance plans": { - "text": "maintenance plans" - }, - "schedule": { - "text": "schedule" - }, - "sections": { - "text": "sections" - }, - "shop drawings": { - "text": "shop drawings" - }, - "submittals": { - "text": "submittals" - }, - "ventilation system": { - "text": "ventilation system" - }, - "windows": { - "text": "windows" - } - } - }, - "building_setting_enum": { - "name": "building_setting_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "urban": { - "text": "urban" - }, - "suburban": { - "text": "suburban" - }, - "exurban": { - "text": "exurban" - }, - "rural": { - "text": "rural" - } - } - }, - "wall_finish_mat_enum": { - "name": "wall_finish_mat_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "plaster": { - "text": "plaster" - }, - "gypsum plaster": { - "text": "gypsum plaster" - }, - "veneer plaster": { - "text": "veneer plaster" - }, - "gypsum board": { - "text": "gypsum board" - }, - "tile": { - "text": "tile" - }, - "terrazzo": { - "text": "terrazzo" - }, - "stone facing": { - "text": "stone facing" - }, - "acoustical treatment": { - "text": "acoustical treatment" - }, - "wood": { - "text": "wood" - }, - "metal": { - "text": "metal" - }, - "masonry": { - "text": "masonry" - } - } - }, - "build_occup_type_enum": { - "name": "build_occup_type_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "office": { - "text": "office" - }, - "market": { - "text": "market" - }, - "restaurant": { - "text": "restaurant" - }, - "residence": { - "text": "residence" - }, - "school": { - "text": "school" - }, - "residential": { - "text": "residential" - }, - "commercial": { - "text": "commercial" - }, - "low rise": { - "text": "low rise" - }, - "high rise": { - "text": "high rise" - }, - "wood framed": { - "text": "wood framed" - }, - "health care": { - "text": "health care" - }, - "airport": { - "text": "airport" - }, - "sports complex": { - "text": "sports complex" - } - } - }, - "ceil_texture_enum": { - "name": "ceil_texture_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "crows feet": { - "text": "crows feet" - }, - "crows-foot stomp": { - "text": "crows-foot stomp" - }, - "double skip": { - "text": "double skip" - }, - "hawk and trowel": { - "text": "hawk and trowel" - }, - "knockdown": { - "text": "knockdown" - }, - "popcorn": { - "text": "popcorn" - }, - "orange peel": { - "text": "orange peel" - }, - "rosebud stomp": { - "text": "rosebud stomp" - }, - "Santa-Fe texture": { - "text": "Santa-Fe texture" - }, - "skip trowel": { - "text": "skip trowel" - }, - "smooth": { - "text": "smooth" - }, - "stomp knockdown": { - "text": "stomp knockdown" - }, - "swirl": { - "text": "swirl" - } - } - }, - "floor_water_mold_enum": { - "name": "floor_water_mold_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "mold odor": { - "text": "mold odor" - }, - "wet floor": { - "text": "wet floor" - }, - "water stains": { - "text": "water stains" - }, - "wall discoloration": { - "text": "wall discoloration" - }, - "floor discoloration": { - "text": "floor discoloration" - }, - "ceiling discoloration": { - "text": "ceiling discoloration" - }, - "peeling paint or wallpaper": { - "text": "peeling paint or wallpaper" - }, - "bulging walls": { - "text": "bulging walls" - }, - "condensation": { - "text": "condensation" - } - } - }, - "ceil_type_enum": { - "name": "ceil_type_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "cathedral": { - "text": "cathedral" - }, - "dropped": { - "text": "dropped" - }, - "concave": { - "text": "concave" - }, - "barrel-shaped": { - "text": "barrel-shaped" - }, - "coffered": { - "text": "coffered" - }, - "cove": { - "text": "cove" - }, - "stretched": { - "text": "stretched" - } - } - }, - "door_loc_enum": { - "name": "door_loc_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "north": { - "text": "north" - }, - "south": { - "text": "south" - }, - "east": { - "text": "east" - }, - "west": { - "text": "west" - } - } - }, - "door_comp_type_enum": { - "name": "door_comp_type_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "metal covered": { - "text": "metal covered" - }, - "revolving": { - "text": "revolving" - }, - "sliding": { - "text": "sliding" - }, - "telescopic": { - "text": "telescopic" - } - } - }, - "mech_struc_enum": { - "name": "mech_struc_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "subway": { - "text": "subway" - }, - "coach": { - "text": "coach" - }, - "carriage": { - "text": "carriage" - }, - "elevator": { - "text": "elevator" - }, - "escalator": { - "text": "escalator" - }, - "boat": { - "text": "boat" - }, - "train": { - "text": "train" - }, - "car": { - "text": "car" - }, - "bus": { - "text": "bus" - } - } - }, - "wall_surf_treatment_enum": { - "name": "wall_surf_treatment_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "painted": { - "text": "painted" - }, - "wall paper": { - "text": "wall paper" - }, - "no treatment": { - "text": "no treatment" - }, - "paneling": { - "text": "paneling" - }, - "stucco": { - "text": "stucco" - }, - "fabric": { - "text": "fabric" - } - } - }, - "room_condt_enum": { - "name": "room_condt_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "new": { - "text": "new" - }, - "visible wear": { - "text": "visible wear" - }, - "needs repair": { - "text": "needs repair" - }, - "damaged": { - "text": "damaged" - }, - "rupture": { - "text": "rupture" - }, - "visible signs of mold/mildew": { - "text": "visible signs of mold/mildew" - } - } - }, - "ext_window_orient_enum": { - "name": "ext_window_orient_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "north": { - "text": "north" - }, - "south": { - "text": "south" - }, - "east": { - "text": "east" - }, - "west": { - "text": "west" - }, - "northeast": { - "text": "northeast" - }, - "southeast": { - "text": "southeast" - }, - "southwest": { - "text": "southwest" - }, - "northwest": { - "text": "northwest" - } - } - }, - "indoor_space_enum": { - "name": "indoor_space_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "bedroom": { - "text": "bedroom" - }, - "office": { - "text": "office" - }, - "bathroom": { - "text": "bathroom" - }, - "foyer": { - "text": "foyer" - }, - "kitchen": { - "text": "kitchen" - }, - "locker room": { - "text": "locker room" - }, - "hallway": { - "text": "hallway" - }, - "elevator": { - "text": "elevator" - } - } - }, - "floor_cond_enum": { - "name": "floor_cond_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "new": { - "text": "new" - }, - "visible wear": { - "text": "visible wear" - }, - "needs repair": { - "text": "needs repair" - }, - "damaged": { - "text": "damaged" - }, - "rupture": { - "text": "rupture" - } - } - }, - "samp_floor_enum": { - "name": "samp_floor_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "1st floor": { - "text": "1st floor" - }, - "2nd floor": { - "text": "2nd floor" - }, - "basement": { - "text": "basement" - }, - "lobby": { - "text": "lobby" - } - } - }, - "filter_type_enum": { - "name": "filter_type_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "particulate air filter": { - "text": "particulate air filter" - }, - "chemical air filter": { - "text": "chemical air filter" - }, - "low-MERV pleated media": { - "text": "low-MERV pleated media" - }, - "HEPA": { - "text": "HEPA" - }, - "electrostatic": { - "text": "electrostatic" - }, - "gas-phase or ultraviolet air treatments": { - "text": "gas-phase or ultraviolet air treatments" - } - } - }, - "train_stop_loc_enum": { - "name": "train_stop_loc_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "end": { - "text": "end" - }, - "mid": { - "text": "mid" - }, - "downtown": { - "text": "downtown" - } - } - }, - "floor_finish_mat_enum": { - "name": "floor_finish_mat_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "tile": { - "text": "tile" - }, - "wood strip or parquet": { - "text": "wood strip or parquet" - }, - "carpet": { - "text": "carpet" - }, - "rug": { - "text": "rug" - }, - "laminate wood": { - "text": "laminate wood" - }, - "lineoleum": { - "text": "lineoleum" - }, - "vinyl composition tile": { - "text": "vinyl composition tile" - }, - "sheet vinyl": { - "text": "sheet vinyl" - }, - "stone": { - "text": "stone" - }, - "bamboo": { - "text": "bamboo" - }, - "cork": { - "text": "cork" - }, - "terrazo": { - "text": "terrazo" - }, - "concrete": { - "text": "concrete" - }, - "none": { - "text": "none" - }, - "sealed": { - "text": "sealed" - }, - "clear finish": { - "text": "clear finish" - }, - "paint": { - "text": "paint" - }, - "none or unfinished": { - "text": "none or unfinished" - } - } - }, - "season_use_enum": { - "name": "season_use_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "Spring": { - "text": "Spring" - }, - "Summer": { - "text": "Summer" - }, - "Fall": { - "text": "Fall" - }, - "Winter": { - "text": "Winter" - } - } - }, - "furniture_enum": { - "name": "furniture_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "cabinet": { - "text": "cabinet" - }, - "chair": { - "text": "chair" - }, - "desks": { - "text": "desks" - } - } - }, - "quad_pos_enum": { - "name": "quad_pos_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "North side": { - "text": "North side" - }, - "West side": { - "text": "West side" - }, - "South side": { - "text": "South side" - }, - "East side": { - "text": "East side" - } - } - }, - "substructure_type_enum": { - "name": "substructure_type_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "crawlspace": { - "text": "crawlspace" - }, - "slab on grade": { - "text": "slab on grade" - }, - "basement": { - "text": "basement" - } - } - }, - "indoor_surf_enum": { - "name": "indoor_surf_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "cabinet": { - "text": "cabinet" - }, - "ceiling": { - "text": "ceiling" - }, - "counter top": { - "text": "counter top" - }, - "door": { - "text": "door" - }, - "shelving": { - "text": "shelving" - }, - "vent cover": { - "text": "vent cover" - }, - "window": { - "text": "window" - }, - "wall": { - "text": "wall" - } - } - }, - "ceil_finish_mat_enum": { - "name": "ceil_finish_mat_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "drywall": { - "text": "drywall" - }, - "mineral fibre": { - "text": "mineral fibre" - }, - "tiles": { - "text": "tiles" - }, - "PVC": { - "text": "PVC" - }, - "plasterboard": { - "text": "plasterboard" - }, - "metal": { - "text": "metal" - }, - "fiberglass": { - "text": "fiberglass" - }, - "stucco": { - "text": "stucco" - }, - "mineral wool/calcium silicate": { - "text": "mineral wool/calcium silicate" - }, - "wood": { - "text": "wood" - } - } - }, - "gender_restroom_enum": { - "name": "gender_restroom_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "all gender": { - "text": "all gender" - }, - "female": { - "text": "female" - }, - "gender neurtral": { - "text": "gender neurtral" - }, - "male": { - "text": "male" - }, - "male and female": { - "text": "male and female" - }, - "unisex": { - "text": "unisex" - } - } - }, - "window_horiz_pos_enum": { - "name": "window_horiz_pos_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "left": { - "text": "left" - }, - "middle": { - "text": "middle" - }, - "right": { - "text": "right" - } - } - }, - "window_vert_pos_enum": { - "name": "window_vert_pos_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "bottom": { - "text": "bottom" - }, - "middle": { - "text": "middle" - }, - "top": { - "text": "top" - }, - "low": { - "text": "low" - }, - "high": { - "text": "high" - } - } - }, - "arch_struc_enum": { - "name": "arch_struc_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "building": { - "text": "building" - }, - "shed": { - "text": "shed" - }, - "home": { - "text": "home" - } - } - }, - "hc_produced_enum": { - "name": "hc_produced_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "Oil": { - "text": "Oil" - }, - "Gas-Condensate": { - "text": "Gas-Condensate" - }, - "Gas": { - "text": "Gas" - }, - "Bitumen": { - "text": "Bitumen" - }, - "Coalbed Methane": { - "text": "Coalbed Methane" - }, - "other": { - "text": "other" - } - } - }, - "hcr_geol_age_enum": { - "name": "hcr_geol_age_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "Archean": { - "text": "Archean" - }, - "Cambrian": { - "text": "Cambrian" - }, - "Carboniferous": { - "text": "Carboniferous" - }, - "Cenozoic": { - "text": "Cenozoic" - }, - "Cretaceous": { - "text": "Cretaceous" - }, - "Devonian": { - "text": "Devonian" - }, - "Jurassic": { - "text": "Jurassic" - }, - "Mesozoic": { - "text": "Mesozoic" - }, - "Neogene": { - "text": "Neogene" - }, - "Ordovician": { - "text": "Ordovician" - }, - "Paleogene": { - "text": "Paleogene" - }, - "Paleozoic": { - "text": "Paleozoic" - }, - "Permian": { - "text": "Permian" - }, - "Precambrian": { - "text": "Precambrian" - }, - "Proterozoic": { - "text": "Proterozoic" - }, - "Silurian": { - "text": "Silurian" - }, - "Triassic": { - "text": "Triassic" - }, - "other": { - "text": "other" - } - } - }, - "samp_collect_point_enum": { - "name": "samp_collect_point_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "well": { - "text": "well" - }, - "test well": { - "text": "test well" - }, - "drilling rig": { - "text": "drilling rig" - }, - "wellhead": { - "text": "wellhead" - }, - "separator": { - "text": "separator" - }, - "storage tank": { - "text": "storage tank" - }, - "other": { - "text": "other" - } - } - }, - "depos_env_enum": { - "name": "depos_env_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "Continental - Alluvial": { - "text": "Continental - Alluvial" - }, - "Continental - Aeolian": { - "text": "Continental - Aeolian" - }, - "Continental - Fluvial": { - "text": "Continental - Fluvial" - }, - "Continental - Lacustrine": { - "text": "Continental - Lacustrine" - }, - "Transitional - Deltaic": { - "text": "Transitional - Deltaic" - }, - "Transitional - Tidal": { - "text": "Transitional - Tidal" - }, - "Transitional - Lagoonal": { - "text": "Transitional - Lagoonal" - }, - "Transitional - Beach": { - "text": "Transitional - Beach" - }, - "Transitional - Lake": { - "text": "Transitional - Lake" - }, - "Marine - Shallow": { - "text": "Marine - Shallow" - }, - "Marine - Deep": { - "text": "Marine - Deep" - }, - "Marine - Reef": { - "text": "Marine - Reef" - }, - "Other - Evaporite": { - "text": "Other - Evaporite" - }, - "Other - Glacial": { - "text": "Other - Glacial" - }, - "Other - Volcanic": { - "text": "Other - Volcanic" - }, - "other": { - "text": "other" - } - } - }, - "oxy_stat_samp_enum": { - "name": "oxy_stat_samp_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "aerobic": { - "text": "aerobic" - }, - "anaerobic": { - "text": "anaerobic" - }, - "other": { - "text": "other" - } - } - }, - "hcr_enum": { - "name": "hcr_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "Oil Reservoir": { - "text": "Oil Reservoir" - }, - "Gas Reservoir": { - "text": "Gas Reservoir" - }, - "Oil Sand": { - "text": "Oil Sand" - }, - "Coalbed": { - "text": "Coalbed" - }, - "Shale": { - "text": "Shale" - }, - "Tight Oil Reservoir": { - "text": "Tight Oil Reservoir" - }, - "Tight Gas Reservoir": { - "text": "Tight Gas Reservoir" - }, - "other": { - "text": "other" - } - } - }, - "samp_subtype_enum": { - "name": "samp_subtype_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "oil phase": { - "text": "oil phase" - }, - "water phase": { - "text": "water phase" - }, - "biofilm": { - "text": "biofilm" - }, - "not applicable": { - "text": "not applicable" - }, - "other": { - "text": "other" - } - } - }, - "lithology_enum": { - "name": "lithology_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "Basement": { - "text": "Basement" - }, - "Chalk": { - "text": "Chalk" - }, - "Chert": { - "text": "Chert" - }, - "Coal": { - "text": "Coal" - }, - "Conglomerate": { - "text": "Conglomerate" - }, - "Diatomite": { - "text": "Diatomite" - }, - "Dolomite": { - "text": "Dolomite" - }, - "Limestone": { - "text": "Limestone" - }, - "Sandstone": { - "text": "Sandstone" - }, - "Shale": { - "text": "Shale" - }, - "Siltstone": { - "text": "Siltstone" - }, - "Volcanic": { - "text": "Volcanic" - }, - "other": { - "text": "other" - } - } - }, - "sr_geol_age_enum": { - "name": "sr_geol_age_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "Archean": { - "text": "Archean" - }, - "Cambrian": { - "text": "Cambrian" - }, - "Carboniferous": { - "text": "Carboniferous" - }, - "Cenozoic": { - "text": "Cenozoic" - }, - "Cretaceous": { - "text": "Cretaceous" - }, - "Devonian": { - "text": "Devonian" - }, - "Jurassic": { - "text": "Jurassic" - }, - "Mesozoic": { - "text": "Mesozoic" - }, - "Neogene": { - "text": "Neogene" - }, - "Ordovician": { - "text": "Ordovician" - }, - "Paleogene": { - "text": "Paleogene" - }, - "Paleozoic": { - "text": "Paleozoic" - }, - "Permian": { - "text": "Permian" - }, - "Precambrian": { - "text": "Precambrian" - }, - "Proterozoic": { - "text": "Proterozoic" - }, - "Silurian": { - "text": "Silurian" - }, - "Triassic": { - "text": "Triassic" - }, - "other": { - "text": "other" - } - } - }, - "sr_dep_env_enum": { - "name": "sr_dep_env_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "Lacustine": { - "text": "Lacustine" - }, - "Fluvioldeltaic": { - "text": "Fluvioldeltaic" - }, - "Fluviomarine": { - "text": "Fluviomarine" - }, - "Marine": { - "text": "Marine" - }, - "other": { - "text": "other" - } - } - }, - "sr_kerog_type_enum": { - "name": "sr_kerog_type_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "Type I": { - "text": "Type I" - }, - "Type II": { - "text": "Type II" - }, - "Type III": { - "text": "Type III" - }, - "Type IV": { - "text": "Type IV" - }, - "other": { - "text": "other" - } - } - }, - "sr_lithology_enum": { - "name": "sr_lithology_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "Clastic": { - "text": "Clastic" - }, - "Carbonate": { - "text": "Carbonate" - }, - "Coal": { - "text": "Coal" - }, - "Biosilicieous": { - "text": "Biosilicieous" - }, - "other": { - "text": "other" - } - } - }, - "biotic_relationship_enum": { - "name": "biotic_relationship_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "free living": { - "text": "free living" - }, - "parasite": { - "text": "parasite" - }, - "commensal": { - "text": "commensal" - }, - "symbiont": { - "text": "symbiont" - } - } - }, - "drainage_class_enum": { - "name": "drainage_class_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "very poorly": { - "text": "very poorly" - }, - "poorly": { - "text": "poorly" - }, - "somewhat poorly": { - "text": "somewhat poorly" - }, - "moderately well": { - "text": "moderately well" - }, - "well": { - "text": "well" - }, - "excessively drained": { - "text": "excessively drained" - } - } - }, - "cur_land_use_enum": { - "name": "cur_land_use_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "badlands": { - "text": "badlands" - }, - "cities": { - "text": "cities" - }, - "conifers": { - "text": "conifers", - "annotations": { - "originally": { - "tag": "originally", - "value": "conifers (e.g. pine,spruce,fir,cypress)" - } - }, - "examples": [ - { - "value": "cypress" - }, - { - "value": "fir" - }, - { - "value": "pine" - }, - { - "value": "spruce" - } - ] - }, - "crop trees": { - "text": "crop trees", - "annotations": { - "originally": { - "tag": "originally", - "value": "crop trees (nuts,fruit,christmas trees,nursery trees)" - } - }, - "examples": [ - { - "value": "christmas trees" - }, - { - "value": "fruit" - }, - { - "value": "nursery trees" - }, - { - "value": "nuts" - } - ] - }, - "farmstead": { - "text": "farmstead" - }, - "gravel": { - "text": "gravel" - }, - "hardwoods": { - "text": "hardwoods", - "annotations": { - "originally": { - "tag": "originally", - "value": "hardwoods (e.g. oak,hickory,elm,aspen)" - } - }, - "examples": [ - { - "value": "aspen" - }, - { - "value": "elm" - }, - { - "value": "hickory" - }, - { - "value": "oak" - } - ] - }, - "hayland": { - "text": "hayland" - }, - "horticultural plants": { - "text": "horticultural plants", - "annotations": { - "originally": { - "tag": "originally", - "value": "horticultural plants (e.g. tulips)" - } - }, - "examples": [ - { - "value": "tulips" - } - ] - }, - "industrial areas": { - "text": "industrial areas" - }, - "intermixed hardwood and conifers": { - "text": "intermixed hardwood and conifers" - }, - "marshlands": { - "text": "marshlands", - "annotations": { - "originally": { - "tag": "originally", - "value": "marshlands (grass,sedges,rushes)" - } - }, - "examples": [ - { - "value": "grass" - }, - { - "value": "rushes" - }, - { - "value": "sedgees" - } - ] - }, - "meadows": { - "text": "meadows", - "annotations": { - "originally": { - "tag": "originally", - "value": "meadows (grasses,alfalfa,fescue,bromegrass,timothy)" - } - }, - "examples": [ - { - "value": "alfalfa" - }, - { - "value": "bromegrass" - }, - { - "value": "fescue" - }, - { - "value": "grasses" - }, - { - "value": "timothy" - } - ] - }, - "mines/quarries": { - "text": "mines/quarries" - }, - "mudflats": { - "text": "mudflats" - }, - "oil waste areas": { - "text": "oil waste areas" - }, - "pastureland": { - "text": "pastureland", - "annotations": { - "originally": { - "tag": "originally", - "value": "pastureland (grasslands used for livestock grazing)" - } - }, - "comments": [ - "grasslands used for livestock grazing" - ] - }, - "permanent snow or ice": { - "text": "permanent snow or ice" - }, - "rainforest": { - "text": "rainforest", - "annotations": { - "originally": { - "tag": "originally", - "value": "rainforest (evergreen forest receiving greater than 406 cm annual rainfall)" - } - }, - "comments": [ - "evergreen forest receiving greater than 406 cm annual rainfall" - ] - }, - "rangeland": { - "text": "rangeland" - }, - "roads/railroads": { - "text": "roads/railroads" - }, - "rock": { - "text": "rock" - }, - "row crops": { - "text": "row crops" - }, - "saline seeps": { - "text": "saline seeps" - }, - "salt flats": { - "text": "salt flats" - }, - "sand": { - "text": "sand" - }, - "shrub crops": { - "text": "shrub crops", - "annotations": { - "originally": { - "tag": "originally", - "value": "shrub crops (blueberries,nursery ornamentals,filberts)" - } - }, - "examples": [ - { - "value": "blueberries" - }, - { - "value": "filberts" - }, - { - "value": "nursery ornamentals" - } - ] - }, - "shrub land": { - "text": "shrub land", - "annotations": { - "originally": { - "tag": "originally", - "value": "shrub land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus)" - } - }, - "examples": [ - { - "value": "creosote bush" - }, - { - "value": "eucalyptus" - }, - { - "value": "mesquite" - }, - { - "value": "sage-brush" - }, - { - "value": "shrub oak" - } - ] - }, - "small grains": { - "text": "small grains" - }, - "successional shrub land": { - "text": "successional shrub land", - "annotations": { - "originally": { - "tag": "originally", - "value": "successional shrub land (tree saplings,hazels,sumacs,chokecherry,shrub dogwoods,blackberries)" - } - }, - "examples": [ - { - "value": "blackberries" - }, - { - "value": "chokecherry" - }, - { - "value": "hazels" - }, - { - "value": "shrub dogwoods" - }, - { - "value": "sumacs" - }, - { - "value": "tree saplings" - } - ] - }, - "swamp": { - "text": "swamp", - "annotations": { - "originally": { - "tag": "originally", - "value": "swamp (permanent or semi-permanent water body dominated by woody plants)" - } - }, - "comments": [ - "permanent or semi-permanent water body dominated by woody plants" - ] - }, - "tropical": { - "text": "tropical", - "annotations": { - "originally": { - "tag": "originally", - "value": "tropical (e.g. mangrove,palms)" - } - }, - "examples": [ - { - "value": "mangrove" - }, - { - "value": "palms" - } - ] - }, - "tundra": { - "text": "tundra", - "annotations": { - "originally": { - "tag": "originally", - "value": "tundra (mosses,lichens)" - } - }, - "examples": [ - { - "value": "lichens" - }, - { - "value": "mosses" - } - ] - }, - "vegetable crops": { - "text": "vegetable crops" - }, - "vine crops": { - "text": "vine crops", - "annotations": { - "originally": { - "tag": "originally", - "value": "vine crops (grapes)" - } - }, - "examples": [ - { - "value": "grapes" - } - ] - } - } - }, - "soil_horizon_enum": { - "name": "soil_horizon_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "O horizon": { - "text": "O horizon" - }, - "A horizon": { - "text": "A horizon" - }, - "E horizon": { - "text": "E horizon" - }, - "B horizon": { - "text": "B horizon" - }, - "C horizon": { - "text": "C horizon" - }, - "R layer": { - "text": "R layer" - }, - "Permafrost": { - "text": "Permafrost" - }, - "M horizon": { - "text": "M horizon" - } - } - }, - "profile_position_enum": { - "name": "profile_position_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "summit": { - "text": "summit" - }, - "shoulder": { - "text": "shoulder" - }, - "backslope": { - "text": "backslope" - }, - "footslope": { - "text": "footslope" - }, - "toeslope": { - "text": "toeslope" - } - } - }, - "tillage_enum": { - "name": "tillage_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "drill": { - "text": "drill" - }, - "cutting disc": { - "text": "cutting disc" - }, - "ridge till": { - "text": "ridge till" - }, - "strip tillage": { - "text": "strip tillage" - }, - "zonal tillage": { - "text": "zonal tillage" - }, - "chisel": { - "text": "chisel" - }, - "tined": { - "text": "tined" - }, - "mouldboard": { - "text": "mouldboard" - }, - "disc plough": { - "text": "disc plough" - } - } - }, - "fao_class_enum": { - "name": "fao_class_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "Acrisols": { - "text": "Acrisols" - }, - "Andosols": { - "text": "Andosols" - }, - "Arenosols": { - "text": "Arenosols" - }, - "Cambisols": { - "text": "Cambisols" - }, - "Chernozems": { - "text": "Chernozems" - }, - "Ferralsols": { - "text": "Ferralsols" - }, - "Fluvisols": { - "text": "Fluvisols" - }, - "Gleysols": { - "text": "Gleysols" - }, - "Greyzems": { - "text": "Greyzems" - }, - "Gypsisols": { - "text": "Gypsisols" - }, - "Histosols": { - "text": "Histosols" - }, - "Kastanozems": { - "text": "Kastanozems" - }, - "Lithosols": { - "text": "Lithosols" - }, - "Luvisols": { - "text": "Luvisols" - }, - "Nitosols": { - "text": "Nitosols" - }, - "Phaeozems": { - "text": "Phaeozems" - }, - "Planosols": { - "text": "Planosols" - }, - "Podzols": { - "text": "Podzols" - }, - "Podzoluvisols": { - "text": "Podzoluvisols" - }, - "Rankers": { - "text": "Rankers" - }, - "Regosols": { - "text": "Regosols" - }, - "Rendzinas": { - "text": "Rendzinas" - }, - "Solonchaks": { - "text": "Solonchaks" - }, - "Solonetz": { - "text": "Solonetz" - }, - "Vertisols": { - "text": "Vertisols" - }, - "Yermosols": { - "text": "Yermosols" - } - } - }, - "samp_capt_status_enum": { - "name": "samp_capt_status_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "active surveillance in response to an outbreak": { - "text": "active surveillance in response to an outbreak" - }, - "active surveillance not initiated by an outbreak": { - "text": "active surveillance not initiated by an outbreak" - }, - "farm sample": { - "text": "farm sample" - }, - "market sample": { - "text": "market sample" - }, - "other": { - "text": "other" - } - } - }, - "plant_sex_enum": { - "name": "plant_sex_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "Androdioecious": { - "text": "Androdioecious" - }, - "Androecious": { - "text": "Androecious" - }, - "Androgynous": { - "text": "Androgynous" - }, - "Androgynomonoecious": { - "text": "Androgynomonoecious" - }, - "Andromonoecious": { - "text": "Andromonoecious" - }, - "Bisexual": { - "text": "Bisexual" - }, - "Dichogamous": { - "text": "Dichogamous" - }, - "Diclinous": { - "text": "Diclinous" - }, - "Dioecious": { - "text": "Dioecious" - }, - "Gynodioecious": { - "text": "Gynodioecious" - }, - "Gynoecious": { - "text": "Gynoecious" - }, - "Gynomonoecious": { - "text": "Gynomonoecious" - }, - "Hermaphroditic": { - "text": "Hermaphroditic" - }, - "Imperfect": { - "text": "Imperfect" - }, - "Monoclinous": { - "text": "Monoclinous" - }, - "Monoecious": { - "text": "Monoecious" - }, - "Perfect": { - "text": "Perfect" - }, - "Polygamodioecious": { - "text": "Polygamodioecious" - }, - "Polygamomonoecious": { - "text": "Polygamomonoecious" - }, - "Polygamous": { - "text": "Polygamous" - }, - "Protandrous": { - "text": "Protandrous" - }, - "Protogynous": { - "text": "Protogynous" - }, - "Subandroecious": { - "text": "Subandroecious" - }, - "Subdioecious": { - "text": "Subdioecious" - }, - "Subgynoecious": { - "text": "Subgynoecious" - }, - "Synoecious": { - "text": "Synoecious" - }, - "Trimonoecious": { - "text": "Trimonoecious" - }, - "Trioecious": { - "text": "Trioecious" - }, - "Unisexual": { - "text": "Unisexual" - } - } - }, - "growth_habit_enum": { - "name": "growth_habit_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "erect": { - "text": "erect" - }, - "semi-erect": { - "text": "semi-erect" - }, - "spreading": { - "text": "spreading" - }, - "prostrate": { - "text": "prostrate" - } - } - }, - "samp_dis_stage_enum": { - "name": "samp_dis_stage_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "dissemination": { - "text": "dissemination" - }, - "growth and reproduction": { - "text": "growth and reproduction" - }, - "infection": { - "text": "infection" - }, - "inoculation": { - "text": "inoculation" - }, - "penetration": { - "text": "penetration" - }, - "other": { - "text": "other" - } - } - }, - "biol_stat_enum": { - "name": "biol_stat_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "wild": { - "text": "wild" - }, - "natural": { - "text": "natural" - }, - "semi-natural": { - "text": "semi-natural" - }, - "inbred line": { - "text": "inbred line" - }, - "breeder's line": { - "text": "breeder's line" - }, - "hybrid": { - "text": "hybrid" - }, - "clonal selection": { - "text": "clonal selection" - }, - "mutant": { - "text": "mutant" - } - } - }, - "tidal_stage_enum": { - "name": "tidal_stage_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "low tide": { - "text": "low tide" - }, - "ebb tide": { - "text": "ebb tide" - }, - "flood tide": { - "text": "flood tide" - }, - "high tide": { - "text": "high tide" - } - } - }, - "sediment_type_enum": { - "name": "sediment_type_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "biogenous": { - "text": "biogenous" - }, - "cosmogenous": { - "text": "cosmogenous" - }, - "hydrogenous": { - "text": "hydrogenous" - }, - "lithogenous": { - "text": "lithogenous" - } - } - }, - "host_sex_enum": { - "name": "host_sex_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "female": { - "text": "female" - }, - "hermaphrodite": { - "text": "hermaphrodite" - }, - "male": { - "text": "male" - }, - "neuter": { - "text": "neuter" - } - } - }, - "analysis_type_enum": { - "name": "analysis_type_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "metabolomics": { - "text": "metabolomics" - }, - "metagenomics": { - "text": "metagenomics" - }, - "metaproteomics": { - "text": "metaproteomics" - }, - "metatranscriptomics": { - "text": "metatranscriptomics" - }, - "natural organic matter": { - "text": "natural organic matter" - } - } - }, - "dna_sample_format_enum": { - "name": "dna_sample_format_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "10 mM Tris-HCl": { - "text": "10 mM Tris-HCl" - }, - "DNAStable": { - "text": "DNAStable" - }, - "Ethanol": { - "text": "Ethanol" - }, - "Low EDTA TE": { - "text": "Low EDTA TE" - }, - "MDA reaction buffer": { - "text": "MDA reaction buffer" - }, - "PBS": { - "text": "PBS" - }, - "Pellet": { - "text": "Pellet" - }, - "RNAStable": { - "text": "RNAStable" - }, - "TE": { - "text": "TE" - }, - "Water": { - "text": "Water" - }, - "Gentegra-DNA": { - "text": "Gentegra-DNA" - }, - "Gentegra-RNA": { - "text": "Gentegra-RNA" - } - } - }, - "rna_sample_format_enum": { - "name": "rna_sample_format_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "10 mM Tris-HCl": { - "text": "10 mM Tris-HCl" - }, - "DNAStable": { - "text": "DNAStable" - }, - "Ethanol": { - "text": "Ethanol" - }, - "Low EDTA TE": { - "text": "Low EDTA TE" - }, - "MDA reaction buffer": { - "text": "MDA reaction buffer" - }, - "PBS": { - "text": "PBS" - }, - "Pellet": { - "text": "Pellet" - }, - "RNAStable": { - "text": "RNAStable" - }, - "TE": { - "text": "TE" - }, - "Water": { - "text": "Water" - }, - "Gentegra-DNA": { - "text": "Gentegra-DNA" - }, - "Gentegra-RNA": { - "text": "Gentegra-RNA" - } - } - }, - "sample_type_enum": { - "name": "sample_type_enum", - "from_schema": "https://example.com/nmdc_submission_schema", - "permissible_values": { - "soil": { - "text": "soil" - }, - "water_extract_soil": { - "text": "water_extract_soil" - } - } - } - }, - "slots": { - "air_data": { - "name": "air_data", - "description": "aggregation slot relating air data collections to a SampleData container", - "from_schema": "https://example.com/nmdc_submission_schema", - "multivalued": true, - "range": "AirInterface", - "inlined": true, - "inlined_as_list": true - }, - "biofilm_data": { - "name": "biofilm_data", - "description": "aggregation slot relating biofilm data collections to a SampleData container", - "from_schema": "https://example.com/nmdc_submission_schema", - "multivalued": true, - "range": "BiofilmInterface", - "inlined": true, - "inlined_as_list": true - }, - "built_env_data": { - "name": "built_env_data", - "description": "aggregation slot relating built_env data collections to a SampleData container", - "from_schema": "https://example.com/nmdc_submission_schema", - "multivalued": true, - "range": "BuiltEnvInterface", - "inlined": true, - "inlined_as_list": true - }, - "emsl_data": { - "name": "emsl_data", - "description": "aggregation slot relating emsl data collections to a SampleData container", - "from_schema": "https://example.com/nmdc_submission_schema", - "multivalued": true, - "range": "EmslInterface", - "inlined": true, - "inlined_as_list": true - }, - "hcr_cores_data": { - "name": "hcr_cores_data", - "description": "aggregation slot relating hcr_cores data collections to a SampleData container", - "from_schema": "https://example.com/nmdc_submission_schema", - "multivalued": true, - "range": "HcrCoresInterface", - "inlined": true, - "inlined_as_list": true - }, - "hcr_fluids_swabs_data": { - "name": "hcr_fluids_swabs_data", - "description": "aggregation slot relating hcr_fluids_swabs data collections to a SampleData container", - "from_schema": "https://example.com/nmdc_submission_schema", - "multivalued": true, - "range": "HcrFluidsSwabsInterface", - "inlined": true, - "inlined_as_list": true - }, - "host_associated_data": { - "name": "host_associated_data", - "description": "aggregation slot relating host_associated data collections to a SampleData container", - "from_schema": "https://example.com/nmdc_submission_schema", - "multivalued": true, - "range": "HostAssociatedInterface", - "inlined": true, - "inlined_as_list": true - }, - "jgi_mg_data": { - "name": "jgi_mg_data", - "description": "aggregation slot relating jgi_mg data collections to a SampleData container", - "from_schema": "https://example.com/nmdc_submission_schema", - "multivalued": true, - "range": "JgiMgInterface", - "inlined": true, - "inlined_as_list": true - }, - "jgi_mt_data": { - "name": "jgi_mt_data", - "description": "aggregation slot relating jgi_mt data collections to a SampleData container", - "from_schema": "https://example.com/nmdc_submission_schema", - "multivalued": true, - "range": "JgiMtInterface", - "inlined": true, - "inlined_as_list": true - }, - "misc_envs_data": { - "name": "misc_envs_data", - "description": "aggregation slot relating misc_envs data collections to a SampleData container", - "from_schema": "https://example.com/nmdc_submission_schema", - "multivalued": true, - "range": "MiscEnvsInterface", - "inlined": true, - "inlined_as_list": true - }, - "plant_associated_data": { - "name": "plant_associated_data", - "description": "aggregation slot relating plant_associated data collections to a SampleData container", - "from_schema": "https://example.com/nmdc_submission_schema", - "multivalued": true, - "range": "PlantAssociatedInterface", - "inlined": true, - "inlined_as_list": true - }, - "sediment_data": { - "name": "sediment_data", - "description": "aggregation slot relating sediment data collections to a SampleData container", - "from_schema": "https://example.com/nmdc_submission_schema", - "multivalued": true, - "range": "SedimentInterface", - "inlined": true, - "inlined_as_list": true - }, - "soil_data": { - "name": "soil_data", - "description": "aggregation slot relating soil data collections to a SampleData container", - "from_schema": "https://example.com/nmdc_submission_schema", - "multivalued": true, - "range": "SoilInterface", - "inlined": true, - "inlined_as_list": true - }, - "wastewater_sludge_data": { - "name": "wastewater_sludge_data", - "description": "aggregation slot relating wastewater_sludge data collections to a SampleData container", - "from_schema": "https://example.com/nmdc_submission_schema", - "multivalued": true, - "range": "WastewaterSludgeInterface", - "inlined": true, - "inlined_as_list": true - }, - "water_data": { - "name": "water_data", - "description": "aggregation slot relating water data collections to a SampleData container", - "from_schema": "https://example.com/nmdc_submission_schema", - "multivalued": true, - "range": "WaterInterface", - "inlined": true, - "inlined_as_list": true - }, - "dh_section": { - "name": "dh_section", - "description": "dh_section grouping slot", - "from_schema": "https://example.com/nmdc_submission_schema" - }, - "emsl_section": { - "name": "emsl_section", - "description": "placeholder", - "title": "EMSL", - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 2, - "is_a": "dh_section" - }, - "jgi_metagenomics_section": { - "name": "jgi_metagenomics_section", - "description": "placeholder", - "title": "JGI-Metagenomics", - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 3, - "is_a": "dh_section" - }, - "jgi_metatranscriptomics_section": { - "name": "jgi_metatranscriptomics_section", - "description": "placeholder", - "title": "JGI-Metatranscriptomics", - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 4, - "is_a": "dh_section" - }, - "mixs_core_section": { - "name": "mixs_core_section", - "description": "placeholder", - "title": "MIxS Core", - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 10, - "is_a": "dh_section" - }, - "mixs_inspired_section": { - "name": "mixs_inspired_section", - "description": "placeholder", - "title": "MIxS Inspired", - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 7, - "is_a": "dh_section" - }, - "mixs_investigation_section": { - "name": "mixs_investigation_section", - "description": "placeholder", - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 8, - "is_a": "dh_section" - }, - "mixs_modified_section": { - "name": "mixs_modified_section", - "description": "placeholder", - "title": "MIxS (modified)", - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 6, - "is_a": "dh_section" - }, - "mixs_nassf_section": { - "name": "mixs_nassf_section", - "description": "placeholder", - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 9, - "is_a": "dh_section" - }, - "mixs_section": { - "name": "mixs_section", - "description": "placeholder", - "title": "MIxS", - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 5, - "is_a": "dh_section" - }, - "sample_id_section": { - "name": "sample_id_section", - "description": "placeholder", - "title": "Sample ID", - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 1, - "is_a": "dh_section" - }, - "abs_air_humidity": { - "name": "abs_air_humidity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram per gram, kilogram per kilogram, kilogram, pound" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Actual mass of water vapor - mh20 - present in the air water vapor mixture", - "title": "absolute air humidity", - "examples": [ - { - "value": "9 gram per gram" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "absolute air humidity" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000122", - "multivalued": false, - "range": "string" - }, - "add_recov_method": { - "name": "add_recov_method", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration;timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "secondary and tertiary recovery methods and start date", - "examples": [ - { - "value": "Polymer Addition;2018-06-21T14:30Z" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "secondary and tertiary recovery methods and start date" - ], - "is_a": "core field", - "slot_uri": "MIXS:0001009", - "multivalued": false, - "range": "string" - }, - "additional_info": { - "name": "additional_info", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary", - "title": "additional info", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "additional info" - ], - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000300", - "multivalued": false, - "range": "string" - }, - "address": { - "name": "address", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The street name and building number where the sampling occurred.", - "title": "address", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "address" - ], - "is_a": "core field", - "string_serialization": "{integer}{text}", - "slot_uri": "MIXS:0000218", - "multivalued": false, - "range": "string" - }, - "adj_room": { - "name": "adj_room", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "room name;room number" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "List of rooms (room number, room name) immediately adjacent to the sampling room", - "title": "adjacent rooms", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "adjacent rooms" - ], - "is_a": "core field", - "string_serialization": "{text};{integer}", - "slot_uri": "MIXS:0000219", - "multivalued": false, - "range": "string" - }, - "aero_struc": { - "name": "aero_struc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together", - "title": "aerospace structure", - "examples": [ - { - "value": "plane" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "aerospace structure" - ], - "is_a": "core field", - "string_serialization": "[plane|glider]", - "slot_uri": "MIXS:0000773", - "multivalued": false, - "range": "string" - }, - "agrochem_addition": { - "name": "agrochem_addition", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "agrochemical name;agrochemical amount;timestamp" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, mole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Addition of fertilizers, pesticides, etc. - amount and time of applications", - "title": "history/agrochemical additions", - "examples": [ - { - "value": "roundup;5 milligram per liter;2018-06-21" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "history/agrochemical additions" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{timestamp}", - "slot_uri": "MIXS:0000639", - "multivalued": false, - "range": "string" - }, - "air_PM_concen": { - "name": "air_PM_concen", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "particulate matter name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micrograms per cubic meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM", - "title": "air particulate matter concentration", - "examples": [ - { - "value": "PM2.5;10 microgram per cubic meter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "air particulate matter concentration" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000108", - "multivalued": false, - "range": "string" - }, - "air_temp": { - "name": "air_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Temperature of the air at the time of sampling", - "title": "air temperature", - "examples": [ - { - "value": "20 degree Celsius" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "air temperature" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000124", - "multivalued": false, - "range": "string" - }, - "air_temp_regm": { - "name": "air_temp_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "temperature value;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens", - "title": "air temperature regimen", - "examples": [ - { - "value": "25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "air temperature regimen" - ], - "is_a": "core field", - "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000551", - "multivalued": false, - "range": "string" - }, - "al_sat": { - "name": "al_sat", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "percentage" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Aluminum saturation (esp. For tropical soils)", - "title": "extreme_unusual_properties/Al saturation", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "extreme_unusual_properties/Al saturation" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000607", - "multivalued": false, - "range": "string" - }, - "al_sat_meth": { - "name": "al_sat_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or URL" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining Al saturation", - "title": "extreme_unusual_properties/Al saturation method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "extreme_unusual_properties/Al saturation method" - ], - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000324", - "multivalued": false, - "range": "string" - }, - "alkalinity": { - "name": "alkalinity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milliequivalent per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate", - "title": "alkalinity", - "examples": [ - { - "value": "50 milligram per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "alkalinity" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000421", - "multivalued": false, - "range": "string" - }, - "alkalinity_method": { - "name": "alkalinity_method", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "description of method" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Method used for alkalinity measurement", - "title": "alkalinity method", - "examples": [ - { - "value": "titration" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "alkalinity method" - ], - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000298", - "multivalued": false, - "range": "string" - }, - "alkyl_diethers": { - "name": "alkyl_diethers", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of alkyl diethers", - "title": "alkyl diethers", - "examples": [ - { - "value": "0.005 mole per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "alkyl diethers" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000490", - "multivalued": false, - "range": "string" - }, - "alt": { - "name": "alt", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - } - }, - "description": "Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air", - "title": "altitude", - "examples": [ - { - "value": "100 meter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "altitude" - ], - "is_a": "environment field", - "slot_uri": "MIXS:0000094", - "multivalued": false, - "range": "string" - }, - "aminopept_act": { - "name": "aminopept_act", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mole per liter per hour" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of aminopeptidase activity", - "title": "aminopeptidase activity", - "examples": [ - { - "value": "0.269 mole per liter per hour" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "aminopeptidase activity" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000172", - "multivalued": false, - "range": "string" - }, - "ammonium": { - "name": "ammonium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of ammonium in the sample", - "title": "ammonium", - "examples": [ - { - "value": "1.5 milligram per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "ammonium" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000427", - "multivalued": false, - "range": "string" - }, - "ammonium_nitrogen": { - "name": "ammonium_nitrogen", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mg/kg" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of ammonium nitrogen in the sample", - "title": "ammonium nitrogen", - "examples": [ - { - "value": "2.3 mg/kg" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "see_also": [ - "https://www.ornl.gov/content/bio-scales-0" - ], - "aliases": [ - "ammonium_nitrogen", - "NH4-N" - ], - "is_a": "attribute", - "multivalued": false, - "range": "string" - }, - "amount_light": { - "name": "amount_light", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "lux, lumens per square meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The unit of illuminance and luminous emittance, measuring luminous flux per unit area", - "title": "amount of light", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "amount of light" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000140", - "multivalued": false, - "range": "string" - }, - "analysis_type": { - "name": "analysis_type", - "description": "Select all the data types associated or available for this biosample", - "title": "analysis/data type", - "examples": [ - { - "value": "metagenomics; metabolomics; proteomics" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "see_also": [ - "MIxS:investigation_type" - ], - "rank": 3, - "multivalued": true, - "slot_group": "Sample ID", - "range": "analysis_type_enum", - "recommended": true - }, - "ances_data": { - "name": "ances_data", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "free text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B)", - "title": "ancestral data", - "examples": [ - { - "value": "A/3*B" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "ancestral data" - ], - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000247", - "multivalued": false, - "range": "string" - }, - "annual_precpt": { - "name": "annual_precpt", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millimeter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps.", - "title": "mean annual precipitation", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "mean annual precipitation" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000644", - "multivalued": false, - "range": "string" - }, - "annual_temp": { - "name": "annual_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Mean annual temperature", - "title": "mean annual temperature", - "examples": [ - { - "value": "12.5 degree Celsius" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "mean annual temperature" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000642", - "multivalued": false, - "range": "string" - }, - "antibiotic_regm": { - "name": "antibiotic_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "antibiotic name;antibiotic amount;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens", - "title": "antibiotic regimen", - "examples": [ - { - "value": "penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "antibiotic regimen" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000553", - "multivalued": false, - "range": "string" - }, - "api": { - "name": "api", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degrees API" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API)", - "title": "API gravity", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "API gravity" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000157", - "multivalued": false, - "range": "string" - }, - "arch_struc": { - "name": "arch_struc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "An architectural structure is a human-made, free-standing, immobile outdoor construction", - "title": "architectural structure", - "examples": [ - { - "value": "shed" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "architectural structure" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000774", - "multivalued": false, - "range": "arch_struc_enum" - }, - "aromatics_pc": { - "name": "aromatics_pc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "percent" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", - "title": "aromatics wt%", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "aromatics wt%" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000133", - "multivalued": false, - "range": "string" - }, - "asphaltenes_pc": { - "name": "asphaltenes_pc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "percent" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", - "title": "asphaltenes wt%", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "asphaltenes wt%" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000135", - "multivalued": false, - "range": "string" - }, - "atmospheric_data": { - "name": "atmospheric_data", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "atmospheric data name;measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Measurement of atmospheric data; can include multiple data", - "title": "atmospheric data", - "examples": [ - { - "value": "wind speed;9 knots" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "atmospheric data" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0001097", - "multivalued": false, - "range": "string" - }, - "avg_dew_point": { - "name": "avg_dew_point", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day", - "title": "average dew point", - "examples": [ - { - "value": "25.5 degree Celsius" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "average dew point" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000141", - "multivalued": false, - "range": "string" - }, - "avg_occup": { - "name": "avg_occup", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Daily average occupancy of room. Indicate the number of person(s) daily occupying the sampling room.", - "title": "average daily occupancy", - "examples": [ - { - "value": "2" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "average daily occupancy" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000775", - "multivalued": false, - "range": "string" - }, - "avg_temp": { - "name": "avg_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day", - "title": "average temperature", - "examples": [ - { - "value": "12.5 degree Celsius" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "average temperature" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000142", - "multivalued": false, - "range": "string" - }, - "bac_prod": { - "name": "bac_prod", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per cubic meter per day" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Bacterial production in the water column measured by isotope uptake", - "title": "bacterial production", - "examples": [ - { - "value": "5 milligram per cubic meter per day" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "bacterial production" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000683", - "multivalued": false, - "range": "string" - }, - "bac_resp": { - "name": "bac_resp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per cubic meter per day, micromole oxygen per liter per hour" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of bacterial respiration in the water column", - "title": "bacterial respiration", - "examples": [ - { - "value": "300 micromole oxygen per liter per hour" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "bacterial respiration" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000684", - "multivalued": false, - "range": "string" - }, - "bacteria_carb_prod": { - "name": "bacteria_carb_prod", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "nanogram per hour" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of bacterial carbon production", - "title": "bacterial carbon production", - "examples": [ - { - "value": "2.53 microgram per liter per hour" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "bacterial carbon production" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000173", - "multivalued": false, - "range": "string" - }, - "barometric_press": { - "name": "barometric_press", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millibar" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Force per unit area exerted against a surface by the weight of air above that surface", - "title": "barometric pressure", - "examples": [ - { - "value": "5 millibar" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "barometric pressure" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000096", - "multivalued": false, - "range": "string" - }, - "basin": { - "name": "basin", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Name of the basin (e.g. Campos)", - "title": "basin name", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "basin name" - ], - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000290", - "multivalued": false, - "range": "string" - }, - "bathroom_count": { - "name": "bathroom_count", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The number of bathrooms in the building", - "title": "bathroom count", - "examples": [ - { - "value": "1" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "bathroom count" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000776", - "multivalued": false, - "range": "string" - }, - "bedroom_count": { - "name": "bedroom_count", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The number of bedrooms in the building", - "title": "bedroom count", - "examples": [ - { - "value": "2" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "bedroom count" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000777", - "multivalued": false, - "range": "string" - }, - "benzene": { - "name": "benzene", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of benzene in the sample", - "title": "benzene", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "benzene" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000153", - "multivalued": false, - "range": "string" - }, - "biochem_oxygen_dem": { - "name": "biochem_oxygen_dem", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period", - "title": "biochemical oxygen demand", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "biochemical oxygen demand" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000653", - "multivalued": false, - "range": "string" - }, - "biocide": { - "name": "biocide", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name;name;timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "List of biocides (commercial name of product and supplier) and date of administration", - "title": "biocide administration", - "examples": [ - { - "value": "ALPHA 1427;Baker Hughes;2008-01-23" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "biocide administration" - ], - "is_a": "core field", - "string_serialization": "{text};{text};{timestamp}", - "slot_uri": "MIXS:0001011", - "multivalued": false, - "range": "string" - }, - "biocide_admin_method": { - "name": "biocide_admin_method", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value;frequency;duration;duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days)", - "title": "biocide administration method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "biocide administration method" - ], - "is_a": "core field", - "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration};{duration}", - "slot_uri": "MIXS:0000456", - "multivalued": false, - "range": "string" - }, - "biol_stat": { - "name": "biol_stat", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The level of genome modification.", - "title": "biological status", - "examples": [ - { - "value": "natural" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "biological status" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000858", - "multivalued": false, - "range": "biol_stat_enum" - }, - "biomass": { - "name": "biomass", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "biomass type;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "ton, kilogram, gram" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements", - "title": "biomass", - "examples": [ - { - "value": "total;20 gram" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "biomass" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000174", - "multivalued": false, - "range": "string" - }, - "biotic_regm": { - "name": "biotic_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "free text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi.", - "title": "biotic regimen", - "examples": [ - { - "value": "sample inoculated with Rhizobium spp. Culture" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "biotic regimen" - ], - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0001038", - "multivalued": false, - "range": "string" - }, - "biotic_relationship": { - "name": "biotic_relationship", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - } - }, - "description": "Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object", - "title": "observed biotic relationship", - "examples": [ - { - "value": "free living" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "observed biotic relationship" - ], - "is_a": "nucleic acid sequence source field", - "slot_uri": "MIXS:0000028", - "multivalued": false, - "range": "biotic_relationship_enum" - }, - "bishomohopanol": { - "name": "bishomohopanol", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter, microgram per gram" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of bishomohopanol", - "title": "bishomohopanol", - "examples": [ - { - "value": "14 microgram per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "bishomohopanol" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000175", - "multivalued": false, - "range": "string" - }, - "blood_press_diast": { - "name": "blood_press_diast", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millimeter mercury" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Resting diastolic blood pressure, measured as mm mercury", - "title": "host blood pressure diastolic", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "host blood pressure diastolic" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000258", - "multivalued": false, - "range": "string" - }, - "blood_press_syst": { - "name": "blood_press_syst", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millimeter mercury" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Resting systolic blood pressure, measured as mm mercury", - "title": "host blood pressure systolic", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "host blood pressure systolic" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000259", - "multivalued": false, - "range": "string" - }, - "bromide": { - "name": "bromide", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of bromide", - "title": "bromide", - "examples": [ - { - "value": "0.05 parts per million" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "bromide" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000176", - "multivalued": false, - "range": "string" - }, - "build_docs": { - "name": "build_docs", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The building design, construction and operation documents", - "title": "design, construction, and operation documents", - "examples": [ - { - "value": "maintenance plans" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "design, construction, and operation documents" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000787", - "multivalued": false, - "range": "build_docs_enum" - }, - "build_occup_type": { - "name": "build_occup_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "The primary function for which a building or discrete part of a building is intended to be used", - "title": "building occupancy type", - "examples": [ - { - "value": "market" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "building occupancy type" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000761", - "multivalued": true, - "range": "build_occup_type_enum" - }, - "building_setting": { - "name": "building_setting", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "A location (geography) where a building is set", - "title": "building setting", - "examples": [ - { - "value": "rural" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "building setting" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000768", - "multivalued": false, - "range": "building_setting_enum" - }, - "built_struc_age": { - "name": "built_struc_age", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "year" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The age of the built structure since construction", - "title": "built structure age", - "examples": [ - { - "value": "15" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "built structure age" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000145", - "multivalued": false, - "range": "string" - }, - "built_struc_set": { - "name": "built_struc_set", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The characterization of the location of the built structure as high or low human density", - "title": "built structure setting", - "examples": [ - { - "value": "rural" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "built structure setting" - ], - "is_a": "core field", - "string_serialization": "[urban|rural]", - "slot_uri": "MIXS:0000778", - "multivalued": false, - "range": "string" - }, - "built_struc_type": { - "name": "built_struc_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "free text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads", - "title": "built structure type", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "built structure type" - ], - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000721", - "multivalued": false, - "range": "string" - }, - "calcium": { - "name": "calcium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, micromole per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of calcium in the sample", - "title": "calcium", - "examples": [ - { - "value": "0.2 micromole per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "calcium" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000432", - "multivalued": false, - "range": "string" - }, - "carb_dioxide": { - "name": "carb_dioxide", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Carbon dioxide (gas) amount or concentration at the time of sampling", - "title": "carbon dioxide", - "examples": [ - { - "value": "410 parts per million" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "carbon dioxide" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000097", - "multivalued": false, - "range": "string" - }, - "carb_monoxide": { - "name": "carb_monoxide", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Carbon monoxide (gas) amount or concentration at the time of sampling", - "title": "carbon monoxide", - "examples": [ - { - "value": "0.1 parts per million" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "carbon monoxide" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000098", - "multivalued": false, - "range": "string" - }, - "carb_nitro_ratio": { - "name": "carb_nitro_ratio", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Ratio of amount or concentrations of carbon to nitrogen", - "title": "carbon/nitrogen ratio", - "examples": [ - { - "value": "0.417361111" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "carbon/nitrogen ratio" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000310", - "multivalued": false, - "range": "string" - }, - "ceil_area": { - "name": "ceil_area", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "square meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The area of the ceiling space within the room", - "title": "ceiling area", - "examples": [ - { - "value": "25 square meter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "ceiling area" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000148", - "multivalued": false, - "range": "string" - }, - "ceil_cond": { - "name": "ceil_cond", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas", - "title": "ceiling condition", - "examples": [ - { - "value": "damaged" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "ceiling condition" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000779", - "multivalued": false, - "range": "ceil_cond_enum" - }, - "ceil_finish_mat": { - "name": "ceil_finish_mat", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of material used to finish a ceiling", - "title": "ceiling finish material", - "examples": [ - { - "value": "stucco" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "ceiling finish material" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000780", - "multivalued": false, - "range": "ceil_finish_mat_enum" - }, - "ceil_struc": { - "name": "ceil_struc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The construction format of the ceiling", - "title": "ceiling structure", - "examples": [ - { - "value": "concrete" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "ceiling structure" - ], - "is_a": "core field", - "string_serialization": "[wood frame|concrete]", - "slot_uri": "MIXS:0000782", - "multivalued": false, - "range": "string" - }, - "ceil_texture": { - "name": "ceil_texture", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The feel, appearance, or consistency of a ceiling surface", - "title": "ceiling texture", - "examples": [ - { - "value": "popcorn" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "ceiling texture" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000783", - "multivalued": false, - "range": "ceil_texture_enum" - }, - "ceil_thermal_mass": { - "name": "ceil_thermal_mass", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "joule per degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow", - "title": "ceiling thermal mass", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "ceiling thermal mass" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000143", - "multivalued": false, - "range": "string" - }, - "ceil_type": { - "name": "ceil_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of ceiling according to the ceiling's appearance or construction", - "title": "ceiling type", - "examples": [ - { - "value": "coffered" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "ceiling type" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000784", - "multivalued": false, - "range": "ceil_type_enum" - }, - "ceil_water_mold": { - "name": "ceil_water_mold", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Signs of the presence of mold or mildew on the ceiling", - "title": "ceiling signs of water/mold", - "examples": [ - { - "value": "presence of mold visible" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "ceiling signs of water/mold" - ], - "is_a": "core field", - "string_serialization": "[presence of mold visible|no presence of mold visible]", - "slot_uri": "MIXS:0000781", - "multivalued": false, - "range": "string" - }, - "chem_administration": { - "name": "chem_administration", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "CHEBI;timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", - "title": "chemical administration", - "examples": [ - { - "value": "agar [CHEBI:2509];2018-05-11T20:00Z" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "chemical administration" - ], - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]};{timestamp}", - "slot_uri": "MIXS:0000751", - "multivalued": false, - "range": "string" - }, - "chem_mutagen": { - "name": "chem_mutagen", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "mutagen name;mutagen amount;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens", - "title": "chemical mutagen", - "examples": [ - { - "value": "nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "chemical mutagen" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000555", - "multivalued": false, - "range": "string" - }, - "chem_oxygen_dem": { - "name": "chem_oxygen_dem", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite", - "title": "chemical oxygen demand", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "chemical oxygen demand" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000656", - "multivalued": false, - "range": "string" - }, - "chem_treat_method": { - "name": "chem_treat_method", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value;frequency;duration;duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days)", - "title": "chemical treatment method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "chemical treatment method" - ], - "is_a": "core field", - "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration};{duration};{duration}", - "slot_uri": "MIXS:0000457", - "multivalued": false, - "range": "string" - }, - "chem_treatment": { - "name": "chem_treatment", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name;name;timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included", - "title": "chemical treatment", - "examples": [ - { - "value": "ACCENT 1125;DOW;2010-11-17" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "chemical treatment" - ], - "is_a": "core field", - "string_serialization": "{text};{text};{timestamp}", - "slot_uri": "MIXS:0001012", - "multivalued": false, - "range": "string" - }, - "chloride": { - "name": "chloride", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of chloride in the sample", - "title": "chloride", - "examples": [ - { - "value": "5000 milligram per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "chloride" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000429", - "multivalued": false, - "range": "string" - }, - "chlorophyll": { - "name": "chlorophyll", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per cubic meter, microgram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of chlorophyll", - "title": "chlorophyll", - "examples": [ - { - "value": "5 milligram per cubic meter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "chlorophyll" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000177", - "multivalued": false, - "range": "string" - }, - "climate_environment": { - "name": "climate_environment", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "climate name;treatment interval and duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates", - "title": "climate environment", - "examples": [ - { - "value": "tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "climate environment" - ], - "is_a": "core field", - "string_serialization": "{text};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0001040", - "multivalued": false, - "range": "string" - }, - "collection_date": { - "name": "collection_date", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "date and time" - } - }, - "description": "The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant", - "title": "collection date", - "examples": [ - { - "value": "2018-05-11T10:00:00+01:00; 2018-05-11" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "collection date" - ], - "is_a": "environment field", - "slot_uri": "MIXS:0000011", - "multivalued": false, - "range": "string" - }, - "collection_date_inc": { - "name": "collection_date_inc", - "description": "Date the incubation was harvested/collected/ended. Only relevant for incubation samples.", - "title": "incubation collection date", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only" - ], - "comments": [ - "Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable." - ], - "examples": [ - { - "value": "2021-04-15, 2021-04 and 2021 are all acceptable." - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "see_also": [ - "MIxS:collection_date" - ], - "rank": 2, - "string_serialization": "{date, arbitrary precision}", - "slot_group": "MIxS Inspired", - "recommended": true - }, - "collection_time": { - "name": "collection_time", - "description": "The time of sampling, either as an instance (single point) or interval.", - "title": "collection time, GMT", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" - ], - "comments": [ - "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" - ], - "examples": [ - { - "value": "13:33 or 13:33:55" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "see_also": [ - "MIxS:collection_date" - ], - "rank": 1, - "string_serialization": "{time, seconds optional}", - "slot_group": "MIxS Inspired", - "recommended": true - }, - "collection_time_inc": { - "name": "collection_time_inc", - "description": "Time the incubation was harvested/collected/ended. Only relevant for incubation samples.", - "title": "incubation collection time, GMT", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" - ], - "comments": [ - "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" - ], - "examples": [ - { - "value": "13:33 or 13:33:55" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "see_also": [ - "MIxS:collection_date" - ], - "rank": 3, - "string_serialization": "{time, seconds optional}", - "slot_group": "MIxS Inspired", - "recommended": true - }, - "conduc": { - "name": "conduc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milliSiemens per centimeter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Electrical conductivity of water", - "title": "conductivity", - "examples": [ - { - "value": "10 milliSiemens per centimeter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "conductivity" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000692", - "multivalued": false, - "range": "string" - }, - "cool_syst_id": { - "name": "cool_syst_id", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "unique identifier" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The cooling system identifier", - "title": "cooling system identifier", - "examples": [ - { - "value": "12345" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "cooling system identifier" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000785", - "multivalued": false, - "range": "string" - }, - "crop_rotation": { - "name": "crop_rotation", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "crop rotation status;schedule" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Whether or not crop is rotated, and if yes, rotation schedule", - "title": "history/crop rotation", - "examples": [ - { - "value": "yes;R2/2017-01-01/2018-12-31/P6M" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "history/crop rotation" - ], - "is_a": "core field", - "string_serialization": "{boolean};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000318", - "multivalued": false, - "range": "string" - }, - "cult_root_med": { - "name": "cult_root_med", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name, PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors.", - "title": "culture rooting medium", - "examples": [ - { - "value": "http://himedialabs.com/TD/PT158.pdf" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "culture rooting medium" - ], - "is_a": "core field", - "string_serialization": "{text}|{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0001041", - "multivalued": false, - "range": "string" - }, - "cur_land_use": { - "name": "cur_land_use", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Present state of sample site", - "title": "current land use", - "examples": [ - { - "value": "conifers" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "current land use" - ], - "is_a": "core field", - "slot_uri": "MIXS:0001080", - "multivalued": false, - "range": "cur_land_use_enum" - }, - "cur_vegetation": { - "name": "cur_vegetation", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "current vegetation type" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Vegetation classification from one or more standard classification systems, or agricultural crop", - "title": "current vegetation", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "current vegetation" - ], - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000312", - "multivalued": false, - "range": "string" - }, - "cur_vegetation_meth": { - "name": "cur_vegetation_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in vegetation classification", - "title": "current vegetation method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "current vegetation method" - ], - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000314", - "multivalued": false, - "range": "string" - }, - "date_last_rain": { - "name": "date_last_rain", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The date of the last time it rained", - "title": "date last rain", - "examples": [ - { - "value": "2018-05-11:T14:30Z" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "date last rain" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000786", - "multivalued": false, - "range": "string" - }, - "density": { - "name": "density", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram per cubic meter, gram per cubic centimeter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Density of the sample, which is its mass per unit volume (aka volumetric mass density)", - "title": "density", - "examples": [ - { - "value": "1000 kilogram per cubic meter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "density" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000435", - "multivalued": false, - "range": "string" - }, - "depos_env": { - "name": "depos_env", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "depositional environment", - "examples": [ - { - "value": "Continental - Alluvial" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "depositional environment" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000992", - "multivalued": false, - "range": "depos_env_enum" - }, - "depth": { - "name": "depth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - } - }, - "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", - "title": "depth", - "examples": [ - { - "value": "10 meter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "depth" - ], - "is_a": "environment field", - "slot_uri": "MIXS:0000018", - "multivalued": false, - "range": "string" - }, - "dew_point": { - "name": "dew_point", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water.", - "title": "dew point", - "examples": [ - { - "value": "22 degree Celsius" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "dew point" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000129", - "multivalued": false, - "range": "string" - }, - "diether_lipids": { - "name": "diether_lipids", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "diether lipid name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "nanogram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Concentration of diether lipids; can include multiple types of diether lipids", - "title": "diether lipids", - "examples": [ - { - "value": "0.2 nanogram per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "diether lipids" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000178", - "multivalued": false, - "range": "string" - }, - "diss_carb_dioxide": { - "name": "diss_carb_dioxide", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample", - "title": "dissolved carbon dioxide", - "examples": [ - { - "value": "5 milligram per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "dissolved carbon dioxide" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000436", - "multivalued": false, - "range": "string" - }, - "diss_hydrogen": { - "name": "diss_hydrogen", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved hydrogen", - "title": "dissolved hydrogen", - "examples": [ - { - "value": "0.3 micromole per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "dissolved hydrogen" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000179", - "multivalued": false, - "range": "string" - }, - "diss_inorg_carb": { - "name": "diss_inorg_carb", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter", - "title": "dissolved inorganic carbon", - "examples": [ - { - "value": "2059 micromole per kilogram" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "dissolved inorganic carbon" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000434", - "multivalued": false, - "range": "string" - }, - "diss_inorg_nitro": { - "name": "diss_inorg_nitro", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter, micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved inorganic nitrogen", - "title": "dissolved inorganic nitrogen", - "examples": [ - { - "value": "761 micromole per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "dissolved inorganic nitrogen" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000698", - "multivalued": false, - "range": "string" - }, - "diss_inorg_phosp": { - "name": "diss_inorg_phosp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved inorganic phosphorus in the sample", - "title": "dissolved inorganic phosphorus", - "examples": [ - { - "value": "56.5 micromole per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "dissolved inorganic phosphorus" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000106", - "multivalued": false, - "range": "string" - }, - "diss_iron": { - "name": "diss_iron", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved iron in the sample", - "title": "dissolved iron", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "dissolved iron" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000139", - "multivalued": false, - "range": "string" - }, - "diss_org_carb": { - "name": "diss_org_carb", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid", - "title": "dissolved organic carbon", - "examples": [ - { - "value": "197 micromole per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "dissolved organic carbon" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000433", - "multivalued": false, - "range": "string" - }, - "diss_org_nitro": { - "name": "diss_org_nitro", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2", - "title": "dissolved organic nitrogen", - "examples": [ - { - "value": "0.05 micromole per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "dissolved organic nitrogen" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000162", - "multivalued": false, - "range": "string" - }, - "diss_oxygen": { - "name": "diss_oxygen", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per kilogram, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved oxygen", - "title": "dissolved oxygen", - "examples": [ - { - "value": "175 micromole per kilogram" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "dissolved oxygen" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000119", - "multivalued": false, - "range": "string" - }, - "diss_oxygen_fluid": { - "name": "diss_oxygen_fluid", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per kilogram, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic).", - "title": "dissolved oxygen in fluids", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "dissolved oxygen in fluids" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000438", - "multivalued": false, - "range": "string" - }, - "dna_absorb1": { - "name": "dna_absorb1", - "description": "260/280 measurement of DNA sample purity", - "title": "DNA absorbance 260/280", - "comments": [ - "Recommended value is between 1 and 3." - ], - "examples": [ - { - "value": "2.02" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 7, - "is_a": "biomaterial_purity", - "string_serialization": "{float}", - "slot_group": "JGI-Metagenomics", - "range": "float", - "recommended": true - }, - "dna_absorb2": { - "name": "dna_absorb2", - "description": "260/230 measurement of DNA sample purity", - "title": "DNA absorbance 260/230", - "comments": [ - "Recommended value is between 1 and 3." - ], - "examples": [ - { - "value": "2.02" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 8, - "is_a": "biomaterial_purity", - "string_serialization": "{float}", - "slot_group": "JGI-Metagenomics", - "range": "float", - "recommended": true - }, - "dna_concentration": { - "name": "dna_concentration", - "title": "DNA concentration in ng/ul", - "comments": [ - "Units must be in ng/uL. Enter the numerical part only. Must be calculated using a fluorometric method. Acceptable values are 0-2000." - ], - "examples": [ - { - "value": "100" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "see_also": [ - "nmdc:nucleic_acid_concentration" - ], - "rank": 5, - "string_serialization": "{float}", - "slot_group": "JGI-Metagenomics", - "range": "float", - "recommended": true, - "minimum_value": 0, - "maximum_value": 2000 - }, - "dna_cont_type": { - "name": "dna_cont_type", - "description": "Tube or plate (96-well)", - "title": "DNA container type", - "examples": [ - { - "value": "plate" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 10, - "slot_group": "JGI-Metagenomics", - "range": "JgiContTypeEnum", - "recommended": true - }, - "dna_cont_well": { - "name": "dna_cont_well", - "title": "DNA plate position", - "comments": [ - "Required when 'plate' is selected for container type.", - "Leave blank if the sample will be shipped in a tube.", - "JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass validation.", - "For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8)." - ], - "examples": [ - { - "value": "B2" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 11, - "string_serialization": "{96 well plate pos}", - "slot_group": "JGI-Metagenomics", - "recommended": true, - "pattern": "^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$" - }, - "dna_container_id": { - "name": "dna_container_id", - "title": "DNA container label", - "comments": [ - "Must be unique across all tubes and plates, and <20 characters. All samples in a plate should have the same plate label." - ], - "examples": [ - { - "value": "Pond_MT_041618" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 9, - "string_serialization": "{text < 20 characters}", - "slot_group": "JGI-Metagenomics", - "recommended": true - }, - "dna_dnase": { - "name": "dna_dnase", - "title": "DNase treatment DNA", - "comments": [ - "Note DNase treatment is required for all RNA samples." - ], - "examples": [ - { - "value": "no" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 13, - "slot_group": "JGI-Metagenomics", - "range": "YesNoEnum", - "recommended": true - }, - "dna_isolate_meth": { - "name": "dna_isolate_meth", - "description": "Describe the method/protocol/kit used to extract DNA/RNA.", - "title": "DNA isolation method", - "examples": [ - { - "value": "phenol/chloroform extraction" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 16, - "string_serialization": "{text}", - "slot_group": "JGI-Metagenomics", - "recommended": true - }, - "dna_project_contact": { - "name": "dna_project_contact", - "title": "DNA seq project contact", - "comments": [ - "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." - ], - "examples": [ - { - "value": "John Jones" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 18, - "string_serialization": "{text}", - "slot_group": "JGI-Metagenomics", - "recommended": true - }, - "dna_samp_id": { - "name": "dna_samp_id", - "title": "DNA sample ID", - "todos": [ - "Removed identifier = TRUE from dna_samp_ID in JGI_sample_slots, as a class can't have two identifiers. How to force uniqueness? Moot because that column will be prefilled?" - ], - "comments": [ - "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." - ], - "examples": [ - { - "value": "187654" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 3, - "string_serialization": "{text}", - "slot_group": "JGI-Metagenomics", - "recommended": true - }, - "dna_sample_format": { - "name": "dna_sample_format", - "description": "Solution in which the DNA sample has been suspended", - "title": "DNA sample format", - "examples": [ - { - "value": "Water" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 12, - "slot_group": "JGI-Metagenomics", - "range": "dna_sample_format_enum", - "recommended": true - }, - "dna_sample_name": { - "name": "dna_sample_name", - "description": "Give the DNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", - "title": "DNA sample name", - "examples": [ - { - "value": "JGI_pond_041618" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 4, - "string_serialization": "{text}", - "slot_group": "JGI-Metagenomics", - "recommended": true - }, - "dna_seq_project": { - "name": "dna_seq_project", - "title": "DNA seq project ID", - "comments": [ - "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." - ], - "examples": [ - { - "value": "1191234" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 1, - "string_serialization": "{text}", - "slot_group": "JGI-Metagenomics", - "recommended": true - }, - "dna_seq_project_name": { - "name": "dna_seq_project_name", - "title": "DNA seq project name", - "comments": [ - "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." - ], - "examples": [ - { - "value": "JGI Pond metagenomics" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 2, - "string_serialization": "{text}", - "slot_group": "JGI-Metagenomics", - "recommended": true - }, - "dna_seq_project_pi": { - "name": "dna_seq_project_pi", - "title": "DNA seq project PI", - "comments": [ - "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." - ], - "examples": [ - { - "value": "Jane Johnson" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 17, - "string_serialization": "{text}", - "slot_group": "JGI-Metagenomics", - "recommended": true - }, - "dna_volume": { - "name": "dna_volume", - "title": "DNA volume in ul", - "comments": [ - "Units must be in uL. Enter the numerical part only. Value must be 0-1000. This form accepts values < 25, but JGI may refuse to process them unless permission has been granted by a project manager" - ], - "examples": [ - { - "value": "25" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 6, - "string_serialization": "{float}", - "slot_group": "JGI-Metagenomics", - "range": "float", - "recommended": true, - "minimum_value": 0, - "maximum_value": 1000 - }, - "dnase_rna": { - "name": "dnase_rna", - "title": "DNase treated", - "comments": [ - "Note DNase treatment is required for all RNA samples." - ], - "examples": [ - { - "value": "no" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 13, - "slot_group": "JGI-Metatranscriptomics", - "range": "YesNoEnum", - "recommended": true - }, - "door_comp_type": { - "name": "door_comp_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The composite type of the door", - "title": "door type, composite", - "examples": [ - { - "value": "revolving" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "door type, composite" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000795", - "multivalued": false, - "range": "door_comp_type_enum" - }, - "door_cond": { - "name": "door_cond", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The phsical condition of the door", - "title": "door condition", - "examples": [ - { - "value": "new" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "door condition" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000788", - "multivalued": false, - "range": "door_cond_enum" - }, - "door_direct": { - "name": "door_direct", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The direction the door opens", - "title": "door direction of opening", - "examples": [ - { - "value": "inward" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "door direction of opening" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000789", - "multivalued": false, - "range": "door_direct_enum" - }, - "door_loc": { - "name": "door_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The relative location of the door in the room", - "title": "door location", - "examples": [ - { - "value": "north" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "door location" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000790", - "multivalued": false, - "range": "door_loc_enum" - }, - "door_mat": { - "name": "door_mat", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The material the door is composed of", - "title": "door material", - "examples": [ - { - "value": "wood" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "door material" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000791", - "multivalued": false, - "range": "door_mat_enum" - }, - "door_move": { - "name": "door_move", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of movement of the door", - "title": "door movement", - "examples": [ - { - "value": "swinging" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "door movement" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000792", - "multivalued": false, - "range": "door_move_enum" - }, - "door_size": { - "name": "door_size", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "square meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The size of the door", - "title": "door area or size", - "examples": [ - { - "value": "2.5 square meter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "door area or size" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000158", - "multivalued": false, - "range": "string" - }, - "door_type": { - "name": "door_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of door material", - "title": "door type", - "examples": [ - { - "value": "wooden" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "door type" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000794", - "multivalued": false, - "range": "door_type_enum" - }, - "door_type_metal": { - "name": "door_type_metal", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of metal door", - "title": "door type, metal", - "examples": [ - { - "value": "hollow" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "door type, metal" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000796", - "multivalued": false, - "range": "door_type_metal_enum" - }, - "door_type_wood": { - "name": "door_type_wood", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of wood door", - "title": "door type, wood", - "examples": [ - { - "value": "battened" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "door type, wood" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000797", - "multivalued": false, - "range": "door_type_wood_enum" - }, - "door_water_mold": { - "name": "door_water_mold", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Signs of the presence of mold or mildew on a door", - "title": "door signs of water/mold", - "examples": [ - { - "value": "presence of mold visible" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "door signs of water/mold" - ], - "is_a": "core field", - "string_serialization": "[presence of mold visible|no presence of mold visible]", - "slot_uri": "MIXS:0000793", - "multivalued": false, - "range": "string" - }, - "down_par": { - "name": "down_par", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microEinstein per square meter per second, microEinstein per square centimeter per second" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Visible waveband radiance and irradiance measurements in the water column", - "title": "downward PAR", - "examples": [ - { - "value": "28.71 microEinstein per square meter per second" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "downward PAR" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000703", - "multivalued": false, - "range": "string" - }, - "drainage_class": { - "name": "drainage_class", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Drainage classification from a standard system such as the USDA system", - "title": "drainage classification", - "examples": [ - { - "value": "well" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "drainage classification" - ], - "is_a": "core field", - "slot_uri": "MIXS:0001085", - "multivalued": false, - "range": "drainage_class_enum" - }, - "drawings": { - "name": "drawings", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents", - "title": "drawings", - "examples": [ - { - "value": "sketch" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "drawings" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000798", - "multivalued": false, - "range": "drawings_enum" - }, - "ecosystem": { - "name": "ecosystem", - "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", - "comments": [ - "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "is_a": "gold_path_field" - }, - "ecosystem_category": { - "name": "ecosystem_category", - "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", - "comments": [ - "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "is_a": "gold_path_field" - }, - "ecosystem_subtype": { - "name": "ecosystem_subtype", - "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", - "comments": [ - "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "is_a": "gold_path_field" - }, - "ecosystem_type": { - "name": "ecosystem_type", - "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", - "comments": [ - "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "is_a": "gold_path_field" - }, - "efficiency_percent": { - "name": "efficiency_percent", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Percentage of volatile solids removed from the anaerobic digestor", - "title": "efficiency percent", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "efficiency percent" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000657", - "multivalued": false, - "range": "string" - }, - "elev": { - "name": "elev", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - } - }, - "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", - "title": "elevation", - "examples": [ - { - "value": "100 meter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "elevation" - ], - "is_a": "environment field", - "slot_uri": "MIXS:0000093", - "multivalued": false, - "range": "string" - }, - "elevator": { - "name": "elevator", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The number of elevators within the built structure", - "title": "elevator count", - "examples": [ - { - "value": "2" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "elevator count" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000799", - "multivalued": false, - "range": "string" - }, - "emsl_store_temp": { - "name": "emsl_store_temp", - "description": "The temperature at which the sample should be stored upon delivery to EMSL", - "title": "EMSL sample storage temperature, deg. C", - "todos": [ - "add 'see_alsos' with link to NEXUS info" - ], - "comments": [ - "Enter a temperature in celsius. Numeric portion only." - ], - "examples": [ - { - "value": "-80" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 4, - "string_serialization": "{float}", - "slot_group": "EMSL", - "recommended": true - }, - "emulsions": { - "name": "emulsions", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "emulsion name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types", - "title": "emulsions", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "emulsions" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000660", - "multivalued": false, - "range": "string" - }, - "env_broad_scale": { - "name": "env_broad_scale", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "The major environment type(s) where the sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes." - } - }, - "description": "Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS", - "title": "broad-scale environmental context", - "examples": [ - { - "value": "oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "broad-scale environmental context" - ], - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000012", - "multivalued": false, - "range": "string" - }, - "env_local_scale": { - "name": "env_local_scale", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "Environmental entities having causal influences upon the entity at time of sampling." - } - }, - "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", - "title": "local environmental context", - "examples": [ - { - "value": "litter layer [ENVO:01000338]; Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]." - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "local environmental context" - ], - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000013", - "multivalued": false, - "range": "string" - }, - "env_medium": { - "name": "env_medium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]." - } - }, - "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", - "title": "environmental medium", - "examples": [ - { - "value": "soil [ENVO:00001998]; Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air [ENVO_00002005]" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "environmental medium" - ], - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000014", - "multivalued": false, - "range": "string" - }, - "env_package": { - "name": "env_package", - "description": "MIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported", - "in_subset": [ - "mixs extension" - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "environmental package" - ], - "is_a": "attribute", - "multivalued": false, - "range": "string" - }, - "escalator": { - "name": "escalator", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The number of escalators within the built structure", - "title": "escalator count", - "examples": [ - { - "value": "4" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "escalator count" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000800", - "multivalued": false, - "range": "string" - }, - "ethylbenzene": { - "name": "ethylbenzene", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of ethylbenzene in the sample", - "title": "ethylbenzene", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "ethylbenzene" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000155", - "multivalued": false, - "range": "string" - }, - "exp_duct": { - "name": "exp_duct", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "square meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The amount of exposed ductwork in the room", - "title": "exposed ductwork", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "exposed ductwork" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000144", - "multivalued": false, - "range": "string" - }, - "exp_pipe": { - "name": "exp_pipe", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The number of exposed pipes in the room", - "title": "exposed pipes", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "exposed pipes" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000220", - "multivalued": false, - "range": "string" - }, - "experimental_factor": { - "name": "experimental_factor", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text or EFO and/or OBI" - } - }, - "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", - "title": "experimental factor", - "examples": [ - { - "value": "time series design [EFO:EFO_0001779]" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "experimental factor" - ], - "is_a": "investigation field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000008", - "multivalued": false, - "range": "string" - }, - "experimental_factor_other": { - "name": "experimental_factor_other", - "description": "Other details about your sample that you feel can't be accurately represented in the available columns.", - "title": "experimental factor- other", - "comments": [ - "This slot accepts open-ended text about your sample.", - "We recommend using key:value pairs.", - "Provided pairs will be considered for inclusion as future slots/terms in this data collection template." - ], - "examples": [ - { - "value": "experimental treatment: value" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "see_also": [ - "MIxS:experimental_factor|additional_info" - ], - "rank": 7, - "string_serialization": "{text}", - "slot_group": "MIxS Inspired", - "recommended": true - }, - "ext_door": { - "name": "ext_door", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The number of exterior doors in the built structure", - "title": "exterior door count", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "exterior door count" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000170", - "multivalued": false, - "range": "string" - }, - "ext_wall_orient": { - "name": "ext_wall_orient", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The orientation of the exterior wall", - "title": "orientations of exterior wall", - "examples": [ - { - "value": "northwest" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "orientations of exterior wall" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000817", - "multivalued": false, - "range": "ext_wall_orient_enum" - }, - "ext_window_orient": { - "name": "ext_window_orient", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The compass direction the exterior window of the room is facing", - "title": "orientations of exterior window", - "examples": [ - { - "value": "southwest" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "orientations of exterior window" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000818", - "multivalued": false, - "range": "ext_window_orient_enum" - }, - "extreme_event": { - "name": "extreme_event", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "date" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Unusual physical events that may have affected microbial populations", - "title": "history/extreme events", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "history/extreme events" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000320", - "multivalued": false, - "range": "string" - }, - "fao_class": { - "name": "fao_class", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups", - "title": "soil_taxonomic/FAO classification", - "examples": [ - { - "value": "Luvisols" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "soil_taxonomic/FAO classification" - ], - "is_a": "core field", - "slot_uri": "MIXS:0001083", - "multivalued": false, - "range": "fao_class_enum" - }, - "fertilizer_regm": { - "name": "fertilizer_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "fertilizer name;fertilizer amount;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, mole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens", - "title": "fertilizer regimen", - "examples": [ - { - "value": "urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "fertilizer regimen" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000556", - "multivalued": false, - "range": "string" - }, - "field": { - "name": "field", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Name of the hydrocarbon field (e.g. Albacora)", - "title": "field name", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "field name" - ], - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000291", - "multivalued": false, - "range": "string" - }, - "filter_method": { - "name": "filter_method", - "description": "Type of filter used or how the sample was filtered", - "title": "filter method", - "comments": [ - "describe the filter or provide a catalog number and manufacturer" - ], - "examples": [ - { - "value": "C18" - }, - { - "value": "Basix PES, 13-100-106 FisherSci" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "see_also": [ - "MIxS:filter_type" - ], - "rank": 6, - "string_serialization": "{text}", - "slot_group": "MIxS Inspired", - "recommended": true - }, - "filter_type": { - "name": "filter_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "A device which removes solid particulates or airborne molecular contaminants", - "title": "filter type", - "examples": [ - { - "value": "HEPA" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "filter type" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000765", - "multivalued": true, - "range": "filter_type_enum" - }, - "fire": { - "name": "fire", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "date" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Historical and/or physical evidence of fire", - "title": "history/fire", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "history/fire" - ], - "is_a": "core field", - "slot_uri": "MIXS:0001086", - "multivalued": false, - "range": "string" - }, - "fireplace_type": { - "name": "fireplace_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "A firebox with chimney", - "title": "fireplace type", - "examples": [ - { - "value": "wood burning" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "fireplace type" - ], - "is_a": "core field", - "string_serialization": "[gas burning|wood burning]", - "slot_uri": "MIXS:0000802", - "multivalued": false, - "range": "string" - }, - "flooding": { - "name": "flooding", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "date" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Historical and/or physical evidence of flooding", - "title": "history/flooding", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "history/flooding" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000319", - "multivalued": false, - "range": "string" - }, - "floor_age": { - "name": "floor_age", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "years, weeks, days" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The time period since installment of the carpet or flooring", - "title": "floor age", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "floor age" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000164", - "multivalued": false, - "range": "string" - }, - "floor_area": { - "name": "floor_area", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "square meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The area of the floor space within the room", - "title": "floor area", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "floor area" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000165", - "multivalued": false, - "range": "string" - }, - "floor_cond": { - "name": "floor_cond", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas", - "title": "floor condition", - "examples": [ - { - "value": "new" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "floor condition" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000803", - "multivalued": false, - "range": "floor_cond_enum" - }, - "floor_count": { - "name": "floor_count", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The number of floors in the building, including basements and mechanical penthouse", - "title": "floor count", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "floor count" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000225", - "multivalued": false, - "range": "string" - }, - "floor_finish_mat": { - "name": "floor_finish_mat", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The floor covering type; the finished surface that is walked on", - "title": "floor finish material", - "examples": [ - { - "value": "carpet" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "floor finish material" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000804", - "multivalued": false, - "range": "floor_finish_mat_enum" - }, - "floor_struc": { - "name": "floor_struc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Refers to the structural elements and subfloor upon which the finish flooring is installed", - "title": "floor structure", - "examples": [ - { - "value": "concrete" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "floor structure" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000806", - "multivalued": false, - "range": "floor_struc_enum" - }, - "floor_thermal_mass": { - "name": "floor_thermal_mass", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "joule per degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The ability of the floor to provide inertia against temperature fluctuations", - "title": "floor thermal mass", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "floor thermal mass" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000166", - "multivalued": false, - "range": "string" - }, - "floor_water_mold": { - "name": "floor_water_mold", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Signs of the presence of mold or mildew in a room", - "title": "floor signs of water/mold", - "examples": [ - { - "value": "ceiling discoloration" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "floor signs of water/mold" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000805", - "multivalued": false, - "range": "floor_water_mold_enum" - }, - "fluor": { - "name": "fluor", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram chlorophyll a per cubic meter, volts" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Raw or converted fluorescence of water", - "title": "fluorescence", - "examples": [ - { - "value": "2.5 volts" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "fluorescence" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000704", - "multivalued": false, - "range": "string" - }, - "freq_clean": { - "name": "freq_clean", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration or {text}" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The number of times the sample location is cleaned. Frequency of cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually.", - "title": "frequency of cleaning", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "frequency of cleaning" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000226", - "multivalued": false, - "range": "string" - }, - "freq_cook": { - "name": "freq_cook", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The number of times a meal is cooked per week", - "title": "frequency of cooking", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "frequency of cooking" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000227", - "multivalued": false, - "range": "string" - }, - "fungicide_regm": { - "name": "fungicide_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "fungicide name;fungicide amount;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, mole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens", - "title": "fungicide regimen", - "examples": [ - { - "value": "bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "fungicide regimen" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000557", - "multivalued": false, - "range": "string" - }, - "furniture": { - "name": "furniture", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The types of furniture present in the sampled room", - "title": "furniture", - "examples": [ - { - "value": "chair" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "furniture" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000807", - "multivalued": false, - "range": "furniture_enum" - }, - "gaseous_environment": { - "name": "gaseous_environment", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "gaseous compound name;gaseous compound amount;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens", - "title": "gaseous environment", - "examples": [ - { - "value": "nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "gaseous environment" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000558", - "multivalued": false, - "range": "string" - }, - "gaseous_substances": { - "name": "gaseous_substances", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "gaseous substance name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances", - "title": "gaseous substances", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "gaseous substances" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000661", - "multivalued": false, - "range": "string" - }, - "gender_restroom": { - "name": "gender_restroom", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The gender type of the restroom", - "title": "gender of restroom", - "examples": [ - { - "value": "male" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "gender of restroom" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000808", - "multivalued": false, - "range": "gender_restroom_enum" - }, - "genetic_mod": { - "name": "genetic_mod", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI,url or free text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection", - "title": "genetic modification", - "examples": [ - { - "value": "aox1A transgenic" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "genetic modification" - ], - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}|{text}", - "slot_uri": "MIXS:0000859", - "multivalued": false, - "range": "string" - }, - "geo_loc_name": { - "name": "geo_loc_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" - } - }, - "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (http://purl.bioontology.org/ontology/GAZ)", - "title": "geographic location (country and/or sea,region)", - "examples": [ - { - "value": "USA: Maryland, Bethesda" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "geographic location (country and/or sea,region)" - ], - "is_a": "environment field", - "string_serialization": "{term}: {term}, {text}", - "slot_uri": "MIXS:0000010", - "multivalued": false, - "range": "string" - }, - "glucosidase_act": { - "name": "glucosidase_act", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mol per liter per hour" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of glucosidase activity", - "title": "glucosidase activity", - "examples": [ - { - "value": "5 mol per liter per hour" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "glucosidase activity" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000137", - "multivalued": false, - "range": "string" - }, - "gravidity": { - "name": "gravidity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "gravidity status;timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used", - "title": "gravidity", - "examples": [ - { - "value": "yes;due date:2018-05-11" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "gravidity" - ], - "is_a": "core field", - "string_serialization": "{boolean};{timestamp}", - "slot_uri": "MIXS:0000875", - "multivalued": false, - "range": "string" - }, - "gravity": { - "name": "gravity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "gravity factor value;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter per square second, g" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments", - "title": "gravity", - "examples": [ - { - "value": "12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "gravity" - ], - "is_a": "core field", - "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000559", - "multivalued": false, - "range": "string" - }, - "growth_facil": { - "name": "growth_facil", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "free text or CO" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Type of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research", - "title": "growth facility", - "examples": [ - { - "value": "Growth chamber [CO_715:0000189]" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "growth facility" - ], - "is_a": "core field", - "string_serialization": "{text}|{termLabel} {[termID]}", - "slot_uri": "MIXS:0001043", - "multivalued": false, - "range": "string" - }, - "growth_habit": { - "name": "growth_habit", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Characteristic shape, appearance or growth form of a plant species", - "title": "growth habit", - "examples": [ - { - "value": "spreading" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "growth habit" - ], - "is_a": "core field", - "slot_uri": "MIXS:0001044", - "multivalued": false, - "range": "growth_habit_enum" - }, - "growth_hormone_regm": { - "name": "growth_hormone_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "growth hormone name;growth hormone amount;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, mole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens", - "title": "growth hormone regimen", - "examples": [ - { - "value": "abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "growth hormone regimen" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000560", - "multivalued": false, - "range": "string" - }, - "hall_count": { - "name": "hall_count", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The total count of hallways and cooridors in the built structure", - "title": "hallway/corridor count", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "hallway/corridor count" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000228", - "multivalued": false, - "range": "string" - }, - "handidness": { - "name": "handidness", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The handidness of the individual sampled", - "title": "handidness", - "examples": [ - { - "value": "right handedness" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "handidness" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000809", - "multivalued": false, - "range": "handidness_enum" - }, - "hc_produced": { - "name": "hc_produced", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "hydrocarbon type produced", - "examples": [ - { - "value": "Gas" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "hydrocarbon type produced" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000989", - "multivalued": false, - "range": "hc_produced_enum" - }, - "hcr": { - "name": "hcr", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Main Hydrocarbon Resource type. The term \"Hydrocarbon Resource\" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "hydrocarbon resource type", - "examples": [ - { - "value": "Oil Sand" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "hydrocarbon resource type" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000988", - "multivalued": false, - "range": "hcr_enum" - }, - "hcr_fw_salinity": { - "name": "hcr_fw_salinity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS", - "title": "formation water salinity", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "formation water salinity" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000406", - "multivalued": false, - "range": "string" - }, - "hcr_geol_age": { - "name": "hcr_geol_age", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "hydrocarbon resource geological age", - "examples": [ - { - "value": "Silurian" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "hydrocarbon resource geological age" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000993", - "multivalued": false, - "range": "hcr_geol_age_enum" - }, - "hcr_pressure": { - "name": "hcr_pressure", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value range" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "atmosphere, kilopascal" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Original pressure of the hydrocarbon resource", - "title": "hydrocarbon resource original pressure", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "hydrocarbon resource original pressure" - ], - "is_a": "core field", - "string_serialization": "{float} - {float} {unit}", - "slot_uri": "MIXS:0000395", - "multivalued": false, - "range": "string" - }, - "hcr_temp": { - "name": "hcr_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value range" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Original temperature of the hydrocarbon resource", - "title": "hydrocarbon resource original temperature", - "examples": [ - { - "value": "150-295 degree Celsius" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "hydrocarbon resource original temperature" - ], - "is_a": "core field", - "string_serialization": "{float} - {float} {unit}", - "slot_uri": "MIXS:0000393", - "multivalued": false, - "range": "string" - }, - "heat_cool_type": { - "name": "heat_cool_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Methods of conditioning or heating a room or building", - "title": "heating and cooling system type", - "examples": [ - { - "value": "heat pump" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "heating and cooling system type" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000766", - "multivalued": true, - "range": "heat_cool_type_enum" - }, - "heat_deliv_loc": { - "name": "heat_deliv_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The location of heat delivery within the room", - "title": "heating delivery locations", - "examples": [ - { - "value": "north" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "heating delivery locations" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000810", - "multivalued": false, - "range": "heat_deliv_loc_enum" - }, - "heat_sys_deliv_meth": { - "name": "heat_sys_deliv_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The method by which the heat is delivered through the system", - "title": "heating system delivery method", - "examples": [ - { - "value": "radiant" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "heating system delivery method" - ], - "is_a": "core field", - "string_serialization": "[conductive|radiant]", - "slot_uri": "MIXS:0000812", - "multivalued": false, - "range": "string" - }, - "heat_system_id": { - "name": "heat_system_id", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "unique identifier" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The heating system identifier", - "title": "heating system identifier", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "heating system identifier" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000833", - "multivalued": false, - "range": "string" - }, - "heavy_metals": { - "name": "heavy_metals", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "heavy metal name;measurement value unit" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per gram" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Heavy metals present in the sequenced sample and their concentrations. For multiple heavy metals and concentrations, add multiple copies of this field.", - "title": "extreme_unusual_properties/heavy metals", - "examples": [ - { - "value": "mercury;0.09 micrograms per gram" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "extreme_unusual_properties/heavy metals" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000652", - "multivalued": false, - "range": "string" - }, - "heavy_metals_meth": { - "name": "heavy_metals_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining heavy metals", - "title": "extreme_unusual_properties/heavy metals method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "extreme_unusual_properties/heavy metals method" - ], - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000343", - "multivalued": false, - "range": "string" - }, - "height_carper_fiber": { - "name": "height_carper_fiber", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "centimeter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The average carpet fiber height in the indoor environment", - "title": "height carpet fiber mat", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "height carpet fiber mat" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000167", - "multivalued": false, - "range": "string" - }, - "herbicide_regm": { - "name": "herbicide_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "herbicide name;herbicide amount;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, mole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", - "title": "herbicide regimen", - "examples": [ - { - "value": "atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "herbicide regimen" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000561", - "multivalued": false, - "range": "string" - }, - "horizon_meth": { - "name": "horizon_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining the horizon", - "title": "soil horizon method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "soil horizon method" - ], - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000321", - "multivalued": false, - "range": "string" - }, - "host_age": { - "name": "host_age", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "year, day, hour" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees", - "title": "host age", - "examples": [ - { - "value": "10 days" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "host age" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000255", - "multivalued": false, - "range": "string" - }, - "host_body_habitat": { - "name": "host_body_habitat", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "free text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Original body habitat where the sample was obtained from", - "title": "host body habitat", - "examples": [ - { - "value": "nasopharynx" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "host body habitat" - ], - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000866", - "multivalued": false, - "range": "string" - }, - "host_body_product": { - "name": "host_body_product", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "FMA or UBERON" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon", - "title": "host body product", - "examples": [ - { - "value": "Portion of mucus [fma66938]" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "host body product" - ], - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000888", - "multivalued": false, - "range": "string" - }, - "host_body_site": { - "name": "host_body_site", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "FMA or UBERON" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON", - "title": "host body site", - "examples": [ - { - "value": "gill [UBERON:0002535]" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "host body site" - ], - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000867", - "multivalued": false, - "range": "string" - }, - "host_body_temp": { - "name": "host_body_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Core body temperature of the host when sample was collected", - "title": "host body temperature", - "examples": [ - { - "value": "15 degree Celsius" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "host body temperature" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000274", - "multivalued": false, - "range": "string" - }, - "host_color": { - "name": "host_color", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "color" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The color of host", - "title": "host color", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "host color" - ], - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000260", - "multivalued": false, - "range": "string" - }, - "host_common_name": { - "name": "host_common_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "common name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Common name of the host.", - "title": "host common name", - "examples": [ - { - "value": "human" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "host common name" - ], - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000248", - "multivalued": false, - "range": "string" - }, - "host_diet": { - "name": "host_diet", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "diet type" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types", - "title": "host diet", - "examples": [ - { - "value": "herbivore" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "host diet" - ], - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000869", - "multivalued": false, - "range": "string" - }, - "host_dry_mass": { - "name": "host_dry_mass", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "kilogram, gram" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of dry mass", - "title": "host dry mass", - "examples": [ - { - "value": "500 gram" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "host dry mass" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000257", - "multivalued": false, - "range": "string" - }, - "host_family_relation": { - "name": "host_family_relation", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "relationship type;arbitrary identifier" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Familial relationships to other hosts in the same study; can include multiple relationships", - "title": "host family relationship", - "examples": [ - { - "value": "offspring;Mussel25" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "host family relationship" - ], - "is_a": "core field", - "string_serialization": "{text};{text}", - "slot_uri": "MIXS:0000872", - "multivalued": false, - "range": "string" - }, - "host_genotype": { - "name": "host_genotype", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "genotype" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Observed genotype", - "title": "host genotype", - "examples": [ - { - "value": "C57BL/6" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "host genotype" - ], - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000365", - "multivalued": false, - "range": "string" - }, - "host_growth_cond": { - "name": "host_growth_cond", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI,url or free text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Literature reference giving growth conditions of the host", - "title": "host growth conditions", - "examples": [ - { - "value": "https://academic.oup.com/icesjms/article/68/2/349/617247" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "host growth conditions" - ], - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}|{text}", - "slot_uri": "MIXS:0000871", - "multivalued": false, - "range": "string" - }, - "host_height": { - "name": "host_height", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "centimeter, millimeter, meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The height of subject", - "title": "host height", - "examples": [ - { - "value": "0.1 meter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "host height" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000264", - "multivalued": false, - "range": "string" - }, - "host_last_meal": { - "name": "host_last_meal", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "content;duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Content of last meal and time since feeding; can include multiple values", - "title": "host last meal", - "examples": [ - { - "value": "corn feed;P2H" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "host last meal" - ], - "is_a": "core field", - "string_serialization": "{text};{duration}", - "slot_uri": "MIXS:0000870", - "multivalued": false, - "range": "string" - }, - "host_length": { - "name": "host_length", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "centimeter, millimeter, meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The length of subject", - "title": "host length", - "examples": [ - { - "value": "1 meter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "host length" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000256", - "multivalued": false, - "range": "string" - }, - "host_life_stage": { - "name": "host_life_stage", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "stage" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Description of life stage of host", - "title": "host life stage", - "examples": [ - { - "value": "adult" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "host life stage" - ], - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000251", - "multivalued": false, - "range": "string" - }, - "host_phenotype": { - "name": "host_phenotype", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PATO or HP" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP", - "title": "host phenotype", - "examples": [ - { - "value": "elongated [PATO:0001154]" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "host phenotype" - ], - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000874", - "multivalued": false, - "range": "string" - }, - "host_sex": { - "name": "host_sex", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Gender or physical sex of the host.", - "title": "host sex", - "examples": [ - { - "value": "non-binary" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "host sex" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000811", - "multivalued": false, - "range": "host_sex_enum" - }, - "host_shape": { - "name": "host_shape", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "shape" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Morphological shape of host", - "title": "host shape", - "examples": [ - { - "value": "round" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "host shape" - ], - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000261", - "multivalued": false, - "range": "string" - }, - "host_subject_id": { - "name": "host_subject_id", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "unique identifier" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "A unique identifier by which each subject can be referred to, de-identified.", - "title": "host subject id", - "examples": [ - { - "value": "MPI123" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "host subject id" - ], - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000861", - "multivalued": false, - "range": "string" - }, - "host_subspecf_genlin": { - "name": "host_subspecf_genlin", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies, e.g. serovar, biotype, ecotype, variety, cultivar." - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about the genetic distinctness of the host organism below the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.", - "title": "host subspecific genetic lineage", - "examples": [ - { - "value": "serovar:Newport, variety:glabrum, cultivar: Red Delicious" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "host subspecific genetic lineage" - ], - "is_a": "core field", - "string_serialization": "{rank name}:{text}", - "slot_uri": "MIXS:0001318", - "multivalued": false, - "range": "string" - }, - "host_substrate": { - "name": "host_substrate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "substrate name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The growth substrate of the host.", - "title": "host substrate", - "examples": [ - { - "value": "rock" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "host substrate" - ], - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000252", - "multivalued": false, - "range": "string" - }, - "host_symbiont": { - "name": "host_symbiont", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "species name or common name" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host.", - "title": "observed host symbionts", - "examples": [ - { - "value": "flukeworms" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "observed host symbionts" - ], - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0001298", - "multivalued": false, - "range": "string" - }, - "host_taxid": { - "name": "host_taxid", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "NCBI taxon identifier" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "NCBI taxon id of the host, e.g. 9606", - "title": "host taxid", - "comments": [ - "Homo sapiens [NCBITaxon:9606] would be a reasonable has_raw_value" - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "host taxid" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000250", - "multivalued": false, - "range": "string" - }, - "host_tot_mass": { - "name": "host_tot_mass", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "kilogram, gram" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Total mass of the host at collection, the unit depends on host", - "title": "host total mass", - "examples": [ - { - "value": "2500 gram" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "host total mass" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000263", - "multivalued": false, - "range": "string" - }, - "host_wet_mass": { - "name": "host_wet_mass", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "kilogram, gram" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of wet mass", - "title": "host wet mass", - "examples": [ - { - "value": "1500 gram" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "host wet mass" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000567", - "multivalued": false, - "range": "string" - }, - "humidity": { - "name": "humidity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram per cubic meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Amount of water vapour in the air, at the time of sampling", - "title": "humidity", - "examples": [ - { - "value": "25 gram per cubic meter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "humidity" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000100", - "multivalued": false, - "range": "string" - }, - "humidity_regm": { - "name": "humidity_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "humidity value;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram per cubic meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", - "title": "humidity regimen", - "examples": [ - { - "value": "25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "humidity regimen" - ], - "is_a": "core field", - "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000568", - "multivalued": false, - "range": "string" - }, - "indoor_space": { - "name": "indoor_space", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "A distinguishable space within a structure, the purpose for which discrete areas of a building is used", - "title": "indoor space", - "examples": [ - { - "value": "foyer" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "indoor space" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000763", - "multivalued": false, - "range": "indoor_space_enum" - }, - "indoor_surf": { - "name": "indoor_surf", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Type of indoor surface", - "title": "indoor surface", - "examples": [ - { - "value": "wall" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "indoor surface" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000764", - "multivalued": false, - "range": "indoor_surf_enum" - }, - "indust_eff_percent": { - "name": "indust_eff_percent", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "percentage" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Percentage of industrial effluents received by wastewater treatment plant", - "title": "industrial effluent percent", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "industrial effluent percent" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000662", - "multivalued": false, - "range": "string" - }, - "inorg_particles": { - "name": "inorg_particles", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "inorganic particle name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles", - "title": "inorganic particles", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "inorganic particles" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000664", - "multivalued": false, - "range": "string" - }, - "inside_lux": { - "name": "inside_lux", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "kilowatt per square metre" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The recorded value at sampling time (power density)", - "title": "inside lux light", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "inside lux light" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000168", - "multivalued": false, - "range": "string" - }, - "int_wall_cond": { - "name": "int_wall_cond", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas", - "title": "interior wall condition", - "examples": [ - { - "value": "damaged" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "interior wall condition" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000813", - "multivalued": false, - "range": "int_wall_cond_enum" - }, - "isotope_exposure": { - "name": "isotope_exposure", - "description": "List isotope exposure or addition applied to your sample.", - "title": "isotope exposure/addition", - "todos": [ - "Can we make the H218O correctly super and subscripted?" - ], - "comments": [ - "This is required when your experimental design includes the use of isotopically labeled compounds" - ], - "examples": [ - { - "value": "13C glucose" - }, - { - "value": "H218O" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "see_also": [ - "MIxS:chem_administration" - ], - "rank": 16, - "string_serialization": "{termLabel} {[termID]}; {timestamp}", - "slot_group": "MIxS Inspired", - "recommended": true - }, - "iw_bt_date_well": { - "name": "iw_bt_date_well", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Injection water breakthrough date per well following a secondary and/or tertiary recovery", - "title": "injection water breakthrough date of specific well", - "examples": [ - { - "value": "2018-05-11" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "injection water breakthrough date of specific well" - ], - "is_a": "core field", - "slot_uri": "MIXS:0001010", - "multivalued": false, - "range": "string" - }, - "iwf": { - "name": "iwf", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "percent" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%)", - "title": "injection water fraction", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "injection water fraction" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000455", - "multivalued": false, - "range": "string" - }, - "last_clean": { - "name": "last_clean", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The last time the floor was cleaned (swept, mopped, vacuumed)", - "title": "last time swept/mopped/vacuumed", - "examples": [ - { - "value": "2018-05-11:T14:30Z" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "last time swept/mopped/vacuumed" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000814", - "multivalued": false, - "range": "string" - }, - "lat_lon": { - "name": "lat_lon", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "decimal degrees, limit to 8 decimal points" - } - }, - "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", - "title": "geographic location (latitude and longitude)", - "examples": [ - { - "value": "50.586825 6.408977" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "geographic location (latitude and longitude)" - ], - "is_a": "environment field", - "string_serialization": "{float} {float}", - "slot_uri": "MIXS:0000009", - "multivalued": false, - "range": "string" - }, - "lbc_thirty": { - "name": "lbc_thirty", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "ppm CaCO3/pH" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "lime buffer capacity, determined after 30 minute incubation", - "title": "lime buffer capacity (at 30 minutes)", - "comments": [ - "This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one pH unit" - ], - "examples": [ - { - "value": "543 mg/kg" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "see_also": [ - "https://www.ornl.gov/content/bio-scales-0", - "https://secure.caes.uga.edu/extension/publications/files/pdf/C%20874_5.PDF" - ], - "aliases": [ - "lbc_thirty", - "lbc30", - "lime buffer capacity (at 30 minutes)" - ], - "is_a": "attribute", - "multivalued": false, - "range": "string" - }, - "lbceq": { - "name": "lbceq", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "ppm CaCO3/pH" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "lime buffer capacity, determined at equilibrium after 5 day incubation", - "title": "lime buffer capacity (after 5 day incubation)", - "comments": [ - "This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one pH unit" - ], - "examples": [ - { - "value": "1575 mg/kg" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "see_also": [ - "https://www.ornl.gov/content/bio-scales-0" - ], - "aliases": [ - "lbceq", - "lime buffer capacity (at 5-day equilibrium)" - ], - "is_a": "attribute", - "multivalued": false, - "range": "string" - }, - "light_intensity": { - "name": "light_intensity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "lux" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of light intensity", - "title": "light intensity", - "examples": [ - { - "value": "0.3 lux" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "light intensity" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000706", - "multivalued": false, - "range": "string" - }, - "light_regm": { - "name": "light_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "exposure type;light intensity;light quality" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "lux; micrometer, nanometer, angstrom" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Information about treatment(s) involving exposure to light, including both light intensity and quality.", - "title": "light regimen", - "examples": [ - { - "value": "incandescant light;10 lux;450 nanometer" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "light regimen" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{float} {unit}", - "slot_uri": "MIXS:0000569", - "multivalued": false, - "range": "string" - }, - "light_type": { - "name": "light_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light", - "title": "light type", - "examples": [ - { - "value": "desk lamp" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "light type" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000769", - "multivalued": true, - "range": "light_type_enum" - }, - "link_class_info": { - "name": "link_class_info", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Link to digitized soil maps or other soil classification information", - "title": "link to classification information", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "link to classification information" - ], - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000329", - "multivalued": false, - "range": "string" - }, - "link_climate_info": { - "name": "link_climate_info", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Link to climate resource", - "title": "link to climate information", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "link to climate information" - ], - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000328", - "multivalued": false, - "range": "string" - }, - "lithology": { - "name": "lithology", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "lithology", - "examples": [ - { - "value": "Volcanic" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "lithology" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000990", - "multivalued": false, - "range": "lithology_enum" - }, - "local_class": { - "name": "local_class", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "local classification name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Soil classification based on local soil classification system", - "title": "soil_taxonomic/local classification", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "soil_taxonomic/local classification" - ], - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000330", - "multivalued": false, - "range": "string" - }, - "local_class_meth": { - "name": "local_class_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining the local soil classification", - "title": "soil_taxonomic/local classification method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "soil_taxonomic/local classification method" - ], - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000331", - "multivalued": false, - "range": "string" - }, - "magnesium": { - "name": "magnesium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mole per liter, milligram per liter, parts per million, micromole per kilogram" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of magnesium in the sample", - "title": "magnesium", - "examples": [ - { - "value": "52.8 micromole per kilogram" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "magnesium" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000431", - "multivalued": false, - "range": "string" - }, - "manganese": { - "name": "manganese", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mg/kg (ppm)" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of manganese in the sample", - "title": "manganese", - "examples": [ - { - "value": "24.7 mg/kg" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "see_also": [ - "https://www.ornl.gov/content/bio-scales-0" - ], - "aliases": [ - "manganese" - ], - "is_a": "attribute", - "multivalued": false, - "range": "string" - }, - "max_occup": { - "name": "max_occup", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The maximum amount of people allowed in the indoor environment", - "title": "maximum occupancy", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "maximum occupancy" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000229", - "multivalued": false, - "range": "string" - }, - "mean_frict_vel": { - "name": "mean_frict_vel", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter per second" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of mean friction velocity", - "title": "mean friction velocity", - "examples": [ - { - "value": "0.5 meter per second" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "mean friction velocity" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000498", - "multivalued": false, - "range": "string" - }, - "mean_peak_frict_vel": { - "name": "mean_peak_frict_vel", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter per second" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of mean peak friction velocity", - "title": "mean peak friction velocity", - "examples": [ - { - "value": "1 meter per second" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "mean peak friction velocity" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000502", - "multivalued": false, - "range": "string" - }, - "mech_struc": { - "name": "mech_struc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "mechanical structure: a moving structure", - "title": "mechanical structure", - "examples": [ - { - "value": "elevator" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "mechanical structure" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000815", - "multivalued": false, - "range": "mech_struc_enum" - }, - "mechanical_damage": { - "name": "mechanical_damage", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "damage type;body site" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about any mechanical damage exerted on the plant; can include multiple damages and sites", - "title": "mechanical damage", - "examples": [ - { - "value": "pruning;bark" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "mechanical damage" - ], - "is_a": "core field", - "string_serialization": "{text};{text}", - "slot_uri": "MIXS:0001052", - "multivalued": false, - "range": "string" - }, - "methane": { - "name": "methane", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, parts per billion, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Methane (gas) amount or concentration at the time of sampling", - "title": "methane", - "examples": [ - { - "value": "1800 parts per billion" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "methane" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000101", - "multivalued": false, - "range": "string" - }, - "micro_biomass_c_meth": { - "name": "micro_biomass_c_meth", - "description": "Reference or method used in determining microbial biomass carbon", - "title": "microbial biomass carbon method", - "todos": [ - "How should we separate values? | or ;? lets be consistent" - ], - "comments": [ - "required if \"microbial_biomass_c\" is provided" - ], - "examples": [ - { - "value": "https://doi.org/10.1016/0038-0717(87)90052-6" - }, - { - "value": "https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "see_also": [ - "MIxS:micro_biomass_meth" - ], - "rank": 11, - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_group": "MIxS Inspired", - "recommended": true - }, - "micro_biomass_meth": { - "name": "micro_biomass_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining microbial biomass", - "title": "microbial biomass method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "microbial biomass method" - ], - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000339", - "multivalued": false, - "range": "string" - }, - "micro_biomass_n_meth": { - "name": "micro_biomass_n_meth", - "description": "Reference or method used in determining microbial biomass nitrogen", - "title": "microbial biomass nitrogen method", - "comments": [ - "required if \"microbial_biomass_n\" is provided" - ], - "examples": [ - { - "value": "https://doi.org/10.1016/0038-0717(87)90052-6" - }, - { - "value": "https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "see_also": [ - "MIxS:micro_biomass_meth" - ], - "rank": 13, - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_group": "MIxS Inspired" - }, - "microbial_biomass": { - "name": "microbial_biomass", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "ton, kilogram, gram per kilogram soil" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units", - "title": "microbial biomass", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "microbial biomass" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000650", - "multivalued": false, - "range": "string" - }, - "microbial_biomass_c": { - "name": "microbial_biomass_c", - "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.", - "title": "microbial biomass carbon", - "comments": [ - "If you provide this, correction factors used for conversion to the final units and method are required" - ], - "examples": [ - { - "value": "0.05 ug C/g dry soil" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "see_also": [ - "MIxS:microbial_biomass" - ], - "rank": 10, - "string_serialization": "{float} {unit}", - "slot_group": "MIxS Inspired" - }, - "microbial_biomass_n": { - "name": "microbial_biomass_n", - "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.", - "title": "microbial biomass nitrogen", - "comments": [ - "If you provide this, correction factors used for conversion to the final units and method are required" - ], - "examples": [ - { - "value": "0.05 ug N/g dry soil" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "see_also": [ - "MIxS:microbial_biomass" - ], - "rank": 12, - "string_serialization": "{float} {unit}", - "slot_group": "MIxS Inspired" - }, - "mineral_nutr_regm": { - "name": "mineral_nutr_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "mineral nutrient name;mineral nutrient amount;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, mole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens", - "title": "mineral nutrient regimen", - "examples": [ - { - "value": "potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "mineral nutrient regimen" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000570", - "multivalued": false, - "range": "string" - }, - "misc_param": { - "name": "misc_param", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "parameter name;measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Any other measurement performed or parameter collected, that is not listed here", - "title": "miscellaneous parameter", - "examples": [ - { - "value": "Bicarbonate ion concentration;2075 micromole per kilogram" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "miscellaneous parameter" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000752", - "multivalued": false, - "range": "string" - }, - "n_alkanes": { - "name": "n_alkanes", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "n-alkane name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Concentration of n-alkanes; can include multiple n-alkanes", - "title": "n-alkanes", - "examples": [ - { - "value": "n-hexadecane;100 milligram per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "n-alkanes" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000503", - "multivalued": false, - "range": "string" - }, - "nitrate": { - "name": "nitrate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of nitrate in the sample", - "title": "nitrate", - "examples": [ - { - "value": "65 micromole per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "nitrate" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000425", - "multivalued": false, - "range": "string" - }, - "nitrate_nitrogen": { - "name": "nitrate_nitrogen", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mg/kg" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of nitrate nitrogen in the sample", - "title": "nitrate_nitrogen", - "comments": [ - "often below some specified limit of detection" - ], - "examples": [ - { - "value": "0.29 mg/kg" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "see_also": [ - "https://www.ornl.gov/content/bio-scales-0" - ], - "aliases": [ - "nitrate_nitrogen", - "NO3-N" - ], - "is_a": "attribute", - "multivalued": false, - "range": "string" - }, - "nitrite": { - "name": "nitrite", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of nitrite in the sample", - "title": "nitrite", - "examples": [ - { - "value": "0.5 micromole per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "nitrite" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000426", - "multivalued": false, - "range": "string" - }, - "nitrite_nitrogen": { - "name": "nitrite_nitrogen", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mg/kg" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of nitrite nitrogen in the sample", - "title": "nitrite_nitrogen", - "examples": [ - { - "value": "1.2 mg/kg" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "see_also": [ - "https://www.ornl.gov/content/bio-scales-0" - ], - "aliases": [ - "nitrite_nitrogen", - "NO2-N" - ], - "is_a": "attribute", - "multivalued": false, - "range": "string" - }, - "nitro": { - "name": "nitro", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of nitrogen (total)", - "title": "nitrogen", - "examples": [ - { - "value": "4.2 micromole per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "nitrogen" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000504", - "multivalued": false, - "range": "string" - }, - "non_microb_biomass": { - "name": "non_microb_biomass", - "description": "Amount of biomass; should include the name for the part of biomass measured, e.g.insect, plant, total. Can include multiple measurements separated by ;", - "title": "non-microbial biomass", - "examples": [ - { - "value": "insect 0.23 ug; plant 1g" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "see_also": [ - "MIxS:biomass|microbial_biomass" - ], - "rank": 8, - "string_serialization": "{text};{float} {unit}", - "slot_group": "MIxS Inspired" - }, - "non_microb_biomass_method": { - "name": "non_microb_biomass_method", - "description": "Reference or method used in determining biomass", - "title": "non-microbial biomass method", - "comments": [ - "required if \"non-microbial biomass\" is provided" - ], - "examples": [ - { - "value": "https://doi.org/10.1038/s41467-021-26181-3" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "see_also": [ - "MIxS:microbial_biomass" - ], - "rank": 9, - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_group": "MIxS Inspired" - }, - "non_min_nutr_regm": { - "name": "non_min_nutr_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "non-mineral nutrient name;non-mineral nutrient amount;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, mole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens", - "title": "non-mineral nutrient regimen", - "examples": [ - { - "value": "carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "non-mineral nutrient regimen" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000571", - "multivalued": false, - "range": "string" - }, - "number_pets": { - "name": "number_pets", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The number of pets residing in the sampled space", - "title": "number of pets", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "number of pets" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000231", - "multivalued": false, - "range": "string" - }, - "number_plants": { - "name": "number_plants", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The number of plant(s) in the sampling space", - "title": "number of houseplants", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "number of houseplants" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000230", - "multivalued": false, - "range": "string" - }, - "number_resident": { - "name": "number_resident", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The number of individuals currently occupying in the sampling location", - "title": "number of residents", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "number of residents" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000232", - "multivalued": false, - "range": "string" - }, - "occup_density_samp": { - "name": "occup_density_samp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Average number of occupants at time of sampling per square footage", - "title": "occupant density at sampling", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "occupant density at sampling" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000217", - "multivalued": false, - "range": "string" - }, - "occup_document": { - "name": "occup_document", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of documentation of occupancy", - "title": "occupancy documentation", - "examples": [ - { - "value": "estimate" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "occupancy documentation" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000816", - "multivalued": false, - "range": "occup_document_enum" - }, - "occup_samp": { - "name": "occup_samp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Number of occupants present at time of sample within the given space", - "title": "occupancy at sampling", - "examples": [ - { - "value": "10" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "occupancy at sampling" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000772", - "multivalued": false, - "range": "string" - }, - "org_carb": { - "name": "org_carb", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of organic carbon", - "title": "organic carbon", - "examples": [ - { - "value": "1.5 microgram per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "organic carbon" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000508", - "multivalued": false, - "range": "string" - }, - "org_count_qpcr_info": { - "name": "org_count_qpcr_info", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "number of cells per gram (or ml or cm^2)" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles)", - "title": "organism count qPCR information", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "organism count qPCR information" - ], - "is_a": "core field", - "string_serialization": "{text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles", - "slot_uri": "MIXS:0000099", - "multivalued": false, - "range": "string" - }, - "org_matter": { - "name": "org_matter", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of organic matter", - "title": "organic matter", - "examples": [ - { - "value": "1.75 milligram per cubic meter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "organic matter" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000204", - "multivalued": false, - "range": "string" - }, - "org_nitro": { - "name": "org_nitro", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of organic nitrogen", - "title": "organic nitrogen", - "examples": [ - { - "value": "4 micromole per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "organic nitrogen" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000205", - "multivalued": false, - "range": "string" - }, - "org_nitro_method": { - "name": "org_nitro_method", - "description": "Method used for obtaining organic nitrogen", - "title": "organic nitrogen method", - "comments": [ - "required if \"org_nitro\" is provided" - ], - "examples": [ - { - "value": "https://doi.org/10.1016/0038-0717(85)90144-0" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "see_also": [ - "MIxS:org_nitro|tot_nitro_cont_meth" - ], - "rank": 14, - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_group": "MIxS Inspired" - }, - "org_particles": { - "name": "org_particles", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "particle name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc.", - "title": "organic particles", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "organic particles" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000665", - "multivalued": false, - "range": "string" - }, - "organism_count": { - "name": "organism_count", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "organism name;measurement value;enumeration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", - "title": "organism count", - "examples": [ - { - "value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "organism count" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000103", - "multivalued": false, - "range": "string" - }, - "other_treatment": { - "name": "other_treatment", - "description": "Other treatments applied to your samples that are not applicable to the provided fields", - "title": "other treatments", - "comments": [ - "This is an open text field to provide any treatments that cannot be captured in the provided slots." - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "see_also": [ - "MIxS:additional_info" - ], - "rank": 15, - "string_serialization": "{text}", - "slot_group": "MIxS Inspired", - "recommended": true - }, - "owc_tvdss": { - "name": "owc_tvdss", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Depth of the original oil water contact (OWC) zone (average) (m TVDSS)", - "title": "oil water contact depth", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "oil water contact depth" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000405", - "multivalued": false, - "range": "string" - }, - "oxy_stat_samp": { - "name": "oxy_stat_samp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Oxygenation status of sample", - "title": "oxygenation status of sample", - "examples": [ - { - "value": "aerobic" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "oxygenation status of sample" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000753", - "multivalued": false, - "range": "OxyStatSampEnum" - }, - "oxygen": { - "name": "oxygen", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Oxygen (gas) amount or concentration at the time of sampling", - "title": "oxygen", - "examples": [ - { - "value": "600 parts per million" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "oxygen" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000104", - "multivalued": false, - "range": "string" - }, - "part_org_carb": { - "name": "part_org_carb", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of particulate organic carbon", - "title": "particulate organic carbon", - "examples": [ - { - "value": "1.92 micromole per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "particulate organic carbon" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000515", - "multivalued": false, - "range": "string" - }, - "part_org_nitro": { - "name": "part_org_nitro", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter, micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of particulate organic nitrogen", - "title": "particulate organic nitrogen", - "examples": [ - { - "value": "0.3 micromole per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "particulate organic nitrogen" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000719", - "multivalued": false, - "range": "string" - }, - "particle_class": { - "name": "particle_class", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "particle name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micrometer" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values", - "title": "particle classification", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "particle classification" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000206", - "multivalued": false, - "range": "string" - }, - "permeability": { - "name": "permeability", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value range" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mD" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))", - "title": "permeability", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "permeability" - ], - "is_a": "core field", - "string_serialization": "{integer} - {integer} {unit}", - "slot_uri": "MIXS:0000404", - "multivalued": false, - "range": "string" - }, - "perturbation": { - "name": "perturbation", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "perturbation type name;perturbation interval and duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types", - "title": "perturbation", - "examples": [ - { - "value": "antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "perturbation" - ], - "is_a": "core field", - "string_serialization": "{text};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000754", - "multivalued": false, - "range": "string" - }, - "pesticide_regm": { - "name": "pesticide_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "pesticide name;pesticide amount;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, mole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens", - "title": "pesticide regimen", - "examples": [ - { - "value": "pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "pesticide regimen" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000573", - "multivalued": false, - "range": "string" - }, - "petroleum_hydrocarb": { - "name": "petroleum_hydrocarb", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of petroleum hydrocarbon", - "title": "petroleum hydrocarbon", - "examples": [ - { - "value": "0.05 micromole per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "petroleum hydrocarbon" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000516", - "multivalued": false, - "range": "string" - }, - "ph": { - "name": "ph", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid", - "title": "pH", - "examples": [ - { - "value": "7.2" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "pH" - ], - "is_a": "core field", - "slot_uri": "MIXS:0001001", - "multivalued": false, - "range": "double" - }, - "ph_meth": { - "name": "ph_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining ph", - "title": "pH method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "pH method" - ], - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0001106", - "multivalued": false, - "range": "string" - }, - "ph_regm": { - "name": "ph_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value;treatment interval and duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen", - "title": "pH regimen", - "examples": [ - { - "value": "7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "pH regimen" - ], - "is_a": "core field", - "string_serialization": "{float};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0001056", - "multivalued": false, - "range": "string" - }, - "phaeopigments": { - "name": "phaeopigments", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "phaeopigment name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per cubic meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Concentration of phaeopigments; can include multiple phaeopigments", - "title": "phaeopigments", - "examples": [ - { - "value": "2.5 milligram per cubic meter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "phaeopigments" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000180", - "multivalued": false, - "range": "string" - }, - "phosphate": { - "name": "phosphate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of phosphate", - "title": "phosphate", - "examples": [ - { - "value": "0.7 micromole per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "phosphate" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000505", - "multivalued": false, - "range": "string" - }, - "phosplipid_fatt_acid": { - "name": "phosplipid_fatt_acid", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "phospholipid fatty acid name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mole per gram, mole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Concentration of phospholipid fatty acids; can include multiple values", - "title": "phospholipid fatty acid", - "examples": [ - { - "value": "2.98 milligram per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "phospholipid fatty acid" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000181", - "multivalued": false, - "range": "string" - }, - "photon_flux": { - "name": "photon_flux", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "number of photons per second per unit area" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of photon flux", - "title": "photon flux", - "examples": [ - { - "value": "3.926 micromole photons per second per square meter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "photon flux" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000725", - "multivalued": false, - "range": "string" - }, - "plant_growth_med": { - "name": "plant_growth_med", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "EO or enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary", - "title": "plant growth medium", - "examples": [ - { - "value": "hydroponic plant culture media [EO:0007067]" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "plant growth medium" - ], - "is_a": "core field", - "slot_uri": "MIXS:0001057", - "multivalued": false, - "range": "string" - }, - "plant_product": { - "name": "plant_product", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "product name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Substance produced by the plant, where the sample was obtained from", - "title": "plant product", - "examples": [ - { - "value": "xylem sap [PO:0025539]" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "plant product" - ], - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0001058", - "multivalued": false, - "range": "string" - }, - "plant_sex": { - "name": "plant_sex", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite.", - "title": "plant sex", - "examples": [ - { - "value": "Hermaphroditic" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "plant sex" - ], - "is_a": "core field", - "slot_uri": "MIXS:0001059", - "multivalued": false, - "range": "plant_sex_enum" - }, - "plant_struc": { - "name": "plant_struc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PO" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here.", - "title": "plant structure", - "examples": [ - { - "value": "epidermis [PO:0005679]" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "plant structure" - ], - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0001060", - "multivalued": false, - "range": "string" - }, - "pollutants": { - "name": "pollutants", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "pollutant name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, mole per liter, milligram per liter, microgram per cubic meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant", - "title": "pollutants", - "examples": [ - { - "value": "lead;0.15 microgram per cubic meter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "pollutants" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000107", - "multivalued": false, - "range": "string" - }, - "porosity": { - "name": "porosity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value or range" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "percentage" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Porosity of deposited sediment is volume of voids divided by the total volume of sample", - "title": "porosity", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "porosity" - ], - "is_a": "core field", - "string_serialization": "{float} - {float} {unit}", - "slot_uri": "MIXS:0000211", - "multivalued": false, - "range": "string" - }, - "potassium": { - "name": "potassium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of potassium in the sample", - "title": "potassium", - "examples": [ - { - "value": "463 milligram per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "potassium" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000430", - "multivalued": false, - "range": "string" - }, - "pour_point": { - "name": "pour_point", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)", - "title": "pour point", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "pour point" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000127", - "multivalued": false, - "range": "string" - }, - "pre_treatment": { - "name": "pre_treatment", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "pre-treatment type" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The process of pre-treatment removes materials that can be easily collected from the raw wastewater", - "title": "pre-treatment", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "pre-treatment" - ], - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000348", - "multivalued": false, - "range": "string" - }, - "pres_animal_insect": { - "name": "pres_animal_insect", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration;count" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type and number of animals or insects present in the sampling space.", - "title": "presence of pets, animals, or insects", - "examples": [ - { - "value": "cat;5" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "presence of pets, animals, or insects" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000819", - "multivalued": false, - "range": "string", - "pattern": "^(cat|dog|rodent|snake|other);\\d+$" - }, - "pressure": { - "name": "pressure", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "atmosphere" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Pressure to which the sample is subject to, in atmospheres", - "title": "pressure", - "examples": [ - { - "value": "50 atmosphere" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "pressure" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000412", - "multivalued": false, - "range": "string" - }, - "prev_land_use_meth": { - "name": "prev_land_use_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining previous land use and dates", - "title": "history/previous land use method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "history/previous land use method" - ], - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000316", - "multivalued": false, - "range": "string" - }, - "previous_land_use": { - "name": "previous_land_use", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "land use name;date" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Previous land use and dates", - "title": "history/previous land use", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "history/previous land use" - ], - "is_a": "core field", - "string_serialization": "{text};{timestamp}", - "slot_uri": "MIXS:0000315", - "multivalued": false, - "range": "string" - }, - "primary_prod": { - "name": "primary_prod", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per cubic meter per day, gram per square meter per day" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of primary production, generally measured as isotope uptake", - "title": "primary production", - "examples": [ - { - "value": "100 milligram per cubic meter per day" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "primary production" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000728", - "multivalued": false, - "range": "string" - }, - "primary_treatment": { - "name": "primary_treatment", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "primary treatment type" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed", - "title": "primary treatment", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "primary treatment" - ], - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000349", - "multivalued": false, - "range": "string" - }, - "prod_rate": { - "name": "prod_rate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "cubic meter per day" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Oil and/or gas production rates per well (e.g. 524 m3 / day)", - "title": "production rate", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "production rate" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000452", - "multivalued": false, - "range": "string" - }, - "prod_start_date": { - "name": "prod_start_date", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Date of field's first production", - "title": "production start date", - "examples": [ - { - "value": "2018-05-11" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "production start date" - ], - "is_a": "core field", - "slot_uri": "MIXS:0001008", - "multivalued": false, - "range": "string" - }, - "profile_position": { - "name": "profile_position", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas", - "title": "profile position", - "examples": [ - { - "value": "summit" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "profile position" - ], - "is_a": "core field", - "slot_uri": "MIXS:0001084", - "multivalued": false, - "range": "profile_position_enum" - }, - "project_id": { - "name": "project_id", - "description": "Proposal IDs or names associated with dataset", - "title": "project ID", - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 1, - "string_serialization": "{text}", - "slot_group": "EMSL", - "recommended": true - }, - "proposal_dna": { - "name": "proposal_dna", - "title": "DNA proposal ID", - "comments": [ - "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." - ], - "examples": [ - { - "value": "504000" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 19, - "string_serialization": "{text}", - "slot_group": "JGI-Metagenomics", - "recommended": true - }, - "proposal_rna": { - "name": "proposal_rna", - "title": "RNA proposal ID", - "comments": [ - "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." - ], - "examples": [ - { - "value": "504000" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 19, - "string_serialization": "{text}", - "slot_group": "JGI-Metatranscriptomics", - "recommended": true - }, - "quad_pos": { - "name": "quad_pos", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The quadrant position of the sampling room within the building", - "title": "quadrant position", - "examples": [ - { - "value": "West side" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "quadrant position" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000820", - "multivalued": false, - "range": "quad_pos_enum" - }, - "radiation_regm": { - "name": "radiation_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "radiation type name;radiation amount;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "rad, gray" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens", - "title": "radiation regimen", - "examples": [ - { - "value": "gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "radiation regimen" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000575", - "multivalued": false, - "range": "string" - }, - "rainfall_regm": { - "name": "rainfall_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millimeter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", - "title": "rainfall regimen", - "examples": [ - { - "value": "15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "rainfall regimen" - ], - "is_a": "core field", - "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000576", - "multivalued": false, - "range": "string" - }, - "reactor_type": { - "name": "reactor_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "reactor type name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage", - "title": "reactor type", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "reactor type" - ], - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000350", - "multivalued": false, - "range": "string" - }, - "redox_potential": { - "name": "redox_potential", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millivolt" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential", - "title": "redox potential", - "examples": [ - { - "value": "300 millivolt" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "redox potential" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000182", - "multivalued": false, - "range": "string" - }, - "rel_air_humidity": { - "name": "rel_air_humidity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "percentage" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air", - "title": "relative air humidity", - "examples": [ - { - "value": "80%" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "relative air humidity" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000121", - "multivalued": false, - "range": "string" - }, - "rel_humidity_out": { - "name": "rel_humidity_out", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram of air, kilogram of air" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The recorded outside relative humidity value at the time of sampling", - "title": "outside relative humidity", - "examples": [ - { - "value": "12 per kilogram of air" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "outside relative humidity" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000188", - "multivalued": false, - "range": "string" - }, - "rel_samp_loc": { - "name": "rel_samp_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The sampling location within the train car", - "title": "relative sampling location", - "examples": [ - { - "value": "center of car" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "relative sampling location" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000821", - "multivalued": false, - "range": "rel_samp_loc_enum" - }, - "replicate_number": { - "name": "replicate_number", - "description": "If sending biological replicates, indicate the rep number here.", - "title": "replicate number", - "comments": [ - "This will guide staff in ensuring your samples are blocked & randomized correctly" - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 6, - "string_serialization": "{integer}", - "slot_group": "EMSL", - "recommended": true - }, - "reservoir": { - "name": "reservoir", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Name of the reservoir (e.g. Carapebus)", - "title": "reservoir name", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "reservoir name" - ], - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000303", - "multivalued": false, - "range": "string" - }, - "resins_pc": { - "name": "resins_pc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "percent" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", - "title": "resins wt%", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "resins wt%" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000134", - "multivalued": false, - "range": "string" - }, - "rna_absorb1": { - "name": "rna_absorb1", - "description": "260/280 measurement of RNA sample purity", - "title": "RNA absorbance 260/280", - "comments": [ - "Recommended value is between 1 and 3." - ], - "examples": [ - { - "value": "2.02" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 7, - "is_a": "biomaterial_purity", - "string_serialization": "{float}", - "slot_group": "JGI-Metatranscriptomics", - "range": "float", - "recommended": true - }, - "rna_absorb2": { - "name": "rna_absorb2", - "description": "260/230 measurement of RNA sample purity", - "title": "RNA absorbance 260/230", - "comments": [ - "Recommended value is between 1 and 3." - ], - "examples": [ - { - "value": "2.02" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 8, - "is_a": "biomaterial_purity", - "string_serialization": "{float}", - "slot_group": "JGI-Metatranscriptomics", - "range": "float", - "recommended": true - }, - "rna_concentration": { - "name": "rna_concentration", - "title": "RNA concentration in ng/ul", - "comments": [ - "Units must be in ng/uL. Enter the numerical part only. Must be calculated using a fluorometric method. Acceptable values are 0-2000." - ], - "examples": [ - { - "value": "100" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "see_also": [ - "nmdc:nucleic_acid_concentration" - ], - "rank": 5, - "string_serialization": "{float}", - "slot_group": "JGI-Metatranscriptomics", - "range": "float", - "recommended": true, - "minimum_value": 0, - "maximum_value": 1000 - }, - "rna_cont_type": { - "name": "rna_cont_type", - "description": "Tube or plate (96-well)", - "title": "RNA container type", - "examples": [ - { - "value": "plate" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 10, - "slot_group": "JGI-Metatranscriptomics", - "range": "JgiContTypeEnum", - "recommended": true - }, - "rna_cont_well": { - "name": "rna_cont_well", - "title": "RNA plate position", - "comments": [ - "Required when 'plate' is selected for container type.", - "Leave blank if the sample will be shipped in a tube.", - "JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass validation.", - "For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8)." - ], - "examples": [ - { - "value": "B2" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 11, - "string_serialization": "{96 well plate pos}", - "slot_group": "JGI-Metatranscriptomics", - "recommended": true, - "pattern": "^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$" - }, - "rna_container_id": { - "name": "rna_container_id", - "title": "RNA container label", - "comments": [ - "Must be unique across all tubes and plates, and <20 characters. All samples in a plate should have the same plate label." - ], - "examples": [ - { - "value": "Pond_MT_041618" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 9, - "string_serialization": "{text < 20 characters}", - "slot_group": "JGI-Metatranscriptomics", - "recommended": true - }, - "rna_isolate_meth": { - "name": "rna_isolate_meth", - "description": "Describe the method/protocol/kit used to extract DNA/RNA.", - "title": "RNA isolation method", - "examples": [ - { - "value": "phenol/chloroform extraction" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 16, - "string_serialization": "{text}", - "slot_group": "JGI-Metatranscriptomics", - "recommended": true - }, - "rna_project_contact": { - "name": "rna_project_contact", - "title": "RNA seq project contact", - "comments": [ - "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." - ], - "examples": [ - { - "value": "John Jones" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 18, - "string_serialization": "{text}", - "slot_group": "JGI-Metatranscriptomics", - "recommended": true - }, - "rna_samp_id": { - "name": "rna_samp_id", - "title": "RNA sample ID", - "comments": [ - "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." - ], - "examples": [ - { - "value": "187654" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 3, - "string_serialization": "{text}", - "slot_group": "JGI-Metatranscriptomics", - "recommended": true - }, - "rna_sample_format": { - "name": "rna_sample_format", - "description": "Solution in which the RNA sample has been suspended", - "title": "RNA sample format", - "examples": [ - { - "value": "Water" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 12, - "slot_group": "JGI-Metatranscriptomics", - "range": "rna_sample_format_enum", - "recommended": true - }, - "rna_sample_name": { - "name": "rna_sample_name", - "description": "Give the RNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", - "title": "RNA sample name", - "examples": [ - { - "value": "JGI_pond_041618" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 4, - "string_serialization": "{text}", - "slot_group": "JGI-Metatranscriptomics", - "recommended": true, - "minimum_value": 0, - "maximum_value": 2000 - }, - "rna_seq_project": { - "name": "rna_seq_project", - "title": "RNA seq project ID", - "comments": [ - "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." - ], - "examples": [ - { - "value": "1191234" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 1, - "string_serialization": "{text}", - "slot_group": "JGI-Metatranscriptomics", - "recommended": true - }, - "rna_seq_project_name": { - "name": "rna_seq_project_name", - "title": "RNA seq project name", - "comments": [ - "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." - ], - "examples": [ - { - "value": "JGI Pond metatranscriptomics" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 2, - "string_serialization": "{text}", - "slot_group": "JGI-Metatranscriptomics", - "recommended": true - }, - "rna_seq_project_pi": { - "name": "rna_seq_project_pi", - "title": "RNA seq project PI", - "comments": [ - "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." - ], - "examples": [ - { - "value": "Jane Johnson" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 17, - "string_serialization": "{text}", - "slot_group": "JGI-Metatranscriptomics", - "recommended": true - }, - "rna_volume": { - "name": "rna_volume", - "title": "RNA volume in ul", - "comments": [ - "Units must be in uL. Enter the numerical part only. Value must be 0-1000. This form accepts values < 25, but JGI may refuse to process them unless permission has been granted by a project manager" - ], - "examples": [ - { - "value": "25" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 6, - "string_serialization": "{float}", - "slot_group": "JGI-Metatranscriptomics", - "range": "float", - "recommended": true, - "minimum_value": 0, - "maximum_value": 1000 - }, - "room_air_exch_rate": { - "name": "room_air_exch_rate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "liter per hour" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The rate at which outside air replaces indoor air in a given space", - "title": "room air exchange rate", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "room air exchange rate" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000169", - "multivalued": false, - "range": "string" - }, - "room_architec_elem": { - "name": "room_architec_elem", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "free text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure", - "title": "room architectural elements", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "room architectural elements" - ], - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000233", - "multivalued": false, - "range": "string" - }, - "room_condt": { - "name": "room_condt", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The condition of the room at the time of sampling", - "title": "room condition", - "examples": [ - { - "value": "new" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "room condition" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000822", - "multivalued": false, - "range": "room_condt_enum" - }, - "room_connected": { - "name": "room_connected", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "List of rooms connected to the sampling room by a doorway", - "title": "rooms connected by a doorway", - "examples": [ - { - "value": "office" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "rooms connected by a doorway" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000826", - "multivalued": false, - "range": "room_connected_enum" - }, - "room_count": { - "name": "room_count", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The total count of rooms in the built structure including all room types", - "title": "room count", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "room count" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000234", - "multivalued": false, - "range": "string" - }, - "room_dim": { - "name": "room_dim", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The length, width and height of sampling room", - "title": "room dimensions", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "room dimensions" - ], - "is_a": "core field", - "string_serialization": "{integer} {unit} x {integer} {unit} x {integer} {unit}", - "slot_uri": "MIXS:0000192", - "multivalued": false, - "range": "string" - }, - "room_door_dist": { - "name": "room_door_dist", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Distance between doors (meters) in the hallway between the sampling room and adjacent rooms", - "title": "room door distance", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "room door distance" - ], - "is_a": "core field", - "string_serialization": "{integer} {unit}", - "slot_uri": "MIXS:0000193", - "multivalued": false, - "range": "string" - }, - "room_door_share": { - "name": "room_door_share", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "room name;room number" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "List of room(s) (room number, room name) sharing a door with the sampling room", - "title": "rooms that share a door with sampling room", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "rooms that share a door with sampling room" - ], - "is_a": "core field", - "string_serialization": "{text};{integer}", - "slot_uri": "MIXS:0000242", - "multivalued": false, - "range": "string" - }, - "room_hallway": { - "name": "room_hallway", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "room name;room number" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "List of room(s) (room number, room name) located in the same hallway as sampling room", - "title": "rooms that are on the same hallway", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "rooms that are on the same hallway" - ], - "is_a": "core field", - "string_serialization": "{text};{integer}", - "slot_uri": "MIXS:0000238", - "multivalued": false, - "range": "string" - }, - "room_loc": { - "name": "room_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The position of the room within the building", - "title": "room location in building", - "examples": [ - { - "value": "interior room" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "room location in building" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000823", - "multivalued": false, - "range": "room_loc_enum" - }, - "room_moist_dam_hist": { - "name": "room_moist_dam_hist", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed", - "title": "room moisture damage or mold history", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "room moisture damage or mold history" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000235", - "multivalued": false, - "range": "integer" - }, - "room_net_area": { - "name": "room_net_area", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "square feet, square meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The net floor area of sampling room. Net area excludes wall thicknesses", - "title": "room net area", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "room net area" - ], - "is_a": "core field", - "string_serialization": "{integer} {unit}", - "slot_uri": "MIXS:0000194", - "multivalued": false, - "range": "string" - }, - "room_occup": { - "name": "room_occup", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Count of room occupancy at time of sampling", - "title": "room occupancy", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "room occupancy" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000236", - "multivalued": false, - "range": "string" - }, - "room_samp_pos": { - "name": "room_samp_pos", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The horizontal sampling position in the room relative to architectural elements", - "title": "room sampling position", - "examples": [ - { - "value": "south corner" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "room sampling position" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000824", - "multivalued": false, - "range": "room_samp_pos_enum" - }, - "room_type": { - "name": "room_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The main purpose or activity of the sampling room. A room is any distinguishable space within a structure", - "title": "room type", - "examples": [ - { - "value": "bathroom" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "room type" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000825", - "multivalued": false, - "range": "room_type_enum" - }, - "room_vol": { - "name": "room_vol", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "cubic feet, cubic meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Volume of sampling room", - "title": "room volume", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "room volume" - ], - "is_a": "core field", - "string_serialization": "{integer} {unit}", - "slot_uri": "MIXS:0000195", - "multivalued": false, - "range": "string" - }, - "room_wall_share": { - "name": "room_wall_share", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "room name;room number" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "List of room(s) (room number, room name) sharing a wall with the sampling room", - "title": "rooms that share a wall with sampling room", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "rooms that share a wall with sampling room" - ], - "is_a": "core field", - "string_serialization": "{text};{integer}", - "slot_uri": "MIXS:0000243", - "multivalued": false, - "range": "string" - }, - "room_window_count": { - "name": "room_window_count", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Number of windows in the room", - "title": "room window count", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "room window count" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000237", - "multivalued": false, - "range": "integer" - }, - "root_cond": { - "name": "root_cond", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI,url or free text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container.", - "title": "rooting conditions", - "examples": [ - { - "value": "http://himedialabs.com/TD/PT158.pdf" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "rooting conditions" - ], - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}|{text}", - "slot_uri": "MIXS:0001061", - "multivalued": false, - "range": "string" - }, - "root_med_carbon": { - "name": "root_med_carbon", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "carbon source name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Source of organic carbon in the culture rooting medium; e.g. sucrose.", - "title": "rooting medium carbon", - "examples": [ - { - "value": "sucrose" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "rooting medium carbon" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000577", - "multivalued": false, - "range": "string" - }, - "root_med_macronutr": { - "name": "root_med_macronutr", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "macronutrient name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L).", - "title": "rooting medium macronutrients", - "examples": [ - { - "value": "KH2PO4;170¬†milligram per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "rooting medium macronutrients" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000578", - "multivalued": false, - "range": "string" - }, - "root_med_micronutr": { - "name": "root_med_micronutr", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "micronutrient name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L).", - "title": "rooting medium micronutrients", - "examples": [ - { - "value": "H3BO3;6.2¬†milligram per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "rooting medium micronutrients" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000579", - "multivalued": false, - "range": "string" - }, - "root_med_ph": { - "name": "root_med_ph", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "pH measurement of the culture rooting medium; e.g. 5.5.", - "title": "rooting medium pH", - "examples": [ - { - "value": "7.5" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "rooting medium pH" - ], - "is_a": "core field", - "slot_uri": "MIXS:0001062", - "multivalued": false, - "range": "string" - }, - "root_med_regl": { - "name": "root_med_regl", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "regulator name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA.", - "title": "rooting medium regulators", - "examples": [ - { - "value": "abscisic acid;0.75 milligram per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "rooting medium regulators" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000581", - "multivalued": false, - "range": "string" - }, - "root_med_solid": { - "name": "root_med_solid", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Specification of the solidifying agent in the culture rooting medium; e.g. agar.", - "title": "rooting medium solidifier", - "examples": [ - { - "value": "agar" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "rooting medium solidifier" - ], - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0001063", - "multivalued": false, - "range": "string" - }, - "root_med_suppl": { - "name": "root_med_suppl", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "supplement name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L).", - "title": "rooting medium organic supplements", - "examples": [ - { - "value": "nicotinic acid;0.5 milligram per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "rooting medium organic supplements" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000580", - "multivalued": false, - "range": "string" - }, - "salinity": { - "name": "salinity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "practical salinity unit, percentage" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", - "title": "salinity", - "examples": [ - { - "value": "25 practical salinity unit" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "salinity" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000183", - "multivalued": false, - "range": "string" - }, - "salinity_meth": { - "name": "salinity_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining salinity", - "title": "salinity method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "salinity method" - ], - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000341", - "multivalued": false, - "range": "string" - }, - "salt_regm": { - "name": "salt_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "salt name;salt amount;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, microgram, mole per liter, gram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens", - "title": "salt regimen", - "examples": [ - { - "value": "NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "salt regimen" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000582", - "multivalued": false, - "range": "string" - }, - "samp_capt_status": { - "name": "samp_capt_status", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reason for the sample", - "title": "sample capture status", - "examples": [ - { - "value": "farm sample" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "sample capture status" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000860", - "multivalued": false, - "range": "samp_capt_status_enum" - }, - "samp_collec_device": { - "name": "samp_collec_device", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "device name" - } - }, - "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", - "title": "sample collection device", - "examples": [ - { - "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "sample collection device" - ], - "is_a": "nucleic acid sequence source field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000002", - "multivalued": false, - "range": "string" - }, - "samp_collec_method": { - "name": "samp_collec_method", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI,url , or text" - } - }, - "description": "The method employed for collecting the sample.", - "title": "sample collection method", - "examples": [ - { - "value": "swabbing" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "sample collection method" - ], - "is_a": "nucleic acid sequence source field", - "string_serialization": "{PMID}|{DOI}|{URL}|{text}", - "slot_uri": "MIXS:0001225", - "multivalued": false, - "range": "string" - }, - "samp_collect_point": { - "name": "samp_collect_point", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "sample collection point", - "examples": [ - { - "value": "well" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "sample collection point" - ], - "is_a": "core field", - "slot_uri": "MIXS:0001015", - "multivalued": false, - "range": "samp_collect_point_enum" - }, - "samp_dis_stage": { - "name": "samp_dis_stage", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen.", - "title": "sample disease stage", - "examples": [ - { - "value": "infection" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "sample disease stage" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000249", - "multivalued": false, - "range": "samp_dis_stage_enum" - }, - "samp_floor": { - "name": "samp_floor", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The floor of the building, where the sampling room is located", - "title": "sampling floor", - "examples": [ - { - "value": "4th floor" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "sampling floor" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000828", - "multivalued": false, - "range": "samp_floor_enum" - }, - "samp_loc_corr_rate": { - "name": "samp_loc_corr_rate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value range" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millimeter per year" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays", - "title": "corrosion rate at sample location", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "corrosion rate at sample location" - ], - "is_a": "core field", - "string_serialization": "{float} - {float} {unit}", - "slot_uri": "MIXS:0000136", - "multivalued": false, - "range": "string" - }, - "samp_mat_process": { - "name": "samp_mat_process", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - } - }, - "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", - "title": "sample material processing", - "examples": [ - { - "value": "filtering of seawater, storing samples in ethanol" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "sample material processing" - ], - "is_a": "nucleic acid sequence source field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000016", - "multivalued": false, - "range": "string" - }, - "samp_md": { - "name": "samp_md", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value;enumeration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "sample measured depth", - "examples": [ - { - "value": "1534 meter;MSL" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "sample measured depth" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000413", - "multivalued": false, - "range": "string" - }, - "samp_name": { - "name": "samp_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - } - }, - "description": "A local identifier or name that for the material sample used for extracting nucleic acids, and subsequent sequencing. It can refer either to the original material collected or to any derived sub-samples. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. INSDC requires every sample name from a single Submitter to be unique. Use of a globally unique identifier for the field source_mat_id is recommended in addition to sample_name.", - "title": "sample name", - "examples": [ - { - "value": "ISDsoil1" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "sample name" - ], - "is_a": "investigation field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0001107", - "multivalued": false, - "range": "string" - }, - "samp_preserv": { - "name": "samp_preserv", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milliliter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml)", - "title": "preservative added to sample", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "preservative added to sample" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000463", - "multivalued": false, - "range": "string" - }, - "samp_room_id": { - "name": "samp_room_id", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Sampling room number. This ID should be consistent with the designations on the building floor plans", - "title": "sampling room ID or name", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "sampling room ID or name" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000244", - "multivalued": false, - "range": "string" - }, - "samp_size": { - "name": "samp_size", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millliter, gram, milligram, liter" - } - }, - "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", - "title": "amount or size of sample collected", - "examples": [ - { - "value": "5 liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "amount or size of sample collected" - ], - "is_a": "nucleic acid sequence source field", - "slot_uri": "MIXS:0000001", - "multivalued": false, - "range": "string" - }, - "samp_sort_meth": { - "name": "samp_sort_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "description of method" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor.", - "title": "sample size sorting method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "sample size sorting method" - ], - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000216", - "multivalued": false, - "range": "string" - }, - "samp_store_dur": { - "name": "samp_store_dur", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Duration for which the sample was stored", - "title": "sample storage duration", - "examples": [ - { - "value": "P1Y6M" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "sample storage duration" - ], - "is_a": "core field", - "string_serialization": "{duration}", - "slot_uri": "MIXS:0000116", - "multivalued": false, - "range": "string" - }, - "samp_store_loc": { - "name": "samp_store_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "location name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Location at which sample was stored, usually name of a specific freezer/room", - "title": "sample storage location", - "examples": [ - { - "value": "Freezer no:5" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "sample storage location" - ], - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000755", - "multivalued": false, - "range": "string" - }, - "samp_store_temp": { - "name": "samp_store_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Temperature at which sample was stored, e.g. -80 degree Celsius", - "title": "sample storage temperature", - "examples": [ - { - "value": "-80 degree Celsius" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "sample storage temperature" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000110", - "multivalued": false, - "range": "string" - }, - "samp_subtype": { - "name": "samp_subtype", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Name of sample sub-type. For example if \"sample type\" is \"Produced Water\" then subtype could be \"Oil Phase\" or \"Water Phase\". If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "sample subtype", - "examples": [ - { - "value": "biofilm" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "sample subtype" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000999", - "multivalued": false, - "range": "samp_subtype_enum" - }, - "samp_time_out": { - "name": "samp_time_out", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "time" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "hour" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The recent and long term history of outside sampling", - "title": "sampling time outside", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "sampling time outside" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000196", - "multivalued": false, - "range": "string" - }, - "samp_transport_cond": { - "name": "samp_transport_cond", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "days;degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C)", - "title": "sample transport conditions", - "examples": [ - { - "value": "5 days;-20 degree Celsius" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "sample transport conditions" - ], - "is_a": "core field", - "string_serialization": "{float} {unit};{float} {unit}", - "slot_uri": "MIXS:0000410", - "multivalued": false, - "range": "string" - }, - "samp_tvdss": { - "name": "samp_tvdss", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value or measurement value range" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m", - "title": "sample true vertical depth subsea", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "sample true vertical depth subsea" - ], - "is_a": "core field", - "string_serialization": "{float}-{float} {unit}", - "slot_uri": "MIXS:0000409", - "multivalued": false, - "range": "string" - }, - "samp_type": { - "name": "samp_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "GENEPIO:0001246" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of material from which the sample was obtained. For the Hydrocarbon package, samples include types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. For the Food Package, samples are usually categorized as food, body products or tissues, or environmental material. This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246).", - "title": "sample type", - "examples": [ - { - "value": "built environment sample [GENEPIO:0001248]" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "sample type" - ], - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000998", - "multivalued": false, - "range": "string" - }, - "samp_weather": { - "name": "samp_weather", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The weather on the sampling day", - "title": "sampling day weather", - "examples": [ - { - "value": "foggy" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "sampling day weather" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000827", - "multivalued": false, - "range": "samp_weather_enum" - }, - "samp_well_name": { - "name": "samp_well_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Name of the well (e.g. BXA1123) where sample was taken", - "title": "sample well name", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "sample well name" - ], - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000296", - "multivalued": false, - "range": "string" - }, - "sample_link": { - "name": "sample_link", - "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", - "title": "sample linkage", - "comments": [ - "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" - ], - "examples": [ - { - "value": "IGSN:DSJ0284" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 5, - "string_serialization": "{text}:{text}", - "multivalued": false, - "slot_group": "Sample ID", - "range": "string", - "recommended": true - }, - "sample_shipped": { - "name": "sample_shipped", - "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent to EMSL.", - "title": "sample shipped amount", - "comments": [ - "This field is only required when completing metadata for samples being submitted to EMSL for analyses." - ], - "examples": [ - { - "value": "15 g" - }, - { - "value": "100 uL" - }, - { - "value": "5 mL" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 3, - "string_serialization": "{float} {unit}", - "slot_group": "EMSL", - "recommended": true - }, - "sample_type": { - "name": "sample_type", - "description": "Type of sample being submitted", - "title": "sample type", - "comments": [ - "This can vary from 'environmental package' if the sample is an extraction." - ], - "examples": [ - { - "value": "water extracted soil" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 2, - "slot_group": "EMSL", - "range": "sample_type_enum", - "recommended": true - }, - "saturates_pc": { - "name": "saturates_pc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "percent" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", - "title": "saturates wt%", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "saturates wt%" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000131", - "multivalued": false, - "range": "string" - }, - "season": { - "name": "season", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "NCIT:C94729" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729).", - "title": "season", - "examples": [ - { - "value": "autumn [NCIT:C94733]" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "season" - ], - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000829", - "multivalued": false, - "range": "string" - }, - "season_environment": { - "name": "season_environment", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "seasonal environment name;treatment interval and duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment", - "title": "seasonal environment", - "examples": [ - { - "value": "rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "seasonal environment" - ], - "is_a": "core field", - "string_serialization": "{text};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0001068", - "multivalued": false, - "range": "string" - }, - "season_precpt": { - "name": "season_precpt", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millimeter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps.", - "title": "mean seasonal precipitation", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "mean seasonal precipitation" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000645", - "multivalued": false, - "range": "string" - }, - "season_temp": { - "name": "season_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Mean seasonal temperature", - "title": "mean seasonal temperature", - "examples": [ - { - "value": "18 degree Celsius" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "mean seasonal temperature" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000643", - "multivalued": false, - "range": "string" - }, - "season_use": { - "name": "season_use", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The seasons the space is occupied", - "title": "seasonal use", - "examples": [ - { - "value": "Winter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "seasonal use" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000830", - "multivalued": false, - "range": "season_use_enum" - }, - "secondary_treatment": { - "name": "secondary_treatment", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "secondary treatment type" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The process for substantially degrading the biological content of the sewage", - "title": "secondary treatment", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "secondary treatment" - ], - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000351", - "multivalued": false, - "range": "string" - }, - "sediment_type": { - "name": "sediment_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Information about the sediment type based on major constituents", - "title": "sediment type", - "examples": [ - { - "value": "biogenous" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "sediment type" - ], - "is_a": "core field", - "slot_uri": "MIXS:0001078", - "multivalued": false, - "range": "sediment_type_enum" - }, - "sewage_type": { - "name": "sewage_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "sewage type name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Type of wastewater treatment plant as municipial or industrial", - "title": "sewage type", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "sewage type" - ], - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000215", - "multivalued": false, - "range": "string" - }, - "shad_dev_water_mold": { - "name": "shad_dev_water_mold", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Signs of the presence of mold or mildew on the shading device", - "title": "shading device signs of water/mold", - "examples": [ - { - "value": "no presence of mold visible" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "shading device signs of water/mold" - ], - "is_a": "core field", - "string_serialization": "[presence of mold visible|no presence of mold visible]", - "slot_uri": "MIXS:0000834", - "multivalued": false, - "range": "string" - }, - "shading_device_cond": { - "name": "shading_device_cond", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The physical condition of the shading device at the time of sampling", - "title": "shading device condition", - "examples": [ - { - "value": "new" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "shading device condition" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000831", - "multivalued": false, - "range": "shading_device_cond_enum" - }, - "shading_device_loc": { - "name": "shading_device_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The location of the shading device in relation to the built structure", - "title": "shading device location", - "examples": [ - { - "value": "exterior" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "shading device location" - ], - "is_a": "core field", - "string_serialization": "[exterior|interior]", - "slot_uri": "MIXS:0000832", - "multivalued": false, - "range": "string" - }, - "shading_device_mat": { - "name": "shading_device_mat", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "material name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The material the shading device is composed of", - "title": "shading device material", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "shading device material" - ], - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000245", - "multivalued": false, - "range": "string" - }, - "shading_device_type": { - "name": "shading_device_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of shading device", - "title": "shading device type", - "examples": [ - { - "value": "slatted aluminum awning" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "shading device type" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000835", - "multivalued": false, - "range": "shading_device_type_enum" - }, - "sieving": { - "name": "sieving", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "design name and/or size;amount" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Collection design of pooled samples and/or sieve size and amount of sample sieved", - "title": "composite design/sieving", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "composite design/sieving" - ], - "is_a": "core field", - "string_serialization": "{{text}|{float} {unit}};{float} {unit}", - "slot_uri": "MIXS:0000322", - "multivalued": false, - "range": "string" - }, - "silicate": { - "name": "silicate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of silicate", - "title": "silicate", - "examples": [ - { - "value": "0.05 micromole per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "silicate" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000184", - "multivalued": false, - "range": "string" - }, - "size_frac": { - "name": "size_frac", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "filter size value range" - } - }, - "description": "Filtering pore size used in sample preparation", - "title": "size fraction selected", - "examples": [ - { - "value": "0-0.22 micrometer" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "size fraction selected" - ], - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float}-{float} {unit}", - "slot_uri": "MIXS:0000017", - "multivalued": false, - "range": "string" - }, - "size_frac_low": { - "name": "size_frac_low", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micrometer" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample", - "title": "size-fraction lower threshold", - "examples": [ - { - "value": "0.2 micrometer" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "size-fraction lower threshold" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000735", - "multivalued": false, - "range": "string" - }, - "size_frac_up": { - "name": "size_frac_up", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micrometer" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample", - "title": "size-fraction upper threshold", - "examples": [ - { - "value": "20 micrometer" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "size-fraction upper threshold" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000736", - "multivalued": false, - "range": "string" - }, - "slope_aspect": { - "name": "slope_aspect", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration.", - "title": "slope aspect", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "slope aspect" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000647", - "multivalued": false, - "range": "string" - }, - "slope_gradient": { - "name": "slope_gradient", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "percentage" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer", - "title": "slope gradient", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "slope gradient" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000646", - "multivalued": false, - "range": "string" - }, - "sludge_retent_time": { - "name": "sludge_retent_time", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "hours" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The time activated sludge remains in reactor", - "title": "sludge retention time", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "sludge retention time" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000669", - "multivalued": false, - "range": "string" - }, - "sodium": { - "name": "sodium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Sodium concentration in the sample", - "title": "sodium", - "examples": [ - { - "value": "10.5 milligram per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "sodium" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000428", - "multivalued": false, - "range": "string" - }, - "soil_horizon": { - "name": "soil_horizon", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath", - "title": "soil horizon", - "examples": [ - { - "value": "A horizon" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "soil horizon" - ], - "is_a": "core field", - "slot_uri": "MIXS:0001082", - "multivalued": false, - "range": "soil_horizon_enum" - }, - "soil_text_measure": { - "name": "soil_text_measure", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional.", - "title": "soil texture measurement", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "soil texture measurement" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000335", - "multivalued": false, - "range": "string" - }, - "soil_texture_meth": { - "name": "soil_texture_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining soil texture", - "title": "soil texture method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "soil texture method" - ], - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000336", - "multivalued": false, - "range": "string" - }, - "soil_type": { - "name": "soil_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "ENVO_00001998" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes.", - "title": "soil type", - "examples": [ - { - "value": "plinthosol [ENVO:00002250]" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "soil type" - ], - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000332", - "multivalued": false, - "range": "string" - }, - "soil_type_meth": { - "name": "soil_type_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining soil series name or other lower-level classification", - "title": "soil type method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "soil type method" - ], - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000334", - "multivalued": false, - "range": "string" - }, - "solar_irradiance": { - "name": "solar_irradiance", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "kilowatts per square meter per day, ergs per square centimeter per second" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The amount of solar energy that arrives at a specific area of a surface during a specific time interval", - "title": "solar irradiance", - "examples": [ - { - "value": "1.36 kilowatts per square meter per day" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "solar irradiance" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000112", - "multivalued": false, - "range": "string" - }, - "soluble_inorg_mat": { - "name": "soluble_inorg_mat", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "soluble inorganic material name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, microgram, mole per liter, gram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc.", - "title": "soluble inorganic material", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "soluble inorganic material" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000672", - "multivalued": false, - "range": "string" - }, - "soluble_org_mat": { - "name": "soluble_org_mat", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "soluble organic material name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, microgram, mole per liter, gram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc.", - "title": "soluble organic material", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "soluble organic material" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000673", - "multivalued": false, - "range": "string" - }, - "soluble_react_phosp": { - "name": "soluble_react_phosp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of soluble reactive phosphorus", - "title": "soluble reactive phosphorus", - "examples": [ - { - "value": "0.1 milligram per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "soluble reactive phosphorus" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000738", - "multivalued": false, - "range": "string" - }, - "source_mat_id": { - "name": "source_mat_id", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "for cultures of microorganisms: identifiers for two culture collections; for other material a unique arbitrary identifer" - } - }, - "description": "A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2).", - "title": "source material identifiers", - "examples": [ - { - "value": "MPI012345" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "source material identifiers" - ], - "is_a": "nucleic acid sequence source field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000026", - "multivalued": false, - "range": "string" - }, - "space_typ_state": { - "name": "space_typ_state", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Customary or normal state of the space", - "title": "space typical state", - "examples": [ - { - "value": "typically occupied" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "space typical state" - ], - "is_a": "core field", - "string_serialization": "[typically occupied|typically unoccupied]", - "slot_uri": "MIXS:0000770", - "multivalued": false, - "range": "string" - }, - "specific": { - "name": "specific", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents", - "title": "specifications", - "examples": [ - { - "value": "construction" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "specifications" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000836", - "multivalued": false, - "range": "specific_enum" - }, - "specific_ecosystem": { - "name": "specific_ecosystem", - "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", - "comments": [ - "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "is_a": "gold_path_field" - }, - "specific_humidity": { - "name": "specific_humidity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram of air, kilogram of air" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound.", - "title": "specific humidity", - "examples": [ - { - "value": "15 per kilogram of air" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "specific humidity" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000214", - "multivalued": false, - "range": "string" - }, - "sr_dep_env": { - "name": "sr_dep_env", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "source rock depositional environment", - "examples": [ - { - "value": "Marine" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "source rock depositional environment" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000996", - "multivalued": false, - "range": "sr_dep_env_enum" - }, - "sr_geol_age": { - "name": "sr_geol_age", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "source rock geological age", - "examples": [ - { - "value": "Silurian" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "source rock geological age" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000997", - "multivalued": false, - "range": "sr_geol_age_enum" - }, - "sr_kerog_type": { - "name": "sr_kerog_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "source rock kerogen type", - "examples": [ - { - "value": "Type IV" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "source rock kerogen type" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000994", - "multivalued": false, - "range": "sr_kerog_type_enum" - }, - "sr_lithology": { - "name": "sr_lithology", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "source rock lithology", - "examples": [ - { - "value": "Coal" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "source rock lithology" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000995", - "multivalued": false, - "range": "sr_lithology_enum" - }, - "standing_water_regm": { - "name": "standing_water_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "standing water type;treatment interval and duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", - "title": "standing water regimen", - "examples": [ - { - "value": "standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "standing water regimen" - ], - "is_a": "core field", - "string_serialization": "{text};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0001069", - "multivalued": false, - "range": "string" - }, - "start_date_inc": { - "name": "start_date_inc", - "description": "Date the incubation was started. Only relevant for incubation samples.", - "title": "incubation start date", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only" - ], - "comments": [ - "Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable." - ], - "examples": [ - { - "value": "2021-04-15, 2021-04 and 2021 are all acceptable." - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "see_also": [ - "MIxS:collection_date" - ], - "rank": 4, - "string_serialization": "{date, arbitrary precision}", - "slot_group": "MIxS Inspired", - "recommended": true - }, - "start_time_inc": { - "name": "start_time_inc", - "description": "Time the incubation was started. Only relevant for incubation samples.", - "title": "incubation start time, GMT", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" - ], - "comments": [ - "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" - ], - "examples": [ - { - "value": "13:33 or 13:33:55" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "see_also": [ - "MIxS:collection_date" - ], - "rank": 5, - "string_serialization": "{time, seconds optional}", - "slot_group": "MIxS Inspired", - "recommended": true - }, - "store_cond": { - "name": "store_cond", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "storage condition type;duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other).", - "title": "storage conditions", - "examples": [ - { - "value": "-20 degree Celsius freezer;P2Y10D" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "storage conditions" - ], - "is_a": "core field", - "string_serialization": "{text};{duration}", - "slot_uri": "MIXS:0000327", - "multivalued": false, - "range": "string" - }, - "substructure_type": { - "name": "substructure_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level", - "title": "substructure type", - "examples": [ - { - "value": "basement" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "substructure type" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000767", - "multivalued": true, - "range": "substructure_type_enum" - }, - "sulfate": { - "name": "sulfate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of sulfate in the sample", - "title": "sulfate", - "examples": [ - { - "value": "5 micromole per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "sulfate" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000423", - "multivalued": false, - "range": "string" - }, - "sulfate_fw": { - "name": "sulfate_fw", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Original sulfate concentration in the hydrocarbon resource", - "title": "sulfate in formation water", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "sulfate in formation water" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000407", - "multivalued": false, - "range": "string" - }, - "sulfide": { - "name": "sulfide", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of sulfide in the sample", - "title": "sulfide", - "examples": [ - { - "value": "2 micromole per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "sulfide" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000424", - "multivalued": false, - "range": "string" - }, - "surf_air_cont": { - "name": "surf_air_cont", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Contaminant identified on surface", - "title": "surface-air contaminant", - "examples": [ - { - "value": "radon" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "surface-air contaminant" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000759", - "multivalued": true, - "range": "surf_air_cont_enum" - }, - "surf_humidity": { - "name": "surf_humidity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "percentage" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Surfaces: water activity as a function of air and material moisture", - "title": "surface humidity", - "examples": [ - { - "value": "10%" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "surface humidity" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000123", - "multivalued": false, - "range": "string" - }, - "surf_material": { - "name": "surf_material", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Surface materials at the point of sampling", - "title": "surface material", - "examples": [ - { - "value": "wood" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "surface material" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000758", - "multivalued": false, - "range": "surf_material_enum" - }, - "surf_moisture": { - "name": "surf_moisture", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "parts per million, gram per cubic meter, gram per square meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Water held on a surface", - "title": "surface moisture", - "examples": [ - { - "value": "0.01 gram per square meter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "surface moisture" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000128", - "multivalued": false, - "range": "string" - }, - "surf_moisture_ph": { - "name": "surf_moisture_ph", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "ph measurement of surface", - "title": "surface moisture pH", - "examples": [ - { - "value": "7" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "surface moisture pH" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000760", - "multivalued": false, - "range": "double" - }, - "surf_temp": { - "name": "surf_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Temperature of the surface at the time of sampling", - "title": "surface temperature", - "examples": [ - { - "value": "15 degree Celsius" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "surface temperature" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000125", - "multivalued": false, - "range": "string" - }, - "suspend_part_matter": { - "name": "suspend_part_matter", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of suspended particulate matter", - "title": "suspended particulate matter", - "examples": [ - { - "value": "0.5 milligram per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "suspended particulate matter" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000741", - "multivalued": false, - "range": "string" - }, - "suspend_solids": { - "name": "suspend_solids", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "suspended solid name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, microgram, milligram per liter, mole per liter, gram per liter, part per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances", - "title": "suspended solids", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "suspended solids" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000150", - "multivalued": false, - "range": "string" - }, - "tan": { - "name": "tan", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)", - "title": "total acid number", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "total acid number" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000120", - "multivalued": false, - "range": "string" - }, - "technical_reps": { - "name": "technical_reps", - "description": "If sending technical replicates of the same sample, indicate the replicate count.", - "title": "number technical replicate", - "comments": [ - "This field is only required when completing metadata for samples being submitted to EMSL for analyses." - ], - "examples": [ - { - "value": "2" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 5, - "string_serialization": "{integer}", - "slot_group": "EMSL", - "recommended": true - }, - "temp": { - "name": "temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - } - }, - "description": "Temperature of the sample at the time of sampling.", - "title": "temperature", - "examples": [ - { - "value": "25 degree Celsius" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "temperature" - ], - "is_a": "environment field", - "slot_uri": "MIXS:0000113", - "multivalued": false, - "range": "string" - }, - "temp_out": { - "name": "temp_out", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The recorded temperature value at sampling time outside", - "title": "temperature outside house", - "examples": [ - { - "value": "5 degree Celsius" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "temperature outside house" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000197", - "multivalued": false, - "range": "string" - }, - "tertiary_treatment": { - "name": "tertiary_treatment", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "tertiary treatment type" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment", - "title": "tertiary treatment", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "tertiary treatment" - ], - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000352", - "multivalued": false, - "range": "string" - }, - "tidal_stage": { - "name": "tidal_stage", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Stage of tide", - "title": "tidal stage", - "examples": [ - { - "value": "high tide" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "tidal stage" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000750", - "multivalued": false, - "range": "tidal_stage_enum" - }, - "tillage": { - "name": "tillage", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Note method(s) used for tilling", - "title": "history/tillage", - "examples": [ - { - "value": "chisel" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "history/tillage" - ], - "is_a": "core field", - "slot_uri": "MIXS:0001081", - "multivalued": true, - "range": "tillage_enum" - }, - "tiss_cult_growth_med": { - "name": "tiss_cult_growth_med", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI,url or free text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Description of plant tissue culture growth media used", - "title": "tissue culture growth media", - "examples": [ - { - "value": "https://link.springer.com/content/pdf/10.1007/BF02796489.pdf" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "tissue culture growth media" - ], - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}|{text}", - "slot_uri": "MIXS:0001070", - "multivalued": false, - "range": "string" - }, - "toluene": { - "name": "toluene", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of toluene in the sample", - "title": "toluene", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "toluene" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000154", - "multivalued": false, - "range": "string" - }, - "tot_carb": { - "name": "tot_carb", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Total carbon content", - "title": "total carbon", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "total carbon" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000525", - "multivalued": false, - "range": "string" - }, - "tot_depth_water_col": { - "name": "tot_depth_water_col", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of total depth of water column", - "title": "total depth of water column", - "examples": [ - { - "value": "500 meter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "total depth of water column" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000634", - "multivalued": false, - "range": "string" - }, - "tot_diss_nitro": { - "name": "tot_diss_nitro", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen", - "title": "total dissolved nitrogen", - "examples": [ - { - "value": "40 microgram per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "total dissolved nitrogen" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000744", - "multivalued": false, - "range": "string" - }, - "tot_inorg_nitro": { - "name": "tot_inorg_nitro", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Total inorganic nitrogen content", - "title": "total inorganic nitrogen", - "examples": [ - { - "value": "40 microgram per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "total inorganic nitrogen" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000745", - "multivalued": false, - "range": "string" - }, - "tot_iron": { - "name": "tot_iron", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, milligram per kilogram" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of total iron in the sample", - "title": "total iron", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "total iron" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000105", - "multivalued": false, - "range": "string" - }, - "tot_nitro": { - "name": "tot_nitro", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter, micromole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen", - "title": "total nitrogen concentration", - "examples": [ - { - "value": "50 micromole per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "total nitrogen concentration" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000102", - "multivalued": false, - "range": "string" - }, - "tot_nitro_cont_meth": { - "name": "tot_nitro_cont_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining the total nitrogen", - "title": "total nitrogen content method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "total nitrogen content method" - ], - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000338", - "multivalued": false, - "range": "string" - }, - "tot_nitro_content": { - "name": "tot_nitro_content", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter, micromole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Total nitrogen content of the sample", - "title": "total nitrogen content", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "total nitrogen content" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000530", - "multivalued": false, - "range": "string" - }, - "tot_org_c_meth": { - "name": "tot_org_c_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining total organic carbon", - "title": "total organic carbon method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "total organic carbon method" - ], - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000337", - "multivalued": false, - "range": "string" - }, - "tot_org_carb": { - "name": "tot_org_carb", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram Carbon per kilogram sample material" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content", - "title": "total organic carbon", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "total organic carbon" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000533", - "multivalued": false, - "range": "string" - }, - "tot_part_carb": { - "name": "tot_part_carb", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter, micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Total particulate carbon content", - "title": "total particulate carbon", - "examples": [ - { - "value": "35 micromole per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "total particulate carbon" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000747", - "multivalued": false, - "range": "string" - }, - "tot_phosp": { - "name": "tot_phosp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus", - "title": "total phosphorus", - "examples": [ - { - "value": "0.03 milligram per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "total phosphorus" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000117", - "multivalued": false, - "range": "string" - }, - "tot_phosphate": { - "name": "tot_phosphate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter, micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Total amount or concentration of phosphate", - "title": "total phosphate", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "total phosphate" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000689", - "multivalued": false, - "range": "string" - }, - "tot_sulfur": { - "name": "tot_sulfur", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of total sulfur in the sample", - "title": "total sulfur", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "total sulfur" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000419", - "multivalued": false, - "range": "string" - }, - "train_line": { - "name": "train_line", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The subway line name", - "title": "train line", - "examples": [ - { - "value": "red" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "train line" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000837", - "multivalued": false, - "range": "train_line_enum" - }, - "train_stat_loc": { - "name": "train_stat_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The train station collection location", - "title": "train station collection location", - "examples": [ - { - "value": "forest hills" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "train station collection location" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000838", - "multivalued": false, - "range": "train_stat_loc_enum" - }, - "train_stop_loc": { - "name": "train_stop_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The train stop collection location", - "title": "train stop collection location", - "examples": [ - { - "value": "end" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "train stop collection location" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000839", - "multivalued": false, - "range": "train_stop_loc_enum" - }, - "turbidity": { - "name": "turbidity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "formazin turbidity unit, formazin nephelometric units" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measure of the amount of cloudiness or haziness in water caused by individual particles", - "title": "turbidity", - "examples": [ - { - "value": "0.3 nephelometric turbidity units" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "turbidity" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000191", - "multivalued": false, - "range": "string" - }, - "tvdss_of_hcr_press": { - "name": "tvdss_of_hcr_press", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m).", - "title": "depth (TVDSS) of hydrocarbon resource pressure", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "depth (TVDSS) of hydrocarbon resource pressure" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000397", - "multivalued": false, - "range": "string" - }, - "tvdss_of_hcr_temp": { - "name": "tvdss_of_hcr_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m).", - "title": "depth (TVDSS) of hydrocarbon resource temperature", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "depth (TVDSS) of hydrocarbon resource temperature" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000394", - "multivalued": false, - "range": "string" - }, - "typ_occup_density": { - "name": "typ_occup_density", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Customary or normal density of occupants", - "title": "typical occupant density", - "examples": [ - { - "value": "25" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "typical occupant density" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000771", - "multivalued": false, - "range": "double" - }, - "ventilation_rate": { - "name": "ventilation_rate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "cubic meter per minute, liters per second" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Ventilation rate of the system in the sampled premises", - "title": "ventilation rate", - "examples": [ - { - "value": "750 cubic meter per minute" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "ventilation rate" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000114", - "multivalued": false, - "range": "string" - }, - "ventilation_type": { - "name": "ventilation_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "ventilation type name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Ventilation system used in the sampled premises", - "title": "ventilation type", - "examples": [ - { - "value": "Operable windows" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "ventilation type" - ], - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000756", - "multivalued": false, - "range": "string" - }, - "vfa": { - "name": "vfa", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of Volatile Fatty Acids in the sample", - "title": "volatile fatty acids", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "volatile fatty acids" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000152", - "multivalued": false, - "range": "string" - }, - "vfa_fw": { - "name": "vfa_fw", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Original volatile fatty acid concentration in the hydrocarbon resource", - "title": "vfa in formation water", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "vfa in formation water" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000408", - "multivalued": false, - "range": "string" - }, - "vis_media": { - "name": "vis_media", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The building visual media", - "title": "visual media", - "examples": [ - { - "value": "3D scans" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "visual media" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000840", - "multivalued": false, - "range": "vis_media_enum" - }, - "viscosity": { - "name": "viscosity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "cP at degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C)", - "title": "viscosity", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "viscosity" - ], - "is_a": "core field", - "string_serialization": "{float} {unit};{float} {unit}", - "slot_uri": "MIXS:0000126", - "multivalued": false, - "range": "string" - }, - "volatile_org_comp": { - "name": "volatile_org_comp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "volatile organic compound name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per cubic meter, parts per million, nanogram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound", - "title": "volatile organic compounds", - "examples": [ - { - "value": "formaldehyde;500 nanogram per liter" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "volatile organic compounds" - ], - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000115", - "multivalued": false, - "range": "string" - }, - "wall_area": { - "name": "wall_area", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "square meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The total area of the sampled room's walls", - "title": "wall area", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "wall area" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000198", - "multivalued": false, - "range": "string" - }, - "wall_const_type": { - "name": "wall_const_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The building class of the wall defined by the composition of the building elements and fire-resistance rating.", - "title": "wall construction type", - "examples": [ - { - "value": "fire resistive" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "wall construction type" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000841", - "multivalued": false, - "range": "wall_const_type_enum" - }, - "wall_finish_mat": { - "name": "wall_finish_mat", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The material utilized to finish the outer most layer of the wall", - "title": "wall finish material", - "examples": [ - { - "value": "wood" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "wall finish material" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000842", - "multivalued": false, - "range": "wall_finish_mat_enum" - }, - "wall_height": { - "name": "wall_height", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "centimeter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The average height of the walls in the sampled room", - "title": "wall height", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "wall height" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000221", - "multivalued": false, - "range": "string" - }, - "wall_loc": { - "name": "wall_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The relative location of the wall within the room", - "title": "wall location", - "examples": [ - { - "value": "north" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "wall location" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000843", - "multivalued": false, - "range": "wall_loc_enum" - }, - "wall_surf_treatment": { - "name": "wall_surf_treatment", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The surface treatment of interior wall", - "title": "wall surface treatment", - "examples": [ - { - "value": "paneling" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "wall surface treatment" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000845", - "multivalued": false, - "range": "wall_surf_treatment_enum" - }, - "wall_texture": { - "name": "wall_texture", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The feel, appearance, or consistency of a wall surface", - "title": "wall texture", - "examples": [ - { - "value": "popcorn" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "wall texture" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000846", - "multivalued": false, - "range": "wall_texture_enum" - }, - "wall_thermal_mass": { - "name": "wall_thermal_mass", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "joule per degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint", - "title": "wall thermal mass", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "wall thermal mass" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000222", - "multivalued": false, - "range": "string" - }, - "wall_water_mold": { - "name": "wall_water_mold", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Signs of the presence of mold or mildew on a wall", - "title": "wall signs of water/mold", - "examples": [ - { - "value": "no presence of mold visible" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "wall signs of water/mold" - ], - "is_a": "core field", - "string_serialization": "[presence of mold visible|no presence of mold visible]", - "slot_uri": "MIXS:0000844", - "multivalued": false, - "range": "string" - }, - "wastewater_type": { - "name": "wastewater_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "wastewater type name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The origin of wastewater such as human waste, rainfall, storm drains, etc.", - "title": "wastewater type", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "wastewater type" - ], - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000353", - "multivalued": false, - "range": "string" - }, - "water_cont_soil_meth": { - "name": "water_cont_soil_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining the water content of soil", - "title": "water content method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "water content method" - ], - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000323", - "multivalued": false, - "range": "string" - }, - "water_content": { - "name": "water_content", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram per gram or cubic centimeter per cubic centimeter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Water content measurement", - "title": "water content", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "water content" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000185", - "multivalued": false, - "range": "string" - }, - "water_current": { - "name": "water_current", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "cubic meter per second, knots" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of magnitude and direction of flow within a fluid", - "title": "water current", - "examples": [ - { - "value": "10 cubic meter per second" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "water current" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000203", - "multivalued": false, - "range": "string" - }, - "water_cut": { - "name": "water_cut", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "percent" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Current amount of water (%) in a produced fluid stream; or the average of the combined streams", - "title": "water cut", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "water cut" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000454", - "multivalued": false, - "range": "string" - }, - "water_feat_size": { - "name": "water_feat_size", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "square meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The size of the water feature", - "title": "water feature size", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "water feature size" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000223", - "multivalued": false, - "range": "string" - }, - "water_feat_type": { - "name": "water_feat_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of water feature present within the building being sampled", - "title": "water feature type", - "examples": [ - { - "value": "stream" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "water feature type" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000847", - "multivalued": false, - "range": "water_feat_type_enum" - }, - "water_prod_rate": { - "name": "water_prod_rate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "cubic meter per day" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Water production rates per well (e.g. 987 m3 / day)", - "title": "water production rate", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "water production rate" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000453", - "multivalued": false, - "range": "string" - }, - "water_temp_regm": { - "name": "water_temp_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", - "title": "water temperature regimen", - "examples": [ - { - "value": "15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "water temperature regimen" - ], - "is_a": "core field", - "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000590", - "multivalued": false, - "range": "string" - }, - "watering_regm": { - "name": "watering_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milliliter, liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", - "title": "watering regimen", - "examples": [ - { - "value": "1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "watering regimen" - ], - "is_a": "core field", - "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000591", - "multivalued": false, - "range": "string" - }, - "weekday": { - "name": "weekday", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The day of the week when sampling occurred", - "title": "weekday", - "examples": [ - { - "value": "Sunday" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "weekday" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000848", - "multivalued": false, - "range": "weekday_enum" - }, - "win": { - "name": "win", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)", - "title": "well identification number", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "well identification number" - ], - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000297", - "multivalued": false, - "range": "string" - }, - "wind_direction": { - "name": "wind_direction", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "wind direction name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Wind direction is the direction from which a wind originates", - "title": "wind direction", - "examples": [ - { - "value": "Northwest" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "wind direction" - ], - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000757", - "multivalued": false, - "range": "string" - }, - "wind_speed": { - "name": "wind_speed", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter per second, kilometer per hour" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Speed of wind measured at the time of sampling", - "title": "wind speed", - "examples": [ - { - "value": "21 kilometer per hour" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "wind speed" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000118", - "multivalued": false, - "range": "string" - }, - "window_cond": { - "name": "window_cond", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The physical condition of the window at the time of sampling", - "title": "window condition", - "examples": [ - { - "value": "rupture" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "window condition" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000849", - "multivalued": false, - "range": "window_cond_enum" - }, - "window_cover": { - "name": "window_cover", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of window covering", - "title": "window covering", - "examples": [ - { - "value": "curtains" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "window covering" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000850", - "multivalued": false, - "range": "window_cover_enum" - }, - "window_horiz_pos": { - "name": "window_horiz_pos", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The horizontal position of the window on the wall", - "title": "window horizontal position", - "examples": [ - { - "value": "middle" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "window horizontal position" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000851", - "multivalued": false, - "range": "window_horiz_pos_enum" - }, - "window_loc": { - "name": "window_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The relative location of the window within the room", - "title": "window location", - "examples": [ - { - "value": "west" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "window location" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000852", - "multivalued": false, - "range": "window_loc_enum" - }, - "window_mat": { - "name": "window_mat", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of material used to finish a window", - "title": "window material", - "examples": [ - { - "value": "wood" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "window material" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000853", - "multivalued": false, - "range": "window_mat_enum" - }, - "window_open_freq": { - "name": "window_open_freq", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The number of times windows are opened per week", - "title": "window open frequency", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "window open frequency" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000246", - "multivalued": false, - "range": "string" - }, - "window_size": { - "name": "window_size", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "inch, meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The window's length and width", - "title": "window area/size", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "window area/size" - ], - "is_a": "core field", - "string_serialization": "{float} {unit} x {float} {unit}", - "slot_uri": "MIXS:0000224", - "multivalued": false, - "range": "string" - }, - "window_status": { - "name": "window_status", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Defines whether the windows were open or closed during environmental testing", - "title": "window status", - "examples": [ - { - "value": "open" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "window status" - ], - "is_a": "core field", - "string_serialization": "[closed|open]", - "slot_uri": "MIXS:0000855", - "multivalued": false, - "range": "string" - }, - "window_type": { - "name": "window_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of windows", - "title": "window type", - "examples": [ - { - "value": "fixed window" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "window type" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000856", - "multivalued": false, - "range": "window_type_enum" - }, - "window_vert_pos": { - "name": "window_vert_pos", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The vertical position of the window on the wall", - "title": "window vertical position", - "examples": [ - { - "value": "middle" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "window vertical position" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000857", - "multivalued": false, - "range": "window_vert_pos_enum" - }, - "window_water_mold": { - "name": "window_water_mold", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Signs of the presence of mold or mildew on the window.", - "title": "window signs of water/mold", - "examples": [ - { - "value": "no presence of mold visible" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "window signs of water/mold" - ], - "is_a": "core field", - "string_serialization": "[presence of mold visible|no presence of mold visible]", - "slot_uri": "MIXS:0000854", - "multivalued": false, - "range": "string" - }, - "xylene": { - "name": "xylene", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of xylene in the sample", - "title": "xylene", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "xylene" - ], - "is_a": "core field", - "slot_uri": "MIXS:0000156", - "multivalued": false, - "range": "string" - }, - "zinc": { - "name": "zinc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mg/kg (ppm)" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of zinc in the sample", - "title": "zinc", - "examples": [ - { - "value": "2.5 mg/kg" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "see_also": [ - "https://www.ornl.gov/content/bio-scales-0" - ], - "aliases": [ - "zinc" - ], - "is_a": "attribute", - "multivalued": false, - "range": "string" - }, - "core field": { - "name": "core field", - "description": "basic fields", - "from_schema": "https://example.com/nmdc_submission_schema", - "abstract": true - }, - "id": { - "name": "id", - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "notes": [ - "abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?", - "a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters will be accepted", - "typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked via per-class id slot usage assertions", - "minting authority shoulders should probably be enumerated and checked in the pattern" - ], - "examples": [ - { - "value": "nmdc:mgmag-00-x012.1_7_c1", - "description": "https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "identifier": true, - "range": "uriorcurie", - "required": true, - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$" - }, - "language": { - "name": "language", - "description": "Should use ISO 639-1 code e.g. \"en\", \"fr\"", - "from_schema": "https://example.com/nmdc_submission_schema", - "range": "language code" - }, - "description": { - "name": "description", - "description": "a human-readable description of a thing", - "from_schema": "https://example.com/nmdc_submission_schema", - "slot_uri": "dcterms:description", - "multivalued": false, - "range": "string" - }, - "nucleic acid sequence source field": { - "name": "nucleic acid sequence source field", - "from_schema": "https://example.com/nmdc_submission_schema", - "abstract": true - }, - "environment field": { - "name": "environment field", - "description": "field describing environmental aspect of a sample", - "from_schema": "https://example.com/nmdc_submission_schema", - "abstract": true - }, - "gold_path_field": { - "name": "gold_path_field", - "description": "This is a grouping for any of the gold path fields", - "from_schema": "https://example.com/nmdc_submission_schema", - "is_a": "attribute", - "abstract": true, - "multivalued": false, - "range": "string" - }, - "alternative_identifiers": { - "name": "alternative_identifiers", - "description": "A list of alternative identifiers for the entity.", - "from_schema": "https://example.com/nmdc_submission_schema", - "multivalued": true, - "range": "uriorcurie", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$" - }, - "name": { - "name": "name", - "description": "A human readable label for an entity", - "from_schema": "https://example.com/nmdc_submission_schema", - "multivalued": false, - "range": "string" - }, - "investigation field": { - "name": "investigation field", - "description": "field describing aspect of the investigation/study to which the sample belongs", - "from_schema": "https://example.com/nmdc_submission_schema", - "abstract": true - }, - "attribute": { - "name": "attribute", - "description": "A attribute of a biosample. Examples: depth, habitat, material. For NMDC, attributes SHOULD be mapped to terms within a MIxS template", - "from_schema": "https://example.com/nmdc_submission_schema", - "aliases": [ - "field", - "property", - "template field", - "key", - "characteristic" - ], - "abstract": true - }, - "biomaterial_purity": { - "name": "biomaterial_purity", - "from_schema": "https://example.com/nmdc_submission_schema", - "multivalued": false, - "range": "string" - } - }, - "classes": { - "AirInterface": { - "name": "AirInterface", - "description": "air dh_interface", - "title": "Air", - "from_schema": "https://example.com/nmdc_submission_schema", - "is_a": "DhInterface", - "mixins": [ - "DhMultiviewCommonColumnsMixin", - "SampIdNewTermsMixin" - ], - "slots": [ - "air_PM_concen", - "alt", - "barometric_press", - "carb_dioxide", - "carb_monoxide", - "chem_administration", - "collection_date", - "depth", - "ecosystem", - "ecosystem_category", - "ecosystem_subtype", - "ecosystem_type", - "elev", - "env_broad_scale", - "env_local_scale", - "env_medium", - "env_package", - "experimental_factor", - "geo_loc_name", - "horizon_meth", - "humidity", - "lat_lon", - "methane", - "misc_param", - "organism_count", - "oxy_stat_samp", - "oxygen", - "perturbation", - "pollutants", - "salinity", - "samp_collec_device", - "samp_collec_method", - "samp_mat_process", - "samp_size", - "samp_store_dur", - "samp_store_loc", - "samp_store_temp", - "sample_link", - "size_frac", - "solar_irradiance", - "specific_ecosystem", - "temp", - "ventilation_rate", - "ventilation_type", - "volatile_org_comp", - "wind_direction", - "wind_speed" - ], - "slot_usage": { - "air_PM_concen": { - "name": "air_PM_concen", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "particulate matter name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micrograms per cubic meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM", - "title": "air particulate matter concentration", - "examples": [ - { - "value": "PM2.5;10 microgram per cubic meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "air particulate matter concentration" - ], - "rank": 48, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000108", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "alt": { - "name": "alt", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - } - }, - "description": "Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air", - "title": "altitude", - "examples": [ - { - "value": "100 meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "altitude" - ], - "rank": 26, - "is_a": "environment field", - "slot_uri": "MIXS:0000094", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HostAssociatedInterface", - "MiscEnvsInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "barometric_press": { - "name": "barometric_press", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millibar" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Force per unit area exerted against a surface by the weight of air above that surface", - "title": "barometric pressure", - "examples": [ - { - "value": "5 millibar" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "barometric pressure" - ], - "rank": 49, - "is_a": "core field", - "slot_uri": "MIXS:0000096", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "carb_dioxide": { - "name": "carb_dioxide", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Carbon dioxide (gas) amount or concentration at the time of sampling", - "title": "carbon dioxide", - "examples": [ - { - "value": "410 parts per million" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "carbon dioxide" - ], - "rank": 50, - "is_a": "core field", - "slot_uri": "MIXS:0000097", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "carb_monoxide": { - "name": "carb_monoxide", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Carbon monoxide (gas) amount or concentration at the time of sampling", - "title": "carbon monoxide", - "examples": [ - { - "value": "0.1 parts per million" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "carbon monoxide" - ], - "rank": 51, - "is_a": "core field", - "slot_uri": "MIXS:0000098", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "chem_administration": { - "name": "chem_administration", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "CHEBI;timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", - "title": "chemical administration", - "examples": [ - { - "value": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22" - }, - { - "value": "agar [CHEBI:2509];2018-05" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "chemical administration" - ], - "rank": 17, - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]};{timestamp}", - "slot_uri": "MIXS:0000751", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" - }, - "collection_date": { - "name": "collection_date", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "date and time" - } - }, - "description": "The date of sampling", - "title": "collection date", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", - "Use modified term (amended definition)" - ], - "examples": [ - { - "value": "2021-04-15" - }, - { - "value": "2021-04" - }, - { - "value": "2021" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "collection date" - ], - "rank": 3, - "is_a": "environment field", - "string_serialization": "{date, arbitrary precision}", - "slot_uri": "MIXS:0000011", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" - }, - "depth": { - "name": "depth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - } - }, - "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", - "title": "depth, meters", - "notes": [ - "Use modified term" - ], - "comments": [ - "All depths must be reported in meters. Provide the numerical portion only." - ], - "examples": [ - { - "value": "0 - 0.1" - }, - { - "value": "1" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "depth" - ], - "rank": 9, - "is_a": "environment field", - "string_serialization": "{float}|{float}-{float}", - "slot_uri": "MIXS:0000018", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$" - }, - "ecosystem": { - "name": "ecosystem", - "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", - "notes": [ - "range: string or EcosystemEnum? The enum could be dynamic or might be soil biased." - ], - "comments": [ - "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 9, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_category": { - "name": "ecosystem_category", - "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", - "notes": [ - "string or EcosystemCategoryEnum range?" - ], - "comments": [ - "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 10, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_subtype": { - "name": "ecosystem_subtype", - "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", - "notes": [ - "string or EcosystemSubtypeEnum range?" - ], - "comments": [ - "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 12, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_type": { - "name": "ecosystem_type", - "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", - "notes": [ - "string or EcosystemTypeEnum range?" - ], - "comments": [ - "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 11, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "elev": { - "name": "elev", - "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", - "title": "elevation, meters", - "comments": [ - "All elevations must be reported in meters. Provide the numerical portion only.", - "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." - ], - "examples": [ - { - "value": "225" - }, - { - "value": "0" - }, - { - "value": "1250" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "slot_uri": "MIXS:0000093", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "float", - "required": true - }, - "env_broad_scale": { - "name": "env_broad_scale", - "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", - "title": "broad-scale environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000012", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_local_scale": { - "name": "env_local_scale", - "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", - "title": "local environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "canopy [ENVO:00000047]" - }, - { - "value": "herb and fern layer [ENVO:01000337]" - }, - { - "value": "litter layer [ENVO:01000338]" - }, - { - "value": "understory [01000335]" - }, - { - "value": "shrub layer [ENVO:01000336]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 7, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000013", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_medium": { - "name": "env_medium", - "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", - "title": "environmental medium", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "soil [ENVO:00001998]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 8, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000014", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_package": { - "name": "env_package", - "description": "Select the MIxS enviromental package that best describes the environment from which your sample was collected.", - "title": "environmental package", - "examples": [ - { - "value": "soil" - } - ], - "in_subset": [ - "mixs extension" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "environmental package" - ], - "rank": 4, - "is_a": "attribute", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true - }, - "experimental_factor": { - "name": "experimental_factor", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text or EFO and/or OBI" - } - }, - "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", - "title": "experimental factor", - "examples": [ - { - "value": "time series design [EFO:EFO_0001779]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "experimental factor" - ], - "rank": 12, - "is_a": "investigation field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000008", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "geo_loc_name": { - "name": "geo_loc_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" - } - }, - "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", - "title": "geographic location (country and/or sea,region)", - "examples": [ - { - "value": "USA: Maryland, Bethesda" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "geographic location (country and/or sea,region)" - ], - "rank": 4, - "is_a": "environment field", - "string_serialization": "{text}: {text}, {text}", - "slot_uri": "MIXS:0000010", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" - }, - "horizon_meth": { - "name": "horizon_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining the horizon", - "title": "horizon method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "soil horizon method" - ], - "rank": 19, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000321", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "humidity": { - "name": "humidity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram per cubic meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Amount of water vapour in the air, at the time of sampling", - "title": "humidity", - "examples": [ - { - "value": "25 gram per cubic meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "humidity" - ], - "rank": 52, - "is_a": "core field", - "slot_uri": "MIXS:0000100", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "lat_lon": { - "name": "lat_lon", - "description": "This is currently a required field but it's not clear if this should be required for human hosts", - "title": "geographic location (latitude and longitude)", - "notes": [ - "required where?", - "This is currently a required field but it's not clear if this should be required for human hosts" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "is_a": "environment field", - "string_serialization": "{lat lon}", - "slot_uri": "MIXS:0000009", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" - }, - "methane": { - "name": "methane", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, parts per billion, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Methane (gas) amount or concentration at the time of sampling", - "title": "methane", - "examples": [ - { - "value": "1800 parts per billion" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "methane" - ], - "rank": 24, - "is_a": "core field", - "slot_uri": "MIXS:0000101", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "SedimentInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "misc_param": { - "name": "misc_param", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "parameter name;measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Any other measurement performed or parameter collected, that is not listed here", - "title": "miscellaneous parameter", - "examples": [ - { - "value": "Bicarbonate ion concentration;2075 micromole per kilogram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "miscellaneous parameter" - ], - "rank": 23, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000752", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "organism_count": { - "name": "organism_count", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "organism name;measurement value;enumeration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", - "title": "organism count", - "examples": [ - { - "value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "organism count" - ], - "rank": 30, - "is_a": "core field", - "slot_uri": "MIXS:0000103", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$" - }, - "oxy_stat_samp": { - "name": "oxy_stat_samp", - "description": "Oxygenation status of sample", - "title": "oxygenation status of sample", - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 25, - "is_a": "core field", - "slot_uri": "MIXS:0000753", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "OxyStatSampEnum" - }, - "oxygen": { - "name": "oxygen", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Oxygen (gas) amount or concentration at the time of sampling", - "title": "oxygen", - "examples": [ - { - "value": "600 parts per million" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "oxygen" - ], - "rank": 53, - "is_a": "core field", - "slot_uri": "MIXS:0000104", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "perturbation": { - "name": "perturbation", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "perturbation type name;perturbation interval and duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types", - "title": "perturbation", - "examples": [ - { - "value": "antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "perturbation" - ], - "rank": 33, - "is_a": "core field", - "string_serialization": "{text};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000754", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "pollutants": { - "name": "pollutants", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "pollutant name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, mole per liter, milligram per liter, microgram per cubic meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant", - "title": "pollutants", - "examples": [ - { - "value": "lead;0.15 microgram per cubic meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "pollutants" - ], - "rank": 54, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000107", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "salinity": { - "name": "salinity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "practical salinity unit, percentage" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", - "title": "salinity", - "examples": [ - { - "value": "25 practical salinity unit" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "salinity" - ], - "rank": 54, - "is_a": "core field", - "slot_uri": "MIXS:0000183", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "samp_collec_device": { - "name": "samp_collec_device", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "device name" - } - }, - "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", - "title": "sample collection device", - "comments": [ - "Report dimensions and details when applicable" - ], - "examples": [ - { - "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection device" - ], - "rank": 14, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000002", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "samp_collec_method": { - "name": "samp_collec_method", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI,url , or text" - } - }, - "description": "The method employed for collecting the sample.", - "title": "sample collection method", - "comments": [ - "This can be a citation or description" - ], - "examples": [ - { - "value": "swabbing" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection method" - ], - "rank": 15, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{PMID}|{DOI}|{URL}|{text}", - "slot_uri": "MIXS:0001225", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_mat_process": { - "name": "samp_mat_process", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - } - }, - "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", - "title": "sample material processing", - "examples": [ - { - "value": "filtering of seawater" - }, - { - "value": "storing samples in ethanol" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample material processing" - ], - "rank": 12, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000016", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_size": { - "name": "samp_size", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millliter, gram, milligram, liter" - } - }, - "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", - "title": "amount or size of sample collected", - "comments": [ - "This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis." - ], - "examples": [ - { - "value": "5 grams" - }, - { - "value": "10 mL" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "amount or size of sample collected" - ], - "rank": 18, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float} {unit}", - "slot_uri": "MIXS:0000001", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" - }, - "samp_store_dur": { - "name": "samp_store_dur", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Duration for which the sample was stored", - "title": "sample storage duration", - "examples": [ - { - "value": "P1Y6M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage duration" - ], - "rank": 353, - "is_a": "core field", - "string_serialization": "{duration}", - "slot_uri": "MIXS:0000116", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_store_loc": { - "name": "samp_store_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "location name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Location at which sample was stored, usually name of a specific freezer/room", - "title": "sample storage location", - "examples": [ - { - "value": "Freezer no:5" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage location" - ], - "rank": 41, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000755", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_store_temp": { - "name": "samp_store_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Temperature at which the sample was stored (degrees are assumed)", - "title": "sample storage temperature", - "examples": [ - { - "value": "-80 Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage temperature" - ], - "rank": 7, - "is_a": "core field", - "slot_uri": "MIXS:0000110", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "sample_link": { - "name": "sample_link", - "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", - "title": "sample linkage", - "notes": [ - "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" - ], - "comments": [ - "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" - ], - "examples": [ - { - "value": "IGSN:DSJ0284" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "string_serialization": "{text}:{text}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface", - "SampIdNewTermsMixin" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true, - "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" - }, - "size_frac": { - "name": "size_frac", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "filter size value range" - } - }, - "description": "Filtering pore size used in sample preparation", - "title": "size fraction selected", - "examples": [ - { - "value": "0-0.22 micrometer" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "size fraction selected" - ], - "rank": 285, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float}-{float} {unit}", - "slot_uri": "MIXS:0000017", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "solar_irradiance": { - "name": "solar_irradiance", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "kilowatts per square meter per day, ergs per square centimeter per second" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The amount of solar energy that arrives at a specific area of a surface during a specific time interval", - "title": "solar irradiance", - "examples": [ - { - "value": "1.36 kilowatts per square meter per day" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "solar irradiance" - ], - "rank": 55, - "is_a": "core field", - "slot_uri": "MIXS:0000112", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "specific_ecosystem": { - "name": "specific_ecosystem", - "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", - "notes": [ - "string or SpecificEcosystemEnum range?" - ], - "comments": [ - "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 13, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "temp": { - "name": "temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - } - }, - "description": "Temperature of the sample at the time of sampling.", - "title": "temperature", - "examples": [ - { - "value": "25 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "temperature" - ], - "rank": 37, - "is_a": "environment field", - "slot_uri": "MIXS:0000113", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "ventilation_rate": { - "name": "ventilation_rate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "cubic meter per minute, liters per second" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Ventilation rate of the system in the sampled premises", - "title": "ventilation rate", - "examples": [ - { - "value": "750 cubic meter per minute" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "ventilation rate" - ], - "rank": 56, - "is_a": "core field", - "slot_uri": "MIXS:0000114", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "ventilation_type": { - "name": "ventilation_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "ventilation type name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Ventilation system used in the sampled premises", - "title": "ventilation type", - "examples": [ - { - "value": "Operable windows" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "ventilation type" - ], - "rank": 57, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000756", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "volatile_org_comp": { - "name": "volatile_org_comp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "volatile organic compound name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per cubic meter, parts per million, nanogram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound", - "title": "volatile organic compounds", - "examples": [ - { - "value": "formaldehyde;500 nanogram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "volatile organic compounds" - ], - "rank": 58, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000115", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "wind_direction": { - "name": "wind_direction", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "wind direction name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Wind direction is the direction from which a wind originates", - "title": "wind direction", - "examples": [ - { - "value": "Northwest" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "wind direction" - ], - "rank": 59, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000757", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "wind_speed": { - "name": "wind_speed", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter per second, kilometer per hour" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Speed of wind measured at the time of sampling", - "title": "wind speed", - "examples": [ - { - "value": "21 kilometer per hour" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "wind speed" - ], - "rank": 60, - "is_a": "core field", - "slot_uri": "MIXS:0000118", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - } - }, - "attributes": { - "air_PM_concen": { - "name": "air_PM_concen", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "particulate matter name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micrograms per cubic meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM", - "title": "air particulate matter concentration", - "examples": [ - { - "value": "PM2.5;10 microgram per cubic meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "air particulate matter concentration" - ], - "rank": 48, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000108", - "multivalued": false, - "alias": "air_PM_concen", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "AirInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "alt": { - "name": "alt", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - } - }, - "description": "Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air", - "title": "altitude", - "examples": [ - { - "value": "100 meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "altitude" - ], - "rank": 26, - "is_a": "environment field", - "slot_uri": "MIXS:0000094", - "multivalued": false, - "alias": "alt", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HostAssociatedInterface", - "MiscEnvsInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "barometric_press": { - "name": "barometric_press", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millibar" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Force per unit area exerted against a surface by the weight of air above that surface", - "title": "barometric pressure", - "examples": [ - { - "value": "5 millibar" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "barometric pressure" - ], - "rank": 49, - "is_a": "core field", - "slot_uri": "MIXS:0000096", - "multivalued": false, - "alias": "barometric_press", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "AirInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "carb_dioxide": { - "name": "carb_dioxide", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Carbon dioxide (gas) amount or concentration at the time of sampling", - "title": "carbon dioxide", - "examples": [ - { - "value": "410 parts per million" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "carbon dioxide" - ], - "rank": 50, - "is_a": "core field", - "slot_uri": "MIXS:0000097", - "multivalued": false, - "alias": "carb_dioxide", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "carb_monoxide": { - "name": "carb_monoxide", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Carbon monoxide (gas) amount or concentration at the time of sampling", - "title": "carbon monoxide", - "examples": [ - { - "value": "0.1 parts per million" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "carbon monoxide" - ], - "rank": 51, - "is_a": "core field", - "slot_uri": "MIXS:0000098", - "multivalued": false, - "alias": "carb_monoxide", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "AirInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "chem_administration": { - "name": "chem_administration", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "CHEBI;timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", - "title": "chemical administration", - "examples": [ - { - "value": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22" - }, - { - "value": "agar [CHEBI:2509];2018-05" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "chemical administration" - ], - "rank": 17, - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]};{timestamp}", - "slot_uri": "MIXS:0000751", - "multivalued": false, - "alias": "chem_administration", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" - }, - "collection_date": { - "name": "collection_date", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "date and time" - } - }, - "description": "The date of sampling", - "title": "collection date", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", - "Use modified term (amended definition)" - ], - "examples": [ - { - "value": "2021-04-15" - }, - { - "value": "2021-04" - }, - { - "value": "2021" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "collection date" - ], - "rank": 3, - "is_a": "environment field", - "string_serialization": "{date, arbitrary precision}", - "slot_uri": "MIXS:0000011", - "multivalued": false, - "alias": "collection_date", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" - }, - "depth": { - "name": "depth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - } - }, - "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", - "title": "depth, meters", - "notes": [ - "Use modified term" - ], - "comments": [ - "All depths must be reported in meters. Provide the numerical portion only." - ], - "examples": [ - { - "value": "0 - 0.1" - }, - { - "value": "1" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "depth" - ], - "rank": 9, - "is_a": "environment field", - "string_serialization": "{float}|{float}-{float}", - "slot_uri": "MIXS:0000018", - "multivalued": false, - "alias": "depth", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$" - }, - "ecosystem": { - "name": "ecosystem", - "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", - "notes": [ - "range: string or EcosystemEnum? The enum could be dynamic or might be soil biased." - ], - "comments": [ - "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 9, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_category": { - "name": "ecosystem_category", - "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", - "notes": [ - "string or EcosystemCategoryEnum range?" - ], - "comments": [ - "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 10, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem_category", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_subtype": { - "name": "ecosystem_subtype", - "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", - "notes": [ - "string or EcosystemSubtypeEnum range?" - ], - "comments": [ - "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 12, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem_subtype", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_type": { - "name": "ecosystem_type", - "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", - "notes": [ - "string or EcosystemTypeEnum range?" - ], - "comments": [ - "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 11, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem_type", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "elev": { - "name": "elev", - "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", - "title": "elevation, meters", - "comments": [ - "All elevations must be reported in meters. Provide the numerical portion only.", - "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." - ], - "examples": [ - { - "value": "225" - }, - { - "value": "0" - }, - { - "value": "1250" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "slot_uri": "MIXS:0000093", - "multivalued": false, - "alias": "elev", - "owner": "AirInterface", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "float", - "required": true - }, - "env_broad_scale": { - "name": "env_broad_scale", - "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", - "title": "broad-scale environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000012", - "multivalued": false, - "alias": "env_broad_scale", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_local_scale": { - "name": "env_local_scale", - "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", - "title": "local environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "canopy [ENVO:00000047]" - }, - { - "value": "herb and fern layer [ENVO:01000337]" - }, - { - "value": "litter layer [ENVO:01000338]" - }, - { - "value": "understory [01000335]" - }, - { - "value": "shrub layer [ENVO:01000336]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 7, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000013", - "multivalued": false, - "alias": "env_local_scale", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_medium": { - "name": "env_medium", - "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", - "title": "environmental medium", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "soil [ENVO:00001998]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 8, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000014", - "multivalued": false, - "alias": "env_medium", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_package": { - "name": "env_package", - "description": "Select the MIxS enviromental package that best describes the environment from which your sample was collected.", - "title": "environmental package", - "examples": [ - { - "value": "soil" - } - ], - "in_subset": [ - "mixs extension" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "environmental package" - ], - "rank": 4, - "is_a": "attribute", - "multivalued": false, - "alias": "env_package", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true - }, - "experimental_factor": { - "name": "experimental_factor", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text or EFO and/or OBI" - } - }, - "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", - "title": "experimental factor", - "examples": [ - { - "value": "time series design [EFO:EFO_0001779]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "experimental factor" - ], - "rank": 12, - "is_a": "investigation field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000008", - "multivalued": false, - "alias": "experimental_factor", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "geo_loc_name": { - "name": "geo_loc_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" - } - }, - "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", - "title": "geographic location (country and/or sea,region)", - "examples": [ - { - "value": "USA: Maryland, Bethesda" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "geographic location (country and/or sea,region)" - ], - "rank": 4, - "is_a": "environment field", - "string_serialization": "{text}: {text}, {text}", - "slot_uri": "MIXS:0000010", - "multivalued": false, - "alias": "geo_loc_name", - "owner": "AirInterface", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" - }, - "horizon_meth": { - "name": "horizon_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining the horizon", - "title": "horizon method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "soil horizon method" - ], - "rank": 19, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000321", - "multivalued": false, - "alias": "horizon_meth", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "humidity": { - "name": "humidity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram per cubic meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Amount of water vapour in the air, at the time of sampling", - "title": "humidity", - "examples": [ - { - "value": "25 gram per cubic meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "humidity" - ], - "rank": 52, - "is_a": "core field", - "slot_uri": "MIXS:0000100", - "multivalued": false, - "alias": "humidity", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "AirInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "lat_lon": { - "name": "lat_lon", - "description": "This is currently a required field but it's not clear if this should be required for human hosts", - "title": "geographic location (latitude and longitude)", - "notes": [ - "required where?", - "This is currently a required field but it's not clear if this should be required for human hosts" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "is_a": "environment field", - "string_serialization": "{lat lon}", - "slot_uri": "MIXS:0000009", - "multivalued": false, - "alias": "lat_lon", - "owner": "AirInterface", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" - }, - "methane": { - "name": "methane", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, parts per billion, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Methane (gas) amount or concentration at the time of sampling", - "title": "methane", - "examples": [ - { - "value": "1800 parts per billion" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "methane" - ], - "rank": 24, - "is_a": "core field", - "slot_uri": "MIXS:0000101", - "multivalued": false, - "alias": "methane", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "SedimentInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "misc_param": { - "name": "misc_param", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "parameter name;measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Any other measurement performed or parameter collected, that is not listed here", - "title": "miscellaneous parameter", - "examples": [ - { - "value": "Bicarbonate ion concentration;2075 micromole per kilogram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "miscellaneous parameter" - ], - "rank": 23, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000752", - "multivalued": false, - "alias": "misc_param", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "organism_count": { - "name": "organism_count", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "organism name;measurement value;enumeration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", - "title": "organism count", - "examples": [ - { - "value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "organism count" - ], - "rank": 30, - "is_a": "core field", - "slot_uri": "MIXS:0000103", - "multivalued": false, - "alias": "organism_count", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$" - }, - "oxy_stat_samp": { - "name": "oxy_stat_samp", - "description": "Oxygenation status of sample", - "title": "oxygenation status of sample", - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 25, - "is_a": "core field", - "slot_uri": "MIXS:0000753", - "multivalued": false, - "alias": "oxy_stat_samp", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "OxyStatSampEnum" - }, - "oxygen": { - "name": "oxygen", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Oxygen (gas) amount or concentration at the time of sampling", - "title": "oxygen", - "examples": [ - { - "value": "600 parts per million" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "oxygen" - ], - "rank": 53, - "is_a": "core field", - "slot_uri": "MIXS:0000104", - "multivalued": false, - "alias": "oxygen", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "AirInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "perturbation": { - "name": "perturbation", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "perturbation type name;perturbation interval and duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types", - "title": "perturbation", - "examples": [ - { - "value": "antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "perturbation" - ], - "rank": 33, - "is_a": "core field", - "string_serialization": "{text};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000754", - "multivalued": false, - "alias": "perturbation", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "pollutants": { - "name": "pollutants", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "pollutant name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, mole per liter, milligram per liter, microgram per cubic meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant", - "title": "pollutants", - "examples": [ - { - "value": "lead;0.15 microgram per cubic meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "pollutants" - ], - "rank": 54, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000107", - "multivalued": false, - "alias": "pollutants", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "AirInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "salinity": { - "name": "salinity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "practical salinity unit, percentage" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", - "title": "salinity", - "examples": [ - { - "value": "25 practical salinity unit" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "salinity" - ], - "rank": 54, - "is_a": "core field", - "slot_uri": "MIXS:0000183", - "multivalued": false, - "alias": "salinity", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "samp_collec_device": { - "name": "samp_collec_device", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "device name" - } - }, - "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", - "title": "sample collection device", - "comments": [ - "Report dimensions and details when applicable" - ], - "examples": [ - { - "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection device" - ], - "rank": 14, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000002", - "multivalued": false, - "alias": "samp_collec_device", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "samp_collec_method": { - "name": "samp_collec_method", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI,url , or text" - } - }, - "description": "The method employed for collecting the sample.", - "title": "sample collection method", - "comments": [ - "This can be a citation or description" - ], - "examples": [ - { - "value": "swabbing" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection method" - ], - "rank": 15, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{PMID}|{DOI}|{URL}|{text}", - "slot_uri": "MIXS:0001225", - "multivalued": false, - "alias": "samp_collec_method", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_mat_process": { - "name": "samp_mat_process", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - } - }, - "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", - "title": "sample material processing", - "examples": [ - { - "value": "filtering of seawater" - }, - { - "value": "storing samples in ethanol" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample material processing" - ], - "rank": 12, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000016", - "multivalued": false, - "alias": "samp_mat_process", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_size": { - "name": "samp_size", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millliter, gram, milligram, liter" - } - }, - "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", - "title": "amount or size of sample collected", - "comments": [ - "This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis." - ], - "examples": [ - { - "value": "5 grams" - }, - { - "value": "10 mL" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "amount or size of sample collected" - ], - "rank": 18, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float} {unit}", - "slot_uri": "MIXS:0000001", - "multivalued": false, - "alias": "samp_size", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" - }, - "samp_store_dur": { - "name": "samp_store_dur", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Duration for which the sample was stored", - "title": "sample storage duration", - "examples": [ - { - "value": "P1Y6M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage duration" - ], - "rank": 353, - "is_a": "core field", - "string_serialization": "{duration}", - "slot_uri": "MIXS:0000116", - "multivalued": false, - "alias": "samp_store_dur", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_store_loc": { - "name": "samp_store_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "location name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Location at which sample was stored, usually name of a specific freezer/room", - "title": "sample storage location", - "examples": [ - { - "value": "Freezer no:5" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage location" - ], - "rank": 41, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000755", - "multivalued": false, - "alias": "samp_store_loc", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_store_temp": { - "name": "samp_store_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Temperature at which the sample was stored (degrees are assumed)", - "title": "sample storage temperature", - "examples": [ - { - "value": "-80 Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage temperature" - ], - "rank": 7, - "is_a": "core field", - "slot_uri": "MIXS:0000110", - "multivalued": false, - "alias": "samp_store_temp", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "sample_link": { - "name": "sample_link", - "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", - "title": "sample linkage", - "notes": [ - "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" - ], - "comments": [ - "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" - ], - "examples": [ - { - "value": "IGSN:DSJ0284" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "string_serialization": "{text}:{text}", - "multivalued": false, - "alias": "sample_link", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface", - "SampIdNewTermsMixin" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true, - "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" - }, - "size_frac": { - "name": "size_frac", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "filter size value range" - } - }, - "description": "Filtering pore size used in sample preparation", - "title": "size fraction selected", - "examples": [ - { - "value": "0-0.22 micrometer" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "size fraction selected" - ], - "rank": 285, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float}-{float} {unit}", - "slot_uri": "MIXS:0000017", - "multivalued": false, - "alias": "size_frac", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "solar_irradiance": { - "name": "solar_irradiance", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "kilowatts per square meter per day, ergs per square centimeter per second" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The amount of solar energy that arrives at a specific area of a surface during a specific time interval", - "title": "solar irradiance", - "examples": [ - { - "value": "1.36 kilowatts per square meter per day" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "solar irradiance" - ], - "rank": 55, - "is_a": "core field", - "slot_uri": "MIXS:0000112", - "multivalued": false, - "alias": "solar_irradiance", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "AirInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "specific_ecosystem": { - "name": "specific_ecosystem", - "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", - "notes": [ - "string or SpecificEcosystemEnum range?" - ], - "comments": [ - "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 13, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "specific_ecosystem", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "temp": { - "name": "temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - } - }, - "description": "Temperature of the sample at the time of sampling.", - "title": "temperature", - "examples": [ - { - "value": "25 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "temperature" - ], - "rank": 37, - "is_a": "environment field", - "slot_uri": "MIXS:0000113", - "multivalued": false, - "alias": "temp", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "ventilation_rate": { - "name": "ventilation_rate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "cubic meter per minute, liters per second" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Ventilation rate of the system in the sampled premises", - "title": "ventilation rate", - "examples": [ - { - "value": "750 cubic meter per minute" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "ventilation rate" - ], - "rank": 56, - "is_a": "core field", - "slot_uri": "MIXS:0000114", - "multivalued": false, - "alias": "ventilation_rate", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "AirInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "ventilation_type": { - "name": "ventilation_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "ventilation type name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Ventilation system used in the sampled premises", - "title": "ventilation type", - "examples": [ - { - "value": "Operable windows" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "ventilation type" - ], - "rank": 57, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000756", - "multivalued": false, - "alias": "ventilation_type", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "volatile_org_comp": { - "name": "volatile_org_comp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "volatile organic compound name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per cubic meter, parts per million, nanogram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound", - "title": "volatile organic compounds", - "examples": [ - { - "value": "formaldehyde;500 nanogram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "volatile organic compounds" - ], - "rank": 58, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000115", - "multivalued": false, - "alias": "volatile_org_comp", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "AirInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "wind_direction": { - "name": "wind_direction", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "wind direction name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Wind direction is the direction from which a wind originates", - "title": "wind direction", - "examples": [ - { - "value": "Northwest" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "wind direction" - ], - "rank": 59, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000757", - "multivalued": false, - "alias": "wind_direction", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "AirInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "wind_speed": { - "name": "wind_speed", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter per second, kilometer per hour" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Speed of wind measured at the time of sampling", - "title": "wind speed", - "examples": [ - { - "value": "21 kilometer per hour" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "wind speed" - ], - "rank": 60, - "is_a": "core field", - "slot_uri": "MIXS:0000118", - "multivalued": false, - "alias": "wind_speed", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "AirInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "analysis_type": { - "name": "analysis_type", - "description": "Select all the data types associated or available for this biosample", - "title": "analysis/data type", - "examples": [ - { - "value": "metagenomics; metabolomics; proteomics" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:investigation_type" - ], - "rank": 3, - "multivalued": true, - "alias": "analysis_type", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin" - ], - "slot_group": "sample_id_section", - "range": "analysis_type_enum", - "required": true, - "recommended": true - }, - "samp_name": { - "name": "samp_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - } - }, - "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", - "title": "sample name", - "comments": [ - "It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." - ], - "examples": [ - { - "value": "Rock core CB1178(5-6) from NSW" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample name" - ], - "rank": 1, - "is_a": "investigation field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0001107", - "multivalued": false, - "identifier": true, - "alias": "samp_name", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true - }, - "source_mat_id": { - "name": "source_mat_id", - "description": "A globally unique identifier assigned to the biological sample.", - "title": "source material identifier", - "todos": [ - "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID.", - "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID." - ], - "notes": [ - "The source material IS the Globally Unique ID" - ], - "comments": [ - "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).", - "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/)." - ], - "examples": [ - { - "value": "IGSN:AU1243" - }, - { - "value": "UUID:24f1467a-40f4-11ed-b878-0242ac120002" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 2, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{text}:{text}", - "slot_uri": "MIXS:0000026", - "multivalued": false, - "alias": "source_mat_id", - "owner": "AirInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin" - ], - "slot_group": "sample_id_section", - "range": "string", - "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" - } - } - }, - "BiofilmInterface": { - "name": "BiofilmInterface", - "description": "biofilm dh_interface", - "title": "Biofilm", - "from_schema": "https://example.com/nmdc_submission_schema", - "is_a": "DhInterface", - "mixins": [ - "DhMultiviewCommonColumnsMixin", - "SampIdNewTermsMixin" - ], - "slots": [ - "alkalinity", - "alkyl_diethers", - "alt", - "aminopept_act", - "ammonium", - "bacteria_carb_prod", - "biomass", - "bishomohopanol", - "bromide", - "calcium", - "carb_nitro_ratio", - "chem_administration", - "chloride", - "chlorophyll", - "collection_date", - "depth", - "diether_lipids", - "diss_carb_dioxide", - "diss_hydrogen", - "diss_inorg_carb", - "diss_org_carb", - "diss_org_nitro", - "diss_oxygen", - "ecosystem", - "ecosystem_category", - "ecosystem_subtype", - "ecosystem_type", - "elev", - "env_broad_scale", - "env_local_scale", - "env_medium", - "env_package", - "experimental_factor", - "geo_loc_name", - "glucosidase_act", - "horizon_meth", - "lat_lon", - "magnesium", - "mean_frict_vel", - "mean_peak_frict_vel", - "methane", - "misc_param", - "n_alkanes", - "nitrate", - "nitrite", - "nitro", - "org_carb", - "org_matter", - "org_nitro", - "organism_count", - "oxy_stat_samp", - "part_org_carb", - "perturbation", - "petroleum_hydrocarb", - "ph", - "ph_meth", - "phaeopigments", - "phosphate", - "phosplipid_fatt_acid", - "potassium", - "pressure", - "redox_potential", - "salinity", - "samp_collec_device", - "samp_collec_method", - "samp_mat_process", - "samp_size", - "samp_store_dur", - "samp_store_loc", - "samp_store_temp", - "sample_link", - "silicate", - "size_frac", - "sodium", - "specific_ecosystem", - "sulfate", - "sulfide", - "temp", - "tot_carb", - "tot_nitro_content", - "tot_org_carb", - "turbidity", - "water_content" - ], - "slot_usage": { - "alkalinity": { - "name": "alkalinity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milliequivalent per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate", - "title": "alkalinity", - "examples": [ - { - "value": "50 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "alkalinity" - ], - "rank": 1, - "is_a": "core field", - "slot_uri": "MIXS:0000421", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "alkyl_diethers": { - "name": "alkyl_diethers", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of alkyl diethers", - "title": "alkyl diethers", - "examples": [ - { - "value": "0.005 mole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "alkyl diethers" - ], - "rank": 2, - "is_a": "core field", - "slot_uri": "MIXS:0000490", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "alt": { - "name": "alt", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - } - }, - "description": "Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air", - "title": "altitude", - "examples": [ - { - "value": "100 meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "altitude" - ], - "rank": 26, - "is_a": "environment field", - "slot_uri": "MIXS:0000094", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HostAssociatedInterface", - "MiscEnvsInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "aminopept_act": { - "name": "aminopept_act", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mole per liter per hour" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of aminopeptidase activity", - "title": "aminopeptidase activity", - "examples": [ - { - "value": "0.269 mole per liter per hour" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "aminopeptidase activity" - ], - "rank": 3, - "is_a": "core field", - "slot_uri": "MIXS:0000172", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "ammonium": { - "name": "ammonium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of ammonium in the sample", - "title": "ammonium", - "examples": [ - { - "value": "1.5 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "ammonium" - ], - "rank": 4, - "is_a": "core field", - "slot_uri": "MIXS:0000427", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "bacteria_carb_prod": { - "name": "bacteria_carb_prod", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "nanogram per hour" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of bacterial carbon production", - "title": "bacterial carbon production", - "examples": [ - { - "value": "2.53 microgram per liter per hour" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "bacterial carbon production" - ], - "rank": 5, - "is_a": "core field", - "slot_uri": "MIXS:0000173", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "biomass": { - "name": "biomass", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "biomass type;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "ton, kilogram, gram" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements", - "title": "biomass", - "examples": [ - { - "value": "total;20 gram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "biomass" - ], - "rank": 6, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000174", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "bishomohopanol": { - "name": "bishomohopanol", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter, microgram per gram" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of bishomohopanol", - "title": "bishomohopanol", - "examples": [ - { - "value": "14 microgram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "bishomohopanol" - ], - "rank": 7, - "is_a": "core field", - "slot_uri": "MIXS:0000175", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "bromide": { - "name": "bromide", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of bromide", - "title": "bromide", - "examples": [ - { - "value": "0.05 parts per million" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "bromide" - ], - "rank": 8, - "is_a": "core field", - "slot_uri": "MIXS:0000176", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "calcium": { - "name": "calcium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, micromole per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of calcium in the sample", - "title": "calcium", - "examples": [ - { - "value": "0.2 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "calcium" - ], - "rank": 9, - "is_a": "core field", - "slot_uri": "MIXS:0000432", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "carb_nitro_ratio": { - "name": "carb_nitro_ratio", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Ratio of amount or concentrations of carbon to nitrogen", - "title": "carbon/nitrogen ratio", - "examples": [ - { - "value": "0.417361111" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "carbon/nitrogen ratio" - ], - "rank": 44, - "is_a": "core field", - "slot_uri": "MIXS:0000310", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "SoilInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "float", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "chem_administration": { - "name": "chem_administration", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "CHEBI;timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. 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In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 11, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "elev": { - "name": "elev", - "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", - "title": "elevation, meters", - "comments": [ - "All elevations must be reported in meters. Provide the numerical portion only.", - "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." - ], - "examples": [ - { - "value": "225" - }, - { - "value": "0" - }, - { - "value": "1250" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "slot_uri": "MIXS:0000093", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "float", - "required": true - }, - "env_broad_scale": { - "name": "env_broad_scale", - "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", - "title": "broad-scale environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000012", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_local_scale": { - "name": "env_local_scale", - "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", - "title": "local environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "canopy [ENVO:00000047]" - }, - { - "value": "herb and fern layer [ENVO:01000337]" - }, - { - "value": "litter layer [ENVO:01000338]" - }, - { - "value": "understory [01000335]" - }, - { - "value": "shrub layer [ENVO:01000336]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 7, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000013", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_medium": { - "name": "env_medium", - "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", - "title": "environmental medium", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "soil [ENVO:00001998]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 8, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000014", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_package": { - "name": "env_package", - "description": "Select the MIxS enviromental package that best describes the environment from which your sample was collected.", - "title": "environmental package", - "examples": [ - { - "value": "soil" - } - ], - "in_subset": [ - "mixs extension" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "environmental package" - ], - "rank": 4, - "is_a": "attribute", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true - }, - "experimental_factor": { - "name": "experimental_factor", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text or EFO and/or OBI" - } - }, - "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", - "title": "experimental factor", - "examples": [ - { - "value": "time series design [EFO:EFO_0001779]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "experimental factor" - ], - "rank": 12, - "is_a": "investigation field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000008", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "geo_loc_name": { - "name": "geo_loc_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" - } - }, - "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", - "title": "geographic location (country and/or sea,region)", - "examples": [ - { - "value": "USA: Maryland, Bethesda" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "geographic location (country and/or sea,region)" - ], - "rank": 4, - "is_a": "environment field", - "string_serialization": "{text}: {text}, {text}", - "slot_uri": "MIXS:0000010", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" - }, - "glucosidase_act": { - "name": "glucosidase_act", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mol per liter per hour" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of glucosidase activity", - "title": "glucosidase activity", - "examples": [ - { - "value": "5 mol per liter per hour" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "glucosidase activity" - ], - "rank": 20, - "is_a": "core field", - "slot_uri": "MIXS:0000137", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "horizon_meth": { - "name": "horizon_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining the horizon", - "title": "horizon method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "soil horizon method" - ], - "rank": 19, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000321", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "lat_lon": { - "name": "lat_lon", - "description": "This is currently a required field but it's not clear if this should be required for human hosts", - "title": "geographic location (latitude and longitude)", - "notes": [ - "required where?", - "This is currently a required field but it's not clear if this should be required for human hosts" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "is_a": "environment field", - "string_serialization": "{lat lon}", - "slot_uri": "MIXS:0000009", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" - }, - "magnesium": { - "name": "magnesium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mole per liter, milligram per liter, parts per million, micromole per kilogram" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of magnesium in the sample", - "title": "magnesium", - "examples": [ - { - "value": "52.8 micromole per kilogram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "magnesium" - ], - "rank": 21, - "is_a": "core field", - "slot_uri": "MIXS:0000431", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "SedimentInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "mean_frict_vel": { - "name": "mean_frict_vel", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter per second" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of mean friction velocity", - "title": "mean friction velocity", - "examples": [ - { - "value": "0.5 meter per second" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "mean friction velocity" - ], - "rank": 22, - "is_a": "core field", - "slot_uri": "MIXS:0000498", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "mean_peak_frict_vel": { - "name": "mean_peak_frict_vel", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter per second" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of mean peak friction velocity", - "title": "mean peak friction velocity", - "examples": [ - { - "value": "1 meter per second" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "mean peak friction velocity" - ], - "rank": 23, - "is_a": "core field", - "slot_uri": "MIXS:0000502", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "methane": { - "name": "methane", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, parts per billion, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Methane (gas) amount or concentration at the time of sampling", - "title": "methane", - "examples": [ - { - "value": "1800 parts per billion" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "methane" - ], - "rank": 24, - "is_a": "core field", - "slot_uri": "MIXS:0000101", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "SedimentInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "misc_param": { - "name": "misc_param", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "parameter name;measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Any other measurement performed or parameter collected, that is not listed here", - "title": "miscellaneous parameter", - "examples": [ - { - "value": "Bicarbonate ion concentration;2075 micromole per kilogram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "miscellaneous parameter" - ], - "rank": 23, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000752", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "n_alkanes": { - "name": "n_alkanes", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "n-alkane name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Concentration of n-alkanes; can include multiple n-alkanes", - "title": "n-alkanes", - "examples": [ - { - "value": "n-hexadecane;100 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "n-alkanes" - ], - "rank": 25, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000503", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "nitrate": { - "name": "nitrate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of nitrate in the sample", - "title": "nitrate", - "examples": [ - { - "value": "65 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "nitrate" - ], - "rank": 26, - "is_a": "core field", - "slot_uri": "MIXS:0000425", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "nitrite": { - "name": "nitrite", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of nitrite in the sample", - "title": "nitrite", - "examples": [ - { - "value": "0.5 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "nitrite" - ], - "rank": 27, - "is_a": "core field", - "slot_uri": "MIXS:0000426", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "nitro": { - "name": "nitro", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of nitrogen (total)", - "title": "nitrogen", - "examples": [ - { - "value": "4.2 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "nitrogen" - ], - "rank": 28, - "is_a": "core field", - "slot_uri": "MIXS:0000504", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "org_carb": { - "name": "org_carb", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of organic carbon", - "title": "organic carbon", - "examples": [ - { - "value": "1.5 microgram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "organic carbon" - ], - "rank": 29, - "is_a": "core field", - "slot_uri": "MIXS:0000508", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "org_matter": { - "name": "org_matter", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of organic matter", - "title": "organic matter", - "examples": [ - { - "value": "1.75 milligram per cubic meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "organic matter" - ], - "rank": 45, - "is_a": "core field", - "slot_uri": "MIXS:0000204", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "org_nitro": { - "name": "org_nitro", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of organic nitrogen", - "title": "organic nitrogen", - "examples": [ - { - "value": "4 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "organic nitrogen" - ], - "rank": 46, - "is_a": "core field", - "slot_uri": "MIXS:0000205", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "organism_count": { - "name": "organism_count", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "organism name;measurement value;enumeration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. 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While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. 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This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", - "title": "sample collection device", - "comments": [ - "Report dimensions and details when applicable" - ], - "examples": [ - { - "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection device" - ], - "rank": 14, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000002", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "samp_collec_method": { - "name": "samp_collec_method", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI,url , or text" - } - }, - "description": "The method employed for collecting the sample.", - "title": "sample collection method", - "comments": [ - "This can be a citation or description" - ], - "examples": [ - { - "value": "swabbing" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection method" - ], - "rank": 15, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{PMID}|{DOI}|{URL}|{text}", - "slot_uri": "MIXS:0001225", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_mat_process": { - "name": "samp_mat_process", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - } - }, - "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", - "title": "sample material processing", - "examples": [ - { - "value": "filtering of seawater" - }, - { - "value": "storing samples in ethanol" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample material processing" - ], - "rank": 12, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000016", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_size": { - "name": "samp_size", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millliter, gram, milligram, liter" - } - }, - "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", - "title": "amount or size of sample collected", - "comments": [ - "This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis." - ], - "examples": [ - { - "value": "5 grams" - }, - { - "value": "10 mL" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "amount or size of sample collected" - ], - "rank": 18, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float} {unit}", - "slot_uri": "MIXS:0000001", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" - }, - "samp_store_dur": { - "name": "samp_store_dur", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Duration for which the sample was stored", - "title": "sample storage duration", - "examples": [ - { - "value": "P1Y6M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage duration" - ], - "rank": 353, - "is_a": "core field", - "string_serialization": "{duration}", - "slot_uri": "MIXS:0000116", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_store_loc": { - "name": "samp_store_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "location name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Location at which sample was stored, usually name of a specific freezer/room", - "title": "sample storage location", - "examples": [ - { - "value": "Freezer no:5" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage location" - ], - "rank": 41, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000755", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_store_temp": { - "name": "samp_store_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Temperature at which the sample was stored (degrees are assumed)", - "title": "sample storage temperature", - "examples": [ - { - "value": "-80 Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage temperature" - ], - "rank": 7, - "is_a": "core field", - "slot_uri": "MIXS:0000110", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "sample_link": { - "name": "sample_link", - "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", - "title": "sample linkage", - "notes": [ - "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" - ], - "comments": [ - "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" - ], - "examples": [ - { - "value": "IGSN:DSJ0284" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "string_serialization": "{text}:{text}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface", - "SampIdNewTermsMixin" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true, - "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" - }, - "silicate": { - "name": "silicate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of silicate", - "title": "silicate", - "examples": [ - { - "value": "0.05 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "silicate" - ], - "rank": 43, - "is_a": "core field", - "slot_uri": "MIXS:0000184", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "size_frac": { - "name": "size_frac", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "filter size value range" - } - }, - "description": "Filtering pore size used in sample preparation", - "title": "size fraction selected", - "examples": [ - { - "value": "0-0.22 micrometer" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "size fraction selected" - ], - "rank": 285, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float}-{float} {unit}", - "slot_uri": "MIXS:0000017", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "sodium": { - "name": "sodium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Sodium concentration in the sample", - "title": "sodium", - "examples": [ - { - "value": "10.5 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sodium" - ], - "rank": 363, - "is_a": "core field", - "slot_uri": "MIXS:0000428", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "specific_ecosystem": { - "name": "specific_ecosystem", - "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", - "notes": [ - "string or SpecificEcosystemEnum range?" - ], - "comments": [ - "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 13, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "sulfate": { - "name": "sulfate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of sulfate in the sample", - "title": "sulfate", - "examples": [ - { - "value": "5 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sulfate" - ], - "rank": 44, - "is_a": "core field", - "slot_uri": "MIXS:0000423", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "sulfide": { - "name": "sulfide", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of sulfide in the sample", - "title": "sulfide", - "examples": [ - { - "value": "2 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sulfide" - ], - "rank": 371, - "is_a": "core field", - "slot_uri": "MIXS:0000424", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "temp": { - "name": "temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - } - }, - "description": "Temperature of the sample at the time of sampling.", - "title": "temperature", - "examples": [ - { - "value": "25 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "temperature" - ], - "rank": 37, - "is_a": "environment field", - "slot_uri": "MIXS:0000113", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tot_carb": { - "name": "tot_carb", - "description": "Total carbon content", - "title": "total carbon", - "todos": [ - "is this inorganic and organic? both? could use some clarification.", - "ug/L doesn't seem like the right units. Should check this slots usage in databases and re-evaluate. I couldn't find any references that provided this data in this format", - "is this inorganic and organic? both? could use some clarification.", - "ug/L doesn't seem like the right units. Should check this slots usage in databases and re-evaluate. I couldn't find any references that provided this data in this format" - ], - "examples": [ - { - "value": "1 ug/L" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 47, - "is_a": "core field", - "slot_uri": "MIXS:0000525", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tot_nitro_content": { - "name": "tot_nitro_content", - "description": "Total nitrogen content of the sample", - "title": "total nitrogen content", - "examples": [ - { - "value": "5 mg N/ L" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 48, - "is_a": "core field", - "slot_uri": "MIXS:0000530", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tot_org_carb": { - "name": "tot_org_carb", - "description": "Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content", - "title": "total organic carbon", - "todos": [ - "check description. How are they different?", - "check description. How are they different?" - ], - "examples": [ - { - "value": "5 mg N/ L" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 50, - "is_a": "core field", - "slot_uri": "MIXS:0000533", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "turbidity": { - "name": "turbidity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "formazin turbidity unit, formazin nephelometric units" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measure of the amount of cloudiness or haziness in water caused by individual particles", - "title": "turbidity", - "examples": [ - { - "value": "0.3 nephelometric turbidity units" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "turbidity" - ], - "rank": 47, - "is_a": "core field", - "slot_uri": "MIXS:0000191", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "water_content": { - "name": "water_content", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "string" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram per gram or cubic centimeter per cubic centimeter" - } - }, - "description": "Water content measurement", - "title": "water content", - "todos": [ - "value in preferred unit is too limiting. need to change this", - "check and correct validation so examples are accepted", - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "how to manage multiple water content methods?", - "value in preferred unit is too limiting. need to change this", - "check and correct validation so examples are accepted", - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "how to manage multiple water content methods?" - ], - "examples": [ - { - "value": "75%" - }, - { - "value": "75 %" - }, - { - "value": "0.75 g water/g dry soil" - }, - { - "value": "75% water holding capacity" - }, - { - "value": "1.1 g fresh weight/ dry weight" - }, - { - "value": "10% water filled pore space" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 39, - "is_a": "core field", - "string_serialization": "{float or pct} {unit}", - "slot_uri": "MIXS:0000185", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?%? \\S.+$" - } - }, - "attributes": { - "alkalinity": { - "name": "alkalinity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milliequivalent per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate", - "title": "alkalinity", - "examples": [ - { - "value": "50 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "alkalinity" - ], - "rank": 1, - "is_a": "core field", - "slot_uri": "MIXS:0000421", - "multivalued": false, - "alias": "alkalinity", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "alkyl_diethers": { - "name": "alkyl_diethers", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of alkyl diethers", - "title": "alkyl diethers", - "examples": [ - { - "value": "0.005 mole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "alkyl diethers" - ], - "rank": 2, - "is_a": "core field", - "slot_uri": "MIXS:0000490", - "multivalued": false, - "alias": "alkyl_diethers", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "alt": { - "name": "alt", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - } - }, - "description": "Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air", - "title": "altitude", - "examples": [ - { - "value": "100 meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "altitude" - ], - "rank": 26, - "is_a": "environment field", - "slot_uri": "MIXS:0000094", - "multivalued": false, - "alias": "alt", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HostAssociatedInterface", - "MiscEnvsInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "aminopept_act": { - "name": "aminopept_act", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mole per liter per hour" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of aminopeptidase activity", - "title": "aminopeptidase activity", - "examples": [ - { - "value": "0.269 mole per liter per hour" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "aminopeptidase activity" - ], - "rank": 3, - "is_a": "core field", - "slot_uri": "MIXS:0000172", - "multivalued": false, - "alias": "aminopept_act", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "ammonium": { - "name": "ammonium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of ammonium in the sample", - "title": "ammonium", - "examples": [ - { - "value": "1.5 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "ammonium" - ], - "rank": 4, - "is_a": "core field", - "slot_uri": "MIXS:0000427", - "multivalued": false, - "alias": "ammonium", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "bacteria_carb_prod": { - "name": "bacteria_carb_prod", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "nanogram per hour" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of bacterial carbon production", - "title": "bacterial carbon production", - "examples": [ - { - "value": "2.53 microgram per liter per hour" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "bacterial carbon production" - ], - "rank": 5, - "is_a": "core field", - "slot_uri": "MIXS:0000173", - "multivalued": false, - "alias": "bacteria_carb_prod", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "biomass": { - "name": "biomass", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "biomass type;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "ton, kilogram, gram" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements", - "title": "biomass", - "examples": [ - { - "value": "total;20 gram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "biomass" - ], - "rank": 6, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000174", - "multivalued": false, - "alias": "biomass", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "bishomohopanol": { - "name": "bishomohopanol", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter, microgram per gram" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of bishomohopanol", - "title": "bishomohopanol", - "examples": [ - { - "value": "14 microgram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "bishomohopanol" - ], - "rank": 7, - "is_a": "core field", - "slot_uri": "MIXS:0000175", - "multivalued": false, - "alias": "bishomohopanol", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "bromide": { - "name": "bromide", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of bromide", - "title": "bromide", - "examples": [ - { - "value": "0.05 parts per million" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "bromide" - ], - "rank": 8, - "is_a": "core field", - "slot_uri": "MIXS:0000176", - "multivalued": false, - "alias": "bromide", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "calcium": { - "name": "calcium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, micromole per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of calcium in the sample", - "title": "calcium", - "examples": [ - { - "value": "0.2 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "calcium" - ], - "rank": 9, - "is_a": "core field", - "slot_uri": "MIXS:0000432", - "multivalued": false, - "alias": "calcium", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "carb_nitro_ratio": { - "name": "carb_nitro_ratio", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Ratio of amount or concentrations of carbon to nitrogen", - "title": "carbon/nitrogen ratio", - "examples": [ - { - "value": "0.417361111" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "carbon/nitrogen ratio" - ], - "rank": 44, - "is_a": "core field", - "slot_uri": "MIXS:0000310", - "multivalued": false, - "alias": "carb_nitro_ratio", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "SoilInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "float", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "chem_administration": { - "name": "chem_administration", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "CHEBI;timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", - "title": "chemical administration", - "examples": [ - { - "value": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22" - }, - { - "value": "agar [CHEBI:2509];2018-05" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "chemical administration" - ], - "rank": 17, - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]};{timestamp}", - "slot_uri": "MIXS:0000751", - "multivalued": false, - "alias": "chem_administration", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" - }, - "chloride": { - "name": "chloride", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of chloride in the sample", - "title": "chloride", - "examples": [ - { - "value": "5000 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "chloride" - ], - "rank": 10, - "is_a": "core field", - "slot_uri": "MIXS:0000429", - "multivalued": false, - "alias": "chloride", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "chlorophyll": { - "name": "chlorophyll", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per cubic meter, microgram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of chlorophyll", - "title": "chlorophyll", - "examples": [ - { - "value": "5 milligram per cubic meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "chlorophyll" - ], - "rank": 11, - "is_a": "core field", - "slot_uri": "MIXS:0000177", - "multivalued": false, - "alias": "chlorophyll", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "collection_date": { - "name": "collection_date", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "date and time" - } - }, - "description": "The date of sampling", - "title": "collection date", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", - "Use modified term (amended definition)" - ], - "examples": [ - { - "value": "2021-04-15" - }, - { - "value": "2021-04" - }, - { - "value": "2021" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "collection date" - ], - "rank": 3, - "is_a": "environment field", - "string_serialization": "{date, arbitrary precision}", - "slot_uri": "MIXS:0000011", - "multivalued": false, - "alias": "collection_date", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" - }, - "depth": { - "name": "depth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - } - }, - "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", - "title": "depth, meters", - "notes": [ - "Use modified term" - ], - "comments": [ - "All depths must be reported in meters. Provide the numerical portion only." - ], - "examples": [ - { - "value": "0 - 0.1" - }, - { - "value": "1" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "depth" - ], - "rank": 9, - "is_a": "environment field", - "string_serialization": "{float}|{float}-{float}", - "slot_uri": "MIXS:0000018", - "multivalued": false, - "alias": "depth", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$" - }, - "diether_lipids": { - "name": "diether_lipids", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "diether lipid name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "nanogram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Concentration of diether lipids; can include multiple types of diether lipids", - "title": "diether lipids", - "examples": [ - { - "value": "0.2 nanogram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "diether lipids" - ], - "rank": 13, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000178", - "multivalued": false, - "alias": "diether_lipids", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "diss_carb_dioxide": { - "name": "diss_carb_dioxide", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample", - "title": "dissolved carbon dioxide", - "examples": [ - { - "value": "5 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved carbon dioxide" - ], - "rank": 14, - "is_a": "core field", - "slot_uri": "MIXS:0000436", - "multivalued": false, - "alias": "diss_carb_dioxide", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_hydrogen": { - "name": "diss_hydrogen", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved hydrogen", - "title": "dissolved hydrogen", - "examples": [ - { - "value": "0.3 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved hydrogen" - ], - "rank": 15, - "is_a": "core field", - "slot_uri": "MIXS:0000179", - "multivalued": false, - "alias": "diss_hydrogen", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_inorg_carb": { - "name": "diss_inorg_carb", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter", - "title": "dissolved inorganic carbon", - "examples": [ - { - "value": "2059 micromole per kilogram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved inorganic carbon" - ], - "rank": 16, - "is_a": "core field", - "slot_uri": "MIXS:0000434", - "multivalued": false, - "alias": "diss_inorg_carb", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_org_carb": { - "name": "diss_org_carb", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid", - "title": "dissolved organic carbon", - "examples": [ - { - "value": "197 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved organic carbon" - ], - "rank": 17, - "is_a": "core field", - "slot_uri": "MIXS:0000433", - "multivalued": false, - "alias": "diss_org_carb", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_org_nitro": { - "name": "diss_org_nitro", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2", - "title": "dissolved organic nitrogen", - "examples": [ - { - "value": "0.05 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved organic nitrogen" - ], - "rank": 18, - "is_a": "core field", - "slot_uri": "MIXS:0000162", - "multivalued": false, - "alias": "diss_org_nitro", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_oxygen": { - "name": "diss_oxygen", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per kilogram, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved oxygen", - "title": "dissolved oxygen", - "examples": [ - { - "value": "175 micromole per kilogram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved oxygen" - ], - "rank": 19, - "is_a": "core field", - "slot_uri": "MIXS:0000119", - "multivalued": false, - "alias": "diss_oxygen", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "ecosystem": { - "name": "ecosystem", - "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", - "notes": [ - "range: string or EcosystemEnum? The enum could be dynamic or might be soil biased." - ], - "comments": [ - "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 9, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_category": { - "name": "ecosystem_category", - "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", - "notes": [ - "string or EcosystemCategoryEnum range?" - ], - "comments": [ - "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 10, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem_category", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_subtype": { - "name": "ecosystem_subtype", - "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", - "notes": [ - "string or EcosystemSubtypeEnum range?" - ], - "comments": [ - "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 12, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem_subtype", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_type": { - "name": "ecosystem_type", - "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", - "notes": [ - "string or EcosystemTypeEnum range?" - ], - "comments": [ - "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 11, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem_type", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "elev": { - "name": "elev", - "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", - "title": "elevation, meters", - "comments": [ - "All elevations must be reported in meters. Provide the numerical portion only.", - "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." - ], - "examples": [ - { - "value": "225" - }, - { - "value": "0" - }, - { - "value": "1250" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "slot_uri": "MIXS:0000093", - "multivalued": false, - "alias": "elev", - "owner": "BiofilmInterface", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "float", - "required": true - }, - "env_broad_scale": { - "name": "env_broad_scale", - "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", - "title": "broad-scale environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000012", - "multivalued": false, - "alias": "env_broad_scale", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_local_scale": { - "name": "env_local_scale", - "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", - "title": "local environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "canopy [ENVO:00000047]" - }, - { - "value": "herb and fern layer [ENVO:01000337]" - }, - { - "value": "litter layer [ENVO:01000338]" - }, - { - "value": "understory [01000335]" - }, - { - "value": "shrub layer [ENVO:01000336]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 7, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000013", - "multivalued": false, - "alias": "env_local_scale", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_medium": { - "name": "env_medium", - "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", - "title": "environmental medium", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "soil [ENVO:00001998]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 8, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000014", - "multivalued": false, - "alias": "env_medium", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_package": { - "name": "env_package", - "description": "Select the MIxS enviromental package that best describes the environment from which your sample was collected.", - "title": "environmental package", - "examples": [ - { - "value": "soil" - } - ], - "in_subset": [ - "mixs extension" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "environmental package" - ], - "rank": 4, - "is_a": "attribute", - "multivalued": false, - "alias": "env_package", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true - }, - "experimental_factor": { - "name": "experimental_factor", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text or EFO and/or OBI" - } - }, - "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", - "title": "experimental factor", - "examples": [ - { - "value": "time series design [EFO:EFO_0001779]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "experimental factor" - ], - "rank": 12, - "is_a": "investigation field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000008", - "multivalued": false, - "alias": "experimental_factor", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "geo_loc_name": { - "name": "geo_loc_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" - } - }, - "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", - "title": "geographic location (country and/or sea,region)", - "examples": [ - { - "value": "USA: Maryland, Bethesda" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "geographic location (country and/or sea,region)" - ], - "rank": 4, - "is_a": "environment field", - "string_serialization": "{text}: {text}, {text}", - "slot_uri": "MIXS:0000010", - "multivalued": false, - "alias": "geo_loc_name", - "owner": "BiofilmInterface", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" - }, - "glucosidase_act": { - "name": "glucosidase_act", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mol per liter per hour" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of glucosidase activity", - "title": "glucosidase activity", - "examples": [ - { - "value": "5 mol per liter per hour" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "glucosidase activity" - ], - "rank": 20, - "is_a": "core field", - "slot_uri": "MIXS:0000137", - "multivalued": false, - "alias": "glucosidase_act", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - 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The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", - "title": "organism count", - "examples": [ - { - "value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "organism count" - ], - "rank": 30, - "is_a": "core field", - "slot_uri": "MIXS:0000103", - "multivalued": false, - "alias": "organism_count", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$" - }, - "oxy_stat_samp": { - "name": "oxy_stat_samp", - "description": "Oxygenation status of sample", - "title": "oxygenation status of sample", - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 25, - "is_a": "core field", - "slot_uri": "MIXS:0000753", - "multivalued": false, - "alias": "oxy_stat_samp", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "OxyStatSampEnum" - }, - "part_org_carb": { - "name": "part_org_carb", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of particulate organic carbon", - "title": "particulate organic carbon", - "examples": [ - { - "value": "1.92 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "particulate organic carbon" - ], - "rank": 31, - "is_a": "core field", - "slot_uri": "MIXS:0000515", - "multivalued": false, - "alias": "part_org_carb", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "perturbation": { - "name": "perturbation", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "perturbation type name;perturbation interval and duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types", - "title": "perturbation", - "examples": [ - { - "value": "antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "perturbation" - ], - "rank": 33, - "is_a": "core field", - "string_serialization": "{text};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000754", - "multivalued": false, - "alias": "perturbation", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "petroleum_hydrocarb": { - "name": "petroleum_hydrocarb", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of petroleum hydrocarbon", - "title": "petroleum hydrocarbon", - "examples": [ - { - "value": "0.05 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "petroleum hydrocarbon" - ], - "rank": 34, - "is_a": "core field", - "slot_uri": "MIXS:0000516", - "multivalued": false, - "alias": "petroleum_hydrocarb", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "ph": { - "name": "ph", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid", - "title": "pH", - "notes": [ - "Use modified term" - ], - "examples": [ - { - "value": "7.2" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "pH" - ], - "rank": 27, - "is_a": "core field", - "string_serialization": "{float}", - "slot_uri": "MIXS:0001001", - "multivalued": false, - "alias": "ph", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "float", - "recommended": true, - "minimum_value": 0, - "maximum_value": 14 - }, - "ph_meth": { - "name": "ph_meth", - "description": "Reference or method used in determining ph", - "title": "pH method", - "comments": [ - "This can include a link to the instrument used or a citation for the method." - ], - "examples": [ - { - "value": "https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB" - }, - { - "value": "https://doi.org/10.2136/sssabookser5.3.c16" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 41, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0001106", - "multivalued": false, - "alias": "ph_meth", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "phaeopigments": { - "name": "phaeopigments", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "phaeopigment name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per cubic meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Concentration of phaeopigments; can include multiple phaeopigments", - "title": "phaeopigments", - "examples": [ - { - "value": "2.5 milligram per cubic meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "phaeopigments" - ], - "rank": 35, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000180", - "multivalued": false, - "alias": "phaeopigments", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "phosphate": { - "name": "phosphate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of phosphate", - "title": "phosphate", - "examples": [ - { - "value": "0.7 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "phosphate" - ], - "rank": 53, - "is_a": "core field", - "slot_uri": "MIXS:0000505", - "multivalued": false, - "alias": "phosphate", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "phosplipid_fatt_acid": { - "name": "phosplipid_fatt_acid", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "phospholipid fatty acid name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mole per gram, mole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Concentration of phospholipid fatty acids; can include multiple values", - "title": "phospholipid fatty acid", - "examples": [ - { - "value": "2.98 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "phospholipid fatty acid" - ], - "rank": 36, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000181", - "multivalued": false, - "alias": "phosplipid_fatt_acid", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "potassium": { - "name": "potassium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of potassium in the sample", - "title": "potassium", - "examples": [ - { - "value": "463 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "potassium" - ], - "rank": 38, - "is_a": "core field", - "slot_uri": "MIXS:0000430", - "multivalued": false, - "alias": "potassium", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "pressure": { - "name": "pressure", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "atmosphere" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Pressure to which the sample is subject to, in atmospheres", - "title": "pressure", - "examples": [ - { - "value": "50 atmosphere" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "pressure" - ], - "rank": 39, - "is_a": "core field", - "slot_uri": "MIXS:0000412", - "multivalued": false, - "alias": "pressure", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "redox_potential": { - "name": "redox_potential", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millivolt" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential", - "title": "redox potential", - "examples": [ - { - "value": "300 millivolt" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "redox potential" - ], - "rank": 40, - "is_a": "core field", - "slot_uri": "MIXS:0000182", - "multivalued": false, - "alias": "redox_potential", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "salinity": { - "name": "salinity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "practical salinity unit, percentage" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", - "title": "salinity", - "examples": [ - { - "value": "25 practical salinity unit" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "salinity" - ], - "rank": 54, - "is_a": "core field", - "slot_uri": "MIXS:0000183", - "multivalued": false, - "alias": "salinity", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "samp_collec_device": { - "name": "samp_collec_device", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "device name" - } - }, - "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", - "title": "sample collection device", - "comments": [ - "Report dimensions and details when applicable" - ], - "examples": [ - { - "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection device" - ], - "rank": 14, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000002", - "multivalued": false, - "alias": "samp_collec_device", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "samp_collec_method": { - "name": "samp_collec_method", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI,url , or text" - } - }, - "description": "The method employed for collecting the sample.", - "title": "sample collection method", - "comments": [ - "This can be a citation or description" - ], - "examples": [ - { - "value": "swabbing" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection method" - ], - "rank": 15, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{PMID}|{DOI}|{URL}|{text}", - "slot_uri": "MIXS:0001225", - "multivalued": false, - "alias": "samp_collec_method", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_mat_process": { - "name": "samp_mat_process", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - } - }, - "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", - "title": "sample material processing", - "examples": [ - { - "value": "filtering of seawater" - }, - { - "value": "storing samples in ethanol" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample material processing" - ], - "rank": 12, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000016", - "multivalued": false, - "alias": "samp_mat_process", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_size": { - "name": "samp_size", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millliter, gram, milligram, liter" - } - }, - "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", - "title": "amount or size of sample collected", - "comments": [ - "This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis." - ], - "examples": [ - { - "value": "5 grams" - }, - { - "value": "10 mL" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "amount or size of sample collected" - ], - "rank": 18, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float} {unit}", - "slot_uri": "MIXS:0000001", - "multivalued": false, - "alias": "samp_size", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" - }, - "samp_store_dur": { - "name": "samp_store_dur", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Duration for which the sample was stored", - "title": "sample storage duration", - "examples": [ - { - "value": "P1Y6M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage duration" - ], - "rank": 353, - "is_a": "core field", - "string_serialization": "{duration}", - "slot_uri": "MIXS:0000116", - "multivalued": false, - "alias": "samp_store_dur", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_store_loc": { - "name": "samp_store_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "location name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Location at which sample was stored, usually name of a specific freezer/room", - "title": "sample storage location", - "examples": [ - { - "value": "Freezer no:5" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage location" - ], - "rank": 41, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000755", - "multivalued": false, - "alias": "samp_store_loc", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_store_temp": { - "name": "samp_store_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Temperature at which the sample was stored (degrees are assumed)", - "title": "sample storage temperature", - "examples": [ - { - "value": "-80 Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage temperature" - ], - "rank": 7, - "is_a": "core field", - "slot_uri": "MIXS:0000110", - "multivalued": false, - "alias": "samp_store_temp", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "sample_link": { - "name": "sample_link", - "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", - "title": "sample linkage", - "notes": [ - "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" - ], - "comments": [ - "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" - ], - "examples": [ - { - "value": "IGSN:DSJ0284" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "string_serialization": "{text}:{text}", - "multivalued": false, - "alias": "sample_link", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface", - "SampIdNewTermsMixin" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true, - "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" - }, - "silicate": { - "name": "silicate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of silicate", - "title": "silicate", - "examples": [ - { - "value": "0.05 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "silicate" - ], - "rank": 43, - "is_a": "core field", - "slot_uri": "MIXS:0000184", - "multivalued": false, - "alias": "silicate", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "size_frac": { - "name": "size_frac", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "filter size value range" - } - }, - "description": "Filtering pore size used in sample preparation", - "title": "size fraction selected", - "examples": [ - { - "value": "0-0.22 micrometer" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "size fraction selected" - ], - "rank": 285, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float}-{float} {unit}", - "slot_uri": "MIXS:0000017", - "multivalued": false, - "alias": "size_frac", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "sodium": { - "name": "sodium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Sodium concentration in the sample", - "title": "sodium", - "examples": [ - { - "value": "10.5 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sodium" - ], - "rank": 363, - "is_a": "core field", - "slot_uri": "MIXS:0000428", - "multivalued": false, - "alias": "sodium", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "specific_ecosystem": { - "name": "specific_ecosystem", - "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", - "notes": [ - "string or SpecificEcosystemEnum range?" - ], - "comments": [ - "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 13, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "specific_ecosystem", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "sulfate": { - "name": "sulfate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of sulfate in the sample", - "title": "sulfate", - "examples": [ - { - "value": "5 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sulfate" - ], - "rank": 44, - "is_a": "core field", - "slot_uri": "MIXS:0000423", - "multivalued": false, - "alias": "sulfate", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "sulfide": { - "name": "sulfide", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of sulfide in the sample", - "title": "sulfide", - "examples": [ - { - "value": "2 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sulfide" - ], - "rank": 371, - "is_a": "core field", - "slot_uri": "MIXS:0000424", - "multivalued": false, - "alias": "sulfide", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "temp": { - "name": "temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - } - }, - "description": "Temperature of the sample at the time of sampling.", - "title": "temperature", - "examples": [ - { - "value": "25 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "temperature" - ], - "rank": 37, - "is_a": "environment field", - "slot_uri": "MIXS:0000113", - "multivalued": false, - "alias": "temp", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tot_carb": { - "name": "tot_carb", - "description": "Total carbon content", - "title": "total carbon", - "todos": [ - "is this inorganic and organic? both? could use some clarification.", - "ug/L doesn't seem like the right units. Should check this slots usage in databases and re-evaluate. I couldn't find any references that provided this data in this format", - "is this inorganic and organic? both? could use some clarification.", - "ug/L doesn't seem like the right units. Should check this slots usage in databases and re-evaluate. I couldn't find any references that provided this data in this format" - ], - "examples": [ - { - "value": "1 ug/L" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 47, - "is_a": "core field", - "slot_uri": "MIXS:0000525", - "multivalued": false, - "alias": "tot_carb", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tot_nitro_content": { - "name": "tot_nitro_content", - "description": "Total nitrogen content of the sample", - "title": "total nitrogen content", - "examples": [ - { - "value": "5 mg N/ L" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 48, - "is_a": "core field", - "slot_uri": "MIXS:0000530", - "multivalued": false, - "alias": "tot_nitro_content", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tot_org_carb": { - "name": "tot_org_carb", - "description": "Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content", - "title": "total organic carbon", - "todos": [ - "check description. How are they different?", - "check description. How are they different?" - ], - "examples": [ - { - "value": "5 mg N/ L" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 50, - "is_a": "core field", - "slot_uri": "MIXS:0000533", - "multivalued": false, - "alias": "tot_org_carb", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "turbidity": { - "name": "turbidity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "formazin turbidity unit, formazin nephelometric units" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measure of the amount of cloudiness or haziness in water caused by individual particles", - "title": "turbidity", - "examples": [ - { - "value": "0.3 nephelometric turbidity units" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "turbidity" - ], - "rank": 47, - "is_a": "core field", - "slot_uri": "MIXS:0000191", - "multivalued": false, - "alias": "turbidity", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "water_content": { - "name": "water_content", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "string" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram per gram or cubic centimeter per cubic centimeter" - } - }, - "description": "Water content measurement", - "title": "water content", - "todos": [ - "value in preferred unit is too limiting. need to change this", - "check and correct validation so examples are accepted", - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "how to manage multiple water content methods?", - "value in preferred unit is too limiting. need to change this", - "check and correct validation so examples are accepted", - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "how to manage multiple water content methods?" - ], - "examples": [ - { - "value": "75%" - }, - { - "value": "75 %" - }, - { - "value": "0.75 g water/g dry soil" - }, - { - "value": "75% water holding capacity" - }, - { - "value": "1.1 g fresh weight/ dry weight" - }, - { - "value": "10% water filled pore space" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 39, - "is_a": "core field", - "string_serialization": "{float or pct} {unit}", - "slot_uri": "MIXS:0000185", - "multivalued": false, - "alias": "water_content", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?%? \\S.+$" - }, - "analysis_type": { - "name": "analysis_type", - "description": "Select all the data types associated or available for this biosample", - "title": "analysis/data type", - "examples": [ - { - "value": "metagenomics; metabolomics; proteomics" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:investigation_type" - ], - "rank": 3, - "multivalued": true, - "alias": "analysis_type", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface" - ], - "slot_group": "sample_id_section", - "range": "analysis_type_enum", - "required": true, - "recommended": true - }, - "samp_name": { - "name": "samp_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - } - }, - "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", - "title": "sample name", - "comments": [ - "It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." - ], - "examples": [ - { - "value": "Rock core CB1178(5-6) from NSW" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample name" - ], - "rank": 1, - "is_a": "investigation field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0001107", - "multivalued": false, - "identifier": true, - "alias": "samp_name", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true - }, - "source_mat_id": { - "name": "source_mat_id", - "description": "A globally unique identifier assigned to the biological sample.", - "title": "source material identifier", - "todos": [ - "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID.", - "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID." - ], - "notes": [ - "The source material IS the Globally Unique ID" - ], - "comments": [ - "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).", - "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/)." - ], - "examples": [ - { - "value": "IGSN:AU1243" - }, - { - "value": "UUID:24f1467a-40f4-11ed-b878-0242ac120002" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 2, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{text}:{text}", - "slot_uri": "MIXS:0000026", - "multivalued": false, - "alias": "source_mat_id", - "owner": "BiofilmInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" - } - } - }, - "BuiltEnvInterface": { - "name": "BuiltEnvInterface", - "description": "built_env dh_interface", - "title": "Built Env", - "from_schema": "https://example.com/nmdc_submission_schema", - "is_a": "DhInterface", - "mixins": [ - "DhMultiviewCommonColumnsMixin", - "SampIdNewTermsMixin" - ], - "slots": [ - "abs_air_humidity", - "address", - "adj_room", - "aero_struc", - "air_temp", - "alt", - "amount_light", - "arch_struc", - "avg_dew_point", - "avg_occup", - "avg_temp", - "bathroom_count", - "bedroom_count", - "build_docs", - "build_occup_type", - "building_setting", - "built_struc_age", - "built_struc_set", - "built_struc_type", - "carb_dioxide", - "ceil_area", - "ceil_cond", - "ceil_finish_mat", - "ceil_struc", - "ceil_texture", - "ceil_thermal_mass", - "ceil_type", - "ceil_water_mold", - "collection_date", - "cool_syst_id", - "date_last_rain", - "depth", - "dew_point", - "door_comp_type", - "door_cond", - "door_direct", - "door_loc", - "door_mat", - "door_move", - "door_size", - "door_type", - "door_type_metal", - "door_type_wood", - "door_water_mold", - "drawings", - "ecosystem", - "ecosystem_category", - "ecosystem_subtype", - "ecosystem_type", - "elev", - "elevator", - "env_broad_scale", - "env_local_scale", - "env_medium", - "env_package", - "escalator", - "exp_duct", - "exp_pipe", - "experimental_factor", - "ext_door", - "ext_wall_orient", - "ext_window_orient", - "filter_type", - "fireplace_type", - "floor_age", - "floor_area", - "floor_cond", - "floor_count", - "floor_finish_mat", - "floor_struc", - "floor_thermal_mass", - "floor_water_mold", - "freq_clean", - "freq_cook", - "furniture", - "gender_restroom", - "geo_loc_name", - "hall_count", - "handidness", - "heat_cool_type", - "heat_deliv_loc", - "heat_sys_deliv_meth", - "heat_system_id", - "height_carper_fiber", - "horizon_meth", - "indoor_space", - "indoor_surf", - "inside_lux", - "int_wall_cond", - "last_clean", - "lat_lon", - "light_type", - "max_occup", - "mech_struc", - "number_pets", - "number_plants", - "number_resident", - "occup_density_samp", - "occup_document", - "occup_samp", - "organism_count", - "pres_animal_insect", - "quad_pos", - "rel_air_humidity", - "rel_humidity_out", - "rel_samp_loc", - "room_air_exch_rate", - "room_architec_elem", - "room_condt", - "room_connected", - "room_count", - "room_dim", - "room_door_dist", - "room_door_share", - "room_hallway", - "room_loc", - "room_moist_dam_hist", - "room_net_area", - "room_occup", - "room_samp_pos", - "room_type", - "room_vol", - "room_wall_share", - "room_window_count", - "samp_floor", - "samp_room_id", - "samp_sort_meth", - "samp_time_out", - "samp_weather", - "sample_link", - "season", - "season_use", - "shad_dev_water_mold", - "shading_device_cond", - "shading_device_loc", - "shading_device_mat", - "shading_device_type", - "size_frac", - "space_typ_state", - "specific", - "specific_ecosystem", - "specific_humidity", - "substructure_type", - "surf_air_cont", - "surf_humidity", - "surf_material", - "surf_moisture", - "surf_moisture_ph", - "surf_temp", - "temp", - "temp_out", - "train_line", - "train_stat_loc", - "train_stop_loc", - "typ_occup_density", - "ventilation_type", - "vis_media", - "wall_area", - "wall_const_type", - "wall_finish_mat", - "wall_height", - "wall_loc", - "wall_surf_treatment", - "wall_texture", - "wall_thermal_mass", - "wall_water_mold", - "water_feat_size", - "water_feat_type", - "weekday", - "window_cond", - "window_cover", - "window_horiz_pos", - "window_loc", - "window_mat", - "window_open_freq", - "window_size", - "window_status", - "window_type", - "window_vert_pos", - "window_water_mold" - ], - "slot_usage": { - "abs_air_humidity": { - "name": "abs_air_humidity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram per gram, kilogram per kilogram, kilogram, pound" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Actual mass of water vapor - mh20 - present in the air water vapor mixture", - "title": "absolute air humidity", - "examples": [ - { - "value": "9 gram per gram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "absolute air humidity" - ], - "rank": 61, - "is_a": "core field", - "slot_uri": "MIXS:0000122", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "address": { - "name": "address", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The street name and building number where the sampling occurred.", - "title": "address", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "address" - ], - "rank": 62, - "is_a": "core field", - "string_serialization": "{integer}{text}", - "slot_uri": "MIXS:0000218", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "adj_room": { - "name": "adj_room", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "room name;room number" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "List of rooms (room number, room name) immediately adjacent to the sampling room", - "title": "adjacent rooms", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "adjacent rooms" - ], - "rank": 63, - "is_a": "core field", - "string_serialization": "{text};{integer}", - "slot_uri": "MIXS:0000219", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "aero_struc": { - "name": "aero_struc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together", - "title": "aerospace structure", - "examples": [ - { - "value": "plane" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "aerospace structure" - ], - "rank": 64, - "is_a": "core field", - "string_serialization": "[plane|glider]", - "slot_uri": "MIXS:0000773", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "air_temp": { - "name": "air_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Temperature of the air at the time of sampling", - "title": "air temperature", - "examples": [ - { - "value": "20 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "air temperature" - ], - "rank": 65, - "is_a": "core field", - "slot_uri": "MIXS:0000124", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "alt": { - "name": "alt", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - } - }, - "description": "Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. 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"aliases": [ - "average temperature" - ], - "rank": 70, - "is_a": "core field", - "slot_uri": "MIXS:0000142", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "bathroom_count": { - "name": "bathroom_count", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The number of bathrooms in the building", - "title": "bathroom count", - "examples": [ - { - "value": "1" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "bathroom count" - ], - "rank": 71, - "is_a": "core field", - "slot_uri": "MIXS:0000776", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "bedroom_count": { - "name": "bedroom_count", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The number of bedrooms in the building", - "title": "bedroom count", - "examples": [ - { - "value": "2" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "bedroom count" - ], - "rank": 72, - "is_a": "core field", - "slot_uri": "MIXS:0000777", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "build_docs": { - "name": "build_docs", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The building design, construction and operation documents", - "title": "design, construction, and operation documents", - "examples": [ - { - 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"owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "build_occup_type_enum" - }, - "building_setting": { - "name": "building_setting", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "A location (geography) where a building is set", - "title": "building setting", - "examples": [ - { - "value": "rural" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "building setting" - ], - "rank": 75, - "is_a": "core field", - "slot_uri": "MIXS:0000768", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "building_setting_enum" - }, - "built_struc_age": { - "name": "built_struc_age", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "year" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The age of the built structure since construction", - "title": "built structure age", - "examples": [ - { - "value": "15" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "built structure age" - ], - "rank": 76, - "is_a": "core field", - "slot_uri": "MIXS:0000145", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "built_struc_set": { - "name": "built_struc_set", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The characterization of the location of the built structure as high or low human density", - "title": "built structure setting", - "examples": [ - { - "value": "rural" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "built structure setting" - ], - "rank": 77, - "is_a": "core field", - "string_serialization": "[urban|rural]", - "slot_uri": "MIXS:0000778", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "built_struc_type": { - "name": "built_struc_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "free text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads", - "title": "built structure type", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "built structure type" - ], - "rank": 78, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000721", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "carb_dioxide": { - "name": "carb_dioxide", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Carbon dioxide (gas) amount or concentration at the time of sampling", - "title": "carbon dioxide", - "examples": [ - { - "value": "410 parts per million" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "carbon dioxide" - ], - "rank": 50, - "is_a": "core field", - "slot_uri": "MIXS:0000097", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "ceil_area": { - "name": "ceil_area", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "square meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The area of the ceiling space within the room", - "title": "ceiling area", - "examples": [ - { - "value": "25 square meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "ceiling area" - ], - "rank": 79, - "is_a": "core field", - "slot_uri": "MIXS:0000148", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "ceil_cond": { - "name": "ceil_cond", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas", - "title": "ceiling condition", - "examples": [ - { - "value": "damaged" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "ceiling condition" - ], - "rank": 80, - "is_a": "core field", - "slot_uri": "MIXS:0000779", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "ceil_cond_enum" - }, - "ceil_finish_mat": { - "name": "ceil_finish_mat", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of material used to finish a ceiling", - "title": "ceiling finish material", - "examples": [ - { - "value": "stucco" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "ceiling finish material" - ], - "rank": 81, - "is_a": "core field", - "slot_uri": "MIXS:0000780", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "ceil_finish_mat_enum" - }, - "ceil_struc": { - "name": "ceil_struc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The construction format of the ceiling", - "title": "ceiling structure", - "examples": [ - { - "value": "concrete" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "ceiling structure" - ], - "rank": 82, - "is_a": "core field", - "string_serialization": "[wood frame|concrete]", - "slot_uri": "MIXS:0000782", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "ceil_texture": { - "name": "ceil_texture", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The feel, appearance, or consistency of a ceiling surface", - "title": "ceiling texture", - "examples": [ - { - "value": "popcorn" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "ceiling texture" - ], - "rank": 83, - "is_a": "core field", - "slot_uri": "MIXS:0000783", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "ceil_texture_enum" - }, - "ceil_thermal_mass": { - "name": "ceil_thermal_mass", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "joule per degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow", - "title": "ceiling thermal mass", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "ceiling thermal mass" - ], - "rank": 84, - "is_a": "core field", - "slot_uri": "MIXS:0000143", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "ceil_type": { - "name": "ceil_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of ceiling according to the ceiling's appearance or construction", - "title": "ceiling type", - "examples": [ - { - "value": "coffered" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "ceiling type" - ], - "rank": 85, - "is_a": "core field", - "slot_uri": "MIXS:0000784", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "ceil_type_enum" - }, - "ceil_water_mold": { - "name": "ceil_water_mold", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Signs of the presence of mold or mildew on the ceiling", - "title": "ceiling signs of water/mold", - "examples": [ - { - "value": "presence of mold visible" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "ceiling signs of water/mold" - ], - "rank": 86, - "is_a": "core field", - "string_serialization": "[presence of mold visible|no presence of mold visible]", - "slot_uri": "MIXS:0000781", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "collection_date": { - "name": "collection_date", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "date and time" - } - }, - "description": "The date of sampling", - "title": "collection date", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", - "Use modified term (amended definition)" - ], - "examples": [ - { - "value": "2021-04-15" - }, - { - "value": "2021-04" - }, - { - "value": "2021" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "collection date" - ], - "rank": 3, - "is_a": "environment field", - "string_serialization": "{date, arbitrary precision}", - "slot_uri": "MIXS:0000011", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" - }, - "cool_syst_id": { - "name": "cool_syst_id", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "unique identifier" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The cooling system identifier", - "title": "cooling system identifier", - "examples": [ - { - "value": "12345" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "cooling system identifier" - ], - "rank": 87, - "is_a": "core field", - "slot_uri": "MIXS:0000785", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "date_last_rain": { - "name": "date_last_rain", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The date of the last time it rained", - "title": "date last rain", - "examples": [ - { - "value": "2018-05-11:T14:30Z" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "date last rain" - ], - "rank": 88, - "is_a": "core field", - "slot_uri": "MIXS:0000786", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "depth": { - "name": "depth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - } - }, - "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", - "title": "depth, meters", - "notes": [ - "Use modified term" - ], - "comments": [ - "All depths must be reported in meters. Provide the numerical portion only." - ], - "examples": [ - { - "value": "0 - 0.1" - }, - { - "value": "1" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "depth" - ], - "rank": 9, - "is_a": "environment field", - "string_serialization": "{float}|{float}-{float}", - "slot_uri": "MIXS:0000018", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$" - }, - "dew_point": { - "name": "dew_point", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water.", - "title": "dew point", - "examples": [ - { - "value": "22 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dew point" - ], - "rank": 89, - "is_a": "core field", - "slot_uri": "MIXS:0000129", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "door_comp_type": { - "name": "door_comp_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The composite type of the door", - "title": "door type, composite", - "examples": [ - { - "value": "revolving" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "door type, composite" - ], - "rank": 90, - "is_a": "core field", - "slot_uri": "MIXS:0000795", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "door_comp_type_enum" - }, - "door_cond": { - "name": "door_cond", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The phsical condition of the door", - "title": "door condition", - "examples": [ - { - "value": "new" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "door condition" - ], - "rank": 91, - "is_a": "core field", - "slot_uri": "MIXS:0000788", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "door_cond_enum" - }, - "door_direct": { - "name": "door_direct", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The direction the door opens", - "title": "door direction of opening", - "examples": [ - { - "value": "inward" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "door direction of opening" - ], - "rank": 92, - "is_a": "core field", - "slot_uri": "MIXS:0000789", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "door_direct_enum" - }, - "door_loc": { - "name": "door_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The relative location of the door in the room", - "title": "door location", - "examples": [ - { - "value": "north" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "door location" - ], - "rank": 93, - "is_a": "core field", - "slot_uri": "MIXS:0000790", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "door_loc_enum" - }, - "door_mat": { - "name": "door_mat", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The material the door is composed of", - "title": "door material", - "examples": [ - { - "value": "wood" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "door material" - ], - "rank": 94, - "is_a": "core field", - "slot_uri": "MIXS:0000791", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "door_mat_enum" - }, - "door_move": { - "name": "door_move", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of movement of the door", - "title": "door movement", - "examples": [ - { - "value": "swinging" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "door movement" - ], - "rank": 95, - "is_a": "core field", - "slot_uri": "MIXS:0000792", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "door_move_enum" - }, - "door_size": { - "name": "door_size", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "square meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The size of the door", - "title": "door area or size", - "examples": [ - { - "value": "2.5 square meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "door area or size" - ], - "rank": 96, - "is_a": "core field", - "slot_uri": "MIXS:0000158", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "door_type": { - "name": "door_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of door material", - "title": "door type", - "examples": [ - { - "value": "wooden" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "door type" - ], - "rank": 97, - "is_a": "core field", - "slot_uri": "MIXS:0000794", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "door_type_enum" - }, - "door_type_metal": { - "name": "door_type_metal", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of metal door", - "title": "door type, metal", - "examples": [ - { - "value": "hollow" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "door type, metal" - ], - "rank": 98, - "is_a": "core field", - "slot_uri": "MIXS:0000796", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "door_type_metal_enum" - }, - "door_type_wood": { - "name": "door_type_wood", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of wood door", - "title": "door type, wood", - "examples": [ - { - "value": "battened" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "door type, wood" - ], - "rank": 99, - "is_a": "core field", - "slot_uri": "MIXS:0000797", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "door_type_wood_enum" - }, - "door_water_mold": { - "name": "door_water_mold", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Signs of the presence of mold or mildew on a door", - "title": "door signs of water/mold", - "examples": [ - { - "value": "presence of mold visible" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "door signs of water/mold" - ], - "rank": 100, - "is_a": "core field", - "string_serialization": "[presence of mold visible|no presence of mold visible]", - "slot_uri": "MIXS:0000793", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "drawings": { - "name": "drawings", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents", - "title": "drawings", - "examples": [ - { - "value": "sketch" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "drawings" - ], - "rank": 101, - "is_a": "core field", - "slot_uri": "MIXS:0000798", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "drawings_enum" - }, - "ecosystem": { - "name": "ecosystem", - "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", - "notes": [ - "range: string or EcosystemEnum? The enum could be dynamic or might be soil biased." - ], - "comments": [ - "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 9, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_category": { - "name": "ecosystem_category", - "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", - "notes": [ - "string or EcosystemCategoryEnum range?" - ], - "comments": [ - "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 10, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_subtype": { - "name": "ecosystem_subtype", - "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", - "notes": [ - "string or EcosystemSubtypeEnum range?" - ], - "comments": [ - "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 12, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_type": { - "name": "ecosystem_type", - "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", - "notes": [ - "string or EcosystemTypeEnum range?" - ], - "comments": [ - "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 11, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "elev": { - "name": "elev", - "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", - "title": "elevation, meters", - "comments": [ - "All elevations must be reported in meters. Provide the numerical portion only.", - "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." - ], - "examples": [ - { - "value": "225" - }, - { - "value": "0" - }, - { - "value": "1250" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "slot_uri": "MIXS:0000093", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "float", - "required": true - }, - "elevator": { - "name": "elevator", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The number of elevators within the built structure", - "title": "elevator count", - "examples": [ - { - "value": "2" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "elevator count" - ], - "rank": 102, - "is_a": "core field", - "slot_uri": "MIXS:0000799", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "env_broad_scale": { - "name": "env_broad_scale", - "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", - "title": "broad-scale environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000012", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_local_scale": { - "name": "env_local_scale", - "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", - "title": "local environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "canopy [ENVO:00000047]" - }, - { - "value": "herb and fern layer [ENVO:01000337]" - }, - { - "value": "litter layer [ENVO:01000338]" - }, - { - "value": "understory [01000335]" - }, - { - "value": "shrub layer [ENVO:01000336]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 7, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000013", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_medium": { - "name": "env_medium", - "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", - "title": "environmental medium", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "soil [ENVO:00001998]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 8, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000014", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_package": { - "name": "env_package", - "description": "Select the MIxS enviromental package that best describes the environment from which your sample was collected.", - "title": "environmental package", - "examples": [ - { - "value": "soil" - } - ], - "in_subset": [ - "mixs extension" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "environmental package" - ], - "rank": 4, - "is_a": "attribute", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true - }, - "escalator": { - "name": "escalator", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The number of escalators within the built structure", - "title": "escalator count", - "examples": [ - { - "value": "4" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "escalator count" - ], - "rank": 103, - "is_a": "core field", - "slot_uri": "MIXS:0000800", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "exp_duct": { - "name": "exp_duct", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "square meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The amount of exposed ductwork in the room", - "title": "exposed ductwork", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "exposed ductwork" - ], - "rank": 104, - "is_a": "core field", - "slot_uri": "MIXS:0000144", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "exp_pipe": { - "name": "exp_pipe", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The number of exposed pipes in the room", - "title": "exposed pipes", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "exposed pipes" - ], - "rank": 105, - "is_a": "core field", - "slot_uri": "MIXS:0000220", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "experimental_factor": { - "name": "experimental_factor", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text or EFO and/or OBI" - } - }, - "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", - "title": "experimental factor", - "examples": [ - { - "value": "time series design [EFO:EFO_0001779]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "experimental factor" - ], - "rank": 12, - "is_a": "investigation field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000008", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "ext_door": { - "name": "ext_door", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The number of exterior doors in the built structure", - "title": "exterior door count", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "exterior door count" - ], - "rank": 106, - "is_a": "core field", - "slot_uri": "MIXS:0000170", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "ext_wall_orient": { - "name": "ext_wall_orient", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The orientation of the exterior wall", - "title": "orientations of exterior wall", - "examples": [ - { - "value": "northwest" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "orientations of exterior wall" - ], - "rank": 107, - "is_a": "core field", - "slot_uri": "MIXS:0000817", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "ext_wall_orient_enum" - }, - "ext_window_orient": { - "name": "ext_window_orient", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The compass direction the exterior window of the room is facing", - "title": "orientations of exterior window", - "examples": [ - { - "value": "southwest" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "orientations of exterior window" - ], - "rank": 108, - "is_a": "core field", - "slot_uri": "MIXS:0000818", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "ext_window_orient_enum" - }, - "filter_type": { - "name": "filter_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "A device which removes solid particulates or airborne molecular contaminants", - "title": "filter type", - "examples": [ - { - "value": "HEPA" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "filter type" - ], - "rank": 109, - "is_a": "core field", - "slot_uri": "MIXS:0000765", - "multivalued": true, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "filter_type_enum" - }, - "fireplace_type": { - "name": "fireplace_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "A firebox with chimney", - "title": "fireplace type", - "examples": [ - { - "value": "wood burning" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "fireplace type" - ], - "rank": 110, - "is_a": "core field", - "string_serialization": "[gas burning|wood burning]", - "slot_uri": "MIXS:0000802", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "floor_age": { - "name": "floor_age", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "years, weeks, days" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The time period since installment of the carpet or flooring", - "title": "floor age", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "floor age" - ], - "rank": 111, - "is_a": "core field", - "slot_uri": "MIXS:0000164", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "floor_area": { - "name": "floor_area", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "square meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The area of the floor space within the room", - "title": "floor area", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "floor area" - ], - "rank": 112, - "is_a": "core field", - "slot_uri": "MIXS:0000165", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "floor_cond": { - "name": "floor_cond", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas", - "title": "floor condition", - "examples": [ - { - "value": "new" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "floor condition" - ], - "rank": 113, - "is_a": "core field", - "slot_uri": "MIXS:0000803", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "floor_cond_enum" - }, - "floor_count": { - "name": "floor_count", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The number of floors in the building, including basements and mechanical penthouse", - "title": "floor count", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "floor count" - ], - "rank": 114, - "is_a": "core field", - "slot_uri": "MIXS:0000225", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "floor_finish_mat": { - "name": "floor_finish_mat", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The floor covering type; the finished surface that is walked on", - "title": "floor finish material", - "examples": [ - { - "value": "carpet" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "floor finish material" - ], - "rank": 115, - "is_a": "core field", - "slot_uri": "MIXS:0000804", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "floor_finish_mat_enum" - }, - "floor_struc": { - "name": "floor_struc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Refers to the structural elements and subfloor upon which the finish flooring is installed", - "title": "floor structure", - "examples": [ - { - "value": "concrete" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "floor structure" - ], - "rank": 116, - "is_a": "core field", - "slot_uri": "MIXS:0000806", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "floor_struc_enum" - }, - "floor_thermal_mass": { - "name": "floor_thermal_mass", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "joule per degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The ability of the floor to provide inertia against temperature fluctuations", - "title": "floor thermal mass", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "floor thermal mass" - ], - "rank": 117, - "is_a": "core field", - "slot_uri": "MIXS:0000166", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "floor_water_mold": { - "name": "floor_water_mold", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Signs of the presence of mold or mildew in a room", - "title": "floor signs of water/mold", - "examples": [ - { - "value": "ceiling discoloration" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "floor signs of water/mold" - ], - "rank": 118, - "is_a": "core field", - "slot_uri": "MIXS:0000805", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "floor_water_mold_enum" - }, - "freq_clean": { - "name": "freq_clean", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration or {text}" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The number of times the sample location is cleaned. 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"is_a": "core field", - "slot_uri": "MIXS:0000227", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "furniture": { - "name": "furniture", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The types of furniture present in the sampled room", - "title": "furniture", - "examples": [ - { - "value": "chair" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "furniture" - ], - "rank": 121, - "is_a": "core field", - "slot_uri": "MIXS:0000807", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "furniture_enum" - }, - "gender_restroom": { - "name": "gender_restroom", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The gender type of the restroom", - "title": "gender of restroom", - "examples": [ - { - "value": "male" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "gender of restroom" - ], - "rank": 122, - "is_a": "core field", - "slot_uri": "MIXS:0000808", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "gender_restroom_enum" - }, - "geo_loc_name": { - "name": "geo_loc_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" - } - }, - "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", - "title": "geographic location (country and/or sea,region)", - "examples": [ - { - "value": "USA: Maryland, Bethesda" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "geographic location (country and/or sea,region)" - ], - "rank": 4, - "is_a": "environment field", - "string_serialization": "{text}: {text}, {text}", - "slot_uri": "MIXS:0000010", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" - }, - "hall_count": { - "name": "hall_count", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The total count of hallways and cooridors in the built structure", - "title": "hallway/corridor count", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "hallway/corridor count" - ], - "rank": 123, - "is_a": "core field", - "slot_uri": "MIXS:0000228", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "handidness": { - "name": "handidness", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The handidness of the individual sampled", - "title": "handidness", - "examples": [ - { - "value": "right handedness" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "handidness" - ], - "rank": 124, - "is_a": "core field", - "slot_uri": "MIXS:0000809", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "handidness_enum" - }, - "heat_cool_type": { - "name": "heat_cool_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Methods of conditioning or heating a room or building", - "title": "heating and cooling system type", - "examples": [ - { - "value": "heat pump" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "heating and cooling system type" - ], - "rank": 125, - "is_a": "core field", - "slot_uri": "MIXS:0000766", - "multivalued": true, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "heat_cool_type_enum" - }, - "heat_deliv_loc": { - "name": "heat_deliv_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The location of heat delivery within the room", - "title": "heating delivery locations", - "examples": [ - { - "value": "north" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "heating delivery locations" - ], - "rank": 126, - "is_a": "core field", - "slot_uri": "MIXS:0000810", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "heat_deliv_loc_enum" - }, - "heat_sys_deliv_meth": { - "name": "heat_sys_deliv_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The method by which the heat is delivered through the system", - "title": "heating system delivery method", - "examples": [ - { - "value": "radiant" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "heating system delivery method" - ], - "rank": 127, - "is_a": "core field", - "string_serialization": "[conductive|radiant]", - "slot_uri": "MIXS:0000812", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "heat_system_id": { - "name": "heat_system_id", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "unique identifier" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The heating system identifier", - "title": "heating system identifier", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "heating system identifier" - ], - "rank": 128, - "is_a": "core field", - "slot_uri": "MIXS:0000833", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "height_carper_fiber": { - "name": "height_carper_fiber", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "centimeter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The average carpet fiber height in the indoor environment", - "title": "height carpet fiber mat", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "height carpet fiber mat" - ], - "rank": 129, - "is_a": "core field", - "slot_uri": "MIXS:0000167", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "horizon_meth": { - "name": "horizon_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining the horizon", - "title": "horizon method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "soil horizon method" - ], - "rank": 19, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000321", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "indoor_space": { - "name": "indoor_space", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "A distinguishable space within a structure, the purpose for which discrete areas of a building is used", - "title": "indoor space", - "examples": [ - { - "value": "foyer" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "indoor space" - ], - "rank": 130, - "is_a": "core field", - "slot_uri": "MIXS:0000763", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "indoor_space_enum" - }, - "indoor_surf": { - "name": "indoor_surf", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Type of indoor surface", - "title": "indoor surface", - "examples": [ - { - "value": "wall" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "indoor surface" - ], - "rank": 131, - "is_a": "core field", - "slot_uri": "MIXS:0000764", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "indoor_surf_enum" - }, - "inside_lux": { - "name": "inside_lux", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "kilowatt per square metre" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The recorded value at sampling time (power density)", - "title": "inside lux light", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "inside lux light" - ], - "rank": 132, - "is_a": "core field", - "slot_uri": "MIXS:0000168", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "int_wall_cond": { - "name": "int_wall_cond", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas", - "title": "interior wall condition", - "examples": [ - { - "value": "damaged" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "interior wall condition" - ], - "rank": 133, - "is_a": "core field", - "slot_uri": "MIXS:0000813", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "int_wall_cond_enum" - }, - "last_clean": { - "name": "last_clean", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The last time the floor was cleaned (swept, mopped, vacuumed)", - "title": "last time swept/mopped/vacuumed", - "examples": [ - { - "value": "2018-05-11:T14:30Z" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "last time swept/mopped/vacuumed" - ], - "rank": 134, - "is_a": "core field", - "slot_uri": "MIXS:0000814", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "lat_lon": { - "name": "lat_lon", - "description": "This is currently a required field but it's not clear if this should be required for human hosts", - "title": "geographic location (latitude and longitude)", - "notes": [ - "required where?", - "This is currently a required field but it's not clear if this should be required for human hosts" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "is_a": "environment field", - "string_serialization": "{lat lon}", - "slot_uri": "MIXS:0000009", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" - }, - "light_type": { - "name": "light_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. 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"domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "mech_struc": { - "name": "mech_struc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "mechanical structure: a moving structure", - "title": "mechanical structure", - "examples": [ - { - "value": "elevator" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "mechanical structure" - ], - "rank": 137, - "is_a": "core field", - "slot_uri": "MIXS:0000815", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "mech_struc_enum" - }, - "number_pets": { - "name": "number_pets", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The number of pets residing in the sampled space", - "title": "number of pets", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "number of pets" - ], - "rank": 138, - "is_a": "core field", - "slot_uri": "MIXS:0000231", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "number_plants": { - "name": "number_plants", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The number of plant(s) in the sampling space", - "title": "number of houseplants", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "number of houseplants" - ], - "rank": 139, - "is_a": "core field", - "slot_uri": "MIXS:0000230", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "number_resident": { - "name": "number_resident", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The number of individuals currently occupying in the sampling location", - "title": "number of residents", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "number of residents" - ], - "rank": 140, - "is_a": "core field", - "slot_uri": "MIXS:0000232", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "occup_density_samp": { - "name": "occup_density_samp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Average number of occupants at time of sampling per square footage", - "title": "occupant density at sampling", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "occupant density at sampling" - ], - "rank": 141, - "is_a": "core field", - "slot_uri": "MIXS:0000217", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "occup_document": { - "name": "occup_document", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of documentation of occupancy", - "title": "occupancy documentation", - "examples": [ - { - "value": "estimate" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "occupancy documentation" - ], - "rank": 142, - "is_a": "core field", - "slot_uri": "MIXS:0000816", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "occup_document_enum" - }, - "occup_samp": { - "name": "occup_samp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Number of occupants present at time of sample within the given space", - "title": "occupancy at sampling", - "examples": [ - { - "value": "10" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - 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"tag": "occurrence", - "value": "1" - } - }, - "description": "The type and number of animals or insects present in the sampling space.", - "title": "presence of pets, animals, or insects", - "examples": [ - { - "value": "cat;5" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "presence of pets, animals, or insects" - ], - "rank": 144, - "is_a": "core field", - "slot_uri": "MIXS:0000819", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^(cat|dog|rodent|snake|other);\\d+$" - }, - "quad_pos": { - "name": "quad_pos", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The quadrant position of the sampling room within the building", - "title": "quadrant position", - "examples": [ - { - "value": "West side" - } - 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"tag": "preferred_unit", - "value": "liter per hour" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The rate at which outside air replaces indoor air in a given space", - "title": "room air exchange rate", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "room air exchange rate" - ], - "rank": 149, - "is_a": "core field", - "slot_uri": "MIXS:0000169", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "room_architec_elem": { - "name": "room_architec_elem", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "free text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure", - 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"domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "room_condt_enum" - }, - "room_connected": { - "name": "room_connected", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "List of rooms connected to the sampling room by a doorway", - "title": "rooms connected by a doorway", - "examples": [ - { - "value": "office" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "rooms connected by a doorway" - ], - "rank": 152, - "is_a": "core field", - "slot_uri": "MIXS:0000826", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "room_connected_enum" - }, - "room_count": { - "name": "room_count", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The total count of rooms in the built structure including all room types", - "title": "room count", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "room count" - ], - "rank": 153, - "is_a": "core field", - "slot_uri": "MIXS:0000234", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "room_dim": { - "name": "room_dim", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The length, width and height of sampling room", - "title": "room dimensions", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "room dimensions" - ], - "rank": 154, - "is_a": "core field", - "string_serialization": "{integer} {unit} x {integer} {unit} x {integer} {unit}", - "slot_uri": "MIXS:0000192", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "room_door_dist": { - "name": "room_door_dist", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Distance between doors (meters) in the hallway between the sampling room and adjacent rooms", - "title": "room door distance", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "room door distance" - ], - "rank": 155, - "is_a": "core field", - "string_serialization": "{integer} {unit}", - "slot_uri": "MIXS:0000193", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "room_door_share": { - "name": "room_door_share", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "room name;room number" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "List of room(s) (room number, room name) sharing a door with the sampling room", - "title": "rooms that share a door with sampling room", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "rooms that share a door with sampling room" - ], - "rank": 156, - "is_a": "core field", - "string_serialization": "{text};{integer}", - "slot_uri": "MIXS:0000242", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "room_hallway": { - "name": "room_hallway", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "room name;room number" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "List of room(s) (room number, room name) located in the same hallway as sampling room", - "title": "rooms that are on the same hallway", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "rooms that are on the same hallway" - ], - "rank": 157, - "is_a": "core field", - "string_serialization": "{text};{integer}", - "slot_uri": "MIXS:0000238", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "room_loc": { - "name": "room_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The position of the room within the building", - "title": "room location in building", - "examples": [ - { - "value": "interior room" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "room location in building" - ], - "rank": 158, - "is_a": "core field", - "slot_uri": "MIXS:0000823", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "room_loc_enum" - }, - "room_moist_dam_hist": { - "name": "room_moist_dam_hist", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed", - "title": "room moisture damage or mold history", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "room moisture damage or mold history" - ], - "rank": 159, - "is_a": "core field", - "slot_uri": "MIXS:0000235", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "integer" - }, - "room_net_area": { - "name": "room_net_area", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "square feet, square meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The net floor area of sampling room. Net area excludes wall thicknesses", - "title": "room net area", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "room net area" - ], - "rank": 160, - "is_a": "core field", - "string_serialization": "{integer} {unit}", - "slot_uri": "MIXS:0000194", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "room_occup": { - "name": "room_occup", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Count of room occupancy at time of sampling", - "title": "room occupancy", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "room occupancy" - ], - "rank": 161, - "is_a": "core field", - "slot_uri": "MIXS:0000236", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "room_samp_pos": { - "name": "room_samp_pos", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The horizontal sampling position in the room relative to architectural elements", - "title": "room sampling position", - "examples": [ - { - "value": "south corner" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "room sampling position" - ], - "rank": 162, - "is_a": "core field", - "slot_uri": "MIXS:0000824", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "room_samp_pos_enum" - }, - "room_type": { - "name": "room_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The main purpose or activity of the sampling room. A room is any distinguishable space within a structure", - "title": "room type", - "examples": [ - { - "value": "bathroom" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "room type" - ], - "rank": 163, - "is_a": "core field", - "slot_uri": "MIXS:0000825", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "room_type_enum" - }, - "room_vol": { - "name": "room_vol", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "cubic feet, cubic meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Volume of sampling room", - "title": "room volume", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "room volume" - ], - "rank": 164, - "is_a": "core field", - "string_serialization": "{integer} {unit}", - "slot_uri": "MIXS:0000195", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "room_wall_share": { - "name": "room_wall_share", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "room name;room number" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "List of room(s) (room number, room name) sharing a wall with the sampling room", - "title": "rooms that share a wall with sampling room", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "rooms that share a wall with sampling room" - ], - "rank": 165, - "is_a": "core field", - "string_serialization": "{text};{integer}", - "slot_uri": "MIXS:0000243", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "room_window_count": { - "name": "room_window_count", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Number of windows in the room", - "title": "room window count", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "room window count" - ], - "rank": 166, - "is_a": "core field", - "slot_uri": "MIXS:0000237", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "integer" - }, - "samp_floor": { - "name": "samp_floor", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The floor of the building, where the sampling room is located", - "title": "sampling floor", - "examples": [ - { - "value": "4th floor" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sampling floor" - ], - "rank": 167, - "is_a": "core field", - "slot_uri": "MIXS:0000828", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "samp_floor_enum" - }, - "samp_room_id": { - "name": "samp_room_id", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Sampling room number. This ID should be consistent with the designations on the building floor plans", - "title": "sampling room ID or name", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sampling room ID or name" - ], - "rank": 168, - "is_a": "core field", - "slot_uri": "MIXS:0000244", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_sort_meth": { - "name": "samp_sort_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "description of method" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor.", - "title": "sample size sorting method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample size sorting method" - ], - "rank": 169, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000216", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_time_out": { - "name": "samp_time_out", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "time" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "hour" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The recent and long term history of outside sampling", - "title": "sampling time outside", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sampling time outside" - ], - "rank": 170, - "is_a": "core field", - "slot_uri": "MIXS:0000196", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_weather": { - "name": "samp_weather", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The weather on the sampling day", - "title": "sampling day weather", - "examples": [ - { - "value": "foggy" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sampling day weather" - ], - "rank": 171, - "is_a": "core field", - "slot_uri": "MIXS:0000827", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "samp_weather_enum" - }, - "sample_link": { - "name": "sample_link", - "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", - "title": "sample linkage", - "notes": [ - "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" - ], - "comments": [ - "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" - ], - "examples": [ - { - "value": "IGSN:DSJ0284" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "string_serialization": "{text}:{text}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface", - "SampIdNewTermsMixin" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true, - "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" - }, - "season": { - "name": "season", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "NCIT:C94729" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729).", - "title": "season", - "examples": [ - { - "value": "autumn [NCIT:C94733]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "season" - ], - "rank": 172, - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000829", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "season_use": { - "name": "season_use", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The seasons the space is occupied", - "title": "seasonal use", - "examples": [ - { - "value": "Winter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "seasonal use" - ], - "rank": 173, - "is_a": "core field", - "slot_uri": "MIXS:0000830", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "season_use_enum" - }, - "shad_dev_water_mold": { - "name": "shad_dev_water_mold", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Signs of the presence of mold or mildew on the shading device", - "title": "shading device signs of water/mold", - "examples": [ - { - "value": "no presence of mold visible" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "shading device signs of water/mold" - ], - "rank": 174, - "is_a": "core field", - "string_serialization": "[presence of mold visible|no presence of mold visible]", - "slot_uri": "MIXS:0000834", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "shading_device_cond": { - "name": "shading_device_cond", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The physical condition of the shading device at the time of sampling", - "title": "shading device condition", - "examples": [ - { - "value": "new" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "shading device condition" - ], - "rank": 175, - "is_a": "core field", - "slot_uri": "MIXS:0000831", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "shading_device_cond_enum" - }, - "shading_device_loc": { - "name": "shading_device_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The location of the shading device in relation to the built structure", - "title": "shading device location", - "examples": [ - { - "value": "exterior" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "shading device location" - ], - "rank": 176, - "is_a": "core field", - "string_serialization": "[exterior|interior]", - "slot_uri": "MIXS:0000832", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "shading_device_mat": { - "name": "shading_device_mat", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "material name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The material the shading device is composed of", - "title": "shading device material", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "shading device material" - ], - "rank": 177, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000245", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "shading_device_type": { - "name": "shading_device_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of shading device", - "title": "shading device type", - "examples": [ - { - "value": "slatted aluminum awning" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "shading device type" - ], - "rank": 178, - "is_a": "core field", - "slot_uri": "MIXS:0000835", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "shading_device_type_enum" - }, - "size_frac": { - "name": "size_frac", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "filter size value range" - } - }, - "description": "Filtering pore size used in sample preparation", - "title": "size fraction selected", - "examples": [ - { - "value": "0-0.22 micrometer" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "size fraction selected" - ], - "rank": 285, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float}-{float} {unit}", - "slot_uri": "MIXS:0000017", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "space_typ_state": { - "name": "space_typ_state", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Customary or normal state of the space", - "title": "space typical state", - "examples": [ - { - "value": "typically occupied" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "space typical state" - ], - "rank": 179, - "is_a": "core field", - "string_serialization": "[typically occupied|typically unoccupied]", - "slot_uri": "MIXS:0000770", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "specific": { - "name": "specific", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents", - "title": "specifications", - "examples": [ - { - "value": "construction" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "specifications" - ], - "rank": 180, - "is_a": "core field", - "slot_uri": "MIXS:0000836", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "specific_enum" - }, - "specific_ecosystem": { - "name": "specific_ecosystem", - "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", - "notes": [ - "string or SpecificEcosystemEnum range?" - ], - "comments": [ - "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 13, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "specific_humidity": { - "name": "specific_humidity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram of air, kilogram of air" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound.", - "title": "specific humidity", - "examples": [ - { - "value": "15 per kilogram of air" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "specific humidity" - ], - "rank": 181, - "is_a": "core field", - "slot_uri": "MIXS:0000214", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "substructure_type": { - "name": "substructure_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level", - "title": "substructure type", - "examples": [ - { - "value": "basement" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "substructure type" - ], - "rank": 182, - "is_a": "core field", - "slot_uri": "MIXS:0000767", - "multivalued": true, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "substructure_type_enum" - }, - "surf_air_cont": { - "name": "surf_air_cont", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Contaminant identified on surface", - "title": "surface-air contaminant", - "examples": [ - { - "value": "radon" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "surface-air contaminant" - ], - "rank": 183, - "is_a": "core field", - "slot_uri": "MIXS:0000759", - "multivalued": true, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "surf_air_cont_enum" - }, - "surf_humidity": { - "name": "surf_humidity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "percentage" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Surfaces: water activity as a function of air and material moisture", - "title": "surface humidity", - "examples": [ - { - "value": "10%" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "surface humidity" - ], - "rank": 184, - "is_a": "core field", - "slot_uri": "MIXS:0000123", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "surf_material": { - "name": "surf_material", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Surface materials at the point of sampling", - "title": "surface material", - "examples": [ - { - "value": "wood" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "surface material" - ], - "rank": 185, - "is_a": "core field", - "slot_uri": "MIXS:0000758", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "surf_material_enum" - }, - "surf_moisture": { - "name": "surf_moisture", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "parts per million, gram per cubic meter, gram per square meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Water held on a surface", - "title": "surface moisture", - "examples": [ - { - "value": "0.01 gram per square meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "surface moisture" - ], - "rank": 186, - "is_a": "core field", - "slot_uri": "MIXS:0000128", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "surf_moisture_ph": { - "name": "surf_moisture_ph", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "ph measurement of surface", - "title": "surface moisture pH", - "examples": [ - { - "value": "7" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "surface moisture pH" - ], - "rank": 187, - "is_a": "core field", - "slot_uri": "MIXS:0000760", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "double" - }, - "surf_temp": { - "name": "surf_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Temperature of the surface at the time of sampling", - "title": "surface temperature", - "examples": [ - { - "value": "15 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "surface temperature" - ], - "rank": 188, - "is_a": "core field", - "slot_uri": "MIXS:0000125", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "temp": { - "name": "temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - } - }, - "description": "Temperature of the sample at the time of sampling.", - "title": "temperature", - "examples": [ - { - "value": "25 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "temperature" - ], - "rank": 37, - "is_a": "environment field", - "slot_uri": "MIXS:0000113", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - 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}, - "train_line": { - "name": "train_line", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The subway line name", - "title": "train line", - "examples": [ - { - "value": "red" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "train line" - ], - "rank": 190, - "is_a": "core field", - "slot_uri": "MIXS:0000837", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "train_line_enum" - }, - "train_stat_loc": { - "name": "train_stat_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The train station collection location", - "title": "train station collection location", - "examples": [ - { - "value": "forest hills" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "train station collection location" - ], - "rank": 191, - "is_a": "core field", - "slot_uri": "MIXS:0000838", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "train_stat_loc_enum" - }, - "train_stop_loc": { - "name": "train_stop_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The train stop collection location", - "title": "train stop collection location", - "examples": [ - { - "value": "end" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "train stop collection location" - ], - "rank": 192, - "is_a": "core field", - "slot_uri": "MIXS:0000839", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "train_stop_loc_enum" - }, - "typ_occup_density": { - "name": "typ_occup_density", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Customary or normal density of occupants", - "title": "typical occupant density", - "examples": [ - { - "value": "25" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "typical occupant density" - ], - "rank": 193, - "is_a": "core field", - "slot_uri": "MIXS:0000771", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "double" - }, - "ventilation_type": { - "name": "ventilation_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "ventilation type name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Ventilation system used in the sampled premises", - "title": "ventilation type", - "examples": [ - { - "value": "Operable windows" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "ventilation type" - ], - "rank": 57, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000756", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "vis_media": { - "name": "vis_media", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The building visual media", - "title": "visual media", - "examples": [ - { - "value": "3D scans" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "visual media" - ], - "rank": 194, - "is_a": "core field", - "slot_uri": "MIXS:0000840", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "vis_media_enum" - }, - "wall_area": { - "name": "wall_area", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "square meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The total area of the sampled room's walls", - "title": "wall area", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "wall area" - ], - "rank": 195, - "is_a": "core field", - "slot_uri": "MIXS:0000198", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "wall_const_type": { - "name": "wall_const_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The building class of the wall defined by the composition of the building elements and fire-resistance rating.", - "title": "wall construction type", - "examples": [ - { - "value": "fire resistive" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "wall construction type" - ], - "rank": 196, - "is_a": "core field", - "slot_uri": "MIXS:0000841", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "wall_const_type_enum" - }, - "wall_finish_mat": { - "name": "wall_finish_mat", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The material utilized to finish the outer most layer of the wall", - "title": "wall finish material", - "examples": [ - { - "value": "wood" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "wall finish material" - ], - "rank": 197, - "is_a": "core field", - "slot_uri": "MIXS:0000842", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "wall_finish_mat_enum" - }, - "wall_height": { - "name": "wall_height", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "centimeter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The average height of the walls in the sampled room", - "title": "wall height", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "wall height" - ], - "rank": 198, - "is_a": "core field", - "slot_uri": "MIXS:0000221", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "wall_loc": { - "name": "wall_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The relative location of the wall within the room", - "title": "wall location", - "examples": [ - { - "value": "north" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "wall location" - ], - "rank": 199, - "is_a": "core field", - "slot_uri": "MIXS:0000843", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "wall_loc_enum" - }, - "wall_surf_treatment": { - "name": "wall_surf_treatment", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The surface treatment of interior wall", - "title": "wall surface treatment", - "examples": [ - { - "value": "paneling" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "wall surface treatment" - ], - "rank": 200, - "is_a": "core field", - "slot_uri": "MIXS:0000845", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "wall_surf_treatment_enum" - }, - "wall_texture": { - "name": "wall_texture", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The feel, appearance, or consistency of a wall surface", - "title": "wall texture", - "examples": [ - { - "value": "popcorn" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "wall texture" - ], - "rank": 201, - "is_a": "core field", - "slot_uri": "MIXS:0000846", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "wall_texture_enum" - }, - "wall_thermal_mass": { - "name": "wall_thermal_mass", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "joule per degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint", - "title": "wall thermal mass", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "wall thermal mass" - ], - "rank": 202, - "is_a": "core field", - "slot_uri": "MIXS:0000222", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "wall_water_mold": { - "name": "wall_water_mold", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Signs of the presence of mold or mildew on a wall", - "title": "wall signs of water/mold", - "examples": [ - { - "value": "no presence of mold visible" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "wall signs of water/mold" - ], - "rank": 203, - "is_a": "core field", - "string_serialization": "[presence of mold visible|no presence of mold visible]", - "slot_uri": "MIXS:0000844", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "water_feat_size": { - "name": "water_feat_size", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "square meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The size of the water feature", - "title": "water feature size", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "water feature size" - ], - "rank": 204, - "is_a": "core field", - "slot_uri": "MIXS:0000223", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "water_feat_type": { - "name": "water_feat_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of water feature present within the building being sampled", - "title": "water feature type", - "examples": [ - { - "value": "stream" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "water feature type" - ], - "rank": 205, - "is_a": "core field", - "slot_uri": "MIXS:0000847", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "water_feat_type_enum" - }, - "weekday": { - "name": "weekday", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The day of the week when sampling occurred", - "title": "weekday", - "examples": [ - { - "value": "Sunday" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "weekday" - ], - "rank": 206, - "is_a": "core field", - "slot_uri": "MIXS:0000848", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "weekday_enum" - }, - "window_cond": { - "name": "window_cond", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The physical condition of the window at the time of sampling", - "title": "window condition", - "examples": [ - { - "value": "rupture" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "window condition" - ], - "rank": 207, - "is_a": "core field", - "slot_uri": "MIXS:0000849", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "window_cond_enum" - }, - "window_cover": { - "name": "window_cover", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of window covering", - "title": "window covering", - "examples": [ - { - "value": "curtains" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "window covering" - ], - "rank": 208, - "is_a": "core field", - "slot_uri": "MIXS:0000850", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "window_cover_enum" - }, - "window_horiz_pos": { - "name": "window_horiz_pos", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The horizontal position of the window on the wall", - "title": "window horizontal position", - "examples": [ - { - "value": "middle" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "window horizontal position" - ], - "rank": 209, - "is_a": "core field", - "slot_uri": "MIXS:0000851", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "window_horiz_pos_enum" - }, - "window_loc": { - "name": "window_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The relative location of the window within the room", - "title": "window location", - "examples": [ - { - "value": "west" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "window location" - ], - "rank": 210, - "is_a": "core field", - "slot_uri": "MIXS:0000852", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "window_loc_enum" - }, - "window_mat": { - "name": "window_mat", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of material used to finish a window", - "title": "window material", - "examples": [ - { - "value": "wood" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "window material" - ], - "rank": 211, - "is_a": "core field", - "slot_uri": "MIXS:0000853", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "window_mat_enum" - }, - "window_open_freq": { - "name": "window_open_freq", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The number of times windows are opened per week", - "title": "window open frequency", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "window open frequency" - ], - "rank": 212, - "is_a": "core field", - "slot_uri": "MIXS:0000246", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "window_size": { - "name": "window_size", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "inch, meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The window's length and width", - "title": "window area/size", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "window area/size" - ], - "rank": 213, - "is_a": "core field", - "string_serialization": "{float} {unit} x {float} {unit}", - "slot_uri": "MIXS:0000224", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "window_status": { - "name": "window_status", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Defines whether the windows were open or closed during environmental testing", - "title": "window status", - "examples": [ - { - "value": "open" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "window status" - ], - "rank": 214, - "is_a": "core field", - "string_serialization": "[closed|open]", - "slot_uri": "MIXS:0000855", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "window_type": { - "name": "window_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of windows", - "title": "window type", - "examples": [ - { - "value": "fixed window" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "window type" - ], - "rank": 215, - "is_a": "core field", - "slot_uri": "MIXS:0000856", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "window_type_enum" - }, - "window_vert_pos": { - "name": "window_vert_pos", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The vertical position of the window on the wall", - "title": "window vertical position", - "examples": [ - { - "value": "middle" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "window vertical position" - ], - "rank": 216, - "is_a": "core field", - "slot_uri": "MIXS:0000857", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "window_vert_pos_enum" - }, - "window_water_mold": { - "name": "window_water_mold", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Signs of the presence of mold or mildew on the window.", - "title": "window signs of water/mold", - "examples": [ - { - "value": "no presence of mold visible" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "window signs of water/mold" - ], - "rank": 217, - "is_a": "core field", - "string_serialization": "[presence of mold visible|no presence of mold visible]", - "slot_uri": "MIXS:0000854", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "oxy_stat_samp": { - "name": "oxy_stat_samp", - "range": "OxyStatSampEnum" - } - }, - "attributes": { - "abs_air_humidity": { - "name": "abs_air_humidity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram per gram, kilogram per kilogram, kilogram, pound" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Actual mass of water vapor - mh20 - present in the air water vapor mixture", - "title": "absolute air humidity", - "examples": [ - { - "value": "9 gram per gram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "absolute air humidity" - ], - "rank": 61, - "is_a": "core field", - "slot_uri": "MIXS:0000122", - "multivalued": false, - "alias": "abs_air_humidity", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "address": { - "name": "address", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The street name and building number where the sampling occurred.", - "title": "address", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "address" - ], - "rank": 62, - "is_a": "core field", - "string_serialization": "{integer}{text}", - "slot_uri": "MIXS:0000218", - "multivalued": false, - "alias": "address", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "adj_room": { - "name": "adj_room", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "room name;room number" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "List of rooms (room number, room name) immediately adjacent to the sampling room", - "title": "adjacent rooms", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "adjacent rooms" - ], - "rank": 63, - "is_a": "core field", - "string_serialization": "{text};{integer}", - "slot_uri": "MIXS:0000219", - "multivalued": false, - "alias": "adj_room", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "aero_struc": { - "name": "aero_struc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Aerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together", - "title": "aerospace structure", - "examples": [ - { - "value": "plane" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "aerospace structure" - ], - "rank": 64, - "is_a": "core field", - "string_serialization": "[plane|glider]", - "slot_uri": "MIXS:0000773", - "multivalued": false, - "alias": "aero_struc", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "air_temp": { - "name": "air_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Temperature of the air at the time of sampling", - "title": "air temperature", - "examples": [ - { - "value": "20 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "air temperature" - ], - "rank": 65, - "is_a": "core field", - "slot_uri": "MIXS:0000124", - "multivalued": false, - "alias": "air_temp", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "alt": { - "name": "alt", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - } - }, - "description": "Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. 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Indicate the number of person(s) daily occupying the sampling room.", - "title": "average daily occupancy", - "examples": [ - { - "value": "2" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "average daily occupancy" - ], - "rank": 69, - "is_a": "core field", - "slot_uri": "MIXS:0000775", - "multivalued": false, - "alias": "avg_occup", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "avg_temp": { - "name": "avg_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day", - "title": "average temperature", - "examples": [ - { - "value": "12.5 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "average temperature" - ], - "rank": 70, - "is_a": "core field", - "slot_uri": "MIXS:0000142", - "multivalued": false, - "alias": "avg_temp", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "bathroom_count": { - "name": "bathroom_count", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The number of bathrooms in the building", - "title": "bathroom count", - "examples": [ - { - "value": "1" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "bathroom count" - ], - "rank": 71, - "is_a": "core field", - "slot_uri": "MIXS:0000776", - "multivalued": false, - "alias": "bathroom_count", - "owner": "BuiltEnvInterface", - "domain_of": [ - 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"description": "The building design, construction and operation documents", - "title": "design, construction, and operation documents", - "examples": [ - { - "value": "maintenance plans" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "design, construction, and operation documents" - ], - "rank": 73, - "is_a": "core field", - "slot_uri": "MIXS:0000787", - "multivalued": false, - "alias": "build_docs", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "build_docs_enum" - }, - "build_occup_type": { - "name": "build_occup_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "The primary function for which a building or discrete part of a building is intended to be used", - "title": "building occupancy type", - "examples": [ - { - "value": "market" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "building occupancy type" - ], - "rank": 74, - "is_a": "core field", - "slot_uri": "MIXS:0000761", - "multivalued": true, - "alias": "build_occup_type", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "build_occup_type_enum" - }, - "building_setting": { - "name": "building_setting", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "A location (geography) where a building is set", - "title": "building setting", - "examples": [ - { - "value": "rural" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "building setting" - ], - "rank": 75, - "is_a": "core field", - "slot_uri": "MIXS:0000768", - "multivalued": false, - "alias": "building_setting", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "building_setting_enum" - }, - "built_struc_age": { - "name": "built_struc_age", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "year" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The age of the built structure since construction", - "title": "built structure age", - "examples": [ - { - "value": "15" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "built structure age" - ], - "rank": 76, - "is_a": "core field", - "slot_uri": "MIXS:0000145", - "multivalued": false, - "alias": "built_struc_age", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "built_struc_set": { - "name": "built_struc_set", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The characterization of the location of the built structure as high or low human density", - "title": "built structure setting", - "examples": [ - { - "value": "rural" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "built structure setting" - ], - "rank": 77, - "is_a": "core field", - "string_serialization": "[urban|rural]", - "slot_uri": "MIXS:0000778", - "multivalued": false, - "alias": "built_struc_set", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "built_struc_type": { - "name": "built_struc_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "free text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads", - "title": "built structure type", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "built structure type" - ], - "rank": 78, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000721", - "multivalued": false, - "alias": "built_struc_type", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "carb_dioxide": { - "name": "carb_dioxide", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Carbon dioxide (gas) amount or concentration at the time of sampling", - "title": "carbon dioxide", - "examples": [ - { - "value": "410 parts per million" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "carbon dioxide" - ], - "rank": 50, - "is_a": "core field", - "slot_uri": "MIXS:0000097", - "multivalued": false, - "alias": "carb_dioxide", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "ceil_area": { - "name": "ceil_area", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "square meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The area of the ceiling space within the room", - "title": "ceiling area", - "examples": [ - { - "value": "25 square meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "ceiling area" - ], - "rank": 79, - "is_a": "core field", - "slot_uri": "MIXS:0000148", - "multivalued": false, - "alias": "ceil_area", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "ceil_cond": { - "name": "ceil_cond", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas", - "title": "ceiling condition", - "examples": [ - { - "value": "damaged" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "ceiling condition" - ], - "rank": 80, - "is_a": "core field", - "slot_uri": "MIXS:0000779", - "multivalued": false, - "alias": "ceil_cond", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "ceil_cond_enum" - }, - "ceil_finish_mat": { - "name": "ceil_finish_mat", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of material used to finish a ceiling", - "title": "ceiling finish material", - "examples": [ - { - "value": "stucco" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "ceiling finish material" - ], - "rank": 81, - "is_a": "core field", - "slot_uri": "MIXS:0000780", - "multivalued": false, - "alias": "ceil_finish_mat", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "ceil_finish_mat_enum" - }, - "ceil_struc": { - "name": "ceil_struc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The construction format of the ceiling", - "title": "ceiling structure", - "examples": [ - { - "value": "concrete" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "ceiling structure" - ], - "rank": 82, - "is_a": "core field", - "string_serialization": "[wood frame|concrete]", - "slot_uri": "MIXS:0000782", - "multivalued": false, - "alias": "ceil_struc", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "ceil_texture": { - "name": "ceil_texture", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The feel, appearance, or consistency of a ceiling surface", - "title": "ceiling texture", - "examples": [ - { - "value": "popcorn" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "ceiling texture" - ], - "rank": 83, - "is_a": "core field", - "slot_uri": "MIXS:0000783", - "multivalued": false, - "alias": "ceil_texture", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "ceil_texture_enum" - }, - "ceil_thermal_mass": { - "name": "ceil_thermal_mass", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "joule per degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow", - "title": "ceiling thermal mass", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "ceiling thermal mass" - ], - "rank": 84, - "is_a": "core field", - "slot_uri": "MIXS:0000143", - "multivalued": false, - "alias": "ceil_thermal_mass", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "ceil_type": { - "name": "ceil_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of ceiling according to the ceiling's appearance or construction", - "title": "ceiling type", - "examples": [ - { - "value": "coffered" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "ceiling type" - ], - "rank": 85, - "is_a": "core field", - "slot_uri": "MIXS:0000784", - "multivalued": false, - "alias": "ceil_type", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "ceil_type_enum" - }, - "ceil_water_mold": { - "name": "ceil_water_mold", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Signs of the presence of mold or mildew on the ceiling", - "title": "ceiling signs of water/mold", - "examples": [ - { - "value": "presence of mold visible" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "ceiling signs of water/mold" - ], - "rank": 86, - "is_a": "core field", - "string_serialization": "[presence of mold visible|no presence of mold visible]", - "slot_uri": "MIXS:0000781", - "multivalued": false, - "alias": "ceil_water_mold", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "collection_date": { - "name": "collection_date", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "date and time" - } - }, - "description": "The date of sampling", - "title": "collection date", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", - "Use modified term (amended definition)" - ], - "examples": [ - { - "value": "2021-04-15" - }, - { - "value": "2021-04" - }, - { - "value": "2021" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "collection date" - ], - "rank": 3, - "is_a": "environment field", - "string_serialization": "{date, arbitrary precision}", - "slot_uri": "MIXS:0000011", - "multivalued": false, - "alias": "collection_date", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" - }, - "cool_syst_id": { - "name": "cool_syst_id", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "unique identifier" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The cooling system identifier", - "title": "cooling system identifier", - "examples": [ - { - "value": "12345" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "cooling system identifier" - ], - "rank": 87, - "is_a": "core field", - "slot_uri": "MIXS:0000785", - "multivalued": false, - "alias": "cool_syst_id", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "date_last_rain": { - "name": "date_last_rain", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The date of the last time it rained", - "title": "date last rain", - "examples": [ - { - "value": "2018-05-11:T14:30Z" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "date last rain" - ], - "rank": 88, - "is_a": "core field", - "slot_uri": "MIXS:0000786", - "multivalued": false, - "alias": "date_last_rain", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "depth": { - "name": "depth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - } - }, - "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", - "title": "depth, meters", - "notes": [ - "Use modified term" - ], - "comments": [ - "All depths must be reported in meters. Provide the numerical portion only." - ], - "examples": [ - { - "value": "0 - 0.1" - }, - { - "value": "1" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "depth" - ], - "rank": 9, - "is_a": "environment field", - "string_serialization": "{float}|{float}-{float}", - "slot_uri": "MIXS:0000018", - "multivalued": false, - "alias": "depth", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$" - }, - "dew_point": { - "name": "dew_point", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water.", - "title": "dew point", - "examples": [ - { - "value": "22 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dew point" - ], - "rank": 89, - "is_a": "core field", - "slot_uri": "MIXS:0000129", - "multivalued": false, - "alias": "dew_point", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "door_comp_type": { - "name": "door_comp_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The composite type of the door", - "title": "door type, composite", - "examples": [ - { - "value": "revolving" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "door type, composite" - ], - "rank": 90, - "is_a": "core field", - "slot_uri": "MIXS:0000795", - "multivalued": false, - "alias": "door_comp_type", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "door_comp_type_enum" - }, - "door_cond": { - "name": "door_cond", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The phsical condition of the door", - "title": "door condition", - "examples": [ - { - "value": "new" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "door condition" - ], - "rank": 91, - "is_a": "core field", - "slot_uri": "MIXS:0000788", - "multivalued": false, - "alias": "door_cond", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "door_cond_enum" - }, - "door_direct": { - "name": "door_direct", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The direction the door opens", - "title": "door direction of opening", - "examples": [ - { - "value": "inward" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "door direction of opening" - ], - "rank": 92, - "is_a": "core field", - "slot_uri": "MIXS:0000789", - "multivalued": false, - "alias": "door_direct", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "door_direct_enum" - }, - "door_loc": { - "name": "door_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The relative location of the door in the room", - "title": "door location", - "examples": [ - { - "value": "north" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "door location" - ], - "rank": 93, - "is_a": "core field", - "slot_uri": "MIXS:0000790", - "multivalued": false, - "alias": "door_loc", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "door_loc_enum" - }, - "door_mat": { - "name": "door_mat", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The material the door is composed of", - "title": "door material", - "examples": [ - { - "value": "wood" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "door material" - ], - "rank": 94, - "is_a": "core field", - "slot_uri": "MIXS:0000791", - "multivalued": false, - "alias": "door_mat", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "door_mat_enum" - }, - "door_move": { - "name": "door_move", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of movement of the door", - "title": "door movement", - "examples": [ - { - "value": "swinging" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "door movement" - ], - "rank": 95, - "is_a": "core field", - "slot_uri": "MIXS:0000792", - "multivalued": false, - "alias": "door_move", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "door_move_enum" - }, - "door_size": { - "name": "door_size", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "square meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The size of the door", - "title": "door area or size", - "examples": [ - { - "value": "2.5 square meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "door area or size" - ], - "rank": 96, - "is_a": "core field", - "slot_uri": "MIXS:0000158", - "multivalued": false, - "alias": "door_size", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "door_type": { - "name": "door_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of door material", - "title": "door type", - "examples": [ - { - "value": "wooden" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "door type" - ], - "rank": 97, - "is_a": "core field", - "slot_uri": "MIXS:0000794", - "multivalued": false, - "alias": "door_type", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "door_type_enum" - }, - "door_type_metal": { - "name": "door_type_metal", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of metal door", - "title": "door type, metal", - "examples": [ - { - "value": "hollow" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "door type, metal" - ], - "rank": 98, - "is_a": "core field", - "slot_uri": "MIXS:0000796", - "multivalued": false, - "alias": "door_type_metal", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "door_type_metal_enum" - }, - "door_type_wood": { - "name": "door_type_wood", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of wood door", - "title": "door type, wood", - "examples": [ - { - "value": "battened" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "door type, wood" - ], - "rank": 99, - "is_a": "core field", - "slot_uri": "MIXS:0000797", - "multivalued": false, - "alias": "door_type_wood", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "door_type_wood_enum" - }, - "door_water_mold": { - "name": "door_water_mold", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Signs of the presence of mold or mildew on a door", - "title": "door signs of water/mold", - "examples": [ - { - "value": "presence of mold visible" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "door signs of water/mold" - ], - "rank": 100, - "is_a": "core field", - "string_serialization": "[presence of mold visible|no presence of mold visible]", - "slot_uri": "MIXS:0000793", - "multivalued": false, - "alias": "door_water_mold", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "drawings": { - "name": "drawings", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents", - "title": "drawings", - "examples": [ - { - "value": "sketch" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "drawings" - ], - "rank": 101, - "is_a": "core field", - "slot_uri": "MIXS:0000798", - "multivalued": false, - "alias": "drawings", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "drawings_enum" - }, - "ecosystem": { - "name": "ecosystem", - "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", - "notes": [ - "range: string or EcosystemEnum? The enum could be dynamic or might be soil biased." - ], - "comments": [ - "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 9, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_category": { - "name": "ecosystem_category", - "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", - "notes": [ - "string or EcosystemCategoryEnum range?" - ], - "comments": [ - "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 10, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem_category", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_subtype": { - "name": "ecosystem_subtype", - "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", - "notes": [ - "string or EcosystemSubtypeEnum range?" - ], - "comments": [ - "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 12, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem_subtype", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_type": { - "name": "ecosystem_type", - "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", - "notes": [ - "string or EcosystemTypeEnum range?" - ], - "comments": [ - "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 11, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem_type", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "elev": { - "name": "elev", - "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", - "title": "elevation, meters", - "comments": [ - "All elevations must be reported in meters. Provide the numerical portion only.", - "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." - ], - "examples": [ - { - "value": "225" - }, - { - "value": "0" - }, - { - "value": "1250" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "slot_uri": "MIXS:0000093", - "multivalued": false, - "alias": "elev", - "owner": "BuiltEnvInterface", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "float", - "required": true - }, - "elevator": { - "name": "elevator", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The number of elevators within the built structure", - "title": "elevator count", - "examples": [ - { - "value": "2" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "elevator count" - ], - "rank": 102, - "is_a": "core field", - "slot_uri": "MIXS:0000799", - "multivalued": false, - "alias": "elevator", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "env_broad_scale": { - "name": "env_broad_scale", - "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", - "title": "broad-scale environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000012", - "multivalued": false, - "alias": "env_broad_scale", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_local_scale": { - "name": "env_local_scale", - "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", - "title": "local environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "canopy [ENVO:00000047]" - }, - { - "value": "herb and fern layer [ENVO:01000337]" - }, - { - "value": "litter layer [ENVO:01000338]" - }, - { - "value": "understory [01000335]" - }, - { - "value": "shrub layer [ENVO:01000336]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 7, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000013", - "multivalued": false, - "alias": "env_local_scale", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_medium": { - "name": "env_medium", - "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", - "title": "environmental medium", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "soil [ENVO:00001998]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 8, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000014", - "multivalued": false, - "alias": "env_medium", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_package": { - "name": "env_package", - "description": "Select the MIxS enviromental package that best describes the environment from which your sample was collected.", - "title": "environmental package", - "examples": [ - { - "value": "soil" - } - ], - "in_subset": [ - "mixs extension" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "environmental package" - ], - "rank": 4, - "is_a": "attribute", - "multivalued": false, - "alias": "env_package", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true - }, - "escalator": { - "name": "escalator", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The number of escalators within the built structure", - "title": "escalator count", - "examples": [ - { - "value": "4" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "escalator count" - ], - "rank": 103, - "is_a": "core field", - "slot_uri": "MIXS:0000800", - "multivalued": false, - "alias": "escalator", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "exp_duct": { - "name": "exp_duct", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "square meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The amount of exposed ductwork in the room", - "title": "exposed ductwork", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "exposed ductwork" - ], - "rank": 104, - "is_a": "core field", - "slot_uri": "MIXS:0000144", - "multivalued": false, - "alias": "exp_duct", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "exp_pipe": { - "name": "exp_pipe", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The number of exposed pipes in the room", - "title": "exposed pipes", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "exposed pipes" - ], - "rank": 105, - "is_a": "core field", - "slot_uri": "MIXS:0000220", - "multivalued": false, - "alias": "exp_pipe", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "experimental_factor": { - "name": "experimental_factor", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text or EFO and/or OBI" - } - }, - "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", - "title": "experimental factor", - "examples": [ - { - "value": "time series design [EFO:EFO_0001779]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "experimental factor" - ], - "rank": 12, - "is_a": "investigation field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000008", - "multivalued": false, - "alias": "experimental_factor", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "ext_door": { - "name": "ext_door", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The number of exterior doors in the built structure", - "title": "exterior door count", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "exterior door count" - ], - "rank": 106, - "is_a": "core field", - "slot_uri": "MIXS:0000170", - "multivalued": false, - "alias": "ext_door", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "ext_wall_orient": { - "name": "ext_wall_orient", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The orientation of the exterior wall", - "title": "orientations of exterior wall", - "examples": [ - { - "value": "northwest" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "orientations of exterior wall" - ], - "rank": 107, - "is_a": "core field", - "slot_uri": "MIXS:0000817", - "multivalued": false, - "alias": "ext_wall_orient", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "ext_wall_orient_enum" - }, - "ext_window_orient": { - "name": "ext_window_orient", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The compass direction the exterior window of the room is facing", - "title": "orientations of exterior window", - "examples": [ - { - "value": "southwest" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "orientations of exterior window" - ], - "rank": 108, - "is_a": "core field", - "slot_uri": "MIXS:0000818", - "multivalued": false, - "alias": "ext_window_orient", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "ext_window_orient_enum" - }, - "filter_type": { - "name": "filter_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "A device which removes solid particulates or airborne molecular contaminants", - "title": "filter type", - "examples": [ - { - "value": "HEPA" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "filter type" - ], - "rank": 109, - "is_a": "core field", - "slot_uri": "MIXS:0000765", - "multivalued": true, - "alias": "filter_type", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "filter_type_enum" - }, - "fireplace_type": { - "name": "fireplace_type", - 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], - "slot_group": "mixs_core_section", - "range": "indoor_space_enum" - }, - "indoor_surf": { - "name": "indoor_surf", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Type of indoor surface", - "title": "indoor surface", - "examples": [ - { - "value": "wall" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "indoor surface" - ], - "rank": 131, - "is_a": "core field", - "slot_uri": "MIXS:0000764", - "multivalued": false, - "alias": "indoor_surf", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "indoor_surf_enum" - }, - "inside_lux": { - "name": "inside_lux", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "kilowatt per square metre" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The recorded value at sampling time (power density)", - "title": "inside lux light", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "inside lux light" - ], - "rank": 132, - "is_a": "core field", - "slot_uri": "MIXS:0000168", - "multivalued": false, - "alias": "inside_lux", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "int_wall_cond": { - "name": "int_wall_cond", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas", - "title": "interior wall condition", - "examples": [ - { - "value": "damaged" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "interior wall condition" - ], - "rank": 133, - "is_a": "core field", - "slot_uri": "MIXS:0000813", - "multivalued": false, - "alias": "int_wall_cond", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "int_wall_cond_enum" - }, - "last_clean": { - "name": "last_clean", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The last time the floor was cleaned (swept, mopped, vacuumed)", - "title": "last time swept/mopped/vacuumed", - "examples": [ - { - "value": "2018-05-11:T14:30Z" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "last time swept/mopped/vacuumed" - ], - "rank": 134, - "is_a": "core field", - "slot_uri": "MIXS:0000814", - "multivalued": false, - "alias": "last_clean", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "lat_lon": { - "name": "lat_lon", - "description": "This is currently a required field but it's not clear if this should be required for human hosts", - "title": "geographic location (latitude and longitude)", - "notes": [ - "required where?", - "This is currently a required field but it's not clear if this should be required for human hosts" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "is_a": "environment field", - "string_serialization": "{lat lon}", - "slot_uri": "MIXS:0000009", - "multivalued": false, - "alias": "lat_lon", - "owner": "BuiltEnvInterface", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" - }, - "light_type": { - "name": "light_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light", - "title": "light type", - "examples": [ - { - "value": "desk lamp" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "light type" - ], - "rank": 135, - "is_a": "core field", - "slot_uri": "MIXS:0000769", - "multivalued": true, - "alias": "light_type", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "light_type_enum" - }, - "max_occup": { - "name": "max_occup", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The maximum amount of people allowed in the indoor environment", - "title": "maximum occupancy", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "maximum occupancy" - ], - "rank": 136, - "is_a": "core field", - "slot_uri": "MIXS:0000229", - "multivalued": false, - "alias": "max_occup", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "mech_struc": { - "name": "mech_struc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "mechanical structure: a moving structure", - "title": "mechanical structure", - "examples": [ - { - "value": "elevator" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "mechanical structure" - ], - "rank": 137, - "is_a": "core field", - "slot_uri": "MIXS:0000815", - "multivalued": false, - "alias": "mech_struc", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "mech_struc_enum" - }, - "number_pets": { - "name": "number_pets", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The number of pets residing in the sampled space", - "title": "number of pets", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "number of pets" - ], - "rank": 138, - "is_a": "core field", - "slot_uri": "MIXS:0000231", - "multivalued": false, - "alias": "number_pets", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "number_plants": { - "name": "number_plants", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The number of plant(s) in the sampling space", - "title": "number of houseplants", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "number of houseplants" - ], - "rank": 139, - "is_a": "core field", - "slot_uri": "MIXS:0000230", - "multivalued": false, - "alias": "number_plants", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "number_resident": { - "name": "number_resident", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The number of individuals currently occupying in the sampling location", - "title": "number of residents", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "number of residents" - ], - "rank": 140, - "is_a": "core field", - "slot_uri": "MIXS:0000232", - "multivalued": false, - "alias": "number_resident", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "occup_density_samp": { - "name": "occup_density_samp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Average number of occupants at time of sampling per square footage", - "title": "occupant density at sampling", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "occupant density at sampling" - ], - "rank": 141, - "is_a": "core field", - "slot_uri": "MIXS:0000217", - "multivalued": false, - "alias": "occup_density_samp", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "occup_document": { - "name": "occup_document", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of documentation of occupancy", - "title": "occupancy documentation", - "examples": [ - { - "value": "estimate" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "occupancy documentation" - ], - "rank": 142, - "is_a": "core field", - "slot_uri": "MIXS:0000816", - "multivalued": false, - "alias": "occup_document", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "occup_document_enum" - }, - "occup_samp": { - "name": "occup_samp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Number of occupants present at time of sample within the given space", - "title": "occupancy at sampling", - "examples": [ - { - "value": "10" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "occupancy at sampling" - ], - "rank": 143, - "is_a": "core field", - "slot_uri": "MIXS:0000772", - "multivalued": false, - "alias": "occup_samp", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "organism_count": { - "name": "organism_count", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "organism name;measurement value;enumeration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", - "title": "organism count", - "examples": [ - { - "value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "organism count" - ], - "rank": 30, - "is_a": "core field", - "slot_uri": "MIXS:0000103", - "multivalued": false, - "alias": "organism_count", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$" - }, - "pres_animal_insect": { - "name": "pres_animal_insect", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration;count" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type and number of animals or insects present in the sampling space.", - "title": "presence of pets, animals, or insects", - "examples": [ - { - "value": "cat;5" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "presence of pets, animals, or insects" - ], - "rank": 144, - "is_a": "core field", - "slot_uri": "MIXS:0000819", - "multivalued": false, - "alias": "pres_animal_insect", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^(cat|dog|rodent|snake|other);\\d+$" - }, - "quad_pos": { - "name": "quad_pos", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The quadrant position of the sampling room within the building", - "title": "quadrant position", - "examples": [ - { - "value": "West side" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "quadrant position" - ], - "rank": 145, - "is_a": "core field", - "slot_uri": "MIXS:0000820", - "multivalued": false, - "alias": "quad_pos", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "quad_pos_enum" - }, - "rel_air_humidity": { - "name": "rel_air_humidity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "percentage" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air", - "title": "relative air humidity", - "examples": [ - { - "value": "80%" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "relative air humidity" - ], - "rank": 146, - "is_a": "core field", - "slot_uri": "MIXS:0000121", - "multivalued": false, - "alias": "rel_air_humidity", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "rel_humidity_out": { - "name": "rel_humidity_out", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram of air, kilogram of air" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The recorded outside relative humidity value at the time of sampling", - "title": "outside relative humidity", - "examples": [ - { - "value": "12 per kilogram of air" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "outside relative humidity" - ], - "rank": 147, - "is_a": "core field", - "slot_uri": "MIXS:0000188", - "multivalued": false, - "alias": "rel_humidity_out", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "rel_samp_loc": { - "name": "rel_samp_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The sampling location within the train car", - "title": "relative sampling location", - "examples": [ - { - "value": "center of car" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "relative sampling location" - ], - "rank": 148, - "is_a": "core field", - "slot_uri": "MIXS:0000821", - "multivalued": false, - "alias": "rel_samp_loc", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "rel_samp_loc_enum" - }, - "room_air_exch_rate": { - "name": "room_air_exch_rate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "liter per hour" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The rate at which outside air replaces indoor air in a given space", - "title": "room air exchange rate", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "room air exchange rate" - ], - "rank": 149, - "is_a": "core field", - "slot_uri": "MIXS:0000169", - "multivalued": false, - "alias": "room_air_exch_rate", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "room_architec_elem": { - "name": "room_architec_elem", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "free text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure", - "title": "room architectural elements", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "room architectural elements" - ], - "rank": 150, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000233", - "multivalued": false, - "alias": "room_architec_elem", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "room_condt": { - "name": "room_condt", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The condition of the room at the time of sampling", - "title": "room condition", - "examples": [ - { - "value": "new" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "room condition" - ], - "rank": 151, - "is_a": "core field", - "slot_uri": "MIXS:0000822", - "multivalued": false, - "alias": "room_condt", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "room_condt_enum" - }, - "room_connected": { - "name": "room_connected", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "List of rooms connected to the sampling room by a doorway", - "title": "rooms connected by a doorway", - "examples": [ - { - "value": "office" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "rooms connected by a doorway" - ], - "rank": 152, - "is_a": "core field", - "slot_uri": "MIXS:0000826", - "multivalued": false, - "alias": "room_connected", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "room_connected_enum" - }, - "room_count": { - "name": "room_count", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The total count of rooms in the built structure including all room types", - "title": "room count", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "room count" - ], - "rank": 153, - "is_a": "core field", - "slot_uri": "MIXS:0000234", - "multivalued": false, - "alias": "room_count", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "room_dim": { - "name": "room_dim", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The length, width and height of sampling room", - "title": "room dimensions", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "room dimensions" - ], - "rank": 154, - "is_a": "core field", - "string_serialization": "{integer} {unit} x {integer} {unit} x {integer} {unit}", - "slot_uri": "MIXS:0000192", - "multivalued": false, - "alias": "room_dim", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "room_door_dist": { - "name": "room_door_dist", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Distance between doors (meters) in the hallway between the sampling room and adjacent rooms", - "title": "room door distance", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "room door distance" - ], - "rank": 155, - "is_a": "core field", - "string_serialization": "{integer} {unit}", - "slot_uri": "MIXS:0000193", - "multivalued": false, - "alias": "room_door_dist", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "room_door_share": { - "name": "room_door_share", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "room name;room number" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "List of room(s) (room number, room name) sharing a door with the sampling room", - "title": "rooms that share a door with sampling room", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "rooms that share a door with sampling room" - ], - "rank": 156, - "is_a": "core field", - "string_serialization": "{text};{integer}", - "slot_uri": "MIXS:0000242", - "multivalued": false, - "alias": "room_door_share", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "room_hallway": { - "name": "room_hallway", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "room name;room number" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "List of room(s) (room number, room name) located in the same hallway as sampling room", - "title": "rooms that are on the same hallway", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "rooms that are on the same hallway" - ], - "rank": 157, - "is_a": "core field", - "string_serialization": "{text};{integer}", - "slot_uri": "MIXS:0000238", - "multivalued": false, - "alias": "room_hallway", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "room_loc": { - "name": "room_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The position of the room within the building", - "title": "room location in building", - "examples": [ - { - "value": "interior room" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "room location in building" - ], - "rank": 158, - "is_a": "core field", - "slot_uri": "MIXS:0000823", - "multivalued": false, - "alias": "room_loc", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "room_loc_enum" - }, - "room_moist_dam_hist": { - "name": "room_moist_dam_hist", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed", - "title": "room moisture damage or mold history", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "room moisture damage or mold history" - ], - "rank": 159, - "is_a": "core field", - "slot_uri": "MIXS:0000235", - "multivalued": false, - "alias": "room_moist_dam_hist", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "integer" - }, - "room_net_area": { - "name": "room_net_area", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "square feet, square meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The net floor area of sampling room. Net area excludes wall thicknesses", - "title": "room net area", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "room net area" - ], - "rank": 160, - "is_a": "core field", - "string_serialization": "{integer} {unit}", - "slot_uri": "MIXS:0000194", - "multivalued": false, - "alias": "room_net_area", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "room_occup": { - "name": "room_occup", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Count of room occupancy at time of sampling", - "title": "room occupancy", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "room occupancy" - ], - "rank": 161, - "is_a": "core field", - "slot_uri": "MIXS:0000236", - "multivalued": false, - "alias": "room_occup", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "room_samp_pos": { - "name": "room_samp_pos", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The horizontal sampling position in the room relative to architectural elements", - "title": "room sampling position", - "examples": [ - { - "value": "south corner" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "room sampling position" - ], - "rank": 162, - "is_a": "core field", - "slot_uri": "MIXS:0000824", - "multivalued": false, - "alias": "room_samp_pos", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "room_samp_pos_enum" - }, - "room_type": { - "name": "room_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The main purpose or activity of the sampling room. A room is any distinguishable space within a structure", - "title": "room type", - "examples": [ - { - "value": "bathroom" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "room type" - ], - "rank": 163, - "is_a": "core field", - "slot_uri": "MIXS:0000825", - "multivalued": false, - "alias": "room_type", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "room_type_enum" - }, - "room_vol": { - "name": "room_vol", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "cubic feet, cubic meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Volume of sampling room", - "title": "room volume", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "room volume" - ], - "rank": 164, - "is_a": "core field", - "string_serialization": "{integer} {unit}", - "slot_uri": "MIXS:0000195", - "multivalued": false, - "alias": "room_vol", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "room_wall_share": { - "name": "room_wall_share", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "room name;room number" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "List of room(s) (room number, room name) sharing a wall with the sampling room", - "title": "rooms that share a wall with sampling room", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "rooms that share a wall with sampling room" - ], - "rank": 165, - "is_a": "core field", - "string_serialization": "{text};{integer}", - "slot_uri": "MIXS:0000243", - "multivalued": false, - "alias": "room_wall_share", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "room_window_count": { - "name": "room_window_count", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Number of windows in the room", - "title": "room window count", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "room window count" - ], - "rank": 166, - "is_a": "core field", - "slot_uri": "MIXS:0000237", - "multivalued": false, - "alias": "room_window_count", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "integer" - }, - "samp_floor": { - "name": "samp_floor", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The floor of the building, where the sampling room is located", - "title": "sampling floor", - "examples": [ - { - "value": "4th floor" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sampling floor" - ], - "rank": 167, - "is_a": "core field", - "slot_uri": "MIXS:0000828", - "multivalued": false, - "alias": "samp_floor", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "samp_floor_enum" - }, - "samp_room_id": { - "name": "samp_room_id", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Sampling room number. This ID should be consistent with the designations on the building floor plans", - "title": "sampling room ID or name", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sampling room ID or name" - ], - "rank": 168, - "is_a": "core field", - "slot_uri": "MIXS:0000244", - "multivalued": false, - "alias": "samp_room_id", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_sort_meth": { - "name": "samp_sort_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "description of method" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Method by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor.", - "title": "sample size sorting method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample size sorting method" - ], - "rank": 169, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000216", - "multivalued": false, - "alias": "samp_sort_meth", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_time_out": { - "name": "samp_time_out", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "time" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "hour" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The recent and long term history of outside sampling", - "title": "sampling time outside", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sampling time outside" - ], - "rank": 170, - "is_a": "core field", - "slot_uri": "MIXS:0000196", - "multivalued": false, - "alias": "samp_time_out", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_weather": { - "name": "samp_weather", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The weather on the sampling day", - "title": "sampling day weather", - "examples": [ - { - "value": "foggy" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sampling day weather" - ], - "rank": 171, - "is_a": "core field", - "slot_uri": "MIXS:0000827", - "multivalued": false, - "alias": "samp_weather", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "samp_weather_enum" - }, - "sample_link": { - "name": "sample_link", - "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", - "title": "sample linkage", - "notes": [ - "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" - ], - "comments": [ - "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" - ], - "examples": [ - { - "value": "IGSN:DSJ0284" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "string_serialization": "{text}:{text}", - "multivalued": false, - "alias": "sample_link", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface", - "SampIdNewTermsMixin" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true, - "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" - }, - "season": { - "name": "season", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "NCIT:C94729" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729).", - "title": "season", - "examples": [ - { - "value": "autumn [NCIT:C94733]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "season" - ], - "rank": 172, - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000829", - "multivalued": false, - "alias": "season", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "season_use": { - "name": "season_use", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The seasons the space is occupied", - "title": "seasonal use", - "examples": [ - { - "value": "Winter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "seasonal use" - ], - "rank": 173, - "is_a": "core field", - "slot_uri": "MIXS:0000830", - "multivalued": false, - "alias": "season_use", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "season_use_enum" - }, - "shad_dev_water_mold": { - "name": "shad_dev_water_mold", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Signs of the presence of mold or mildew on the shading device", - "title": "shading device signs of water/mold", - "examples": [ - { - "value": "no presence of mold visible" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "shading device signs of water/mold" - ], - "rank": 174, - "is_a": "core field", - "string_serialization": "[presence of mold visible|no presence of mold visible]", - "slot_uri": "MIXS:0000834", - "multivalued": false, - "alias": "shad_dev_water_mold", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "shading_device_cond": { - "name": "shading_device_cond", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The physical condition of the shading device at the time of sampling", - "title": "shading device condition", - "examples": [ - { - "value": "new" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "shading device condition" - ], - "rank": 175, - "is_a": "core field", - "slot_uri": "MIXS:0000831", - "multivalued": false, - "alias": "shading_device_cond", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "shading_device_cond_enum" - }, - "shading_device_loc": { - "name": "shading_device_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The location of the shading device in relation to the built structure", - "title": "shading device location", - "examples": [ - { - "value": "exterior" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "shading device location" - ], - "rank": 176, - "is_a": "core field", - "string_serialization": "[exterior|interior]", - "slot_uri": "MIXS:0000832", - "multivalued": false, - "alias": "shading_device_loc", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "shading_device_mat": { - "name": "shading_device_mat", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "material name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The material the shading device is composed of", - "title": "shading device material", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "shading device material" - ], - "rank": 177, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000245", - "multivalued": false, - "alias": "shading_device_mat", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "shading_device_type": { - "name": "shading_device_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of shading device", - "title": "shading device type", - "examples": [ - { - "value": "slatted aluminum awning" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "shading device type" - ], - "rank": 178, - "is_a": "core field", - "slot_uri": "MIXS:0000835", - "multivalued": false, - "alias": "shading_device_type", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "shading_device_type_enum" - }, - "size_frac": { - "name": "size_frac", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "filter size value range" - } - }, - "description": "Filtering pore size used in sample preparation", - "title": "size fraction selected", - "examples": [ - { - "value": "0-0.22 micrometer" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "size fraction selected" - ], - "rank": 285, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float}-{float} {unit}", - "slot_uri": "MIXS:0000017", - "multivalued": false, - "alias": "size_frac", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "space_typ_state": { - "name": "space_typ_state", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Customary or normal state of the space", - "title": "space typical state", - "examples": [ - { - "value": "typically occupied" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "space typical state" - ], - "rank": 179, - "is_a": "core field", - "string_serialization": "[typically occupied|typically unoccupied]", - "slot_uri": "MIXS:0000770", - "multivalued": false, - "alias": "space_typ_state", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "specific": { - "name": "specific", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The building specifications. 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"aliases": [ - "temperature outside house" - ], - "rank": 189, - "is_a": "core field", - "slot_uri": "MIXS:0000197", - "multivalued": false, - "alias": "temp_out", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "train_line": { - "name": "train_line", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The subway line name", - "title": "train line", - "examples": [ - { - "value": "red" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "train line" - ], - "rank": 190, - "is_a": "core field", - "slot_uri": "MIXS:0000837", - "multivalued": false, - "alias": "train_line", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - 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], - "slot_group": "mixs_core_section", - "range": "string" - }, - "vis_media": { - "name": "vis_media", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The building visual media", - "title": "visual media", - "examples": [ - { - "value": "3D scans" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "visual media" - ], - "rank": 194, - "is_a": "core field", - "slot_uri": "MIXS:0000840", - "multivalued": false, - "alias": "vis_media", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "vis_media_enum" - }, - "wall_area": { - "name": "wall_area", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "square meter" - }, - "occurrence": { - "tag": "occurrence", - 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"aliases": [ - "wall construction type" - ], - "rank": 196, - "is_a": "core field", - "slot_uri": "MIXS:0000841", - "multivalued": false, - "alias": "wall_const_type", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "wall_const_type_enum" - }, - "wall_finish_mat": { - "name": "wall_finish_mat", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The material utilized to finish the outer most layer of the wall", - "title": "wall finish material", - "examples": [ - { - "value": "wood" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "wall finish material" - ], - "rank": 197, - "is_a": "core field", - "slot_uri": "MIXS:0000842", - "multivalued": false, - "alias": "wall_finish_mat", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - 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"value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The relative location of the wall within the room", - "title": "wall location", - "examples": [ - { - "value": "north" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "wall location" - ], - "rank": 199, - "is_a": "core field", - "slot_uri": "MIXS:0000843", - "multivalued": false, - "alias": "wall_loc", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "wall_loc_enum" - }, - "wall_surf_treatment": { - "name": "wall_surf_treatment", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The surface treatment of interior wall", - "title": "wall surface treatment", - "examples": [ - { - "value": "paneling" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "wall surface treatment" - ], - "rank": 200, - "is_a": "core field", - "slot_uri": "MIXS:0000845", - "multivalued": false, - "alias": "wall_surf_treatment", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "wall_surf_treatment_enum" - }, - "wall_texture": { - "name": "wall_texture", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The feel, appearance, or consistency of a wall surface", - "title": "wall texture", - "examples": [ - { - "value": "popcorn" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "wall texture" - ], - "rank": 201, - "is_a": "core field", - "slot_uri": "MIXS:0000846", - "multivalued": false, - "alias": "wall_texture", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "wall_texture_enum" - }, - "wall_thermal_mass": { - "name": "wall_thermal_mass", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "joule per degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint", - "title": "wall thermal mass", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "wall thermal mass" - ], - "rank": 202, - "is_a": "core field", - "slot_uri": "MIXS:0000222", - "multivalued": false, - "alias": "wall_thermal_mass", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "wall_water_mold": { - "name": "wall_water_mold", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Signs of the presence of mold or mildew on a wall", - "title": "wall signs of water/mold", - "examples": [ - { - "value": "no presence of mold visible" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "wall signs of water/mold" - ], - "rank": 203, - "is_a": "core field", - "string_serialization": "[presence of mold visible|no presence of mold visible]", - "slot_uri": "MIXS:0000844", - "multivalued": false, - "alias": "wall_water_mold", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "water_feat_size": { - "name": "water_feat_size", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "square meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The size of the water feature", - "title": "water feature size", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "water feature size" - ], - "rank": 204, - "is_a": "core field", - "slot_uri": "MIXS:0000223", - "multivalued": false, - "alias": "water_feat_size", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "water_feat_type": { - "name": "water_feat_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of water feature present within the building being sampled", - "title": "water feature type", - "examples": [ - { - "value": "stream" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "water feature type" - ], - "rank": 205, - "is_a": "core field", - "slot_uri": "MIXS:0000847", - "multivalued": false, - "alias": "water_feat_type", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "water_feat_type_enum" - }, - "weekday": { - "name": "weekday", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The day of the week when sampling occurred", - "title": "weekday", - "examples": [ - { - "value": "Sunday" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "weekday" - ], - "rank": 206, - "is_a": "core field", - "slot_uri": "MIXS:0000848", - "multivalued": false, - "alias": "weekday", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "weekday_enum" - }, - "window_cond": { - "name": "window_cond", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The physical condition of the window at the time of sampling", - "title": "window condition", - "examples": [ - { - "value": "rupture" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "window condition" - ], - "rank": 207, - "is_a": "core field", - "slot_uri": "MIXS:0000849", - "multivalued": false, - "alias": "window_cond", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "window_cond_enum" - }, - "window_cover": { - "name": "window_cover", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of window covering", - "title": "window covering", - "examples": [ - { - "value": "curtains" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "window covering" - ], - "rank": 208, - "is_a": "core field", - "slot_uri": "MIXS:0000850", - "multivalued": false, - "alias": "window_cover", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "window_cover_enum" - }, - "window_horiz_pos": { - "name": "window_horiz_pos", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The horizontal position of the window on the wall", - "title": "window horizontal position", - "examples": [ - { - "value": "middle" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "window horizontal position" - ], - "rank": 209, - "is_a": "core field", - "slot_uri": "MIXS:0000851", - "multivalued": false, - "alias": "window_horiz_pos", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "window_horiz_pos_enum" - }, - "window_loc": { - "name": "window_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The relative location of the window within the room", - "title": "window location", - "examples": [ - { - "value": "west" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "window location" - ], - "rank": 210, - "is_a": "core field", - "slot_uri": "MIXS:0000852", - "multivalued": false, - "alias": "window_loc", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "window_loc_enum" - }, - "window_mat": { - "name": "window_mat", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of material used to finish a window", - "title": "window material", - "examples": [ - { - "value": "wood" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "window material" - ], - "rank": 211, - "is_a": "core field", - "slot_uri": "MIXS:0000853", - "multivalued": false, - "alias": "window_mat", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "window_mat_enum" - }, - "window_open_freq": { - "name": "window_open_freq", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The number of times windows are opened per week", - "title": "window open frequency", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "window open frequency" - ], - "rank": 212, - "is_a": "core field", - "slot_uri": "MIXS:0000246", - "multivalued": false, - "alias": "window_open_freq", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "window_size": { - "name": "window_size", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "inch, meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The window's length and width", - "title": "window area/size", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "window area/size" - ], - "rank": 213, - "is_a": "core field", - "string_serialization": "{float} {unit} x {float} {unit}", - "slot_uri": "MIXS:0000224", - "multivalued": false, - "alias": "window_size", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "window_status": { - "name": "window_status", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Defines whether the windows were open or closed during environmental testing", - "title": "window status", - "examples": [ - { - "value": "open" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "window status" - ], - "rank": 214, - "is_a": "core field", - "string_serialization": "[closed|open]", - "slot_uri": "MIXS:0000855", - "multivalued": false, - "alias": "window_status", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "window_type": { - "name": "window_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of windows", - "title": "window type", - "examples": [ - { - "value": "fixed window" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "window type" - ], - "rank": 215, - "is_a": "core field", - "slot_uri": "MIXS:0000856", - "multivalued": false, - "alias": "window_type", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "window_type_enum" - }, - "window_vert_pos": { - "name": "window_vert_pos", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The vertical position of the window on the wall", - "title": "window vertical position", - "examples": [ - { - "value": "middle" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "window vertical position" - ], - "rank": 216, - "is_a": "core field", - "slot_uri": "MIXS:0000857", - "multivalued": false, - "alias": "window_vert_pos", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "window_vert_pos_enum" - }, - "window_water_mold": { - "name": "window_water_mold", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Signs of the presence of mold or mildew on the window.", - "title": "window signs of water/mold", - "examples": [ - { - "value": "no presence of mold visible" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "window signs of water/mold" - ], - "rank": 217, - "is_a": "core field", - "string_serialization": "[presence of mold visible|no presence of mold visible]", - "slot_uri": "MIXS:0000854", - "multivalued": false, - "alias": "window_water_mold", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "BuiltEnvInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "analysis_type": { - "name": "analysis_type", - "description": "Select all the data types associated or available for this biosample", - "title": "analysis/data type", - "examples": [ - { - "value": "metagenomics; metabolomics; proteomics" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:investigation_type" - ], - "rank": 3, - "multivalued": true, - "alias": "analysis_type", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface" - ], - "slot_group": "sample_id_section", - "range": "analysis_type_enum", - "required": true, - "recommended": true - }, - "samp_name": { - "name": "samp_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - } - }, - "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", - "title": "sample name", - "comments": [ - "It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." - ], - "examples": [ - { - "value": "Rock core CB1178(5-6) from NSW" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample name" - ], - "rank": 1, - "is_a": "investigation field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0001107", - "multivalued": false, - "identifier": true, - "alias": "samp_name", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true - }, - "source_mat_id": { - "name": "source_mat_id", - "description": "A globally unique identifier assigned to the biological sample.", - "title": "source material identifier", - "todos": [ - "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID.", - "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID." - ], - "notes": [ - "The source material IS the Globally Unique ID" - ], - "comments": [ - "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).", - "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/)." - ], - "examples": [ - { - "value": "IGSN:AU1243" - }, - { - "value": "UUID:24f1467a-40f4-11ed-b878-0242ac120002" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 2, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{text}:{text}", - "slot_uri": "MIXS:0000026", - "multivalued": false, - "alias": "source_mat_id", - "owner": "BuiltEnvInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" - } - } - }, - "EmslInterface": { - "name": "EmslInterface", - "description": "emsl dh_interface", - "title": "Emsl", - "from_schema": "https://example.com/nmdc_submission_schema", - "is_a": "DhInterface", - "mixins": [ - "DhMultiviewCommonColumnsMixin" - ], - "slots": [ - "emsl_store_temp", - "project_id", - "replicate_number", - "sample_shipped", - "sample_type", - "technical_reps", - "emsl_store_temp", - "project_id", - "replicate_number", - "sample_shipped", - "sample_type", - "technical_reps" - ], - "slot_usage": { - "emsl_store_temp": { - "name": "emsl_store_temp", - "description": "The temperature at which the sample should be stored upon delivery to EMSL", - "title": "EMSL sample storage temperature, deg. C", - "todos": [ - "add 'see_alsos' with link to NEXUS info" - ], - "comments": [ - "Enter a temperature in celsius. Numeric portion only." - ], - "examples": [ - { - "value": "-80" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 4, - "string_serialization": "{float}", - "owner": "Biosample", - "domain_of": [ - "EmslInterface" - ], - "slot_group": "emsl_section", - "range": "float", - "required": true, - "recommended": true - }, - "project_id": { - "name": "project_id", - "description": "Proposal IDs or names associated with dataset", - "title": "project ID", - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 1, - "string_serialization": "{text}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "EmslInterface" - ], - "slot_group": "emsl_section", - "range": "string", - "required": true, - "recommended": true - }, - "replicate_number": { - "name": "replicate_number", - "description": "If sending biological replicates, indicate the rep number here.", - "title": "replicate number", - "comments": [ - "This will guide staff in ensuring your samples are blocked & randomized correctly" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "string_serialization": "{integer}", - "owner": "Biosample", - "domain_of": [ - "Biosample", - "EmslInterface" - ], - "slot_group": "emsl_section", - "range": "integer", - "recommended": true - }, - "sample_shipped": { - "name": "sample_shipped", - "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent to EMSL.", - "title": "sample shipped amount", - "comments": [ - "This field is only required when completing metadata for samples being submitted to EMSL for analyses." - ], - "examples": [ - { - "value": "15 g" - }, - { - "value": "100 uL" - }, - { - "value": "5 mL" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 3, - "string_serialization": "{float} {unit}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "EmslInterface" - ], - "slot_group": "emsl_section", - "range": "string", - "required": true, - "recommended": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" - }, - "sample_type": { - "name": "sample_type", - "description": "Type of sample being submitted", - "title": "sample type", - "comments": [ - "This can vary from 'environmental package' if the sample is an extraction." - ], - "examples": [ - { - "value": "water extracted soil" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 2, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "EmslInterface" - ], - "slot_group": "emsl_section", - "range": "sample_type_enum", - "required": true, - "recommended": true - }, - "technical_reps": { - "name": "technical_reps", - "description": "If sending technical replicates of the same sample, indicate the replicate count.", - "title": "number technical replicate", - "comments": [ - "This field is only required when completing metadata for samples being submitted to EMSL for analyses." - ], - "examples": [ - { - "value": "2" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "string_serialization": "{integer}", - "owner": "Biosample", - "domain_of": [ - "Biosample", - "EmslInterface" - ], - "slot_group": "emsl_section", - "range": "integer", - "recommended": true - }, - "oxy_stat_samp": { - "name": "oxy_stat_samp", - "range": "OxyStatSampEnum" - } - }, - "attributes": { - "emsl_store_temp": { - "name": "emsl_store_temp", - "description": "The temperature at which the sample should be stored upon delivery to EMSL", - "title": "EMSL sample storage temperature, deg. C", - "todos": [ - "add 'see_alsos' with link to NEXUS info" - ], - "comments": [ - "Enter a temperature in celsius. Numeric portion only." - ], - "examples": [ - { - "value": "-80" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 4, - "string_serialization": "{float}", - "alias": "emsl_store_temp", - "owner": "EmslInterface", - "domain_of": [ - "EmslInterface" - ], - "slot_group": "emsl_section", - "range": "float", - "required": true, - "recommended": true - }, - "project_id": { - "name": "project_id", - "description": "Proposal IDs or names associated with dataset", - "title": "project ID", - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 1, - "string_serialization": "{text}", - "multivalued": false, - "alias": "project_id", - "owner": "EmslInterface", - "domain_of": [ - "Biosample", - "EmslInterface" - ], - "slot_group": "emsl_section", - "range": "string", - "required": true, - "recommended": true - }, - "replicate_number": { - "name": "replicate_number", - "description": "If sending biological replicates, indicate the rep number here.", - "title": "replicate number", - "comments": [ - "This will guide staff in ensuring your samples are blocked & randomized correctly" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "string_serialization": "{integer}", - "alias": "replicate_number", - "owner": "EmslInterface", - "domain_of": [ - "Biosample", - "EmslInterface" - ], - "slot_group": "emsl_section", - "range": "integer", - "recommended": true - }, - "sample_shipped": { - "name": "sample_shipped", - "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent to EMSL.", - "title": "sample shipped amount", - "comments": [ - "This field is only required when completing metadata for samples being submitted to EMSL for analyses." - ], - "examples": [ - { - "value": "15 g" - }, - { - "value": "100 uL" - }, - { - "value": "5 mL" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 3, - "string_serialization": "{float} {unit}", - "multivalued": false, - "alias": "sample_shipped", - "owner": "EmslInterface", - "domain_of": [ - "Biosample", - "EmslInterface" - ], - "slot_group": "emsl_section", - "range": "string", - "required": true, - "recommended": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" - }, - "sample_type": { - "name": "sample_type", - "description": "Type of sample being submitted", - "title": "sample type", - "comments": [ - "This can vary from 'environmental package' if the sample is an extraction." - ], - "examples": [ - { - "value": "water extracted soil" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 2, - "alias": "sample_type", - "owner": "EmslInterface", - "domain_of": [ - "Biosample", - "EmslInterface" - ], - "slot_group": "emsl_section", - "range": "sample_type_enum", - "required": true, - "recommended": true - }, - "technical_reps": { - "name": "technical_reps", - "description": "If sending technical replicates of the same sample, indicate the replicate count.", - "title": "number technical replicate", - "comments": [ - "This field is only required when completing metadata for samples being submitted to EMSL for analyses." - ], - "examples": [ - { - "value": "2" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "string_serialization": "{integer}", - "alias": "technical_reps", - "owner": "EmslInterface", - "domain_of": [ - "Biosample", - "EmslInterface" - ], - "slot_group": "emsl_section", - "range": "integer", - "recommended": true - }, - "analysis_type": { - "name": "analysis_type", - "description": "Select all the data types associated or available for this biosample", - "title": "analysis/data type", - "examples": [ - { - "value": "metagenomics; metabolomics; proteomics" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:investigation_type" - ], - "rank": 3, - "multivalued": true, - "alias": "analysis_type", - "owner": "EmslInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface" - ], - "slot_group": "sample_id_section", - "range": "analysis_type_enum", - "required": true, - "recommended": true - }, - "samp_name": { - "name": "samp_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - } - }, - "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", - "title": "sample name", - "comments": [ - "It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." - ], - "examples": [ - { - "value": "Rock core CB1178(5-6) from NSW" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample name" - ], - "rank": 1, - "is_a": "investigation field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0001107", - "multivalued": false, - "identifier": true, - "alias": "samp_name", - "owner": "EmslInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true - }, - "source_mat_id": { - "name": "source_mat_id", - "description": "A globally unique identifier assigned to the biological sample.", - "title": "source material identifier", - "todos": [ - "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID.", - "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID." - ], - "notes": [ - "The source material IS the Globally Unique ID" - ], - "comments": [ - "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).", - "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/)." - ], - "examples": [ - { - "value": "IGSN:AU1243" - }, - { - "value": "UUID:24f1467a-40f4-11ed-b878-0242ac120002" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 2, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{text}:{text}", - "slot_uri": "MIXS:0000026", - "multivalued": false, - "alias": "source_mat_id", - "owner": "EmslInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" - } - } - }, - "HcrCoresInterface": { - "name": "HcrCoresInterface", - "description": "hcr_cores dh_interface", - "title": "Hcr Cores", - "from_schema": "https://example.com/nmdc_submission_schema", - "is_a": "DhInterface", - "mixins": [ - "DhMultiviewCommonColumnsMixin" - ], - "slots": [ - "additional_info", - "alkalinity", - "alkalinity_method", - "ammonium", - "api", - "aromatics_pc", - "asphaltenes_pc", - "basin", - "benzene", - "calcium", - "chem_administration", - "chloride", - "collection_date", - "density", - "depos_env", - "depth", - "diss_carb_dioxide", - "diss_inorg_carb", - "diss_inorg_phosp", - "diss_iron", - "diss_org_carb", - "diss_oxygen_fluid", - "ecosystem", - "ecosystem_category", - "ecosystem_subtype", - "ecosystem_type", - "elev", - "env_broad_scale", - "env_local_scale", - "env_medium", - "env_package", - "ethylbenzene", - "experimental_factor", - "field", - "geo_loc_name", - "hc_produced", - "hcr", - "hcr_fw_salinity", - "hcr_geol_age", - "hcr_pressure", - "hcr_temp", - "horizon_meth", - "lat_lon", - "lithology", - "magnesium", - "misc_param", - "nitrate", - "nitrite", - "org_count_qpcr_info", - "organism_count", - "owc_tvdss", - "oxy_stat_samp", - "permeability", - "ph", - "ph_meth", - "porosity", - "potassium", - "pour_point", - "pressure", - "reservoir", - "resins_pc", - "salinity", - "samp_collec_device", - "samp_collec_method", - "samp_mat_process", - "samp_md", - "samp_size", - "samp_store_dur", - "samp_store_loc", - "samp_store_temp", - "samp_subtype", - "samp_transport_cond", - "samp_tvdss", - "samp_type", - "samp_well_name", - "sample_link", - "saturates_pc", - "size_frac", - "sodium", - "specific_ecosystem", - "sr_dep_env", - "sr_geol_age", - "sr_kerog_type", - "sr_lithology", - "sulfate", - "sulfate_fw", - "sulfide", - "suspend_solids", - "tan", - "temp", - "toluene", - "tot_iron", - "tot_nitro", - "tot_phosp", - "tot_sulfur", - "tvdss_of_hcr_press", - "tvdss_of_hcr_temp", - "vfa", - "vfa_fw", - "viscosity", - "win", - "xylene" - ], - "slot_usage": { - "additional_info": { - "name": "additional_info", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary", - "title": "additional info", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "additional info" - ], - "rank": 290, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000300", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "alkalinity": { - "name": "alkalinity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milliequivalent per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate", - "title": "alkalinity", - "examples": [ - { - "value": "50 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "alkalinity" - ], - "rank": 1, - "is_a": "core field", - "slot_uri": "MIXS:0000421", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "alkalinity_method": { - "name": "alkalinity_method", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "description of method" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Method used for alkalinity measurement", - "title": "alkalinity method", - "examples": [ - { - "value": "titration" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "alkalinity method" - ], - "rank": 218, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000298", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "ammonium": { - "name": "ammonium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of ammonium in the sample", - "title": "ammonium", - "examples": [ - { - "value": "1.5 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "ammonium" - ], - "rank": 4, - "is_a": "core field", - "slot_uri": "MIXS:0000427", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "api": { - "name": "api", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degrees API" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API)", - "title": "API gravity", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "API gravity" - ], - "rank": 291, - "is_a": "core field", - "slot_uri": "MIXS:0000157", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "aromatics_pc": { - "name": "aromatics_pc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "percent" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", - "title": "aromatics wt%", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "aromatics wt%" - ], - "rank": 292, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000133", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" - }, - "asphaltenes_pc": { - "name": "asphaltenes_pc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "percent" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", - "title": "asphaltenes wt%", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "asphaltenes wt%" - ], - "rank": 293, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000135", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" - }, - "basin": { - "name": "basin", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Name of the basin (e.g. Campos)", - "title": "basin name", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "basin name" - ], - "rank": 294, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000290", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "benzene": { - "name": "benzene", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of benzene in the sample", - "title": "benzene", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "benzene" - ], - "rank": 295, - "is_a": "core field", - "slot_uri": "MIXS:0000153", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "calcium": { - "name": "calcium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, micromole per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of calcium in the sample", - "title": "calcium", - "examples": [ - { - "value": "0.2 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "calcium" - ], - "rank": 9, - "is_a": "core field", - "slot_uri": "MIXS:0000432", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "chem_administration": { - "name": "chem_administration", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "CHEBI;timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", - "title": "chemical administration", - "examples": [ - { - "value": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22" - }, - { - "value": "agar [CHEBI:2509];2018-05" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "chemical administration" - ], - "rank": 17, - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]};{timestamp}", - "slot_uri": "MIXS:0000751", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" - }, - "chloride": { - "name": "chloride", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of chloride in the sample", - "title": "chloride", - "examples": [ - { - "value": "5000 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "chloride" - ], - "rank": 10, - "is_a": "core field", - "slot_uri": "MIXS:0000429", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "collection_date": { - "name": "collection_date", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "date and time" - } - }, - "description": "The date of sampling", - "title": "collection date", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", - "Use modified term (amended definition)" - ], - "examples": [ - { - "value": "2021-04-15" - }, - { - "value": "2021-04" - }, - { - "value": "2021" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "collection date" - ], - "rank": 3, - "is_a": "environment field", - "string_serialization": "{date, arbitrary precision}", - "slot_uri": "MIXS:0000011", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" - }, - "density": { - "name": "density", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram per cubic meter, gram per cubic centimeter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Density of the sample, which is its mass per unit volume (aka volumetric mass density)", - "title": "density", - "examples": [ - { - "value": "1000 kilogram per cubic meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "density" - ], - "rank": 12, - "is_a": "core field", - "slot_uri": "MIXS:0000435", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "depos_env": { - "name": "depos_env", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "depositional environment", - "examples": [ - { - "value": "Continental - Alluvial" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "depositional environment" - ], - "rank": 304, - "is_a": "core field", - "slot_uri": "MIXS:0000992", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "depos_env_enum" - }, - "depth": { - "name": "depth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - } - }, - "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", - "title": "depth, meters", - "notes": [ - "Use modified term" - ], - "comments": [ - "All depths must be reported in meters. Provide the numerical portion only." - ], - "examples": [ - { - "value": "0 - 0.1" - }, - { - "value": "1" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "depth" - ], - "rank": 9, - "is_a": "environment field", - "string_serialization": "{float}|{float}-{float}", - "slot_uri": "MIXS:0000018", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$" - }, - "diss_carb_dioxide": { - "name": "diss_carb_dioxide", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample", - "title": "dissolved carbon dioxide", - "examples": [ - { - "value": "5 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved carbon dioxide" - ], - "rank": 14, - "is_a": "core field", - "slot_uri": "MIXS:0000436", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_inorg_carb": { - "name": "diss_inorg_carb", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter", - "title": "dissolved inorganic carbon", - "examples": [ - { - "value": "2059 micromole per kilogram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved inorganic carbon" - ], - "rank": 16, - "is_a": "core field", - "slot_uri": "MIXS:0000434", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_inorg_phosp": { - "name": "diss_inorg_phosp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved inorganic phosphorus in the sample", - "title": "dissolved inorganic phosphorus", - "examples": [ - { - "value": "56.5 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved inorganic phosphorus" - ], - "rank": 224, - "is_a": "core field", - "slot_uri": "MIXS:0000106", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_iron": { - "name": "diss_iron", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved iron in the sample", - "title": "dissolved iron", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved iron" - ], - "rank": 305, - "is_a": "core field", - "slot_uri": "MIXS:0000139", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_org_carb": { - "name": "diss_org_carb", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid", - "title": "dissolved organic carbon", - "examples": [ - { - "value": "197 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved organic carbon" - ], - "rank": 17, - "is_a": "core field", - "slot_uri": "MIXS:0000433", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_oxygen_fluid": { - "name": "diss_oxygen_fluid", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per kilogram, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic).", - "title": "dissolved oxygen in fluids", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved oxygen in fluids" - ], - "rank": 306, - "is_a": "core field", - "slot_uri": "MIXS:0000438", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "ecosystem": { - "name": "ecosystem", - "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", - "notes": [ - "range: string or EcosystemEnum? The enum could be dynamic or might be soil biased." - ], - "comments": [ - "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 9, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_category": { - "name": "ecosystem_category", - "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", - "notes": [ - "string or EcosystemCategoryEnum range?" - ], - "comments": [ - "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 10, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_subtype": { - "name": "ecosystem_subtype", - "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", - "notes": [ - "string or EcosystemSubtypeEnum range?" - ], - "comments": [ - "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 12, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_type": { - "name": "ecosystem_type", - "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", - "notes": [ - "string or EcosystemTypeEnum range?" - ], - "comments": [ - "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 11, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "elev": { - "name": "elev", - "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", - "title": "elevation, meters", - "comments": [ - "All elevations must be reported in meters. Provide the numerical portion only.", - "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." - ], - "examples": [ - { - "value": "225" - }, - { - "value": "0" - }, - { - "value": "1250" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "slot_uri": "MIXS:0000093", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "float", - "required": true - }, - "env_broad_scale": { - "name": "env_broad_scale", - "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", - "title": "broad-scale environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000012", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_local_scale": { - "name": "env_local_scale", - "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", - "title": "local environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "canopy [ENVO:00000047]" - }, - { - "value": "herb and fern layer [ENVO:01000337]" - }, - { - "value": "litter layer [ENVO:01000338]" - }, - { - "value": "understory [01000335]" - }, - { - "value": "shrub layer [ENVO:01000336]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 7, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000013", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_medium": { - "name": "env_medium", - "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", - "title": "environmental medium", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "soil [ENVO:00001998]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 8, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000014", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_package": { - "name": "env_package", - "description": "Select the MIxS enviromental package that best describes the environment from which your sample was collected.", - "title": "environmental package", - "examples": [ - { - "value": "soil" - } - ], - "in_subset": [ - "mixs extension" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "environmental package" - ], - "rank": 4, - "is_a": "attribute", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true - }, - "ethylbenzene": { - "name": "ethylbenzene", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of ethylbenzene in the sample", - "title": "ethylbenzene", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "ethylbenzene" - ], - "rank": 309, - "is_a": "core field", - "slot_uri": "MIXS:0000155", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "experimental_factor": { - "name": "experimental_factor", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text or EFO and/or OBI" - } - }, - "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", - "title": "experimental factor", - "examples": [ - { - "value": "time series design [EFO:EFO_0001779]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "experimental factor" - ], - "rank": 12, - "is_a": "investigation field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000008", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "field": { - "name": "field", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Name of the hydrocarbon field (e.g. Albacora)", - "title": "field name", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "field name" - ], - "rank": 310, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000291", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "geo_loc_name": { - "name": "geo_loc_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" - } - }, - "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", - "title": "geographic location (country and/or sea,region)", - "examples": [ - { - "value": "USA: Maryland, Bethesda" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "geographic location (country and/or sea,region)" - ], - "rank": 4, - "is_a": "environment field", - "string_serialization": "{text}: {text}, {text}", - "slot_uri": "MIXS:0000010", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" - }, - "hc_produced": { - "name": "hc_produced", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "hydrocarbon type produced", - "examples": [ - { - "value": "Gas" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "hydrocarbon type produced" - ], - "rank": 313, - "is_a": "core field", - "slot_uri": "MIXS:0000989", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "hc_produced_enum" - }, - "hcr": { - "name": "hcr", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Main Hydrocarbon Resource type. The term \"Hydrocarbon Resource\" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "hydrocarbon resource type", - "examples": [ - { - "value": "Oil Sand" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "hydrocarbon resource type" - ], - "rank": 314, - "is_a": "core field", - "slot_uri": "MIXS:0000988", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "hcr_enum" - }, - "hcr_fw_salinity": { - "name": "hcr_fw_salinity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS", - "title": "formation water salinity", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "formation water salinity" - ], - "rank": 315, - "is_a": "core field", - "slot_uri": "MIXS:0000406", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "hcr_geol_age": { - "name": "hcr_geol_age", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "hydrocarbon resource geological age", - "examples": [ - { - "value": "Silurian" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "hydrocarbon resource geological age" - ], - "rank": 316, - "is_a": "core field", - "slot_uri": "MIXS:0000993", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "hcr_geol_age_enum" - }, - "hcr_pressure": { - "name": "hcr_pressure", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value range" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "atmosphere, kilopascal" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Original pressure of the hydrocarbon resource", - "title": "hydrocarbon resource original pressure", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "hydrocarbon resource original pressure" - ], - "rank": 317, - "is_a": "core field", - "string_serialization": "{float} - {float} {unit}", - "slot_uri": "MIXS:0000395", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "hcr_temp": { - "name": "hcr_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value range" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Original temperature of the hydrocarbon resource", - "title": "hydrocarbon resource original temperature", - "examples": [ - { - "value": "150-295 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "hydrocarbon resource original temperature" - ], - "rank": 318, - "is_a": "core field", - "string_serialization": "{float} - {float} {unit}", - "slot_uri": "MIXS:0000393", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "horizon_meth": { - "name": "horizon_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining the horizon", - "title": "horizon method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "soil horizon method" - ], - "rank": 19, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000321", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "lat_lon": { - "name": "lat_lon", - "description": "This is currently a required field but it's not clear if this should be required for human hosts", - "title": "geographic location (latitude and longitude)", - "notes": [ - "required where?", - "This is currently a required field but it's not clear if this should be required for human hosts" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "is_a": "environment field", - "string_serialization": "{lat lon}", - "slot_uri": "MIXS:0000009", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" - }, - "lithology": { - "name": "lithology", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "lithology", - "examples": [ - { - "value": "Volcanic" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "lithology" - ], - "rank": 336, - "is_a": "core field", - "slot_uri": "MIXS:0000990", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "lithology_enum" - }, - "magnesium": { - "name": "magnesium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mole per liter, milligram per liter, parts per million, micromole per kilogram" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of magnesium in the sample", - "title": "magnesium", - "examples": [ - { - "value": "52.8 micromole per kilogram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "magnesium" - ], - "rank": 21, - "is_a": "core field", - "slot_uri": "MIXS:0000431", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "SedimentInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "misc_param": { - "name": "misc_param", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "parameter name;measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Any other measurement performed or parameter collected, that is not listed here", - "title": "miscellaneous parameter", - "examples": [ - { - "value": "Bicarbonate ion concentration;2075 micromole per kilogram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "miscellaneous parameter" - ], - "rank": 23, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000752", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "nitrate": { - "name": "nitrate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of nitrate in the sample", - "title": "nitrate", - "examples": [ - { - "value": "65 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "nitrate" - ], - "rank": 26, - "is_a": "core field", - "slot_uri": "MIXS:0000425", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "nitrite": { - "name": "nitrite", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of nitrite in the sample", - "title": "nitrite", - "examples": [ - { - "value": "0.5 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "nitrite" - ], - "rank": 27, - "is_a": "core field", - "slot_uri": "MIXS:0000426", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "org_count_qpcr_info": { - "name": "org_count_qpcr_info", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "number of cells per gram (or ml or cm^2)" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles)", - "title": "organism count qPCR information", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "organism count qPCR information" - ], - "rank": 337, - "is_a": "core field", - "string_serialization": "{text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles", - "slot_uri": "MIXS:0000099", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "organism_count": { - "name": "organism_count", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "organism name;measurement value;enumeration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", - "title": "organism count", - "examples": [ - { - "value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "organism count" - ], - "rank": 30, - "is_a": "core field", - "slot_uri": "MIXS:0000103", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$" - }, - "owc_tvdss": { - "name": "owc_tvdss", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Depth of the original oil water contact (OWC) zone (average) (m TVDSS)", - "title": "oil water contact depth", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "oil water contact depth" - ], - "rank": 339, - "is_a": "core field", - "slot_uri": "MIXS:0000405", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "oxy_stat_samp": { - "name": "oxy_stat_samp", - "description": "Oxygenation status of sample", - "title": "oxygenation status of sample", - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 25, - "is_a": "core field", - "slot_uri": "MIXS:0000753", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "OxyStatSampEnum" - }, - "permeability": { - "name": "permeability", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value range" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mD" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))", - "title": "permeability", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "permeability" - ], - "rank": 340, - "is_a": "core field", - "string_serialization": "{integer} - {integer} {unit}", - "slot_uri": "MIXS:0000404", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "ph": { - "name": "ph", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid", - "title": "pH", - "notes": [ - "Use modified term" - ], - "examples": [ - { - "value": "7.2" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "pH" - ], - "rank": 27, - "is_a": "core field", - "string_serialization": "{float}", - "slot_uri": "MIXS:0001001", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "float", - "recommended": true, - "minimum_value": 0, - "maximum_value": 14 - }, - "ph_meth": { - "name": "ph_meth", - "description": "Reference or method used in determining ph", - "title": "pH method", - "comments": [ - "This can include a link to the instrument used or a citation for the method." - ], - "examples": [ - { - "value": "https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB" - }, - { - "value": "https://doi.org/10.2136/sssabookser5.3.c16" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 41, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0001106", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "porosity": { - "name": "porosity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value or range" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "percentage" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Porosity of deposited sediment is volume of voids divided by the total volume of sample", - "title": "porosity", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "porosity" - ], - "rank": 37, - "is_a": "core field", - "string_serialization": "{float} - {float} {unit}", - "slot_uri": "MIXS:0000211", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "SedimentInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "potassium": { - "name": "potassium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of potassium in the sample", - "title": "potassium", - "examples": [ - { - "value": "463 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "potassium" - ], - "rank": 38, - "is_a": "core field", - "slot_uri": "MIXS:0000430", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "pour_point": { - "name": "pour_point", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)", - "title": "pour point", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "pour point" - ], - "rank": 341, - "is_a": "core field", - "slot_uri": "MIXS:0000127", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "pressure": { - "name": "pressure", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "atmosphere" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Pressure to which the sample is subject to, in atmospheres", - "title": "pressure", - "examples": [ - { - "value": "50 atmosphere" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "pressure" - ], - "rank": 39, - "is_a": "core field", - "slot_uri": "MIXS:0000412", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "reservoir": { - "name": "reservoir", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Name of the reservoir (e.g. Carapebus)", - "title": "reservoir name", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "reservoir name" - ], - "rank": 347, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000303", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "resins_pc": { - "name": "resins_pc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "percent" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", - "title": "resins wt%", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "resins wt%" - ], - "rank": 348, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000134", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" - }, - "salinity": { - "name": "salinity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "practical salinity unit, percentage" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", - "title": "salinity", - "examples": [ - { - "value": "25 practical salinity unit" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "salinity" - ], - "rank": 54, - "is_a": "core field", - "slot_uri": "MIXS:0000183", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "samp_collec_device": { - "name": "samp_collec_device", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "device name" - } - }, - "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", - "title": "sample collection device", - "comments": [ - "Report dimensions and details when applicable" - ], - "examples": [ - { - "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection device" - ], - "rank": 14, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000002", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "samp_collec_method": { - "name": "samp_collec_method", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI,url , or text" - } - }, - "description": "The method employed for collecting the sample.", - "title": "sample collection method", - "comments": [ - "This can be a citation or description" - ], - "examples": [ - { - "value": "swabbing" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection method" - ], - "rank": 15, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{PMID}|{DOI}|{URL}|{text}", - "slot_uri": "MIXS:0001225", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_mat_process": { - "name": "samp_mat_process", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - } - }, - "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", - "title": "sample material processing", - "examples": [ - { - "value": "filtering of seawater" - }, - { - "value": "storing samples in ethanol" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample material processing" - ], - "rank": 12, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000016", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_md": { - "name": "samp_md", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value;enumeration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "sample measured depth", - "examples": [ - { - "value": "1534 meter;MSL" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample measured depth" - ], - "rank": 351, - "is_a": "core field", - "slot_uri": "MIXS:0000413", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "samp_size": { - "name": "samp_size", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millliter, gram, milligram, liter" - } - }, - "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", - "title": "amount or size of sample collected", - "comments": [ - "This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis." - ], - "examples": [ - { - "value": "5 grams" - }, - { - "value": "10 mL" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "amount or size of sample collected" - ], - "rank": 18, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float} {unit}", - "slot_uri": "MIXS:0000001", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" - }, - "samp_store_dur": { - "name": "samp_store_dur", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Duration for which the sample was stored", - "title": "sample storage duration", - "examples": [ - { - "value": "P1Y6M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage duration" - ], - "rank": 353, - "is_a": "core field", - "string_serialization": "{duration}", - "slot_uri": "MIXS:0000116", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_store_loc": { - "name": "samp_store_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "location name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Location at which sample was stored, usually name of a specific freezer/room", - "title": "sample storage location", - "examples": [ - { - "value": "Freezer no:5" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage location" - ], - "rank": 41, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000755", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_store_temp": { - "name": "samp_store_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Temperature at which the sample was stored (degrees are assumed)", - "title": "sample storage temperature", - "examples": [ - { - "value": "-80 Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage temperature" - ], - "rank": 7, - "is_a": "core field", - "slot_uri": "MIXS:0000110", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "samp_subtype": { - "name": "samp_subtype", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Name of sample sub-type. For example if \"sample type\" is \"Produced Water\" then subtype could be \"Oil Phase\" or \"Water Phase\". If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "sample subtype", - "examples": [ - { - "value": "biofilm" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample subtype" - ], - "rank": 354, - "is_a": "core field", - "slot_uri": "MIXS:0000999", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "samp_subtype_enum" - }, - "samp_transport_cond": { - "name": "samp_transport_cond", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "days;degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C)", - "title": "sample transport conditions", - "examples": [ - { - "value": "5 days;-20 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample transport conditions" - ], - "rank": 355, - "is_a": "core field", - "string_serialization": "{float} {unit};{float} {unit}", - "slot_uri": "MIXS:0000410", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_tvdss": { - "name": "samp_tvdss", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value or measurement value range" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m", - "title": "sample true vertical depth subsea", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample true vertical depth subsea" - ], - "rank": 356, - "is_a": "core field", - "string_serialization": "{float}-{float} {unit}", - "slot_uri": "MIXS:0000409", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_type": { - "name": "samp_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "GENEPIO:0001246" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of material from which the sample was obtained. For the Hydrocarbon package, samples include types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. For the Food Package, samples are usually categorized as food, body products or tissues, or environmental material. This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246).", - "title": "sample type", - "examples": [ - { - "value": "built environment sample [GENEPIO:0001248]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample type" - ], - "rank": 357, - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000998", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "samp_well_name": { - "name": "samp_well_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Name of the well (e.g. BXA1123) where sample was taken", - "title": "sample well name", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample well name" - ], - "rank": 358, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000296", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "sample_link": { - "name": "sample_link", - "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", - "title": "sample linkage", - "notes": [ - "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" - ], - "comments": [ - "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" - ], - "examples": [ - { - "value": "IGSN:DSJ0284" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "string_serialization": "{text}:{text}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface", - "SampIdNewTermsMixin" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true, - "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" - }, - "saturates_pc": { - "name": "saturates_pc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "percent" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", - "title": "saturates wt%", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "saturates wt%" - ], - "rank": 359, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000131", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" - }, - "size_frac": { - "name": "size_frac", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "filter size value range" - } - }, - "description": "Filtering pore size used in sample preparation", - "title": "size fraction selected", - "examples": [ - { - "value": "0-0.22 micrometer" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "size fraction selected" - ], - "rank": 285, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float}-{float} {unit}", - "slot_uri": "MIXS:0000017", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "sodium": { - "name": "sodium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Sodium concentration in the sample", - "title": "sodium", - "examples": [ - { - "value": "10.5 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sodium" - ], - "rank": 363, - "is_a": "core field", - "slot_uri": "MIXS:0000428", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "specific_ecosystem": { - "name": "specific_ecosystem", - "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", - "notes": [ - "string or SpecificEcosystemEnum range?" - ], - "comments": [ - "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 13, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "sr_dep_env": { - "name": "sr_dep_env", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "source rock depositional environment", - "examples": [ - { - "value": "Marine" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "source rock depositional environment" - ], - "rank": 366, - "is_a": "core field", - "slot_uri": "MIXS:0000996", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface" - ], - "slot_group": "mixs_core_section", - "range": "sr_dep_env_enum" - }, - "sr_geol_age": { - "name": "sr_geol_age", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "source rock geological age", - "examples": [ - { - "value": "Silurian" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "source rock geological age" - ], - "rank": 367, - "is_a": "core field", - "slot_uri": "MIXS:0000997", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface" - ], - "slot_group": "mixs_core_section", - "range": "sr_geol_age_enum" - }, - "sr_kerog_type": { - "name": "sr_kerog_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "source rock kerogen type", - "examples": [ - { - "value": "Type IV" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "source rock kerogen type" - ], - "rank": 368, - "is_a": "core field", - "slot_uri": "MIXS:0000994", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface" - ], - "slot_group": "mixs_core_section", - "range": "sr_kerog_type_enum" - }, - "sr_lithology": { - "name": "sr_lithology", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "source rock lithology", - "examples": [ - { - "value": "Coal" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "source rock lithology" - ], - "rank": 369, - "is_a": "core field", - "slot_uri": "MIXS:0000995", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface" - ], - "slot_group": "mixs_core_section", - "range": "sr_lithology_enum" - }, - "sulfate": { - "name": "sulfate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of sulfate in the sample", - "title": "sulfate", - "examples": [ - { - "value": "5 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sulfate" - ], - "rank": 44, - "is_a": "core field", - "slot_uri": "MIXS:0000423", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "sulfate_fw": { - "name": "sulfate_fw", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Original sulfate concentration in the hydrocarbon resource", - "title": "sulfate in formation water", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sulfate in formation water" - ], - "rank": 370, - "is_a": "core field", - "slot_uri": "MIXS:0000407", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "sulfide": { - "name": "sulfide", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of sulfide in the sample", - "title": "sulfide", - "examples": [ - { - "value": "2 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sulfide" - ], - "rank": 371, - "is_a": "core field", - "slot_uri": "MIXS:0000424", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "suspend_solids": { - "name": "suspend_solids", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "suspended solid name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, microgram, milligram per liter, mole per liter, gram per liter, part per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances", - "title": "suspended solids", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "suspended solids" - ], - "rank": 372, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000150", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "WastewaterSludgeInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? 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"aliases": [ - "total sulfur" - ], - "rank": 379, - "is_a": "core field", - "slot_uri": "MIXS:0000419", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tvdss_of_hcr_press": { - "name": "tvdss_of_hcr_press", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m).", - "title": "depth (TVDSS) of hydrocarbon resource pressure", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "depth (TVDSS) of hydrocarbon resource pressure" - 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"value": "text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)", - "title": "well identification number", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "well identification number" - ], - "rank": 388, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000297", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "xylene": { - "name": "xylene", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of xylene in the sample", - "title": "xylene", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "xylene" - ], - "rank": 389, - "is_a": "core field", - "slot_uri": "MIXS:0000156", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - } - }, - "attributes": { - "additional_info": { - "name": "additional_info", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary", - "title": "additional info", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "additional info" - ], - "rank": 290, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000300", - "multivalued": false, - "alias": "additional_info", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "alkalinity": { - "name": "alkalinity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milliequivalent per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate", - "title": "alkalinity", - "examples": [ - { - "value": "50 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "alkalinity" - ], - "rank": 1, - "is_a": "core field", - "slot_uri": "MIXS:0000421", - "multivalued": false, - "alias": "alkalinity", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "alkalinity_method": { - "name": "alkalinity_method", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "description of method" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Method used for alkalinity measurement", - "title": "alkalinity method", - "examples": [ - { - "value": "titration" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "alkalinity method" - ], - "rank": 218, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000298", - "multivalued": false, - "alias": "alkalinity_method", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "ammonium": { - "name": "ammonium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of ammonium in the sample", - "title": "ammonium", - "examples": [ - { - "value": "1.5 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "ammonium" - ], - "rank": 4, - "is_a": "core field", - "slot_uri": "MIXS:0000427", - "multivalued": false, - "alias": "ammonium", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "api": { - "name": "api", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degrees API" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API)", - "title": "API gravity", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "API gravity" - ], - "rank": 291, - "is_a": "core field", - "slot_uri": "MIXS:0000157", - "multivalued": false, - "alias": "api", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "aromatics_pc": { - "name": "aromatics_pc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "percent" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", - "title": "aromatics wt%", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "aromatics wt%" - ], - "rank": 292, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000133", - "multivalued": false, - "alias": "aromatics_pc", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" - }, - "asphaltenes_pc": { - "name": "asphaltenes_pc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "percent" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", - "title": "asphaltenes wt%", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "asphaltenes wt%" - ], - "rank": 293, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000135", - "multivalued": false, - "alias": "asphaltenes_pc", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" - }, - "basin": { - "name": "basin", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Name of the basin (e.g. Campos)", - "title": "basin name", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "basin name" - ], - "rank": 294, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000290", - "multivalued": false, - "alias": "basin", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "benzene": { - "name": "benzene", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of benzene in the sample", - "title": "benzene", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "benzene" - ], - "rank": 295, - "is_a": "core field", - "slot_uri": "MIXS:0000153", - "multivalued": false, - "alias": "benzene", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "calcium": { - "name": "calcium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, micromole per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of calcium in the sample", - "title": "calcium", - "examples": [ - { - "value": "0.2 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "calcium" - ], - "rank": 9, - "is_a": "core field", - "slot_uri": "MIXS:0000432", - "multivalued": false, - "alias": "calcium", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "chem_administration": { - "name": "chem_administration", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "CHEBI;timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", - "title": "chemical administration", - "examples": [ - { - "value": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22" - }, - { - "value": "agar [CHEBI:2509];2018-05" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "chemical administration" - ], - "rank": 17, - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]};{timestamp}", - "slot_uri": "MIXS:0000751", - "multivalued": false, - "alias": "chem_administration", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" - }, - "chloride": { - "name": "chloride", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of chloride in the sample", - "title": "chloride", - "examples": [ - { - "value": "5000 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "chloride" - ], - "rank": 10, - "is_a": "core field", - "slot_uri": "MIXS:0000429", - "multivalued": false, - "alias": "chloride", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "collection_date": { - "name": "collection_date", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "date and time" - } - }, - "description": "The date of sampling", - "title": "collection date", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", - "Use modified term (amended definition)" - ], - "examples": [ - { - "value": "2021-04-15" - }, - { - "value": "2021-04" - }, - { - "value": "2021" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "collection date" - ], - "rank": 3, - "is_a": "environment field", - "string_serialization": "{date, arbitrary precision}", - "slot_uri": "MIXS:0000011", - "multivalued": false, - "alias": "collection_date", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" - }, - "density": { - "name": "density", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram per cubic meter, gram per cubic centimeter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Density of the sample, which is its mass per unit volume (aka volumetric mass density)", - "title": "density", - "examples": [ - { - "value": "1000 kilogram per cubic meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "density" - ], - "rank": 12, - "is_a": "core field", - "slot_uri": "MIXS:0000435", - "multivalued": false, - "alias": "density", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "depos_env": { - "name": "depos_env", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "depositional environment", - "examples": [ - { - "value": "Continental - Alluvial" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "depositional environment" - ], - "rank": 304, - "is_a": "core field", - "slot_uri": "MIXS:0000992", - "multivalued": false, - "alias": "depos_env", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "depos_env_enum" - }, - "depth": { - "name": "depth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - } - }, - "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", - "title": "depth, meters", - "notes": [ - "Use modified term" - ], - "comments": [ - "All depths must be reported in meters. Provide the numerical portion only." - ], - "examples": [ - { - "value": "0 - 0.1" - }, - { - "value": "1" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "depth" - ], - "rank": 9, - "is_a": "environment field", - "string_serialization": "{float}|{float}-{float}", - "slot_uri": "MIXS:0000018", - "multivalued": false, - "alias": "depth", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$" - }, - "diss_carb_dioxide": { - "name": "diss_carb_dioxide", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample", - "title": "dissolved carbon dioxide", - "examples": [ - { - "value": "5 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved carbon dioxide" - ], - "rank": 14, - "is_a": "core field", - "slot_uri": "MIXS:0000436", - "multivalued": false, - "alias": "diss_carb_dioxide", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_inorg_carb": { - "name": "diss_inorg_carb", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter", - "title": "dissolved inorganic carbon", - "examples": [ - { - "value": "2059 micromole per kilogram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved inorganic carbon" - ], - "rank": 16, - "is_a": "core field", - "slot_uri": "MIXS:0000434", - "multivalued": false, - "alias": "diss_inorg_carb", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_inorg_phosp": { - "name": "diss_inorg_phosp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved inorganic phosphorus in the sample", - "title": "dissolved inorganic phosphorus", - "examples": [ - { - "value": "56.5 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved inorganic phosphorus" - ], - "rank": 224, - "is_a": "core field", - "slot_uri": "MIXS:0000106", - "multivalued": false, - "alias": "diss_inorg_phosp", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_iron": { - "name": "diss_iron", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved iron in the sample", - "title": "dissolved iron", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved iron" - ], - "rank": 305, - "is_a": "core field", - "slot_uri": "MIXS:0000139", - "multivalued": false, - "alias": "diss_iron", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_org_carb": { - "name": "diss_org_carb", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid", - "title": "dissolved organic carbon", - "examples": [ - { - "value": "197 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved organic carbon" - ], - "rank": 17, - "is_a": "core field", - "slot_uri": "MIXS:0000433", - "multivalued": false, - "alias": "diss_org_carb", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_oxygen_fluid": { - "name": "diss_oxygen_fluid", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per kilogram, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic).", - "title": "dissolved oxygen in fluids", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved oxygen in fluids" - ], - "rank": 306, - "is_a": "core field", - "slot_uri": "MIXS:0000438", - "multivalued": false, - "alias": "diss_oxygen_fluid", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "ecosystem": { - "name": "ecosystem", - "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", - "notes": [ - "range: string or EcosystemEnum? The enum could be dynamic or might be soil biased." - ], - "comments": [ - "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 9, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_category": { - "name": "ecosystem_category", - "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", - "notes": [ - "string or EcosystemCategoryEnum range?" - ], - "comments": [ - "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 10, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem_category", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_subtype": { - "name": "ecosystem_subtype", - "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", - "notes": [ - "string or EcosystemSubtypeEnum range?" - ], - "comments": [ - "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 12, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem_subtype", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_type": { - "name": "ecosystem_type", - "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", - "notes": [ - "string or EcosystemTypeEnum range?" - ], - "comments": [ - "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 11, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem_type", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "elev": { - "name": "elev", - "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", - "title": "elevation, meters", - "comments": [ - "All elevations must be reported in meters. Provide the numerical portion only.", - "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." - ], - "examples": [ - { - "value": "225" - }, - { - "value": "0" - }, - { - "value": "1250" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "slot_uri": "MIXS:0000093", - "multivalued": false, - "alias": "elev", - "owner": "HcrCoresInterface", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "float", - "required": true - }, - "env_broad_scale": { - "name": "env_broad_scale", - "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", - "title": "broad-scale environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000012", - "multivalued": false, - "alias": "env_broad_scale", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_local_scale": { - "name": "env_local_scale", - "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", - "title": "local environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "canopy [ENVO:00000047]" - }, - { - "value": "herb and fern layer [ENVO:01000337]" - }, - { - "value": "litter layer [ENVO:01000338]" - }, - { - "value": "understory [01000335]" - }, - { - "value": "shrub layer [ENVO:01000336]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 7, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000013", - "multivalued": false, - "alias": "env_local_scale", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_medium": { - "name": "env_medium", - "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", - "title": "environmental medium", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "soil [ENVO:00001998]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 8, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000014", - "multivalued": false, - "alias": "env_medium", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_package": { - "name": "env_package", - "description": "Select the MIxS enviromental package that best describes the environment from which your sample was collected.", - "title": "environmental package", - "examples": [ - { - "value": "soil" - } - ], - "in_subset": [ - "mixs extension" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "environmental package" - ], - "rank": 4, - "is_a": "attribute", - "multivalued": false, - "alias": "env_package", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true - }, - "ethylbenzene": { - "name": "ethylbenzene", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of ethylbenzene in the sample", - "title": "ethylbenzene", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "ethylbenzene" - ], - "rank": 309, - "is_a": "core field", - "slot_uri": "MIXS:0000155", - "multivalued": false, - "alias": "ethylbenzene", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "experimental_factor": { - "name": "experimental_factor", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text or EFO and/or OBI" - } - }, - "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", - "title": "experimental factor", - "examples": [ - { - "value": "time series design [EFO:EFO_0001779]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "experimental factor" - ], - "rank": 12, - "is_a": "investigation field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000008", - "multivalued": false, - "alias": "experimental_factor", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "field": { - "name": "field", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Name of the hydrocarbon field (e.g. Albacora)", - "title": "field name", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "field name" - ], - "rank": 310, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000291", - "multivalued": false, - "alias": "field", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "geo_loc_name": { - "name": "geo_loc_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" - } - }, - "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", - "title": "geographic location (country and/or sea,region)", - "examples": [ - { - "value": "USA: Maryland, Bethesda" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "geographic location (country and/or sea,region)" - ], - "rank": 4, - "is_a": "environment field", - "string_serialization": "{text}: {text}, {text}", - "slot_uri": "MIXS:0000010", - "multivalued": false, - "alias": "geo_loc_name", - "owner": "HcrCoresInterface", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" - }, - "hc_produced": { - "name": "hc_produced", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "hydrocarbon type produced", - "examples": [ - { - "value": "Gas" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "hydrocarbon type produced" - ], - "rank": 313, - "is_a": "core field", - "slot_uri": "MIXS:0000989", - "multivalued": false, - "alias": "hc_produced", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "hc_produced_enum" - }, - "hcr": { - "name": "hcr", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Main Hydrocarbon Resource type. The term \"Hydrocarbon Resource\" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "hydrocarbon resource type", - "examples": [ - { - "value": "Oil Sand" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "hydrocarbon resource type" - ], - "rank": 314, - "is_a": "core field", - "slot_uri": "MIXS:0000988", - "multivalued": false, - "alias": "hcr", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "hcr_enum" - }, - "hcr_fw_salinity": { - "name": "hcr_fw_salinity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS", - "title": "formation water salinity", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "formation water salinity" - ], - "rank": 315, - "is_a": "core field", - "slot_uri": "MIXS:0000406", - "multivalued": false, - "alias": "hcr_fw_salinity", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "hcr_geol_age": { - "name": "hcr_geol_age", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "hydrocarbon resource geological age", - "examples": [ - { - "value": "Silurian" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "hydrocarbon resource geological age" - ], - "rank": 316, - "is_a": "core field", - "slot_uri": "MIXS:0000993", - "multivalued": false, - "alias": "hcr_geol_age", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "hcr_geol_age_enum" - }, - "hcr_pressure": { - "name": "hcr_pressure", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value range" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "atmosphere, kilopascal" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Original pressure of the hydrocarbon resource", - "title": "hydrocarbon resource original pressure", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "hydrocarbon resource original pressure" - ], - "rank": 317, - "is_a": "core field", - "string_serialization": "{float} - {float} {unit}", - "slot_uri": "MIXS:0000395", - "multivalued": false, - "alias": "hcr_pressure", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "hcr_temp": { - "name": "hcr_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value range" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Original temperature of the hydrocarbon resource", - "title": "hydrocarbon resource original temperature", - "examples": [ - { - "value": "150-295 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "hydrocarbon resource original temperature" - ], - "rank": 318, - "is_a": "core field", - "string_serialization": "{float} - {float} {unit}", - "slot_uri": "MIXS:0000393", - "multivalued": false, - "alias": "hcr_temp", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "horizon_meth": { - "name": "horizon_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining the horizon", - "title": "horizon method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "soil horizon method" - ], - "rank": 19, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000321", - "multivalued": false, - "alias": "horizon_meth", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "lat_lon": { - "name": "lat_lon", - "description": "This is currently a required field but it's not clear if this should be required for human hosts", - "title": "geographic location (latitude and longitude)", - "notes": [ - "required where?", - "This is currently a required field but it's not clear if this should be required for human hosts" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "is_a": "environment field", - "string_serialization": "{lat lon}", - "slot_uri": "MIXS:0000009", - "multivalued": false, - "alias": "lat_lon", - "owner": "HcrCoresInterface", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" - }, - "lithology": { - "name": "lithology", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "lithology", - "examples": [ - { - "value": "Volcanic" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "lithology" - ], - "rank": 336, - "is_a": "core field", - "slot_uri": "MIXS:0000990", - "multivalued": false, - "alias": "lithology", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "lithology_enum" - }, - "magnesium": { - "name": "magnesium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mole per liter, milligram per liter, parts per million, micromole per kilogram" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of magnesium in the sample", - "title": "magnesium", - "examples": [ - { - "value": "52.8 micromole per kilogram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "magnesium" - ], - "rank": 21, - "is_a": "core field", - "slot_uri": "MIXS:0000431", - "multivalued": false, - "alias": "magnesium", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "SedimentInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "misc_param": { - "name": "misc_param", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "parameter name;measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Any other measurement performed or parameter collected, that is not listed here", - "title": "miscellaneous parameter", - "examples": [ - { - "value": "Bicarbonate ion concentration;2075 micromole per kilogram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "miscellaneous parameter" - ], - "rank": 23, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000752", - "multivalued": false, - "alias": "misc_param", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "nitrate": { - "name": "nitrate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of nitrate in the sample", - "title": "nitrate", - "examples": [ - { - "value": "65 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "nitrate" - ], - "rank": 26, - "is_a": "core field", - "slot_uri": "MIXS:0000425", - "multivalued": false, - "alias": "nitrate", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "nitrite": { - "name": "nitrite", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of nitrite in the sample", - "title": "nitrite", - "examples": [ - { - "value": "0.5 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "nitrite" - ], - "rank": 27, - "is_a": "core field", - "slot_uri": "MIXS:0000426", - "multivalued": false, - "alias": "nitrite", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "org_count_qpcr_info": { - "name": "org_count_qpcr_info", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "number of cells per gram (or ml or cm^2)" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles)", - "title": "organism count qPCR information", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "organism count qPCR information" - ], - "rank": 337, - "is_a": "core field", - "string_serialization": "{text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles", - "slot_uri": "MIXS:0000099", - "multivalued": false, - "alias": "org_count_qpcr_info", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "organism_count": { - "name": "organism_count", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "organism name;measurement value;enumeration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", - "title": "organism count", - "examples": [ - { - "value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "organism count" - ], - "rank": 30, - "is_a": "core field", - "slot_uri": "MIXS:0000103", - "multivalued": false, - "alias": "organism_count", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$" - }, - "owc_tvdss": { - "name": "owc_tvdss", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Depth of the original oil water contact (OWC) zone (average) (m TVDSS)", - "title": "oil water contact depth", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "oil water contact depth" - ], - "rank": 339, - "is_a": "core field", - "slot_uri": "MIXS:0000405", - "multivalued": false, - "alias": "owc_tvdss", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "oxy_stat_samp": { - "name": "oxy_stat_samp", - "description": "Oxygenation status of sample", - "title": "oxygenation status of sample", - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 25, - "is_a": "core field", - "slot_uri": "MIXS:0000753", - "multivalued": false, - "alias": "oxy_stat_samp", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "OxyStatSampEnum" - }, - "permeability": { - "name": "permeability", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value range" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mD" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))", - "title": "permeability", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "permeability" - ], - "rank": 340, - "is_a": "core field", - "string_serialization": "{integer} - {integer} {unit}", - "slot_uri": "MIXS:0000404", - "multivalued": false, - "alias": "permeability", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "ph": { - "name": "ph", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid", - "title": "pH", - "notes": [ - "Use modified term" - ], - "examples": [ - { - "value": "7.2" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "pH" - ], - "rank": 27, - "is_a": "core field", - "string_serialization": "{float}", - "slot_uri": "MIXS:0001001", - "multivalued": false, - "alias": "ph", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "float", - "recommended": true, - "minimum_value": 0, - "maximum_value": 14 - }, - "ph_meth": { - "name": "ph_meth", - "description": "Reference or method used in determining ph", - "title": "pH method", - "comments": [ - "This can include a link to the instrument used or a citation for the method." - ], - "examples": [ - { - "value": "https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB" - }, - { - "value": "https://doi.org/10.2136/sssabookser5.3.c16" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 41, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0001106", - "multivalued": false, - "alias": "ph_meth", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "porosity": { - "name": "porosity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value or range" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "percentage" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Porosity of deposited sediment is volume of voids divided by the total volume of sample", - "title": "porosity", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "porosity" - ], - "rank": 37, - "is_a": "core field", - "string_serialization": "{float} - {float} {unit}", - "slot_uri": "MIXS:0000211", - "multivalued": false, - "alias": "porosity", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "SedimentInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "potassium": { - "name": "potassium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of potassium in the sample", - "title": "potassium", - "examples": [ - { - "value": "463 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "potassium" - ], - "rank": 38, - "is_a": "core field", - "slot_uri": "MIXS:0000430", - "multivalued": false, - "alias": "potassium", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "pour_point": { - "name": "pour_point", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)", - "title": "pour point", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "pour point" - ], - "rank": 341, - "is_a": "core field", - "slot_uri": "MIXS:0000127", - "multivalued": false, - "alias": "pour_point", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "pressure": { - "name": "pressure", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "atmosphere" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Pressure to which the sample is subject to, in atmospheres", - "title": "pressure", - "examples": [ - { - "value": "50 atmosphere" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "pressure" - ], - "rank": 39, - "is_a": "core field", - "slot_uri": "MIXS:0000412", - "multivalued": false, - "alias": "pressure", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "reservoir": { - "name": "reservoir", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Name of the reservoir (e.g. Carapebus)", - "title": "reservoir name", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "reservoir name" - ], - "rank": 347, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000303", - "multivalued": false, - "alias": "reservoir", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "resins_pc": { - "name": "resins_pc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "percent" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", - "title": "resins wt%", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "resins wt%" - ], - "rank": 348, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000134", - "multivalued": false, - "alias": "resins_pc", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" - }, - "salinity": { - "name": "salinity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "practical salinity unit, percentage" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", - "title": "salinity", - "examples": [ - { - "value": "25 practical salinity unit" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "salinity" - ], - "rank": 54, - "is_a": "core field", - "slot_uri": "MIXS:0000183", - "multivalued": false, - "alias": "salinity", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "samp_collec_device": { - "name": "samp_collec_device", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "device name" - } - }, - "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", - "title": "sample collection device", - "comments": [ - "Report dimensions and details when applicable" - ], - "examples": [ - { - "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection device" - ], - "rank": 14, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000002", - "multivalued": false, - "alias": "samp_collec_device", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "samp_collec_method": { - "name": "samp_collec_method", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI,url , or text" - } - }, - "description": "The method employed for collecting the sample.", - "title": "sample collection method", - "comments": [ - "This can be a citation or description" - ], - "examples": [ - { - "value": "swabbing" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection method" - ], - "rank": 15, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{PMID}|{DOI}|{URL}|{text}", - "slot_uri": "MIXS:0001225", - "multivalued": false, - "alias": "samp_collec_method", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_mat_process": { - "name": "samp_mat_process", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - } - }, - "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", - "title": "sample material processing", - "examples": [ - { - "value": "filtering of seawater" - }, - { - "value": "storing samples in ethanol" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample material processing" - ], - "rank": 12, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000016", - "multivalued": false, - "alias": "samp_mat_process", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_md": { - "name": "samp_md", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value;enumeration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "In non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "sample measured depth", - "examples": [ - { - "value": "1534 meter;MSL" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample measured depth" - ], - "rank": 351, - "is_a": "core field", - "slot_uri": "MIXS:0000413", - "multivalued": false, - "alias": "samp_md", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "samp_size": { - "name": "samp_size", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millliter, gram, milligram, liter" - } - }, - "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", - "title": "amount or size of sample collected", - "comments": [ - "This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis." - ], - "examples": [ - { - "value": "5 grams" - }, - { - "value": "10 mL" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "amount or size of sample collected" - ], - "rank": 18, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float} {unit}", - "slot_uri": "MIXS:0000001", - "multivalued": false, - "alias": "samp_size", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" - }, - "samp_store_dur": { - "name": "samp_store_dur", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Duration for which the sample was stored", - "title": "sample storage duration", - "examples": [ - { - "value": "P1Y6M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage duration" - ], - "rank": 353, - "is_a": "core field", - "string_serialization": "{duration}", - "slot_uri": "MIXS:0000116", - "multivalued": false, - "alias": "samp_store_dur", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_store_loc": { - "name": "samp_store_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "location name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Location at which sample was stored, usually name of a specific freezer/room", - "title": "sample storage location", - "examples": [ - { - "value": "Freezer no:5" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage location" - ], - "rank": 41, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000755", - "multivalued": false, - "alias": "samp_store_loc", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_store_temp": { - "name": "samp_store_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Temperature at which the sample was stored (degrees are assumed)", - "title": "sample storage temperature", - "examples": [ - { - "value": "-80 Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage temperature" - ], - "rank": 7, - "is_a": "core field", - "slot_uri": "MIXS:0000110", - "multivalued": false, - "alias": "samp_store_temp", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "samp_subtype": { - "name": "samp_subtype", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Name of sample sub-type. For example if \"sample type\" is \"Produced Water\" then subtype could be \"Oil Phase\" or \"Water Phase\". If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "sample subtype", - "examples": [ - { - "value": "biofilm" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample subtype" - ], - "rank": 354, - "is_a": "core field", - "slot_uri": "MIXS:0000999", - "multivalued": false, - "alias": "samp_subtype", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "samp_subtype_enum" - }, - "samp_transport_cond": { - "name": "samp_transport_cond", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "days;degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C)", - "title": "sample transport conditions", - "examples": [ - { - "value": "5 days;-20 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample transport conditions" - ], - "rank": 355, - "is_a": "core field", - "string_serialization": "{float} {unit};{float} {unit}", - "slot_uri": "MIXS:0000410", - "multivalued": false, - "alias": "samp_transport_cond", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_tvdss": { - "name": "samp_tvdss", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value or measurement value range" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Depth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m", - "title": "sample true vertical depth subsea", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample true vertical depth subsea" - ], - "rank": 356, - "is_a": "core field", - "string_serialization": "{float}-{float} {unit}", - "slot_uri": "MIXS:0000409", - "multivalued": false, - "alias": "samp_tvdss", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_type": { - "name": "samp_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "GENEPIO:0001246" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of material from which the sample was obtained. For the Hydrocarbon package, samples include types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. For the Food Package, samples are usually categorized as food, body products or tissues, or environmental material. This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246).", - "title": "sample type", - "examples": [ - { - "value": "built environment sample [GENEPIO:0001248]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample type" - ], - "rank": 357, - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000998", - "multivalued": false, - "alias": "samp_type", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "samp_well_name": { - "name": "samp_well_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Name of the well (e.g. BXA1123) where sample was taken", - "title": "sample well name", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample well name" - ], - "rank": 358, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000296", - "multivalued": false, - "alias": "samp_well_name", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "sample_link": { - "name": "sample_link", - "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", - "title": "sample linkage", - "notes": [ - "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" - ], - "comments": [ - "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" - ], - "examples": [ - { - "value": "IGSN:DSJ0284" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "string_serialization": "{text}:{text}", - "multivalued": false, - "alias": "sample_link", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface", - "SampIdNewTermsMixin" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true, - "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" - }, - "saturates_pc": { - "name": "saturates_pc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "percent" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", - "title": "saturates wt%", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "saturates wt%" - ], - "rank": 359, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000131", - "multivalued": false, - "alias": "saturates_pc", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" - }, - "size_frac": { - "name": "size_frac", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "filter size value range" - } - }, - "description": "Filtering pore size used in sample preparation", - "title": "size fraction selected", - "examples": [ - { - "value": "0-0.22 micrometer" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "size fraction selected" - ], - "rank": 285, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float}-{float} {unit}", - "slot_uri": "MIXS:0000017", - "multivalued": false, - "alias": "size_frac", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "sodium": { - "name": "sodium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Sodium concentration in the sample", - "title": "sodium", - "examples": [ - { - "value": "10.5 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sodium" - ], - "rank": 363, - "is_a": "core field", - "slot_uri": "MIXS:0000428", - "multivalued": false, - "alias": "sodium", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "specific_ecosystem": { - "name": "specific_ecosystem", - "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", - "notes": [ - "string or SpecificEcosystemEnum range?" - ], - "comments": [ - "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 13, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "specific_ecosystem", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "sr_dep_env": { - "name": "sr_dep_env", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "source rock depositional environment", - "examples": [ - { - "value": "Marine" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "source rock depositional environment" - ], - "rank": 366, - "is_a": "core field", - "slot_uri": "MIXS:0000996", - "multivalued": false, - "alias": "sr_dep_env", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface" - ], - "slot_group": "mixs_core_section", - "range": "sr_dep_env_enum" - }, - "sr_geol_age": { - "name": "sr_geol_age", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "source rock geological age", - "examples": [ - { - "value": "Silurian" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "source rock geological age" - ], - "rank": 367, - "is_a": "core field", - "slot_uri": "MIXS:0000997", - "multivalued": false, - "alias": "sr_geol_age", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface" - ], - "slot_group": "mixs_core_section", - "range": "sr_geol_age_enum" - }, - "sr_kerog_type": { - "name": "sr_kerog_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "source rock kerogen type", - "examples": [ - { - "value": "Type IV" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "source rock kerogen type" - ], - "rank": 368, - "is_a": "core field", - "slot_uri": "MIXS:0000994", - "multivalued": false, - "alias": "sr_kerog_type", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface" - ], - "slot_group": "mixs_core_section", - "range": "sr_kerog_type_enum" - }, - "sr_lithology": { - "name": "sr_lithology", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "source rock lithology", - "examples": [ - { - "value": "Coal" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "source rock lithology" - ], - "rank": 369, - "is_a": "core field", - "slot_uri": "MIXS:0000995", - "multivalued": false, - "alias": "sr_lithology", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface" - ], - "slot_group": "mixs_core_section", - "range": "sr_lithology_enum" - }, - "sulfate": { - "name": "sulfate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of sulfate in the sample", - "title": "sulfate", - "examples": [ - { - "value": "5 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sulfate" - ], - "rank": 44, - "is_a": "core field", - "slot_uri": "MIXS:0000423", - "multivalued": false, - "alias": "sulfate", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "sulfate_fw": { - "name": "sulfate_fw", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Original sulfate concentration in the hydrocarbon resource", - "title": "sulfate in formation water", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sulfate in formation water" - ], - "rank": 370, - "is_a": "core field", - "slot_uri": "MIXS:0000407", - "multivalued": false, - "alias": "sulfate_fw", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "sulfide": { - "name": "sulfide", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of sulfide in the sample", - "title": "sulfide", - "examples": [ - { - "value": "2 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sulfide" - ], - "rank": 371, - "is_a": "core field", - "slot_uri": "MIXS:0000424", - "multivalued": false, - "alias": "sulfide", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "suspend_solids": { - "name": "suspend_solids", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "suspended solid name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, microgram, milligram per liter, mole per liter, gram per liter, part per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances", - "title": "suspended solids", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "suspended solids" - ], - "rank": 372, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000150", - "multivalued": false, - "alias": "suspend_solids", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "WastewaterSludgeInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "tan": { - "name": "tan", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)", - "title": "total acid number", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "total acid number" - ], - "rank": 373, - "is_a": "core field", - "slot_uri": "MIXS:0000120", - "multivalued": false, - "alias": "tan", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "temp": { - "name": "temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - } - }, - "description": "Temperature of the sample at the time of sampling.", - "title": "temperature", - "examples": [ - { - "value": "25 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "temperature" - ], - "rank": 37, - "is_a": "environment field", - "slot_uri": "MIXS:0000113", - "multivalued": false, - "alias": "temp", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "toluene": { - "name": "toluene", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of toluene in the sample", - "title": "toluene", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "toluene" - ], - "rank": 375, - "is_a": "core field", - "slot_uri": "MIXS:0000154", - "multivalued": false, - "alias": "toluene", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tot_iron": { - "name": "tot_iron", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, milligram per kilogram" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of total iron in the sample", - "title": "total iron", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "total iron" - ], - "rank": 376, - "is_a": "core field", - "slot_uri": "MIXS:0000105", - "multivalued": false, - "alias": "tot_iron", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tot_nitro": { - "name": "tot_nitro", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter, micromole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen", - "title": "total nitrogen concentration", - "examples": [ - { - "value": "50 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "total nitrogen concentration" - ], - "rank": 377, - "is_a": "core field", - "slot_uri": "MIXS:0000102", - "multivalued": false, - "alias": "tot_nitro", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tot_phosp": { - "name": "tot_phosp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus", - "title": "total phosphorus", - "examples": [ - { - "value": "0.03 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "total phosphorus" - ], - "rank": 52, - "is_a": "core field", - "slot_uri": "MIXS:0000117", - "multivalued": false, - "alias": "tot_phosp", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tot_sulfur": { - "name": "tot_sulfur", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of total sulfur in the sample", - "title": "total sulfur", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "total sulfur" - ], - "rank": 379, - "is_a": "core field", - "slot_uri": "MIXS:0000419", - "multivalued": false, - "alias": "tot_sulfur", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tvdss_of_hcr_press": { - "name": "tvdss_of_hcr_press", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m).", - "title": "depth (TVDSS) of hydrocarbon resource pressure", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "depth (TVDSS) of hydrocarbon resource pressure" - ], - "rank": 380, - "is_a": "core field", - "slot_uri": "MIXS:0000397", - "multivalued": false, - "alias": "tvdss_of_hcr_press", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tvdss_of_hcr_temp": { - "name": "tvdss_of_hcr_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m).", - "title": "depth (TVDSS) of hydrocarbon resource temperature", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "depth (TVDSS) of hydrocarbon resource temperature" - ], - "rank": 381, - "is_a": "core field", - "slot_uri": "MIXS:0000394", - "multivalued": false, - "alias": "tvdss_of_hcr_temp", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "vfa": { - "name": "vfa", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of Volatile Fatty Acids in the sample", - "title": "volatile fatty acids", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "volatile fatty acids" - ], - "rank": 382, - "is_a": "core field", - "slot_uri": "MIXS:0000152", - "multivalued": false, - "alias": "vfa", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "vfa_fw": { - "name": "vfa_fw", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Original volatile fatty acid concentration in the hydrocarbon resource", - "title": "vfa in formation water", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "vfa in formation water" - ], - "rank": 383, - "is_a": "core field", - "slot_uri": "MIXS:0000408", - "multivalued": false, - "alias": "vfa_fw", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "viscosity": { - "name": "viscosity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "cP at degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C)", - "title": "viscosity", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "viscosity" - ], - "rank": 384, - "is_a": "core field", - "string_serialization": "{float} {unit};{float} {unit}", - "slot_uri": "MIXS:0000126", - "multivalued": false, - "alias": "viscosity", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "win": { - "name": "win", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)", - "title": "well identification number", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "well identification number" - ], - "rank": 388, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000297", - "multivalued": false, - "alias": "win", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "xylene": { - "name": "xylene", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of xylene in the sample", - "title": "xylene", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "xylene" - ], - "rank": 389, - "is_a": "core field", - "slot_uri": "MIXS:0000156", - "multivalued": false, - "alias": "xylene", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "analysis_type": { - "name": "analysis_type", - "description": "Select all the data types associated or available for this biosample", - "title": "analysis/data type", - "examples": [ - { - "value": "metagenomics; metabolomics; proteomics" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:investigation_type" - ], - "rank": 3, - "multivalued": true, - "alias": "analysis_type", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "EmslInterface" - ], - "slot_group": "sample_id_section", - "range": "analysis_type_enum", - "required": true, - "recommended": true - }, - "samp_name": { - "name": "samp_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - } - }, - "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", - "title": "sample name", - "comments": [ - "It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." - ], - "examples": [ - { - "value": "Rock core CB1178(5-6) from NSW" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample name" - ], - "rank": 1, - "is_a": "investigation field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0001107", - "multivalued": false, - "identifier": true, - "alias": "samp_name", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "EmslInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true - }, - "source_mat_id": { - "name": "source_mat_id", - "description": "A globally unique identifier assigned to the biological sample.", - "title": "source material identifier", - "todos": [ - "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID.", - "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID." - ], - "notes": [ - "The source material IS the Globally Unique ID" - ], - "comments": [ - "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).", - "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/)." - ], - "examples": [ - { - "value": "IGSN:AU1243" - }, - { - "value": "UUID:24f1467a-40f4-11ed-b878-0242ac120002" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 2, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{text}:{text}", - "slot_uri": "MIXS:0000026", - "multivalued": false, - "alias": "source_mat_id", - "owner": "HcrCoresInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "EmslInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" - } - } - }, - "HcrFluidsSwabsInterface": { - "name": "HcrFluidsSwabsInterface", - "description": "hcr_fluids_swabs dh_interface", - "title": "Hcr Fluids Swabs", - "from_schema": "https://example.com/nmdc_submission_schema", - "is_a": "DhInterface", - "mixins": [ - "DhMultiviewCommonColumnsMixin" - ], - "slots": [ - "add_recov_method", - "additional_info", - "alkalinity", - "alkalinity_method", - "ammonium", - "api", - "aromatics_pc", - "asphaltenes_pc", - "basin", - "benzene", - "biocide", - "biocide_admin_method", - "calcium", - "chem_administration", - "chem_treat_method", - "chem_treatment", - "chloride", - "collection_date", - "density", - "depos_env", - "depth", - "diss_carb_dioxide", - "diss_inorg_carb", - "diss_inorg_phosp", - "diss_iron", - "diss_org_carb", - "diss_oxygen_fluid", - "ecosystem", - "ecosystem_category", - "ecosystem_subtype", - "ecosystem_type", - "elev", - "env_broad_scale", - "env_local_scale", - "env_medium", - "env_package", - "ethylbenzene", - "experimental_factor", - "field", - "geo_loc_name", - "hc_produced", - "hcr", - "hcr_fw_salinity", - "hcr_geol_age", - "hcr_pressure", - "hcr_temp", - "horizon_meth", - "iw_bt_date_well", - "iwf", - "lat_lon", - "lithology", - "magnesium", - "misc_param", - "nitrate", - "nitrite", - "org_count_qpcr_info", - "organism_count", - "oxy_stat_samp", - "ph", - "ph_meth", - "potassium", - "pour_point", - "pressure", - "prod_rate", - "prod_start_date", - "reservoir", - "resins_pc", - "salinity", - "samp_collec_device", - "samp_collec_method", - "samp_collect_point", - "samp_loc_corr_rate", - "samp_mat_process", - "samp_preserv", - "samp_size", - "samp_store_dur", - "samp_store_loc", - "samp_store_temp", - "samp_subtype", - "samp_transport_cond", - "samp_type", - "samp_well_name", - "sample_link", - "saturates_pc", - "size_frac", - "sodium", - "specific_ecosystem", - "sulfate", - "sulfate_fw", - "sulfide", - "suspend_solids", - "tan", - "temp", - "toluene", - "tot_iron", - "tot_nitro", - "tot_phosp", - "tot_sulfur", - "tvdss_of_hcr_press", - "tvdss_of_hcr_temp", - "vfa", - "vfa_fw", - "viscosity", - "water_cut", - "water_prod_rate", - "win", - "xylene" - ], - "slot_usage": { - "add_recov_method": { - "name": "add_recov_method", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration;timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "secondary and tertiary recovery methods and start date", - "examples": [ - { - "value": "Polymer Addition;2018-06-21T14:30Z" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "secondary and tertiary recovery methods and start date" - ], - "rank": 289, - "is_a": "core field", - "slot_uri": "MIXS:0001009", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "additional_info": { - "name": "additional_info", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary", - "title": "additional info", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "additional info" - ], - "rank": 290, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000300", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "alkalinity": { - "name": "alkalinity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milliequivalent per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate", - "title": "alkalinity", - "examples": [ - { - "value": "50 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "alkalinity" - ], - "rank": 1, - "is_a": "core field", - "slot_uri": "MIXS:0000421", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "alkalinity_method": { - "name": "alkalinity_method", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "description of method" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Method used for alkalinity measurement", - "title": "alkalinity method", - "examples": [ - { - "value": "titration" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "alkalinity method" - ], - "rank": 218, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000298", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "ammonium": { - "name": "ammonium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of ammonium in the sample", - "title": "ammonium", - "examples": [ - { - "value": "1.5 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "ammonium" - ], - "rank": 4, - "is_a": "core field", - "slot_uri": "MIXS:0000427", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "api": { - "name": "api", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degrees API" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "API gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1¬∞ API)", - "title": "API gravity", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "API gravity" - ], - "rank": 291, - "is_a": "core field", - "slot_uri": "MIXS:0000157", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "aromatics_pc": { - "name": "aromatics_pc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "percent" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", - "title": "aromatics wt%", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "aromatics wt%" - ], - "rank": 292, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000133", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" - }, - "asphaltenes_pc": { - "name": "asphaltenes_pc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "percent" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", - "title": "asphaltenes wt%", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "asphaltenes wt%" - ], - "rank": 293, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000135", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" - }, - "basin": { - "name": "basin", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Name of the basin (e.g. Campos)", - "title": "basin name", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "basin name" - ], - "rank": 294, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000290", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "benzene": { - "name": "benzene", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of benzene in the sample", - "title": "benzene", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "benzene" - ], - "rank": 295, - "is_a": "core field", - "slot_uri": "MIXS:0000153", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "biocide": { - "name": "biocide", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name;name;timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "List of biocides (commercial name of product and supplier) and date of administration", - "title": "biocide administration", - "examples": [ - { - "value": "ALPHA 1427;Baker Hughes;2008-01-23" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "biocide administration" - ], - "rank": 297, - "is_a": "core field", - "string_serialization": "{text};{text};{timestamp}", - "slot_uri": "MIXS:0001011", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "biocide_admin_method": { - "name": "biocide_admin_method", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value;frequency;duration;duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days)", - "title": "biocide administration method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "biocide administration method" - ], - "rank": 298, - "is_a": "core field", - "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration};{duration}", - "slot_uri": "MIXS:0000456", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "calcium": { - "name": "calcium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, micromole per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of calcium in the sample", - "title": "calcium", - "examples": [ - { - "value": "0.2 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "calcium" - ], - "rank": 9, - "is_a": "core field", - "slot_uri": "MIXS:0000432", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "chem_administration": { - "name": "chem_administration", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "CHEBI;timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", - "title": "chemical administration", - "examples": [ - { - "value": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22" - }, - { - "value": "agar [CHEBI:2509];2018-05" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "chemical administration" - ], - "rank": 17, - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]};{timestamp}", - "slot_uri": "MIXS:0000751", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" - }, - "chem_treat_method": { - "name": "chem_treat_method", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value;frequency;duration;duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days)", - "title": "chemical treatment method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "chemical treatment method" - ], - "rank": 302, - "is_a": "core field", - "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration};{duration};{duration}", - "slot_uri": "MIXS:0000457", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "chem_treatment": { - "name": "chem_treatment", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name;name;timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included", - "title": "chemical treatment", - "examples": [ - { - "value": "ACCENT 1125;DOW;2010-11-17" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "chemical treatment" - ], - "rank": 303, - "is_a": "core field", - "string_serialization": "{text};{text};{timestamp}", - "slot_uri": "MIXS:0001012", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "chloride": { - "name": "chloride", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of chloride in the sample", - "title": "chloride", - "examples": [ - { - "value": "5000 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "chloride" - ], - "rank": 10, - "is_a": "core field", - "slot_uri": "MIXS:0000429", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "collection_date": { - "name": "collection_date", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "date and time" - } - }, - "description": "The date of sampling", - "title": "collection date", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", - "Use modified term (amended definition)" - ], - "examples": [ - { - "value": "2021-04-15" - }, - { - "value": "2021-04" - }, - { - "value": "2021" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "collection date" - ], - "rank": 3, - "is_a": "environment field", - "string_serialization": "{date, arbitrary precision}", - "slot_uri": "MIXS:0000011", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" - }, - "density": { - "name": "density", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram per cubic meter, gram per cubic centimeter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Density of the sample, which is its mass per unit volume (aka volumetric mass density)", - "title": "density", - "examples": [ - { - "value": "1000 kilogram per cubic meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "density" - ], - "rank": 12, - "is_a": "core field", - "slot_uri": "MIXS:0000435", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "depos_env": { - "name": "depos_env", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "depositional environment", - "examples": [ - { - "value": "Continental - Alluvial" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "depositional environment" - ], - "rank": 304, - "is_a": "core field", - "slot_uri": "MIXS:0000992", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "depos_env_enum" - }, - "depth": { - "name": "depth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - } - }, - "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. 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Provide the numerical portion only." - ], - "examples": [ - { - "value": "0 - 0.1" - }, - { - "value": "1" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "depth" - ], - "rank": 9, - "is_a": "environment field", - "string_serialization": "{float}|{float}-{float}", - "slot_uri": "MIXS:0000018", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$" - }, - "diss_carb_dioxide": { - "name": "diss_carb_dioxide", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample", - "title": "dissolved carbon dioxide", - "examples": [ - { - "value": "5 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved carbon dioxide" - ], - "rank": 14, - "is_a": "core field", - "slot_uri": "MIXS:0000436", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_inorg_carb": { - "name": "diss_inorg_carb", - "annotations": { - "expected_value": { - 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}, - "diss_inorg_phosp": { - "name": "diss_inorg_phosp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved inorganic phosphorus in the sample", - "title": "dissolved inorganic phosphorus", - "examples": [ - { - "value": "56.5 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved inorganic phosphorus" - ], - "rank": 224, - "is_a": "core field", - "slot_uri": "MIXS:0000106", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_iron": { - "name": "diss_iron", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved iron in the sample", - "title": "dissolved iron", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved iron" - ], - "rank": 305, - "is_a": "core field", - "slot_uri": "MIXS:0000139", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_org_carb": { - "name": "diss_org_carb", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid", - "title": "dissolved organic carbon", - "examples": [ - { - "value": "197 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved organic carbon" - ], - "rank": 17, - "is_a": "core field", - "slot_uri": "MIXS:0000433", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_oxygen_fluid": { - "name": "diss_oxygen_fluid", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per kilogram, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic).", - "title": "dissolved oxygen in fluids", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved oxygen in fluids" - ], - "rank": 306, - "is_a": "core field", - "slot_uri": "MIXS:0000438", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "ecosystem": { - "name": "ecosystem", - "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", - "notes": [ - "range: string or EcosystemEnum? The enum could be dynamic or might be soil biased." - ], - "comments": [ - "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 9, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_category": { - "name": "ecosystem_category", - "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", - "notes": [ - "string or EcosystemCategoryEnum range?" - ], - "comments": [ - "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 10, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_subtype": { - "name": "ecosystem_subtype", - "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", - "notes": [ - "string or EcosystemSubtypeEnum range?" - ], - "comments": [ - "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 12, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_type": { - "name": "ecosystem_type", - "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", - "notes": [ - "string or EcosystemTypeEnum range?" - ], - "comments": [ - "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 11, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "elev": { - "name": "elev", - "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", - "title": "elevation, meters", - "comments": [ - "All elevations must be reported in meters. Provide the numerical portion only.", - "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." - ], - "examples": [ - { - "value": "225" - }, - { - "value": "0" - }, - { - "value": "1250" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "slot_uri": "MIXS:0000093", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "float", - "required": true - }, - "env_broad_scale": { - "name": "env_broad_scale", - "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", - "title": "broad-scale environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000012", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_local_scale": { - "name": "env_local_scale", - "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", - "title": "local environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "canopy [ENVO:00000047]" - }, - { - "value": "herb and fern layer [ENVO:01000337]" - }, - { - "value": "litter layer [ENVO:01000338]" - }, - { - "value": "understory [01000335]" - }, - { - "value": "shrub layer [ENVO:01000336]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 7, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000013", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_medium": { - "name": "env_medium", - "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", - "title": "environmental medium", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "soil [ENVO:00001998]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 8, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000014", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_package": { - "name": "env_package", - "description": "Select the MIxS enviromental package that best describes the environment from which your sample was collected.", - "title": "environmental package", - "examples": [ - { - "value": "soil" - } - ], - "in_subset": [ - "mixs extension" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "environmental package" - ], - "rank": 4, - "is_a": "attribute", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true - }, - "ethylbenzene": { - "name": "ethylbenzene", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of ethylbenzene in the sample", - "title": "ethylbenzene", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "ethylbenzene" - ], - "rank": 309, - "is_a": "core field", - "slot_uri": "MIXS:0000155", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "experimental_factor": { - "name": "experimental_factor", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text or EFO and/or OBI" - } - }, - "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", - "title": "experimental factor", - "examples": [ - { - "value": "time series design [EFO:EFO_0001779]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "experimental factor" - ], - "rank": 12, - "is_a": "investigation field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000008", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "field": { - "name": "field", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Name of the hydrocarbon field (e.g. Albacora)", - "title": "field name", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "field name" - ], - "rank": 310, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000291", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "geo_loc_name": { - "name": "geo_loc_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" - } - }, - "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", - "title": "geographic location (country and/or sea,region)", - "examples": [ - { - "value": "USA: Maryland, Bethesda" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "geographic location (country and/or sea,region)" - ], - "rank": 4, - "is_a": "environment field", - "string_serialization": "{text}: {text}, {text}", - "slot_uri": "MIXS:0000010", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" - }, - "hc_produced": { - "name": "hc_produced", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "hydrocarbon type produced", - "examples": [ - { - "value": "Gas" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "hydrocarbon type produced" - ], - "rank": 313, - "is_a": "core field", - "slot_uri": "MIXS:0000989", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "hc_produced_enum" - }, - "hcr": { - "name": "hcr", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Main Hydrocarbon Resource type. The term \"Hydrocarbon Resource\" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "hydrocarbon resource type", - "examples": [ - { - "value": "Oil Sand" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "hydrocarbon resource type" - ], - "rank": 314, - "is_a": "core field", - "slot_uri": "MIXS:0000988", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "hcr_enum" - }, - "hcr_fw_salinity": { - "name": "hcr_fw_salinity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS", - "title": "formation water salinity", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "formation water salinity" - ], - "rank": 315, - "is_a": "core field", - "slot_uri": "MIXS:0000406", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "hcr_geol_age": { - "name": "hcr_geol_age", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "hydrocarbon resource geological age", - "examples": [ - { - "value": "Silurian" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "hydrocarbon resource geological age" - ], - "rank": 316, - "is_a": "core field", - "slot_uri": "MIXS:0000993", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "hcr_geol_age_enum" - }, - "hcr_pressure": { - "name": "hcr_pressure", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value range" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "atmosphere, kilopascal" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Original pressure of the hydrocarbon resource", - "title": "hydrocarbon resource original pressure", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "hydrocarbon resource original pressure" - ], - "rank": 317, - "is_a": "core field", - "string_serialization": "{float} - {float} {unit}", - "slot_uri": "MIXS:0000395", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "hcr_temp": { - "name": "hcr_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value range" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Original temperature of the hydrocarbon resource", - "title": "hydrocarbon resource original temperature", - "examples": [ - { - "value": "150-295 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "hydrocarbon resource original temperature" - ], - "rank": 318, - "is_a": "core field", - "string_serialization": "{float} - {float} {unit}", - "slot_uri": "MIXS:0000393", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "horizon_meth": { - "name": "horizon_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining the horizon", - "title": "horizon method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "soil horizon method" - ], - "rank": 19, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000321", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "iw_bt_date_well": { - "name": "iw_bt_date_well", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Injection water breakthrough date per well following a secondary and/or tertiary recovery", - "title": "injection water breakthrough date of specific well", - "examples": [ - { - "value": "2018-05-11" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "injection water breakthrough date of specific well" - ], - "rank": 334, - "is_a": "core field", - "slot_uri": "MIXS:0001010", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "iwf": { - "name": "iwf", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "percent" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%)", - "title": "injection water fraction", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "injection water fraction" - ], - "rank": 335, - "is_a": "core field", - "slot_uri": "MIXS:0000455", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "lat_lon": { - "name": "lat_lon", - "description": "This is currently a required field but it's not clear if this should be required for human hosts", - "title": "geographic location (latitude and longitude)", - "notes": [ - "required where?", - "This is currently a required field but it's not clear if this should be required for human hosts" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "is_a": "environment field", - "string_serialization": "{lat lon}", - "slot_uri": "MIXS:0000009", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" - }, - "lithology": { - "name": "lithology", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "lithology", - "examples": [ - { - "value": "Volcanic" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "lithology" - ], - "rank": 336, - "is_a": "core field", - "slot_uri": "MIXS:0000990", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "lithology_enum" - }, - "magnesium": { - "name": "magnesium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mole per liter, milligram per liter, parts per million, micromole per kilogram" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of magnesium in the sample", - "title": "magnesium", - "examples": [ - { - "value": "52.8 micromole per kilogram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "magnesium" - ], - "rank": 21, - "is_a": "core field", - "slot_uri": "MIXS:0000431", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "SedimentInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "misc_param": { - "name": "misc_param", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "parameter name;measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Any other measurement performed or parameter collected, that is not listed here", - "title": "miscellaneous parameter", - "examples": [ - { - "value": "Bicarbonate ion concentration;2075 micromole per kilogram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "miscellaneous parameter" - ], - "rank": 23, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000752", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "nitrate": { - "name": "nitrate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of nitrate in the sample", - "title": "nitrate", - "examples": [ - { - "value": "65 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "nitrate" - ], - "rank": 26, - "is_a": "core field", - "slot_uri": "MIXS:0000425", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "nitrite": { - "name": "nitrite", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of nitrite in the sample", - "title": "nitrite", - "examples": [ - { - "value": "0.5 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "nitrite" - ], - "rank": 27, - "is_a": "core field", - "slot_uri": "MIXS:0000426", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "org_count_qpcr_info": { - "name": "org_count_qpcr_info", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "number of cells per gram (or ml or cm^2)" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles)", - "title": "organism count qPCR information", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "organism count qPCR information" - ], - "rank": 337, - "is_a": "core field", - "string_serialization": "{text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles", - "slot_uri": "MIXS:0000099", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "organism_count": { - "name": "organism_count", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "organism name;measurement value;enumeration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", - "title": "organism count", - "examples": [ - { - "value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "organism count" - ], - "rank": 30, - "is_a": "core field", - "slot_uri": "MIXS:0000103", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$" - }, - "oxy_stat_samp": { - "name": "oxy_stat_samp", - "description": "Oxygenation status of sample", - "title": "oxygenation status of sample", - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 25, - "is_a": "core field", - "slot_uri": "MIXS:0000753", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "OxyStatSampEnum" - }, - "ph": { - "name": "ph", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid", - "title": "pH", - "notes": [ - "Use modified term" - ], - "examples": [ - { - "value": "7.2" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "pH" - ], - "rank": 27, - "is_a": "core field", - "string_serialization": "{float}", - "slot_uri": "MIXS:0001001", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "float", - "recommended": true, - "minimum_value": 0, - "maximum_value": 14 - }, - "ph_meth": { - "name": "ph_meth", - "description": "Reference or method used in determining ph", - "title": "pH method", - "comments": [ - "This can include a link to the instrument used or a citation for the method." - ], - "examples": [ - { - "value": "https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB" - }, - { - "value": "https://doi.org/10.2136/sssabookser5.3.c16" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 41, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0001106", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "potassium": { - "name": "potassium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of potassium in the sample", - "title": "potassium", - "examples": [ - { - "value": "463 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "potassium" - ], - "rank": 38, - "is_a": "core field", - "slot_uri": "MIXS:0000430", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "pour_point": { - "name": "pour_point", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)", - "title": "pour point", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "pour point" - ], - "rank": 341, - "is_a": "core field", - "slot_uri": "MIXS:0000127", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "pressure": { - "name": "pressure", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "atmosphere" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Pressure to which the sample is subject to, in atmospheres", - "title": "pressure", - "examples": [ - { - "value": "50 atmosphere" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "pressure" - ], - "rank": 39, - "is_a": "core field", - "slot_uri": "MIXS:0000412", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "prod_rate": { - "name": "prod_rate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "cubic meter per day" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Oil and/or gas production rates per well (e.g. 524 m3 / day)", - "title": "production rate", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "production rate" - ], - "rank": 344, - "is_a": "core field", - "slot_uri": "MIXS:0000452", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "prod_start_date": { - "name": "prod_start_date", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Date of field's first production", - "title": "production start date", - "examples": [ - { - "value": "2018-05-11" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "production start date" - ], - "rank": 345, - "is_a": "core field", - "slot_uri": "MIXS:0001008", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "reservoir": { - "name": "reservoir", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Name of the reservoir (e.g. Carapebus)", - "title": "reservoir name", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "reservoir name" - ], - "rank": 347, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000303", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "resins_pc": { - "name": "resins_pc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "percent" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", - "title": "resins wt%", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "resins wt%" - ], - "rank": 348, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000134", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" - }, - "salinity": { - "name": "salinity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "practical salinity unit, percentage" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", - "title": "salinity", - "examples": [ - { - "value": "25 practical salinity unit" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "salinity" - ], - "rank": 54, - "is_a": "core field", - "slot_uri": "MIXS:0000183", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "samp_collec_device": { - "name": "samp_collec_device", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "device name" - } - }, - "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", - "title": "sample collection device", - "comments": [ - "Report dimensions and details when applicable" - ], - "examples": [ - { - "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection device" - ], - "rank": 14, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000002", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "samp_collec_method": { - "name": "samp_collec_method", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI,url , or text" - } - }, - "description": "The method employed for collecting the sample.", - "title": "sample collection method", - "comments": [ - "This can be a citation or description" - ], - "examples": [ - { - "value": "swabbing" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection method" - ], - "rank": 15, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{PMID}|{DOI}|{URL}|{text}", - "slot_uri": "MIXS:0001225", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_collect_point": { - "name": "samp_collect_point", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "sample collection point", - "examples": [ - { - "value": "well" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection point" - ], - "rank": 349, - "is_a": "core field", - "slot_uri": "MIXS:0001015", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "samp_collect_point_enum" - }, - "samp_loc_corr_rate": { - "name": "samp_loc_corr_rate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value range" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millimeter per year" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays", - "title": "corrosion rate at sample location", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "corrosion rate at sample location" - ], - "rank": 350, - "is_a": "core field", - "string_serialization": "{float} - {float} {unit}", - "slot_uri": "MIXS:0000136", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_mat_process": { - "name": "samp_mat_process", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - } - }, - "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", - "title": "sample material processing", - "examples": [ - { - "value": "filtering of seawater" - }, - { - "value": "storing samples in ethanol" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample material processing" - ], - "rank": 12, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000016", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_preserv": { - "name": "samp_preserv", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milliliter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml)", - "title": "preservative added to sample", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "preservative added to sample" - ], - "rank": 352, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000463", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" - }, - "samp_size": { - "name": "samp_size", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millliter, gram, milligram, liter" - } - }, - "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", - "title": "amount or size of sample collected", - "comments": [ - "This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis." - ], - "examples": [ - { - "value": "5 grams" - }, - { - "value": "10 mL" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "amount or size of sample collected" - ], - "rank": 18, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float} {unit}", - "slot_uri": "MIXS:0000001", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" - }, - "samp_store_dur": { - "name": "samp_store_dur", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Duration for which the sample was stored", - "title": "sample storage duration", - "examples": [ - { - "value": "P1Y6M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage duration" - ], - "rank": 353, - "is_a": "core field", - "string_serialization": "{duration}", - "slot_uri": "MIXS:0000116", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_store_loc": { - "name": "samp_store_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "location name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Location at which sample was stored, usually name of a specific freezer/room", - "title": "sample storage location", - "examples": [ - { - "value": "Freezer no:5" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage location" - ], - "rank": 41, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000755", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_store_temp": { - "name": "samp_store_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Temperature at which the sample was stored (degrees are assumed)", - "title": "sample storage temperature", - "examples": [ - { - "value": "-80 Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage temperature" - ], - "rank": 7, - "is_a": "core field", - "slot_uri": "MIXS:0000110", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "samp_subtype": { - "name": "samp_subtype", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Name of sample sub-type. For example if \"sample type\" is \"Produced Water\" then subtype could be \"Oil Phase\" or \"Water Phase\". If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "sample subtype", - "examples": [ - { - "value": "biofilm" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample subtype" - ], - "rank": 354, - "is_a": "core field", - "slot_uri": "MIXS:0000999", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "samp_subtype_enum" - }, - "samp_transport_cond": { - "name": "samp_transport_cond", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "days;degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C)", - "title": "sample transport conditions", - "examples": [ - { - "value": "5 days;-20 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample transport conditions" - ], - "rank": 355, - "is_a": "core field", - "string_serialization": "{float} {unit};{float} {unit}", - "slot_uri": "MIXS:0000410", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_type": { - "name": "samp_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "GENEPIO:0001246" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of material from which the sample was obtained. For the Hydrocarbon package, samples include types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. For the Food Package, samples are usually categorized as food, body products or tissues, or environmental material. This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246).", - "title": "sample type", - "examples": [ - { - "value": "built environment sample [GENEPIO:0001248]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample type" - ], - "rank": 357, - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000998", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "samp_well_name": { - "name": "samp_well_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Name of the well (e.g. BXA1123) where sample was taken", - "title": "sample well name", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample well name" - ], - "rank": 358, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000296", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "sample_link": { - "name": "sample_link", - "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", - "title": "sample linkage", - "notes": [ - "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" - ], - "comments": [ - "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" - ], - "examples": [ - { - "value": "IGSN:DSJ0284" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "string_serialization": "{text}:{text}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface", - "SampIdNewTermsMixin" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true, - "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" - }, - "saturates_pc": { - "name": "saturates_pc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "percent" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", - "title": "saturates wt%", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "saturates wt%" - ], - "rank": 359, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000131", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" - }, - "size_frac": { - "name": "size_frac", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "filter size value range" - } - }, - "description": "Filtering pore size used in sample preparation", - "title": "size fraction selected", - "examples": [ - { - "value": "0-0.22 micrometer" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "size fraction selected" - ], - "rank": 285, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float}-{float} {unit}", - "slot_uri": "MIXS:0000017", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "sodium": { - "name": "sodium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Sodium concentration in the sample", - "title": "sodium", - "examples": [ - { - "value": "10.5 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sodium" - ], - "rank": 363, - "is_a": "core field", - "slot_uri": "MIXS:0000428", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "specific_ecosystem": { - "name": "specific_ecosystem", - "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", - "notes": [ - "string or SpecificEcosystemEnum range?" - ], - "comments": [ - "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 13, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "sulfate": { - "name": "sulfate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of sulfate in the sample", - "title": "sulfate", - "examples": [ - { - "value": "5 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sulfate" - ], - "rank": 44, - "is_a": "core field", - "slot_uri": "MIXS:0000423", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "sulfate_fw": { - "name": "sulfate_fw", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Original sulfate concentration in the hydrocarbon resource", - "title": "sulfate in formation water", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sulfate in formation water" - ], - "rank": 370, - "is_a": "core field", - "slot_uri": "MIXS:0000407", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "sulfide": { - "name": "sulfide", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of sulfide in the sample", - "title": "sulfide", - "examples": [ - { - "value": "2 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sulfide" - ], - "rank": 371, - "is_a": "core field", - "slot_uri": "MIXS:0000424", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "suspend_solids": { - "name": "suspend_solids", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "suspended solid name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, microgram, milligram per liter, mole per liter, gram per liter, part per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances", - "title": "suspended solids", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "suspended solids" - ], - "rank": 372, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000150", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "WastewaterSludgeInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "tan": { - "name": "tan", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)", - "title": "total acid number", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "total acid number" - ], - "rank": 373, - "is_a": "core field", - "slot_uri": "MIXS:0000120", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "temp": { - "name": "temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - } - }, - "description": "Temperature of the sample at the time of sampling.", - "title": "temperature", - "examples": [ - { - "value": "25 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "temperature" - ], - "rank": 37, - "is_a": "environment field", - "slot_uri": "MIXS:0000113", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "toluene": { - "name": "toluene", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of toluene in the sample", - "title": "toluene", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "toluene" - ], - "rank": 375, - "is_a": "core field", - "slot_uri": "MIXS:0000154", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tot_iron": { - "name": "tot_iron", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, milligram per kilogram" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of total iron in the sample", - "title": "total iron", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "total iron" - ], - "rank": 376, - "is_a": "core field", - "slot_uri": "MIXS:0000105", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tot_nitro": { - "name": "tot_nitro", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter, micromole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen", - "title": "total nitrogen concentration", - "examples": [ - { - "value": "50 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "total nitrogen concentration" - ], - "rank": 377, - "is_a": "core field", - "slot_uri": "MIXS:0000102", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tot_phosp": { - "name": "tot_phosp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus", - 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[^;\\t\\r\\x0A\\|]+$" - }, - "asphaltenes_pc": { - "name": "asphaltenes_pc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "percent" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", - "title": "asphaltenes wt%", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "asphaltenes wt%" - ], - "rank": 293, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000135", - "multivalued": false, - "alias": "asphaltenes_pc", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" - }, - "basin": { - "name": "basin", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Name of the basin (e.g. Campos)", - "title": "basin name", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "basin name" - ], - "rank": 294, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000290", - "multivalued": false, - "alias": "basin", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "benzene": { - "name": "benzene", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of benzene in the sample", - "title": "benzene", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "benzene" - ], - "rank": 295, - "is_a": "core field", - "slot_uri": "MIXS:0000153", - "multivalued": false, - "alias": "benzene", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "biocide": { - "name": "biocide", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name;name;timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "List of biocides (commercial name of product and supplier) and date of administration", - "title": "biocide administration", - "examples": [ - { - "value": "ALPHA 1427;Baker Hughes;2008-01-23" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "biocide administration" - ], - "rank": 297, - "is_a": "core field", - "string_serialization": "{text};{text};{timestamp}", - "slot_uri": "MIXS:0001011", - "multivalued": false, - "alias": "biocide", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "biocide_admin_method": { - "name": "biocide_admin_method", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value;frequency;duration;duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days)", - "title": "biocide administration method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "biocide administration method" - ], - "rank": 298, - "is_a": "core field", - "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration};{duration}", - "slot_uri": "MIXS:0000456", - "multivalued": false, - "alias": "biocide_admin_method", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "calcium": { - "name": "calcium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, micromole per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of calcium in the sample", - "title": "calcium", - "examples": [ - { - "value": "0.2 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "calcium" - ], - "rank": 9, - "is_a": "core field", - "slot_uri": "MIXS:0000432", - "multivalued": false, - "alias": "calcium", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "chem_administration": { - "name": "chem_administration", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "CHEBI;timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", - "title": "chemical administration", - "examples": [ - { - "value": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22" - }, - { - "value": "agar [CHEBI:2509];2018-05" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "chemical administration" - ], - "rank": 17, - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]};{timestamp}", - "slot_uri": "MIXS:0000751", - "multivalued": false, - "alias": "chem_administration", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" - }, - "chem_treat_method": { - "name": "chem_treat_method", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value;frequency;duration;duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days)", - "title": "chemical treatment method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "chemical treatment method" - ], - "rank": 302, - "is_a": "core field", - "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration};{duration};{duration}", - "slot_uri": "MIXS:0000457", - "multivalued": false, - "alias": "chem_treat_method", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "chem_treatment": { - "name": "chem_treatment", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name;name;timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "List of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included", - "title": "chemical treatment", - "examples": [ - { - "value": "ACCENT 1125;DOW;2010-11-17" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "chemical treatment" - ], - "rank": 303, - "is_a": "core field", - "string_serialization": "{text};{text};{timestamp}", - "slot_uri": "MIXS:0001012", - "multivalued": false, - "alias": "chem_treatment", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "chloride": { - "name": "chloride", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of chloride in the sample", - "title": "chloride", - "examples": [ - { - "value": "5000 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "chloride" - ], - "rank": 10, - "is_a": "core field", - "slot_uri": "MIXS:0000429", - "multivalued": false, - "alias": "chloride", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "collection_date": { - "name": "collection_date", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "date and time" - } - }, - "description": "The date of sampling", - "title": "collection date", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", - "Use modified term (amended definition)" - ], - "examples": [ - { - "value": "2021-04-15" - }, - { - "value": "2021-04" - }, - { - "value": "2021" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "collection date" - ], - "rank": 3, - "is_a": "environment field", - "string_serialization": "{date, arbitrary precision}", - "slot_uri": "MIXS:0000011", - "multivalued": false, - "alias": "collection_date", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" - }, - "density": { - "name": "density", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram per cubic meter, gram per cubic centimeter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Density of the sample, which is its mass per unit volume (aka volumetric mass density)", - "title": "density", - "examples": [ - { - "value": "1000 kilogram per cubic meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "density" - ], - "rank": 12, - "is_a": "core field", - "slot_uri": "MIXS:0000435", - "multivalued": false, - "alias": "density", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "depos_env": { - "name": "depos_env", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "depositional environment", - "examples": [ - { - "value": "Continental - Alluvial" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "depositional environment" - ], - "rank": 304, - "is_a": "core field", - "slot_uri": "MIXS:0000992", - "multivalued": false, - "alias": "depos_env", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "depos_env_enum" - }, - "depth": { - "name": "depth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - } - }, - "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", - "title": "depth, meters", - "notes": [ - "Use modified term" - ], - "comments": [ - "All depths must be reported in meters. Provide the numerical portion only." - ], - "examples": [ - { - "value": "0 - 0.1" - }, - { - "value": "1" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "depth" - ], - "rank": 9, - "is_a": "environment field", - "string_serialization": "{float}|{float}-{float}", - "slot_uri": "MIXS:0000018", - "multivalued": false, - "alias": "depth", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$" - }, - "diss_carb_dioxide": { - "name": "diss_carb_dioxide", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample", - "title": "dissolved carbon dioxide", - "examples": [ - { - "value": "5 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved carbon dioxide" - ], - "rank": 14, - "is_a": "core field", - "slot_uri": "MIXS:0000436", - "multivalued": false, - "alias": "diss_carb_dioxide", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - 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"HcrFluidsSwabsInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_iron": { - "name": "diss_iron", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved iron in the sample", - "title": "dissolved iron", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved iron" - ], - "rank": 305, - "is_a": "core field", - "slot_uri": "MIXS:0000139", - "multivalued": false, - "alias": "diss_iron", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_org_carb": { - "name": "diss_org_carb", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid", - "title": "dissolved organic carbon", - "examples": [ - { - "value": "197 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved organic carbon" - ], - "rank": 17, - "is_a": "core field", - "slot_uri": "MIXS:0000433", - "multivalued": false, - "alias": "diss_org_carb", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_oxygen_fluid": { - "name": "diss_oxygen_fluid", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per kilogram, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic).", - "title": "dissolved oxygen in fluids", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved oxygen in fluids" - ], - "rank": 306, - "is_a": "core field", - "slot_uri": "MIXS:0000438", - "multivalued": false, - "alias": "diss_oxygen_fluid", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "ecosystem": { - "name": "ecosystem", - "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", - "notes": [ - "range: string or EcosystemEnum? The enum could be dynamic or might be soil biased." - ], - "comments": [ - "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 9, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_category": { - "name": "ecosystem_category", - "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", - "notes": [ - "string or EcosystemCategoryEnum range?" - ], - "comments": [ - "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 10, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem_category", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_subtype": { - "name": "ecosystem_subtype", - "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", - "notes": [ - "string or EcosystemSubtypeEnum range?" - ], - "comments": [ - "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 12, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem_subtype", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_type": { - "name": "ecosystem_type", - "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", - "notes": [ - "string or EcosystemTypeEnum range?" - ], - "comments": [ - "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 11, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem_type", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "elev": { - "name": "elev", - "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", - "title": "elevation, meters", - "comments": [ - "All elevations must be reported in meters. Provide the numerical portion only.", - "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." - ], - "examples": [ - { - "value": "225" - }, - { - "value": "0" - }, - { - "value": "1250" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "slot_uri": "MIXS:0000093", - "multivalued": false, - "alias": "elev", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "float", - "required": true - }, - "env_broad_scale": { - "name": "env_broad_scale", - "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", - "title": "broad-scale environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000012", - "multivalued": false, - "alias": "env_broad_scale", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_local_scale": { - "name": "env_local_scale", - "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", - "title": "local environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "canopy [ENVO:00000047]" - }, - { - "value": "herb and fern layer [ENVO:01000337]" - }, - { - "value": "litter layer [ENVO:01000338]" - }, - { - "value": "understory [01000335]" - }, - { - "value": "shrub layer [ENVO:01000336]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 7, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000013", - "multivalued": false, - "alias": "env_local_scale", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_medium": { - "name": "env_medium", - "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", - "title": "environmental medium", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "soil [ENVO:00001998]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 8, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000014", - "multivalued": false, - "alias": "env_medium", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_package": { - "name": "env_package", - "description": "Select the MIxS enviromental package that best describes the environment from which your sample was collected.", - "title": "environmental package", - "examples": [ - { - "value": "soil" - } - ], - "in_subset": [ - "mixs extension" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "environmental package" - ], - "rank": 4, - "is_a": "attribute", - "multivalued": false, - "alias": "env_package", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true - }, - "ethylbenzene": { - "name": "ethylbenzene", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of ethylbenzene in the sample", - "title": "ethylbenzene", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "ethylbenzene" - ], - "rank": 309, - "is_a": "core field", - "slot_uri": "MIXS:0000155", - "multivalued": false, - "alias": "ethylbenzene", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "experimental_factor": { - "name": "experimental_factor", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text or EFO and/or OBI" - } - }, - "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", - "title": "experimental factor", - "examples": [ - { - "value": "time series design [EFO:EFO_0001779]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "experimental factor" - ], - "rank": 12, - "is_a": "investigation field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000008", - "multivalued": false, - "alias": "experimental_factor", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "field": { - "name": "field", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Name of the hydrocarbon field (e.g. Albacora)", - "title": "field name", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "field name" - ], - "rank": 310, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000291", - "multivalued": false, - "alias": "field", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "geo_loc_name": { - "name": "geo_loc_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" - } - }, - "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", - "title": "geographic location (country and/or sea,region)", - "examples": [ - { - "value": "USA: Maryland, Bethesda" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "geographic location (country and/or sea,region)" - ], - "rank": 4, - "is_a": "environment field", - "string_serialization": "{text}: {text}, {text}", - "slot_uri": "MIXS:0000010", - "multivalued": false, - "alias": "geo_loc_name", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" - }, - "hc_produced": { - "name": "hc_produced", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "hydrocarbon type produced", - "examples": [ - { - "value": "Gas" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "hydrocarbon type produced" - ], - "rank": 313, - "is_a": "core field", - "slot_uri": "MIXS:0000989", - "multivalued": false, - "alias": "hc_produced", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "hc_produced_enum" - }, - "hcr": { - "name": "hcr", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Main Hydrocarbon Resource type. The term \"Hydrocarbon Resource\" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "hydrocarbon resource type", - "examples": [ - { - "value": "Oil Sand" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "hydrocarbon resource type" - ], - "rank": 314, - "is_a": "core field", - "slot_uri": "MIXS:0000988", - "multivalued": false, - "alias": "hcr", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "hcr_enum" - }, - "hcr_fw_salinity": { - "name": "hcr_fw_salinity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS", - "title": "formation water salinity", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "formation water salinity" - ], - "rank": 315, - "is_a": "core field", - "slot_uri": "MIXS:0000406", - "multivalued": false, - "alias": "hcr_fw_salinity", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "hcr_geol_age": { - "name": "hcr_geol_age", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "hydrocarbon resource geological age", - "examples": [ - { - "value": "Silurian" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "hydrocarbon resource geological age" - ], - "rank": 316, - "is_a": "core field", - "slot_uri": "MIXS:0000993", - "multivalued": false, - "alias": "hcr_geol_age", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "hcr_geol_age_enum" - }, - "hcr_pressure": { - "name": "hcr_pressure", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value range" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "atmosphere, kilopascal" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Original pressure of the hydrocarbon resource", - "title": "hydrocarbon resource original pressure", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "hydrocarbon resource original pressure" - ], - "rank": 317, - "is_a": "core field", - "string_serialization": "{float} - {float} {unit}", - "slot_uri": "MIXS:0000395", - "multivalued": false, - "alias": "hcr_pressure", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "hcr_temp": { - "name": "hcr_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value range" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Original temperature of the hydrocarbon resource", - "title": "hydrocarbon resource original temperature", - "examples": [ - { - "value": "150-295 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "hydrocarbon resource original temperature" - ], - "rank": 318, - "is_a": "core field", - "string_serialization": "{float} - {float} {unit}", - "slot_uri": "MIXS:0000393", - "multivalued": false, - "alias": "hcr_temp", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "horizon_meth": { - "name": "horizon_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining the horizon", - "title": "horizon method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "soil horizon method" - ], - "rank": 19, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000321", - "multivalued": false, - "alias": "horizon_meth", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "iw_bt_date_well": { - "name": "iw_bt_date_well", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Injection water breakthrough date per well following a secondary and/or tertiary recovery", - "title": "injection water breakthrough date of specific well", - "examples": [ - { - "value": "2018-05-11" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "injection water breakthrough date of specific well" - ], - "rank": 334, - "is_a": "core field", - "slot_uri": "MIXS:0001010", - "multivalued": false, - "alias": "iw_bt_date_well", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "iwf": { - "name": "iwf", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "percent" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%)", - "title": "injection water fraction", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "injection water fraction" - ], - "rank": 335, - "is_a": "core field", - "slot_uri": "MIXS:0000455", - "multivalued": false, - "alias": "iwf", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "lat_lon": { - "name": "lat_lon", - "description": "This is currently a required field but it's not clear if this should be required for human hosts", - "title": "geographic location (latitude and longitude)", - "notes": [ - "required where?", - "This is currently a required field but it's not clear if this should be required for human hosts" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "is_a": "environment field", - "string_serialization": "{lat lon}", - "slot_uri": "MIXS:0000009", - "multivalued": false, - "alias": "lat_lon", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" - }, - "lithology": { - "name": "lithology", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "lithology", - "examples": [ - { - "value": "Volcanic" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "lithology" - ], - "rank": 336, - "is_a": "core field", - "slot_uri": "MIXS:0000990", - "multivalued": false, - "alias": "lithology", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "lithology_enum" - }, - "magnesium": { - "name": "magnesium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mole per liter, milligram per liter, parts per million, micromole per kilogram" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of magnesium in the sample", - "title": "magnesium", - "examples": [ - { - "value": "52.8 micromole per kilogram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "magnesium" - ], - "rank": 21, - "is_a": "core field", - "slot_uri": "MIXS:0000431", - "multivalued": false, - "alias": "magnesium", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "SedimentInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "misc_param": { - "name": "misc_param", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "parameter name;measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Any other measurement performed or parameter collected, that is not listed here", - "title": "miscellaneous parameter", - "examples": [ - { - "value": "Bicarbonate ion concentration;2075 micromole per kilogram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "miscellaneous parameter" - ], - "rank": 23, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000752", - "multivalued": false, - "alias": "misc_param", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "nitrate": { - "name": "nitrate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of nitrate in the sample", - "title": "nitrate", - "examples": [ - { - "value": "65 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "nitrate" - ], - "rank": 26, - "is_a": "core field", - "slot_uri": "MIXS:0000425", - "multivalued": false, - "alias": "nitrate", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "nitrite": { - "name": "nitrite", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of nitrite in the sample", - "title": "nitrite", - "examples": [ - { - "value": "0.5 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "nitrite" - ], - "rank": 27, - "is_a": "core field", - "slot_uri": "MIXS:0000426", - "multivalued": false, - "alias": "nitrite", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "org_count_qpcr_info": { - "name": "org_count_qpcr_info", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "number of cells per gram (or ml or cm^2)" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "If qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles)", - "title": "organism count qPCR information", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "organism count qPCR information" - ], - "rank": 337, - "is_a": "core field", - "string_serialization": "{text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles", - "slot_uri": "MIXS:0000099", - "multivalued": false, - "alias": "org_count_qpcr_info", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "organism_count": { - "name": "organism_count", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "organism name;measurement value;enumeration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", - "title": "organism count", - "examples": [ - { - "value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "organism count" - ], - "rank": 30, - "is_a": "core field", - "slot_uri": "MIXS:0000103", - "multivalued": false, - "alias": "organism_count", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$" - }, - "oxy_stat_samp": { - "name": "oxy_stat_samp", - "description": "Oxygenation status of sample", - "title": "oxygenation status of sample", - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 25, - "is_a": "core field", - "slot_uri": "MIXS:0000753", - "multivalued": false, - "alias": "oxy_stat_samp", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "OxyStatSampEnum" - }, - "ph": { - "name": "ph", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid", - "title": "pH", - "notes": [ - "Use modified term" - ], - "examples": [ - { - "value": "7.2" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "pH" - ], - "rank": 27, - "is_a": "core field", - "string_serialization": "{float}", - "slot_uri": "MIXS:0001001", - "multivalued": false, - "alias": "ph", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "float", - "recommended": true, - "minimum_value": 0, - "maximum_value": 14 - }, - "ph_meth": { - "name": "ph_meth", - "description": "Reference or method used in determining ph", - "title": "pH method", - "comments": [ - "This can include a link to the instrument used or a citation for the method." - ], - "examples": [ - { - "value": "https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB" - }, - { - "value": "https://doi.org/10.2136/sssabookser5.3.c16" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 41, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0001106", - "multivalued": false, - "alias": "ph_meth", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "potassium": { - "name": "potassium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of potassium in the sample", - "title": "potassium", - "examples": [ - { - "value": "463 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "potassium" - ], - "rank": 38, - "is_a": "core field", - "slot_uri": "MIXS:0000430", - "multivalued": false, - "alias": "potassium", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "pour_point": { - "name": "pour_point", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)", - "title": "pour point", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "pour point" - ], - "rank": 341, - "is_a": "core field", - "slot_uri": "MIXS:0000127", - "multivalued": false, - "alias": "pour_point", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "pressure": { - "name": "pressure", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "atmosphere" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Pressure to which the sample is subject to, in atmospheres", - "title": "pressure", - "examples": [ - { - "value": "50 atmosphere" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "pressure" - ], - "rank": 39, - "is_a": "core field", - "slot_uri": "MIXS:0000412", - "multivalued": false, - "alias": "pressure", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "prod_rate": { - "name": "prod_rate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "cubic meter per day" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Oil and/or gas production rates per well (e.g. 524 m3 / day)", - "title": "production rate", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "production rate" - ], - "rank": 344, - "is_a": "core field", - "slot_uri": "MIXS:0000452", - "multivalued": false, - "alias": "prod_rate", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "prod_start_date": { - "name": "prod_start_date", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Date of field's first production", - "title": "production start date", - "examples": [ - { - "value": "2018-05-11" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "production start date" - ], - "rank": 345, - "is_a": "core field", - "slot_uri": "MIXS:0001008", - "multivalued": false, - "alias": "prod_start_date", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "reservoir": { - "name": "reservoir", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Name of the reservoir (e.g. Carapebus)", - "title": "reservoir name", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "reservoir name" - ], - "rank": 347, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000303", - "multivalued": false, - "alias": "reservoir", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "resins_pc": { - "name": "resins_pc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "percent" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", - "title": "resins wt%", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "resins wt%" - ], - "rank": 348, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000134", - "multivalued": false, - "alias": "resins_pc", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" - }, - "salinity": { - "name": "salinity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "practical salinity unit, percentage" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", - "title": "salinity", - "examples": [ - { - "value": "25 practical salinity unit" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "salinity" - ], - "rank": 54, - "is_a": "core field", - "slot_uri": "MIXS:0000183", - "multivalued": false, - "alias": "salinity", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "samp_collec_device": { - "name": "samp_collec_device", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "device name" - } - }, - "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", - "title": "sample collection device", - "comments": [ - "Report dimensions and details when applicable" - ], - "examples": [ - { - "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection device" - ], - "rank": 14, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000002", - "multivalued": false, - "alias": "samp_collec_device", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "samp_collec_method": { - "name": "samp_collec_method", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI,url , or text" - } - }, - "description": "The method employed for collecting the sample.", - "title": "sample collection method", - "comments": [ - "This can be a citation or description" - ], - "examples": [ - { - "value": "swabbing" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection method" - ], - "rank": 15, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{PMID}|{DOI}|{URL}|{text}", - "slot_uri": "MIXS:0001225", - "multivalued": false, - "alias": "samp_collec_method", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_collect_point": { - "name": "samp_collect_point", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Sampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "sample collection point", - "examples": [ - { - "value": "well" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection point" - ], - "rank": 349, - "is_a": "core field", - "slot_uri": "MIXS:0001015", - "multivalued": false, - "alias": "samp_collect_point", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "samp_collect_point_enum" - }, - "samp_loc_corr_rate": { - "name": "samp_loc_corr_rate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value range" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millimeter per year" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Metal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays", - "title": "corrosion rate at sample location", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "corrosion rate at sample location" - ], - "rank": 350, - "is_a": "core field", - "string_serialization": "{float} - {float} {unit}", - "slot_uri": "MIXS:0000136", - "multivalued": false, - "alias": "samp_loc_corr_rate", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_mat_process": { - "name": "samp_mat_process", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - } - }, - "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", - "title": "sample material processing", - "examples": [ - { - "value": "filtering of seawater" - }, - { - "value": "storing samples in ethanol" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample material processing" - ], - "rank": 12, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000016", - "multivalued": false, - "alias": "samp_mat_process", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_preserv": { - "name": "samp_preserv", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milliliter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml)", - "title": "preservative added to sample", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "preservative added to sample" - ], - "rank": 352, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000463", - "multivalued": false, - "alias": "samp_preserv", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" - }, - "samp_size": { - "name": "samp_size", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millliter, gram, milligram, liter" - } - }, - "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", - "title": "amount or size of sample collected", - "comments": [ - "This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis." - ], - "examples": [ - { - "value": "5 grams" - }, - { - "value": "10 mL" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "amount or size of sample collected" - ], - "rank": 18, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float} {unit}", - "slot_uri": "MIXS:0000001", - "multivalued": false, - "alias": "samp_size", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" - }, - "samp_store_dur": { - "name": "samp_store_dur", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Duration for which the sample was stored", - "title": "sample storage duration", - "examples": [ - { - "value": "P1Y6M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage duration" - ], - "rank": 353, - "is_a": "core field", - "string_serialization": "{duration}", - "slot_uri": "MIXS:0000116", - "multivalued": false, - "alias": "samp_store_dur", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_store_loc": { - "name": "samp_store_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "location name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Location at which sample was stored, usually name of a specific freezer/room", - "title": "sample storage location", - "examples": [ - { - "value": "Freezer no:5" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage location" - ], - "rank": 41, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000755", - "multivalued": false, - "alias": "samp_store_loc", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_store_temp": { - "name": "samp_store_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Temperature at which the sample was stored (degrees are assumed)", - "title": "sample storage temperature", - "examples": [ - { - "value": "-80 Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage temperature" - ], - "rank": 7, - "is_a": "core field", - "slot_uri": "MIXS:0000110", - "multivalued": false, - "alias": "samp_store_temp", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "samp_subtype": { - "name": "samp_subtype", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Name of sample sub-type. For example if \"sample type\" is \"Produced Water\" then subtype could be \"Oil Phase\" or \"Water Phase\". If \"other\" is specified, please propose entry in \"additional info\" field", - "title": "sample subtype", - "examples": [ - { - "value": "biofilm" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample subtype" - ], - "rank": 354, - "is_a": "core field", - "slot_uri": "MIXS:0000999", - "multivalued": false, - "alias": "samp_subtype", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "samp_subtype_enum" - }, - "samp_transport_cond": { - "name": "samp_transport_cond", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "days;degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C)", - "title": "sample transport conditions", - "examples": [ - { - "value": "5 days;-20 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample transport conditions" - ], - "rank": 355, - "is_a": "core field", - "string_serialization": "{float} {unit};{float} {unit}", - "slot_uri": "MIXS:0000410", - "multivalued": false, - "alias": "samp_transport_cond", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_type": { - "name": "samp_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "GENEPIO:0001246" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The type of material from which the sample was obtained. For the Hydrocarbon package, samples include types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. For the Food Package, samples are usually categorized as food, body products or tissues, or environmental material. This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246).", - "title": "sample type", - "examples": [ - { - "value": "built environment sample [GENEPIO:0001248]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample type" - ], - "rank": 357, - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000998", - "multivalued": false, - "alias": "samp_type", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "samp_well_name": { - "name": "samp_well_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Name of the well (e.g. BXA1123) where sample was taken", - "title": "sample well name", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample well name" - ], - "rank": 358, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000296", - "multivalued": false, - "alias": "samp_well_name", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "sample_link": { - "name": "sample_link", - "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", - "title": "sample linkage", - "notes": [ - "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" - ], - "comments": [ - "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" - ], - "examples": [ - { - "value": "IGSN:DSJ0284" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "string_serialization": "{text}:{text}", - "multivalued": false, - "alias": "sample_link", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface", - "SampIdNewTermsMixin" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true, - "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" - }, - "saturates_pc": { - "name": "saturates_pc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "percent" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)", - "title": "saturates wt%", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "saturates wt%" - ], - "rank": 359, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000131", - "multivalued": false, - "alias": "saturates_pc", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" - }, - "size_frac": { - "name": "size_frac", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "filter size value range" - } - }, - "description": "Filtering pore size used in sample preparation", - "title": "size fraction selected", - "examples": [ - { - "value": "0-0.22 micrometer" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "size fraction selected" - ], - "rank": 285, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float}-{float} {unit}", - "slot_uri": "MIXS:0000017", - "multivalued": false, - "alias": "size_frac", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "sodium": { - "name": "sodium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Sodium concentration in the sample", - "title": "sodium", - "examples": [ - { - "value": "10.5 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sodium" - ], - "rank": 363, - "is_a": "core field", - "slot_uri": "MIXS:0000428", - "multivalued": false, - "alias": "sodium", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "specific_ecosystem": { - "name": "specific_ecosystem", - "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", - "notes": [ - "string or SpecificEcosystemEnum range?" - ], - "comments": [ - "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 13, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "specific_ecosystem", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "sulfate": { - "name": "sulfate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of sulfate in the sample", - "title": "sulfate", - "examples": [ - { - "value": "5 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sulfate" - ], - "rank": 44, - "is_a": "core field", - "slot_uri": "MIXS:0000423", - "multivalued": false, - "alias": "sulfate", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "sulfate_fw": { - "name": "sulfate_fw", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Original sulfate concentration in the hydrocarbon resource", - "title": "sulfate in formation water", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sulfate in formation water" - ], - "rank": 370, - "is_a": "core field", - "slot_uri": "MIXS:0000407", - "multivalued": false, - "alias": "sulfate_fw", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "sulfide": { - "name": "sulfide", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of sulfide in the sample", - "title": "sulfide", - "examples": [ - { - "value": "2 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sulfide" - ], - "rank": 371, - "is_a": "core field", - "slot_uri": "MIXS:0000424", - "multivalued": false, - "alias": "sulfide", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "suspend_solids": { - "name": "suspend_solids", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "suspended solid name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, microgram, milligram per liter, mole per liter, gram per liter, part per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances", - "title": "suspended solids", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "suspended solids" - ], - "rank": 372, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000150", - "multivalued": false, - "alias": "suspend_solids", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "WastewaterSludgeInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "tan": { - "name": "tan", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)", - "title": "total acid number", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "total acid number" - ], - "rank": 373, - "is_a": "core field", - "slot_uri": "MIXS:0000120", - "multivalued": false, - "alias": "tan", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "temp": { - "name": "temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - } - }, - "description": "Temperature of the sample at the time of sampling.", - "title": "temperature", - "examples": [ - { - "value": "25 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "temperature" - ], - "rank": 37, - "is_a": "environment field", - "slot_uri": "MIXS:0000113", - "multivalued": false, - "alias": "temp", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "toluene": { - "name": "toluene", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of toluene in the sample", - "title": "toluene", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "toluene" - ], - "rank": 375, - "is_a": "core field", - "slot_uri": "MIXS:0000154", - "multivalued": false, - "alias": "toluene", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tot_iron": { - "name": "tot_iron", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, milligram per kilogram" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of total iron in the sample", - "title": "total iron", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "total iron" - ], - "rank": 376, - "is_a": "core field", - "slot_uri": "MIXS:0000105", - "multivalued": false, - "alias": "tot_iron", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tot_nitro": { - "name": "tot_nitro", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter, micromole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen", - "title": "total nitrogen concentration", - "examples": [ - { - "value": "50 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "total nitrogen concentration" - ], - "rank": 377, - "is_a": "core field", - "slot_uri": "MIXS:0000102", - "multivalued": false, - "alias": "tot_nitro", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tot_phosp": { - "name": "tot_phosp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus", - "title": "total phosphorus", - "examples": [ - { - "value": "0.03 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "total phosphorus" - ], - "rank": 52, - "is_a": "core field", - "slot_uri": "MIXS:0000117", - "multivalued": false, - "alias": "tot_phosp", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tot_sulfur": { - "name": "tot_sulfur", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of total sulfur in the sample", - "title": "total sulfur", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "total sulfur" - ], - "rank": 379, - "is_a": "core field", - "slot_uri": "MIXS:0000419", - "multivalued": false, - "alias": "tot_sulfur", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tvdss_of_hcr_press": { - "name": "tvdss_of_hcr_press", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m).", - "title": "depth (TVDSS) of hydrocarbon resource pressure", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "depth (TVDSS) of hydrocarbon resource pressure" - ], - "rank": 380, - "is_a": "core field", - "slot_uri": "MIXS:0000397", - "multivalued": false, - "alias": "tvdss_of_hcr_press", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tvdss_of_hcr_temp": { - "name": "tvdss_of_hcr_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m).", - "title": "depth (TVDSS) of hydrocarbon resource temperature", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "depth (TVDSS) of hydrocarbon resource temperature" - ], - "rank": 381, - "is_a": "core field", - "slot_uri": "MIXS:0000394", - "multivalued": false, - "alias": "tvdss_of_hcr_temp", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "vfa": { - "name": "vfa", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of Volatile Fatty Acids in the sample", - "title": "volatile fatty acids", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "volatile fatty acids" - ], - "rank": 382, - "is_a": "core field", - "slot_uri": "MIXS:0000152", - "multivalued": false, - "alias": "vfa", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "vfa_fw": { - "name": "vfa_fw", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Original volatile fatty acid concentration in the hydrocarbon resource", - "title": "vfa in formation water", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "vfa in formation water" - ], - "rank": 383, - "is_a": "core field", - "slot_uri": "MIXS:0000408", - "multivalued": false, - "alias": "vfa_fw", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "viscosity": { - "name": "viscosity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "cP at degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C)", - "title": "viscosity", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "viscosity" - ], - "rank": 384, - "is_a": "core field", - "string_serialization": "{float} {unit};{float} {unit}", - "slot_uri": "MIXS:0000126", - "multivalued": false, - "alias": "viscosity", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "water_cut": { - "name": "water_cut", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "percent" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Current amount of water (%) in a produced fluid stream; or the average of the combined streams", - "title": "water cut", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "water cut" - ], - "rank": 386, - "is_a": "core field", - "slot_uri": "MIXS:0000454", - "multivalued": false, - "alias": "water_cut", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "water_prod_rate": { - "name": "water_prod_rate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "cubic meter per day" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Water production rates per well (e.g. 987 m3 / day)", - "title": "water production rate", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "water production rate" - ], - "rank": 387, - "is_a": "core field", - "slot_uri": "MIXS:0000453", - "multivalued": false, - "alias": "water_prod_rate", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "win": { - "name": "win", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "A unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)", - "title": "well identification number", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "well identification number" - ], - "rank": 388, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000297", - "multivalued": false, - "alias": "win", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "xylene": { - "name": "xylene", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of xylene in the sample", - "title": "xylene", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "xylene" - ], - "rank": 389, - "is_a": "core field", - "slot_uri": "MIXS:0000156", - "multivalued": false, - "alias": "xylene", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "analysis_type": { - "name": "analysis_type", - "description": "Select all the data types associated or available for this biosample", - "title": "analysis/data type", - "examples": [ - { - "value": "metagenomics; metabolomics; proteomics" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:investigation_type" - ], - "rank": 3, - "multivalued": true, - "alias": "analysis_type", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "EmslInterface", - "HcrCoresInterface" - ], - "slot_group": "sample_id_section", - "range": "analysis_type_enum", - "required": true, - "recommended": true - }, - "samp_name": { - "name": "samp_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - } - }, - "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", - "title": "sample name", - "comments": [ - "It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." - ], - "examples": [ - { - "value": "Rock core CB1178(5-6) from NSW" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample name" - ], - "rank": 1, - "is_a": "investigation field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0001107", - "multivalued": false, - "identifier": true, - "alias": "samp_name", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "EmslInterface", - "HcrCoresInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true - }, - "source_mat_id": { - "name": "source_mat_id", - "description": "A globally unique identifier assigned to the biological sample.", - "title": "source material identifier", - "todos": [ - "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID.", - "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID." - ], - "notes": [ - "The source material IS the Globally Unique ID" - ], - "comments": [ - "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).", - "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/)." - ], - "examples": [ - { - "value": "IGSN:AU1243" - }, - { - "value": "UUID:24f1467a-40f4-11ed-b878-0242ac120002" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 2, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{text}:{text}", - "slot_uri": "MIXS:0000026", - "multivalued": false, - "alias": "source_mat_id", - "owner": "HcrFluidsSwabsInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "EmslInterface", - "HcrCoresInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" - } - } - }, - "HostAssociatedInterface": { - "name": "HostAssociatedInterface", - "description": "host_associated dh_interface", - "title": "Host Associated", - "from_schema": "https://example.com/nmdc_submission_schema", - "is_a": "DhInterface", - "mixins": [ - "DhMultiviewCommonColumnsMixin", - "SampIdNewTermsMixin" - ], - "slots": [ - "alt", - "ances_data", - "biol_stat", - "blood_press_diast", - "blood_press_syst", - "chem_administration", - "collection_date", - "depth", - "ecosystem", - "ecosystem_category", - "ecosystem_subtype", - "ecosystem_type", - "elev", - "env_broad_scale", - "env_local_scale", - "env_medium", - "env_package", - "experimental_factor", - "genetic_mod", - "geo_loc_name", - "gravidity", - "horizon_meth", - "host_age", - "host_body_habitat", - "host_body_product", - "host_body_site", - "host_body_temp", - "host_color", - "host_common_name", - "host_diet", - "host_dry_mass", - "host_family_relation", - "host_genotype", - "host_growth_cond", - "host_height", - "host_last_meal", - "host_length", - "host_life_stage", - "host_phenotype", - "host_sex", - "host_shape", - "host_subject_id", - "host_subspecf_genlin", - "host_substrate", - "host_symbiont", - "host_taxid", - "host_tot_mass", - "lat_lon", - "misc_param", - "organism_count", - "oxy_stat_samp", - "perturbation", - "salinity", - "samp_capt_status", - "samp_collec_device", - "samp_collec_method", - "samp_dis_stage", - "samp_mat_process", - "samp_size", - "samp_store_dur", - "samp_store_loc", - "samp_store_temp", - "sample_link", - "size_frac", - "specific_ecosystem", - "temp" - ], - "slot_usage": { - "alt": { - "name": "alt", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - } - }, - "description": "Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air", - "title": "altitude", - "examples": [ - { - "value": "100 meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "altitude" - ], - "rank": 26, - "is_a": "environment field", - "slot_uri": "MIXS:0000094", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HostAssociatedInterface", - "MiscEnvsInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "ances_data": { - "name": "ances_data", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "free text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B)", - "title": "ancestral data", - "examples": [ - { - "value": "A/3*B" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "ancestral data" - ], - "rank": 237, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000247", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "biol_stat": { - "name": "biol_stat", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The level of genome modification.", - "title": "biological status", - "examples": [ - { - "value": "natural" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "biological status" - ], - "rank": 239, - "is_a": "core field", - "slot_uri": "MIXS:0000858", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "biol_stat_enum" - }, - "blood_press_diast": { - "name": "blood_press_diast", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millimeter mercury" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Resting diastolic blood pressure, measured as mm mercury", - "title": "host blood pressure diastolic", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host blood pressure diastolic" - ], - "rank": 299, - "is_a": "core field", - "slot_uri": "MIXS:0000258", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "blood_press_syst": { - "name": "blood_press_syst", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millimeter mercury" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Resting systolic blood pressure, measured as mm mercury", - "title": "host blood pressure systolic", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host blood pressure systolic" - ], - "rank": 300, - "is_a": "core field", - "slot_uri": "MIXS:0000259", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "chem_administration": { - "name": "chem_administration", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "CHEBI;timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", - "title": "chemical administration", - "examples": [ - { - "value": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22" - }, - { - "value": "agar [CHEBI:2509];2018-05" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "chemical administration" - ], - "rank": 17, - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]};{timestamp}", - "slot_uri": "MIXS:0000751", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" - }, - "collection_date": { - "name": "collection_date", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "date and time" - } - }, - "description": "The date of sampling", - "title": "collection date", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", - "Use modified term (amended definition)" - ], - "examples": [ - { - "value": "2021-04-15" - }, - { - "value": "2021-04" - }, - { - "value": "2021" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "collection date" - ], - "rank": 3, - "is_a": "environment field", - "string_serialization": "{date, arbitrary precision}", - "slot_uri": "MIXS:0000011", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" - }, - "depth": { - "name": "depth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - } - }, - "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", - "title": "depth, meters", - "notes": [ - "Use modified term" - ], - "comments": [ - "All depths must be reported in meters. Provide the numerical portion only." - ], - "examples": [ - { - "value": "0 - 0.1" - }, - { - "value": "1" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "depth" - ], - "rank": 9, - "is_a": "environment field", - "string_serialization": "{float}|{float}-{float}", - "slot_uri": "MIXS:0000018", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$" - }, - "ecosystem": { - "name": "ecosystem", - "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", - "notes": [ - "range: string or EcosystemEnum? The enum could be dynamic or might be soil biased." - ], - "comments": [ - "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 9, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_category": { - "name": "ecosystem_category", - "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", - "notes": [ - "string or EcosystemCategoryEnum range?" - ], - "comments": [ - "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 10, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_subtype": { - "name": "ecosystem_subtype", - "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", - "notes": [ - "string or EcosystemSubtypeEnum range?" - ], - "comments": [ - "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 12, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_type": { - "name": "ecosystem_type", - "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", - "notes": [ - "string or EcosystemTypeEnum range?" - ], - "comments": [ - "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 11, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "elev": { - "name": "elev", - "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", - "title": "elevation, meters", - "comments": [ - "All elevations must be reported in meters. Provide the numerical portion only.", - "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." - ], - "examples": [ - { - "value": "225" - }, - { - "value": "0" - }, - { - "value": "1250" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "slot_uri": "MIXS:0000093", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "float", - "required": true - }, - "env_broad_scale": { - "name": "env_broad_scale", - "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", - "title": "broad-scale environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000012", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_local_scale": { - "name": "env_local_scale", - "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", - "title": "local environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "canopy [ENVO:00000047]" - }, - { - "value": "herb and fern layer [ENVO:01000337]" - }, - { - "value": "litter layer [ENVO:01000338]" - }, - { - "value": "understory [01000335]" - }, - { - "value": "shrub layer [ENVO:01000336]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 7, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000013", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_medium": { - "name": "env_medium", - "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", - "title": "environmental medium", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "soil [ENVO:00001998]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 8, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000014", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_package": { - "name": "env_package", - "description": "Select the MIxS enviromental package that best describes the environment from which your sample was collected.", - "title": "environmental package", - "examples": [ - { - "value": "soil" - } - ], - "in_subset": [ - "mixs extension" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "environmental package" - ], - "rank": 4, - "is_a": "attribute", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true - }, - "experimental_factor": { - "name": "experimental_factor", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text or EFO and/or OBI" - } - }, - "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", - "title": "experimental factor", - "examples": [ - { - "value": "time series design [EFO:EFO_0001779]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "experimental factor" - ], - "rank": 12, - "is_a": "investigation field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000008", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "genetic_mod": { - "name": "genetic_mod", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI,url or free text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection", - "title": "genetic modification", - "examples": [ - { - "value": "aox1A transgenic" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "genetic modification" - ], - "rank": 244, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}|{text}", - "slot_uri": "MIXS:0000859", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "geo_loc_name": { - "name": "geo_loc_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" - } - }, - "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", - "title": "geographic location (country and/or sea,region)", - "examples": [ - { - "value": "USA: Maryland, Bethesda" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "geographic location (country and/or sea,region)" - ], - "rank": 4, - "is_a": "environment field", - "string_serialization": "{text}: {text}, {text}", - "slot_uri": "MIXS:0000010", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" - }, - "gravidity": { - "name": "gravidity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "gravidity status;timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used", - "title": "gravidity", - "examples": [ - { - "value": "yes;due date:2018-05-11" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "gravidity" - ], - "rank": 312, - "is_a": "core field", - "string_serialization": "{boolean};{timestamp}", - "slot_uri": "MIXS:0000875", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "horizon_meth": { - "name": "horizon_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining the horizon", - "title": "horizon method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "soil horizon method" - ], - "rank": 19, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000321", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "host_age": { - "name": "host_age", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "year, day, hour" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees", - "title": "host age", - "examples": [ - { - "value": "10 days" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host age" - ], - "rank": 249, - "is_a": "core field", - "slot_uri": "MIXS:0000255", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "host_body_habitat": { - "name": "host_body_habitat", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "free text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Original body habitat where the sample was obtained from", - "title": "host body habitat", - "examples": [ - { - "value": "nasopharynx" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host body habitat" - ], - "rank": 319, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000866", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_body_product": { - "name": "host_body_product", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "FMA or UBERON" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon", - "title": "host body product", - "examples": [ - { - "value": "Portion of mucus [fma66938]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host body product" - ], - "rank": 320, - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000888", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "host_body_site": { - "name": "host_body_site", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "FMA or UBERON" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON", - "title": "host body site", - "examples": [ - { - "value": "gill [UBERON:0002535]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host body site" - ], - "rank": 321, - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000867", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "host_body_temp": { - "name": "host_body_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Core body temperature of the host when sample was collected", - "title": "host body temperature", - "examples": [ - { - "value": "15 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host body temperature" - ], - "rank": 322, - "is_a": "core field", - "slot_uri": "MIXS:0000274", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "host_color": { - "name": "host_color", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "color" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The color of host", - "title": "host color", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host color" - ], - "rank": 323, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000260", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_common_name": { - "name": "host_common_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "common name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Common name of the host.", - "title": "host common name", - "examples": [ - { - "value": "human" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host common name" - ], - "rank": 250, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000248", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_diet": { - "name": "host_diet", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "diet type" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types", - "title": "host diet", - "examples": [ - { - "value": "herbivore" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host diet" - ], - "rank": 324, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000869", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_dry_mass": { - "name": "host_dry_mass", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "kilogram, gram" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of dry mass", - "title": "host dry mass", - "examples": [ - { - "value": "500 gram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host dry mass" - ], - "rank": 251, - "is_a": "core field", - "slot_uri": "MIXS:0000257", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "host_family_relation": { - "name": "host_family_relation", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "relationship type;arbitrary identifier" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Familial relationships to other hosts in the same study; can include multiple relationships", - "title": "host family relationship", - "examples": [ - { - "value": "offspring;Mussel25" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host family relationship" - ], - "rank": 325, - "is_a": "core field", - "string_serialization": "{text};{text}", - "slot_uri": "MIXS:0000872", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_genotype": { - "name": "host_genotype", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "genotype" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Observed genotype", - "title": "host genotype", - "examples": [ - { - "value": "C57BL/6" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host genotype" - ], - "rank": 252, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000365", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_growth_cond": { - "name": "host_growth_cond", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI,url or free text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Literature reference giving growth conditions of the host", - "title": "host growth conditions", - "examples": [ - { - "value": "https://academic.oup.com/icesjms/article/68/2/349/617247" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host growth conditions" - ], - "rank": 326, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}|{text}", - "slot_uri": "MIXS:0000871", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_height": { - "name": "host_height", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "centimeter, millimeter, meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The height of subject", - "title": "host height", - "examples": [ - { - "value": "0.1 meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host height" - ], - "rank": 253, - "is_a": "core field", - "slot_uri": "MIXS:0000264", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "host_last_meal": { - "name": "host_last_meal", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "content;duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Content of last meal and time since feeding; can include multiple values", - "title": "host last meal", - "examples": [ - { - "value": "corn feed;P2H" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host last meal" - ], - "rank": 327, - "is_a": "core field", - "string_serialization": "{text};{duration}", - "slot_uri": "MIXS:0000870", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_length": { - "name": "host_length", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "centimeter, millimeter, meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The length of subject", - "title": "host length", - "examples": [ - { - "value": "1 meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host length" - ], - "rank": 254, - "is_a": "core field", - "slot_uri": "MIXS:0000256", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "host_life_stage": { - "name": "host_life_stage", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "stage" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Description of life stage of host", - "title": "host life stage", - "examples": [ - { - "value": "adult" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host life stage" - ], - "rank": 255, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000251", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_phenotype": { - "name": "host_phenotype", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PATO or HP" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP", - "title": "host phenotype", - "examples": [ - { - "value": "elongated [PATO:0001154]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host phenotype" - ], - "rank": 256, - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000874", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "host_sex": { - "name": "host_sex", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Gender or physical sex of the host.", - "title": "host sex", - "examples": [ - { - "value": "non-binary" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host sex" - ], - "rank": 328, - "is_a": "core field", - "slot_uri": "MIXS:0000811", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "host_sex_enum" - }, - "host_shape": { - "name": "host_shape", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "shape" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Morphological shape of host", - "title": "host shape", - "examples": [ - { - "value": "round" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host shape" - ], - "rank": 329, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000261", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_subject_id": { - "name": "host_subject_id", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "unique identifier" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "A unique identifier by which each subject can be referred to, de-identified.", - "title": "host subject id", - "examples": [ - { - "value": "MPI123" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host subject id" - ], - "rank": 330, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000861", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_subspecf_genlin": { - "name": "host_subspecf_genlin", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies, e.g. serovar, biotype, ecotype, variety, cultivar." - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about the genetic distinctness of the host organism below the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.", - "title": "host subspecific genetic lineage", - "examples": [ - { - "value": "serovar:Newport, variety:glabrum, cultivar: Red Delicious" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host subspecific genetic lineage" - ], - "rank": 257, - "is_a": "core field", - "string_serialization": "{rank name}:{text}", - "slot_uri": "MIXS:0001318", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_substrate": { - "name": "host_substrate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "substrate name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The growth substrate of the host.", - "title": "host substrate", - "examples": [ - { - "value": "rock" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host substrate" - ], - "rank": 331, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000252", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_symbiont": { - "name": "host_symbiont", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "species name or common name" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host.", - "title": "observed host symbionts", - "examples": [ - { - "value": "flukeworms" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "observed host symbionts" - ], - "rank": 258, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0001298", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_taxid": { - "name": "host_taxid", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "NCBI taxon identifier" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "NCBI taxon id of the host, e.g. 9606", - "title": "host taxid", - "comments": [ - "Homo sapiens [NCBITaxon:9606] would be a reasonable has_raw_value" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host taxid" - ], - "rank": 259, - "is_a": "core field", - "slot_uri": "MIXS:0000250", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_tot_mass": { - "name": "host_tot_mass", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "kilogram, gram" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Total mass of the host at collection, the unit depends on host", - "title": "host total mass", - "examples": [ - { - "value": "2500 gram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host total mass" - ], - "rank": 260, - "is_a": "core field", - "slot_uri": "MIXS:0000263", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "lat_lon": { - "name": "lat_lon", - "description": "This is currently a required field but it's not clear if this should be required for human hosts", - "title": "geographic location (latitude and longitude)", - "notes": [ - "required where?", - "This is currently a required field but it's not clear if this should be required for human hosts" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "is_a": "environment field", - "string_serialization": "{lat lon}", - "slot_uri": "MIXS:0000009", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" - }, - "misc_param": { - "name": "misc_param", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "parameter name;measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Any other measurement performed or parameter collected, that is not listed here", - "title": "miscellaneous parameter", - "examples": [ - { - "value": "Bicarbonate ion concentration;2075 micromole per kilogram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "miscellaneous parameter" - ], - "rank": 23, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000752", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "organism_count": { - "name": "organism_count", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "organism name;measurement value;enumeration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", - "title": "organism count", - "examples": [ - { - "value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "organism count" - ], - "rank": 30, - "is_a": "core field", - "slot_uri": "MIXS:0000103", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$" - }, - "oxy_stat_samp": { - "name": "oxy_stat_samp", - "description": "Oxygenation status of sample", - "title": "oxygenation status of sample", - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 25, - "is_a": "core field", - "slot_uri": "MIXS:0000753", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "OxyStatSampEnum" - }, - "perturbation": { - "name": "perturbation", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "perturbation type name;perturbation interval and duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types", - "title": "perturbation", - "examples": [ - { - "value": "antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "perturbation" - ], - "rank": 33, - "is_a": "core field", - "string_serialization": "{text};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000754", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "salinity": { - "name": "salinity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "practical salinity unit, percentage" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", - "title": "salinity", - "examples": [ - { - "value": "25 practical salinity unit" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "salinity" - ], - "rank": 54, - "is_a": "core field", - "slot_uri": "MIXS:0000183", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "samp_capt_status": { - "name": "samp_capt_status", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reason for the sample", - "title": "sample capture status", - "examples": [ - { - "value": "farm sample" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample capture status" - ], - "rank": 282, - "is_a": "core field", - "slot_uri": "MIXS:0000860", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "samp_capt_status_enum" - }, - "samp_collec_device": { - "name": "samp_collec_device", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "device name" - } - }, - "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", - "title": "sample collection device", - "comments": [ - "Report dimensions and details when applicable" - ], - "examples": [ - { - "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection device" - ], - "rank": 14, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000002", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "samp_collec_method": { - "name": "samp_collec_method", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI,url , or text" - } - }, - "description": "The method employed for collecting the sample.", - "title": "sample collection method", - "comments": [ - "This can be a citation or description" - ], - "examples": [ - { - "value": "swabbing" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection method" - ], - "rank": 15, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{PMID}|{DOI}|{URL}|{text}", - "slot_uri": "MIXS:0001225", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_dis_stage": { - "name": "samp_dis_stage", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen.", - "title": "sample disease stage", - "examples": [ - { - "value": "infection" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample disease stage" - ], - "rank": 283, - "is_a": "core field", - "slot_uri": "MIXS:0000249", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "samp_dis_stage_enum" - }, - "samp_mat_process": { - "name": "samp_mat_process", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - } - }, - "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", - "title": "sample material processing", - "examples": [ - { - "value": "filtering of seawater" - }, - { - "value": "storing samples in ethanol" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample material processing" - ], - "rank": 12, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000016", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_size": { - "name": "samp_size", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millliter, gram, milligram, liter" - } - }, - "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", - "title": "amount or size of sample collected", - "comments": [ - "This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis." - ], - "examples": [ - { - "value": "5 grams" - }, - { - "value": "10 mL" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "amount or size of sample collected" - ], - "rank": 18, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float} {unit}", - "slot_uri": "MIXS:0000001", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" - }, - "samp_store_dur": { - "name": "samp_store_dur", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Duration for which the sample was stored", - "title": "sample storage duration", - "examples": [ - { - "value": "P1Y6M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage duration" - ], - "rank": 353, - "is_a": "core field", - "string_serialization": "{duration}", - "slot_uri": "MIXS:0000116", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_store_loc": { - "name": "samp_store_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "location name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Location at which sample was stored, usually name of a specific freezer/room", - "title": "sample storage location", - "examples": [ - { - "value": "Freezer no:5" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage location" - ], - "rank": 41, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000755", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_store_temp": { - "name": "samp_store_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Temperature at which the sample was stored (degrees are assumed)", - "title": "sample storage temperature", - "examples": [ - { - "value": "-80 Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage temperature" - ], - "rank": 7, - "is_a": "core field", - "slot_uri": "MIXS:0000110", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "sample_link": { - "name": "sample_link", - "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", - "title": "sample linkage", - "notes": [ - "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" - ], - "comments": [ - "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" - ], - "examples": [ - { - "value": "IGSN:DSJ0284" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "string_serialization": "{text}:{text}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface", - "SampIdNewTermsMixin" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true, - "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" - }, - "size_frac": { - "name": "size_frac", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "filter size value range" - } - }, - "description": "Filtering pore size used in sample preparation", - "title": "size fraction selected", - "examples": [ - { - "value": "0-0.22 micrometer" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "size fraction selected" - ], - "rank": 285, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float}-{float} {unit}", - "slot_uri": "MIXS:0000017", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "specific_ecosystem": { - "name": "specific_ecosystem", - "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", - "notes": [ - "string or SpecificEcosystemEnum range?" - ], - "comments": [ - "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 13, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "temp": { - "name": "temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - } - }, - "description": "Temperature of the sample at the time of sampling.", - "title": "temperature", - "examples": [ - { - "value": "25 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "temperature" - ], - "rank": 37, - "is_a": "environment field", - "slot_uri": "MIXS:0000113", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - } - }, - "attributes": { - "alt": { - "name": "alt", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - } - }, - "description": "Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air", - "title": "altitude", - "examples": [ - { - "value": "100 meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "altitude" - ], - "rank": 26, - "is_a": "environment field", - "slot_uri": "MIXS:0000094", - "multivalued": false, - "alias": "alt", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HostAssociatedInterface", - "MiscEnvsInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "ances_data": { - "name": "ances_data", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "free text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B)", - "title": "ancestral data", - "examples": [ - { - "value": "A/3*B" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "ancestral data" - ], - "rank": 237, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000247", - "multivalued": false, - "alias": "ances_data", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "biol_stat": { - "name": "biol_stat", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The level of genome modification.", - "title": "biological status", - "examples": [ - { - "value": "natural" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "biological status" - ], - "rank": 239, - "is_a": "core field", - "slot_uri": "MIXS:0000858", - "multivalued": false, - "alias": "biol_stat", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "biol_stat_enum" - }, - "blood_press_diast": { - "name": "blood_press_diast", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millimeter mercury" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Resting diastolic blood pressure, measured as mm mercury", - "title": "host blood pressure diastolic", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host blood pressure diastolic" - ], - "rank": 299, - "is_a": "core field", - "slot_uri": "MIXS:0000258", - "multivalued": false, - "alias": "blood_press_diast", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "blood_press_syst": { - "name": "blood_press_syst", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millimeter mercury" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Resting systolic blood pressure, measured as mm mercury", - "title": "host blood pressure systolic", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host blood pressure systolic" - ], - "rank": 300, - "is_a": "core field", - "slot_uri": "MIXS:0000259", - "multivalued": false, - "alias": "blood_press_syst", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "chem_administration": { - "name": "chem_administration", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "CHEBI;timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", - "title": "chemical administration", - "examples": [ - { - "value": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22" - }, - { - "value": "agar [CHEBI:2509];2018-05" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "chemical administration" - ], - "rank": 17, - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]};{timestamp}", - "slot_uri": "MIXS:0000751", - "multivalued": false, - "alias": "chem_administration", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" - }, - "collection_date": { - "name": "collection_date", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "date and time" - } - }, - "description": "The date of sampling", - "title": "collection date", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", - "Use modified term (amended definition)" - ], - "examples": [ - { - "value": "2021-04-15" - }, - { - "value": "2021-04" - }, - { - "value": "2021" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "collection date" - ], - "rank": 3, - "is_a": "environment field", - "string_serialization": "{date, arbitrary precision}", - "slot_uri": "MIXS:0000011", - "multivalued": false, - "alias": "collection_date", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" - }, - "depth": { - "name": "depth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - } - }, - "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", - "title": "depth, meters", - "notes": [ - "Use modified term" - ], - "comments": [ - "All depths must be reported in meters. Provide the numerical portion only." - ], - "examples": [ - { - "value": "0 - 0.1" - }, - { - "value": "1" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "depth" - ], - "rank": 9, - "is_a": "environment field", - "string_serialization": "{float}|{float}-{float}", - "slot_uri": "MIXS:0000018", - "multivalued": false, - "alias": "depth", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$" - }, - "ecosystem": { - "name": "ecosystem", - "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", - "notes": [ - "range: string or EcosystemEnum? The enum could be dynamic or might be soil biased." - ], - "comments": [ - "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 9, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_category": { - "name": "ecosystem_category", - "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", - "notes": [ - "string or EcosystemCategoryEnum range?" - ], - "comments": [ - "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 10, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem_category", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_subtype": { - "name": "ecosystem_subtype", - "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", - "notes": [ - "string or EcosystemSubtypeEnum range?" - ], - "comments": [ - "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 12, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem_subtype", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_type": { - "name": "ecosystem_type", - "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", - "notes": [ - "string or EcosystemTypeEnum range?" - ], - "comments": [ - "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 11, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem_type", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "elev": { - "name": "elev", - "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", - "title": "elevation, meters", - "comments": [ - "All elevations must be reported in meters. Provide the numerical portion only.", - "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." - ], - "examples": [ - { - "value": "225" - }, - { - "value": "0" - }, - { - "value": "1250" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "slot_uri": "MIXS:0000093", - "multivalued": false, - "alias": "elev", - "owner": "HostAssociatedInterface", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "float", - "required": true - }, - "env_broad_scale": { - "name": "env_broad_scale", - "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", - "title": "broad-scale environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000012", - "multivalued": false, - "alias": "env_broad_scale", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_local_scale": { - "name": "env_local_scale", - "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", - "title": "local environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "canopy [ENVO:00000047]" - }, - { - "value": "herb and fern layer [ENVO:01000337]" - }, - { - "value": "litter layer [ENVO:01000338]" - }, - { - "value": "understory [01000335]" - }, - { - "value": "shrub layer [ENVO:01000336]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 7, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000013", - "multivalued": false, - "alias": "env_local_scale", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_medium": { - "name": "env_medium", - "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", - "title": "environmental medium", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "soil [ENVO:00001998]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 8, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000014", - "multivalued": false, - "alias": "env_medium", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_package": { - "name": "env_package", - "description": "Select the MIxS enviromental package that best describes the environment from which your sample was collected.", - "title": "environmental package", - "examples": [ - { - "value": "soil" - } - ], - "in_subset": [ - "mixs extension" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "environmental package" - ], - "rank": 4, - "is_a": "attribute", - "multivalued": false, - "alias": "env_package", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true - }, - "experimental_factor": { - "name": "experimental_factor", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text or EFO and/or OBI" - } - }, - "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", - "title": "experimental factor", - "examples": [ - { - "value": "time series design [EFO:EFO_0001779]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "experimental factor" - ], - "rank": 12, - "is_a": "investigation field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000008", - "multivalued": false, - "alias": "experimental_factor", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "genetic_mod": { - "name": "genetic_mod", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI,url or free text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection", - "title": "genetic modification", - "examples": [ - { - "value": "aox1A transgenic" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "genetic modification" - ], - "rank": 244, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}|{text}", - "slot_uri": "MIXS:0000859", - "multivalued": false, - "alias": "genetic_mod", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "geo_loc_name": { - "name": "geo_loc_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" - } - }, - "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", - "title": "geographic location (country and/or sea,region)", - "examples": [ - { - "value": "USA: Maryland, Bethesda" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "geographic location (country and/or sea,region)" - ], - "rank": 4, - "is_a": "environment field", - "string_serialization": "{text}: {text}, {text}", - "slot_uri": "MIXS:0000010", - "multivalued": false, - "alias": "geo_loc_name", - "owner": "HostAssociatedInterface", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" - }, - "gravidity": { - "name": "gravidity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "gravidity status;timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used", - "title": "gravidity", - "examples": [ - { - "value": "yes;due date:2018-05-11" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "gravidity" - ], - "rank": 312, - "is_a": "core field", - "string_serialization": "{boolean};{timestamp}", - "slot_uri": "MIXS:0000875", - "multivalued": false, - "alias": "gravidity", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "horizon_meth": { - "name": "horizon_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining the horizon", - "title": "horizon method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "soil horizon method" - ], - "rank": 19, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000321", - "multivalued": false, - "alias": "horizon_meth", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "host_age": { - "name": "host_age", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "year, day, hour" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees", - "title": "host age", - "examples": [ - { - "value": "10 days" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host age" - ], - "rank": 249, - "is_a": "core field", - "slot_uri": "MIXS:0000255", - "multivalued": false, - "alias": "host_age", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "host_body_habitat": { - "name": "host_body_habitat", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "free text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Original body habitat where the sample was obtained from", - "title": "host body habitat", - "examples": [ - { - "value": "nasopharynx" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host body habitat" - ], - "rank": 319, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000866", - "multivalued": false, - "alias": "host_body_habitat", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_body_product": { - "name": "host_body_product", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "FMA or UBERON" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon", - "title": "host body product", - "examples": [ - { - "value": "Portion of mucus [fma66938]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host body product" - ], - "rank": 320, - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000888", - "multivalued": false, - "alias": "host_body_product", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "host_body_site": { - "name": "host_body_site", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "FMA or UBERON" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON", - "title": "host body site", - "examples": [ - { - "value": "gill [UBERON:0002535]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host body site" - ], - "rank": 321, - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000867", - "multivalued": false, - "alias": "host_body_site", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "host_body_temp": { - "name": "host_body_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Core body temperature of the host when sample was collected", - "title": "host body temperature", - "examples": [ - { - "value": "15 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host body temperature" - ], - "rank": 322, - "is_a": "core field", - "slot_uri": "MIXS:0000274", - "multivalued": false, - "alias": "host_body_temp", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "host_color": { - "name": "host_color", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "color" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The color of host", - "title": "host color", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host color" - ], - "rank": 323, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000260", - "multivalued": false, - "alias": "host_color", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_common_name": { - "name": "host_common_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "common name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Common name of the host.", - "title": "host common name", - "examples": [ - { - "value": "human" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host common name" - ], - "rank": 250, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000248", - "multivalued": false, - "alias": "host_common_name", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_diet": { - "name": "host_diet", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "diet type" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types", - "title": "host diet", - "examples": [ - { - "value": "herbivore" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host diet" - ], - "rank": 324, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000869", - "multivalued": false, - "alias": "host_diet", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_dry_mass": { - "name": "host_dry_mass", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "kilogram, gram" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of dry mass", - "title": "host dry mass", - "examples": [ - { - "value": "500 gram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host dry mass" - ], - "rank": 251, - "is_a": "core field", - "slot_uri": "MIXS:0000257", - "multivalued": false, - "alias": "host_dry_mass", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "host_family_relation": { - "name": "host_family_relation", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "relationship type;arbitrary identifier" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Familial relationships to other hosts in the same study; can include multiple relationships", - "title": "host family relationship", - "examples": [ - { - "value": "offspring;Mussel25" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host family relationship" - ], - "rank": 325, - "is_a": "core field", - "string_serialization": "{text};{text}", - "slot_uri": "MIXS:0000872", - "multivalued": false, - "alias": "host_family_relation", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_genotype": { - "name": "host_genotype", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "genotype" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Observed genotype", - "title": "host genotype", - "examples": [ - { - "value": "C57BL/6" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host genotype" - ], - "rank": 252, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000365", - "multivalued": false, - "alias": "host_genotype", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_growth_cond": { - "name": "host_growth_cond", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI,url or free text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Literature reference giving growth conditions of the host", - "title": "host growth conditions", - "examples": [ - { - "value": "https://academic.oup.com/icesjms/article/68/2/349/617247" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host growth conditions" - ], - "rank": 326, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}|{text}", - "slot_uri": "MIXS:0000871", - "multivalued": false, - "alias": "host_growth_cond", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_height": { - "name": "host_height", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "centimeter, millimeter, meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The height of subject", - "title": "host height", - "examples": [ - { - "value": "0.1 meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host height" - ], - "rank": 253, - "is_a": "core field", - "slot_uri": "MIXS:0000264", - "multivalued": false, - "alias": "host_height", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "host_last_meal": { - "name": "host_last_meal", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "content;duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Content of last meal and time since feeding; can include multiple values", - "title": "host last meal", - "examples": [ - { - "value": "corn feed;P2H" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host last meal" - ], - "rank": 327, - "is_a": "core field", - "string_serialization": "{text};{duration}", - "slot_uri": "MIXS:0000870", - "multivalued": false, - "alias": "host_last_meal", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_length": { - "name": "host_length", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "centimeter, millimeter, meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The length of subject", - "title": "host length", - "examples": [ - { - "value": "1 meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host length" - ], - "rank": 254, - "is_a": "core field", - "slot_uri": "MIXS:0000256", - "multivalued": false, - "alias": "host_length", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "host_life_stage": { - "name": "host_life_stage", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "stage" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Description of life stage of host", - "title": "host life stage", - "examples": [ - { - "value": "adult" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host life stage" - ], - "rank": 255, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000251", - "multivalued": false, - "alias": "host_life_stage", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_phenotype": { - "name": "host_phenotype", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PATO or HP" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP", - "title": "host phenotype", - "examples": [ - { - "value": "elongated [PATO:0001154]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host phenotype" - ], - "rank": 256, - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000874", - "multivalued": false, - "alias": "host_phenotype", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "host_sex": { - "name": "host_sex", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Gender or physical sex of the host.", - "title": "host sex", - "examples": [ - { - "value": "non-binary" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host sex" - ], - "rank": 328, - "is_a": "core field", - "slot_uri": "MIXS:0000811", - "multivalued": false, - "alias": "host_sex", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "host_sex_enum" - }, - "host_shape": { - "name": "host_shape", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "shape" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Morphological shape of host", - "title": "host shape", - "examples": [ - { - "value": "round" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host shape" - ], - "rank": 329, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000261", - "multivalued": false, - "alias": "host_shape", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_subject_id": { - "name": "host_subject_id", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "unique identifier" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "A unique identifier by which each subject can be referred to, de-identified.", - "title": "host subject id", - "examples": [ - { - "value": "MPI123" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host subject id" - ], - "rank": 330, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000861", - "multivalued": false, - "alias": "host_subject_id", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_subspecf_genlin": { - "name": "host_subspecf_genlin", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies, e.g. serovar, biotype, ecotype, variety, cultivar." - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about the genetic distinctness of the host organism below the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.", - "title": "host subspecific genetic lineage", - "examples": [ - { - "value": "serovar:Newport, variety:glabrum, cultivar: Red Delicious" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host subspecific genetic lineage" - ], - "rank": 257, - "is_a": "core field", - "string_serialization": "{rank name}:{text}", - "slot_uri": "MIXS:0001318", - "multivalued": false, - "alias": "host_subspecf_genlin", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_substrate": { - "name": "host_substrate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "substrate name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The growth substrate of the host.", - "title": "host substrate", - "examples": [ - { - "value": "rock" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host substrate" - ], - "rank": 331, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000252", - "multivalued": false, - "alias": "host_substrate", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_symbiont": { - "name": "host_symbiont", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "species name or common name" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host.", - "title": "observed host symbionts", - "examples": [ - { - "value": "flukeworms" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "observed host symbionts" - ], - "rank": 258, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0001298", - "multivalued": false, - "alias": "host_symbiont", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_taxid": { - "name": "host_taxid", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "NCBI taxon identifier" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "NCBI taxon id of the host, e.g. 9606", - "title": "host taxid", - "comments": [ - "Homo sapiens [NCBITaxon:9606] would be a reasonable has_raw_value" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host taxid" - ], - "rank": 259, - "is_a": "core field", - "slot_uri": "MIXS:0000250", - "multivalued": false, - "alias": "host_taxid", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_tot_mass": { - "name": "host_tot_mass", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "kilogram, gram" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Total mass of the host at collection, the unit depends on host", - "title": "host total mass", - "examples": [ - { - "value": "2500 gram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host total mass" - ], - "rank": 260, - "is_a": "core field", - "slot_uri": "MIXS:0000263", - "multivalued": false, - "alias": "host_tot_mass", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "lat_lon": { - "name": "lat_lon", - "description": "This is currently a required field but it's not clear if this should be required for human hosts", - "title": "geographic location (latitude and longitude)", - "notes": [ - "required where?", - "This is currently a required field but it's not clear if this should be required for human hosts" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "is_a": "environment field", - "string_serialization": "{lat lon}", - "slot_uri": "MIXS:0000009", - "multivalued": false, - "alias": "lat_lon", - "owner": "HostAssociatedInterface", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" - }, - "misc_param": { - "name": "misc_param", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "parameter name;measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Any other measurement performed or parameter collected, that is not listed here", - "title": "miscellaneous parameter", - "examples": [ - { - "value": "Bicarbonate ion concentration;2075 micromole per kilogram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "miscellaneous parameter" - ], - "rank": 23, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000752", - "multivalued": false, - "alias": "misc_param", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "organism_count": { - "name": "organism_count", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "organism name;measurement value;enumeration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", - "title": "organism count", - "examples": [ - { - "value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "organism count" - ], - "rank": 30, - "is_a": "core field", - "slot_uri": "MIXS:0000103", - "multivalued": false, - "alias": "organism_count", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$" - }, - "oxy_stat_samp": { - "name": "oxy_stat_samp", - "description": "Oxygenation status of sample", - "title": "oxygenation status of sample", - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 25, - "is_a": "core field", - "slot_uri": "MIXS:0000753", - "multivalued": false, - "alias": "oxy_stat_samp", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "OxyStatSampEnum" - }, - "perturbation": { - "name": "perturbation", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "perturbation type name;perturbation interval and duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types", - "title": "perturbation", - "examples": [ - { - "value": "antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "perturbation" - ], - "rank": 33, - "is_a": "core field", - "string_serialization": "{text};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000754", - "multivalued": false, - "alias": "perturbation", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "salinity": { - "name": "salinity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "practical salinity unit, percentage" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", - "title": "salinity", - "examples": [ - { - "value": "25 practical salinity unit" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "salinity" - ], - "rank": 54, - "is_a": "core field", - "slot_uri": "MIXS:0000183", - "multivalued": false, - "alias": "salinity", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "samp_capt_status": { - "name": "samp_capt_status", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reason for the sample", - "title": "sample capture status", - "examples": [ - { - "value": "farm sample" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample capture status" - ], - "rank": 282, - "is_a": "core field", - "slot_uri": "MIXS:0000860", - "multivalued": false, - "alias": "samp_capt_status", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "samp_capt_status_enum" - }, - "samp_collec_device": { - "name": "samp_collec_device", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "device name" - } - }, - "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", - "title": "sample collection device", - "comments": [ - "Report dimensions and details when applicable" - ], - "examples": [ - { - "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection device" - ], - "rank": 14, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000002", - "multivalued": false, - "alias": "samp_collec_device", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "samp_collec_method": { - "name": "samp_collec_method", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI,url , or text" - } - }, - "description": "The method employed for collecting the sample.", - "title": "sample collection method", - "comments": [ - "This can be a citation or description" - ], - "examples": [ - { - "value": "swabbing" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection method" - ], - "rank": 15, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{PMID}|{DOI}|{URL}|{text}", - "slot_uri": "MIXS:0001225", - "multivalued": false, - "alias": "samp_collec_method", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_dis_stage": { - "name": "samp_dis_stage", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen.", - "title": "sample disease stage", - "examples": [ - { - "value": "infection" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample disease stage" - ], - "rank": 283, - "is_a": "core field", - "slot_uri": "MIXS:0000249", - "multivalued": false, - "alias": "samp_dis_stage", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "samp_dis_stage_enum" - }, - "samp_mat_process": { - "name": "samp_mat_process", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - } - }, - "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", - "title": "sample material processing", - "examples": [ - { - "value": "filtering of seawater" - }, - { - "value": "storing samples in ethanol" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample material processing" - ], - "rank": 12, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000016", - "multivalued": false, - "alias": "samp_mat_process", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_size": { - "name": "samp_size", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millliter, gram, milligram, liter" - } - }, - "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", - "title": "amount or size of sample collected", - "comments": [ - "This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis." - ], - "examples": [ - { - "value": "5 grams" - }, - { - "value": "10 mL" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "amount or size of sample collected" - ], - "rank": 18, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float} {unit}", - "slot_uri": "MIXS:0000001", - "multivalued": false, - "alias": "samp_size", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" - }, - "samp_store_dur": { - "name": "samp_store_dur", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Duration for which the sample was stored", - "title": "sample storage duration", - "examples": [ - { - "value": "P1Y6M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage duration" - ], - "rank": 353, - "is_a": "core field", - "string_serialization": "{duration}", - "slot_uri": "MIXS:0000116", - "multivalued": false, - "alias": "samp_store_dur", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_store_loc": { - "name": "samp_store_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "location name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Location at which sample was stored, usually name of a specific freezer/room", - "title": "sample storage location", - "examples": [ - { - "value": "Freezer no:5" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage location" - ], - "rank": 41, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000755", - "multivalued": false, - "alias": "samp_store_loc", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_store_temp": { - "name": "samp_store_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Temperature at which the sample was stored (degrees are assumed)", - "title": "sample storage temperature", - "examples": [ - { - "value": "-80 Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage temperature" - ], - "rank": 7, - "is_a": "core field", - "slot_uri": "MIXS:0000110", - "multivalued": false, - "alias": "samp_store_temp", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "sample_link": { - "name": "sample_link", - "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", - "title": "sample linkage", - "notes": [ - "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" - ], - "comments": [ - "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" - ], - "examples": [ - { - "value": "IGSN:DSJ0284" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "string_serialization": "{text}:{text}", - "multivalued": false, - "alias": "sample_link", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface", - "SampIdNewTermsMixin" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true, - "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" - }, - "size_frac": { - "name": "size_frac", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "filter size value range" - } - }, - "description": "Filtering pore size used in sample preparation", - "title": "size fraction selected", - "examples": [ - { - "value": "0-0.22 micrometer" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "size fraction selected" - ], - "rank": 285, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float}-{float} {unit}", - "slot_uri": "MIXS:0000017", - "multivalued": false, - "alias": "size_frac", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "specific_ecosystem": { - "name": "specific_ecosystem", - "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", - "notes": [ - "string or SpecificEcosystemEnum range?" - ], - "comments": [ - "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 13, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "specific_ecosystem", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "temp": { - "name": "temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - } - }, - "description": "Temperature of the sample at the time of sampling.", - "title": "temperature", - "examples": [ - { - "value": "25 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "temperature" - ], - "rank": 37, - "is_a": "environment field", - "slot_uri": "MIXS:0000113", - "multivalued": false, - "alias": "temp", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "analysis_type": { - "name": "analysis_type", - "description": "Select all the data types associated or available for this biosample", - "title": "analysis/data type", - "examples": [ - { - "value": "metagenomics; metabolomics; proteomics" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:investigation_type" - ], - "rank": 3, - "multivalued": true, - "alias": "analysis_type", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "EmslInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "sample_id_section", - "range": "analysis_type_enum", - "required": true, - "recommended": true - }, - "samp_name": { - "name": "samp_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - } - }, - "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", - "title": "sample name", - "comments": [ - "It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." - ], - "examples": [ - { - "value": "Rock core CB1178(5-6) from NSW" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample name" - ], - "rank": 1, - "is_a": "investigation field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0001107", - "multivalued": false, - "identifier": true, - "alias": "samp_name", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "EmslInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true - }, - "source_mat_id": { - "name": "source_mat_id", - "description": "A globally unique identifier assigned to the biological sample.", - "title": "source material identifier", - "todos": [ - "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID.", - "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID." - ], - "notes": [ - "The source material IS the Globally Unique ID" - ], - "comments": [ - "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).", - "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/)." - ], - "examples": [ - { - "value": "IGSN:AU1243" - }, - { - "value": "UUID:24f1467a-40f4-11ed-b878-0242ac120002" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 2, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{text}:{text}", - "slot_uri": "MIXS:0000026", - "multivalued": false, - "alias": "source_mat_id", - "owner": "HostAssociatedInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "EmslInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" - } - } - }, - "JgiMgInterface": { - "name": "JgiMgInterface", - "description": "jgi_mg dh_interface", - "title": "JGI MG", - "from_schema": "https://example.com/nmdc_submission_schema", - "is_a": "DhInterface", - "mixins": [ - "DhMultiviewCommonColumnsMixin" - ], - "slots": [ - "dna_absorb1", - "dna_absorb2", - "dna_concentration", - "dna_cont_type", - "dna_cont_well", - "dna_container_id", - "dna_dnase", - "dna_isolate_meth", - "dna_project_contact", - "dna_samp_id", - "dna_sample_format", - "dna_sample_name", - "dna_seq_project", - "dna_seq_project_name", - "dna_seq_project_pi", - "dna_volume", - "proposal_dna", - "dna_absorb1", - "dna_absorb2", - "dna_concentration", - "dna_cont_type", - "dna_cont_well", - "dna_container_id", - "dna_dnase", - "dna_isolate_meth", - "dna_project_contact", - "dna_samp_id", - "dna_sample_format", - "dna_sample_name", - "dna_seq_project", - "dna_seq_project_name", - "dna_seq_project_pi", - "dna_volume", - "proposal_dna" - ], - "slot_usage": { - "dna_absorb1": { - "name": "dna_absorb1", - "description": "260/280 measurement of DNA sample purity", - "title": "DNA absorbance 260/280", - "comments": [ - "Recommended value is between 1 and 3." - ], - "examples": [ - { - "value": "2.02" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 7, - "is_a": "biomaterial_purity", - "string_serialization": "{float}", - "owner": "Biosample", - "domain_of": [ - "Biosample", - "ProcessedSample", - "JgiMgInterface" - ], - "slot_group": "jgi_metagenomics_section", - "range": "float", - "recommended": true - }, - "dna_absorb2": { - "name": "dna_absorb2", - "description": "260/230 measurement of DNA sample purity", - "title": "DNA absorbance 260/230", - "comments": [ - "Recommended value is between 1 and 3." - ], - "examples": [ - { - "value": "2.02" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 8, - "is_a": "biomaterial_purity", - "string_serialization": "{float}", - "owner": "Biosample", - "domain_of": [ - "Biosample", - "JgiMgInterface" - ], - "slot_group": "jgi_metagenomics_section", - "range": "float", - "recommended": true - }, - "dna_concentration": { - "name": "dna_concentration", - "title": "DNA concentration in ng/ul", - "comments": [ - "Units must be in ng/uL. Enter the numerical part only. Must be calculated using a fluorometric method. Acceptable values are 0-2000." - ], - "examples": [ - { - "value": "100" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "nmdc:nucleic_acid_concentration" - ], - "rank": 5, - "string_serialization": "{float}", - "owner": "Biosample", - "domain_of": [ - "Biosample", - "ProcessedSample", - "JgiMgInterface" - ], - "slot_group": "jgi_metagenomics_section", - "range": "float", - "required": true, - "recommended": true, - "minimum_value": 0, - "maximum_value": 2000 - }, - "dna_cont_type": { - "name": "dna_cont_type", - "description": "Tube or plate (96-well)", - "title": "DNA container type", - "examples": [ - { - "value": "plate" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 10, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "JgiMgInterface" - ], - "slot_group": "jgi_metagenomics_section", - "range": "JgiContTypeEnum", - "required": true, - "recommended": true - }, - "dna_cont_well": { - "name": "dna_cont_well", - "title": "DNA plate position", - "comments": [ - "Required when 'plate' is selected for container type.", - "Leave blank if the sample will be shipped in a tube.", - "JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass validation.", - "For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8)." - ], - "examples": [ - { - "value": "B2" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 11, - "string_serialization": "{96 well plate pos}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "JgiMgInterface" - ], - "slot_group": "jgi_metagenomics_section", - "range": "string", - "recommended": true, - "pattern": "^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$" - }, - "dna_container_id": { - "name": "dna_container_id", - "title": "DNA container label", - "comments": [ - "Must be unique across all tubes and plates, and <20 characters. All samples in a plate should have the same plate label." - ], - "examples": [ - { - "value": "Pond_MT_041618" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 9, - "string_serialization": "{text < 20 characters}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "JgiMgInterface" - ], - "slot_group": "jgi_metagenomics_section", - "range": "string", - "required": true, - "recommended": true, - "pattern": "^.{1,20}$" - }, - "dna_dnase": { - "name": "dna_dnase", - "title": "DNase treatment DNA", - "comments": [ - "Note DNase treatment is required for all RNA samples." - ], - "examples": [ - { - "value": "no" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 13, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "JgiMgInterface" - ], - "slot_group": "jgi_metagenomics_section", - "range": "YesNoEnum", - "required": true, - "recommended": true - }, - "dna_isolate_meth": { - "name": "dna_isolate_meth", - "description": "Describe the method/protocol/kit used to extract DNA/RNA.", - "title": "DNA isolation method", - "examples": [ - { - "value": "phenol/chloroform extraction" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 16, - "string_serialization": "{text}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "JgiMgInterface" - ], - "slot_group": "jgi_metagenomics_section", - "range": "string", - "required": true, - "recommended": true - }, - "dna_project_contact": { - "name": "dna_project_contact", - "title": "DNA seq project contact", - "comments": [ - "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." - ], - "examples": [ - { - "value": "John Jones" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 18, - "string_serialization": "{text}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "JgiMgInterface" - ], - "slot_group": "jgi_metagenomics_section", - "range": "string", - "required": true, - "recommended": true - }, - "dna_samp_id": { - "name": "dna_samp_id", - "title": "DNA sample ID", - "todos": [ - "Removed identifier = TRUE from dna_samp_ID in JGI_sample_slots, as a class can't have two identifiers. How to force uniqueness? Moot because that column will be prefilled?" - ], - "comments": [ - "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." - ], - "examples": [ - { - "value": "187654" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 3, - "string_serialization": "{text}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "JgiMgInterface" - ], - "slot_group": "jgi_metagenomics_section", - "range": "string", - "required": true, - "recommended": true - }, - "dna_sample_format": { - "name": "dna_sample_format", - "description": "Solution in which the DNA sample has been suspended", - "title": "DNA sample format", - "examples": [ - { - "value": "Water" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 12, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "JgiMgInterface" - ], - "slot_group": "jgi_metagenomics_section", - "range": "dna_sample_format_enum", - "required": true, - "recommended": true - }, - "dna_sample_name": { - "name": "dna_sample_name", - "description": "Give the DNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", - "title": "DNA sample name", - "examples": [ - { - "value": "JGI_pond_041618" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 4, - "string_serialization": "{text}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "JgiMgInterface" - ], - "slot_group": "jgi_metagenomics_section", - "range": "string", - "required": true, - "recommended": true - }, - "dna_seq_project": { - "name": "dna_seq_project", - "title": "DNA seq project ID", - "comments": [ - "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." - ], - "examples": [ - { - "value": "1191234" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 1, - "string_serialization": "{text}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "JgiMgInterface" - ], - "slot_group": "jgi_metagenomics_section", - "range": "string", - "required": true, - "recommended": true - }, - "dna_seq_project_name": { - "name": "dna_seq_project_name", - "title": "DNA seq project name", - "comments": [ - "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." - ], - "examples": [ - { - "value": "JGI Pond metagenomics" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 2, - "string_serialization": "{text}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "JgiMgInterface" - ], - "slot_group": "jgi_metagenomics_section", - "range": "string", - "required": true, - "recommended": true - }, - "dna_seq_project_pi": { - "name": "dna_seq_project_pi", - "title": "DNA seq project PI", - "comments": [ - "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." - ], - "examples": [ - { - "value": "Jane Johnson" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 17, - "string_serialization": "{text}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "JgiMgInterface" - ], - "slot_group": "jgi_metagenomics_section", - "range": "string", - "required": true, - "recommended": true - }, - "dna_volume": { - "name": "dna_volume", - "title": "DNA volume in ul", - "comments": [ - "Units must be in uL. Enter the numerical part only. Value must be 0-1000. This form accepts values < 25, but JGI may refuse to process them unless permission has been granted by a project manager" - ], - "examples": [ - { - "value": "25" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "string_serialization": "{float}", - "owner": "Biosample", - "domain_of": [ - "Biosample", - "JgiMgInterface" - ], - "slot_group": "jgi_metagenomics_section", - "range": "float", - "required": true, - "recommended": true, - "minimum_value": 0, - "maximum_value": 1000 - }, - "proposal_dna": { - "name": "proposal_dna", - "title": "DNA proposal ID", - "comments": [ - "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." - ], - "examples": [ - { - "value": "504000" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 19, - "string_serialization": "{text}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "JgiMgInterface" - ], - "slot_group": "jgi_metagenomics_section", - "range": "string", - "required": true, - "recommended": true - }, - "oxy_stat_samp": { - "name": "oxy_stat_samp", - "range": "OxyStatSampEnum" - } - }, - "attributes": { - "dna_absorb1": { - "name": "dna_absorb1", - "description": "260/280 measurement of DNA sample purity", - "title": "DNA absorbance 260/280", - "comments": [ - "Recommended value is between 1 and 3." - ], - "examples": [ - { - "value": "2.02" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 7, - "is_a": "biomaterial_purity", - "string_serialization": "{float}", - "alias": "dna_absorb1", - "owner": "JgiMgInterface", - "domain_of": [ - "Biosample", - "ProcessedSample", - "JgiMgInterface" - ], - "slot_group": "jgi_metagenomics_section", - "range": "float", - "recommended": true - }, - "dna_absorb2": { - "name": "dna_absorb2", - "description": "260/230 measurement of DNA sample purity", - "title": "DNA absorbance 260/230", - "comments": [ - "Recommended value is between 1 and 3." - ], - "examples": [ - { - "value": "2.02" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 8, - "is_a": "biomaterial_purity", - "string_serialization": "{float}", - "alias": "dna_absorb2", - "owner": "JgiMgInterface", - "domain_of": [ - "Biosample", - "JgiMgInterface" - ], - "slot_group": "jgi_metagenomics_section", - "range": "float", - "recommended": true - }, - "dna_concentration": { - "name": "dna_concentration", - "title": "DNA concentration in ng/ul", - "comments": [ - "Units must be in ng/uL. Enter the numerical part only. Must be calculated using a fluorometric method. Acceptable values are 0-2000." - ], - "examples": [ - { - "value": "100" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "nmdc:nucleic_acid_concentration" - ], - "rank": 5, - "string_serialization": "{float}", - "alias": "dna_concentration", - "owner": "JgiMgInterface", - "domain_of": [ - "Biosample", - "ProcessedSample", - "JgiMgInterface" - ], - "slot_group": "jgi_metagenomics_section", - "range": "float", - "required": true, - "recommended": true, - "minimum_value": 0, - "maximum_value": 2000 - }, - "dna_cont_type": { - "name": "dna_cont_type", - "description": "Tube or plate (96-well)", - "title": "DNA container type", - "examples": [ - { - "value": "plate" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 10, - "alias": "dna_cont_type", - "owner": "JgiMgInterface", - "domain_of": [ - "Biosample", - "JgiMgInterface" - ], - "slot_group": "jgi_metagenomics_section", - "range": "JgiContTypeEnum", - "required": true, - "recommended": true - }, - "dna_cont_well": { - "name": "dna_cont_well", - "title": "DNA plate position", - "comments": [ - "Required when 'plate' is selected for container type.", - "Leave blank if the sample will be shipped in a tube.", - "JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass validation.", - "For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8)." - ], - "examples": [ - { - "value": "B2" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 11, - "string_serialization": "{96 well plate pos}", - "multivalued": false, - "alias": "dna_cont_well", - "owner": "JgiMgInterface", - "domain_of": [ - "Biosample", - "JgiMgInterface" - ], - "slot_group": "jgi_metagenomics_section", - "range": "string", - "recommended": true, - "pattern": "^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$" - }, - "dna_container_id": { - "name": "dna_container_id", - "title": "DNA container label", - "comments": [ - "Must be unique across all tubes and plates, and <20 characters. All samples in a plate should have the same plate label." - ], - "examples": [ - { - "value": "Pond_MT_041618" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 9, - "string_serialization": "{text < 20 characters}", - "multivalued": false, - "alias": "dna_container_id", - "owner": "JgiMgInterface", - "domain_of": [ - "Biosample", - "JgiMgInterface" - ], - "slot_group": "jgi_metagenomics_section", - "range": "string", - "required": true, - "recommended": true, - "pattern": "^.{1,20}$" - }, - "dna_dnase": { - "name": "dna_dnase", - "title": "DNase treatment DNA", - "comments": [ - "Note DNase treatment is required for all RNA samples." - ], - "examples": [ - { - "value": "no" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 13, - "alias": "dna_dnase", - "owner": "JgiMgInterface", - "domain_of": [ - "Biosample", - "JgiMgInterface" - ], - "slot_group": "jgi_metagenomics_section", - "range": "YesNoEnum", - "required": true, - "recommended": true - }, - "dna_isolate_meth": { - "name": "dna_isolate_meth", - "description": "Describe the method/protocol/kit used to extract DNA/RNA.", - "title": "DNA isolation method", - "examples": [ - { - "value": "phenol/chloroform extraction" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 16, - "string_serialization": "{text}", - "multivalued": false, - "alias": "dna_isolate_meth", - "owner": "JgiMgInterface", - "domain_of": [ - "Biosample", - "JgiMgInterface" - ], - "slot_group": "jgi_metagenomics_section", - "range": "string", - "required": true, - "recommended": true - }, - "dna_project_contact": { - "name": "dna_project_contact", - "title": "DNA seq project contact", - "comments": [ - "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." - ], - "examples": [ - { - "value": "John Jones" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 18, - "string_serialization": "{text}", - "multivalued": false, - "alias": "dna_project_contact", - "owner": "JgiMgInterface", - "domain_of": [ - "Biosample", - "JgiMgInterface" - ], - "slot_group": "jgi_metagenomics_section", - "range": "string", - "required": true, - "recommended": true - }, - "dna_samp_id": { - "name": "dna_samp_id", - "title": "DNA sample ID", - "todos": [ - "Removed identifier = TRUE from dna_samp_ID in JGI_sample_slots, as a class can't have two identifiers. How to force uniqueness? Moot because that column will be prefilled?" - ], - "comments": [ - "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." - ], - "examples": [ - { - "value": "187654" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 3, - "string_serialization": "{text}", - "multivalued": false, - "alias": "dna_samp_id", - "owner": "JgiMgInterface", - "domain_of": [ - "Biosample", - "JgiMgInterface" - ], - "slot_group": "jgi_metagenomics_section", - "range": "string", - "required": true, - "recommended": true - }, - "dna_sample_format": { - "name": "dna_sample_format", - "description": "Solution in which the DNA sample has been suspended", - "title": "DNA sample format", - "examples": [ - { - "value": "Water" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 12, - "alias": "dna_sample_format", - "owner": "JgiMgInterface", - "domain_of": [ - "Biosample", - "JgiMgInterface" - ], - "slot_group": "jgi_metagenomics_section", - "range": "dna_sample_format_enum", - "required": true, - "recommended": true - }, - "dna_sample_name": { - "name": "dna_sample_name", - "description": "Give the DNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", - "title": "DNA sample name", - "examples": [ - { - "value": "JGI_pond_041618" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 4, - "string_serialization": "{text}", - "multivalued": false, - "alias": "dna_sample_name", - "owner": "JgiMgInterface", - "domain_of": [ - "Biosample", - "JgiMgInterface" - ], - "slot_group": "jgi_metagenomics_section", - "range": "string", - "required": true, - "recommended": true - }, - "dna_seq_project": { - "name": "dna_seq_project", - "title": "DNA seq project ID", - "comments": [ - "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." - ], - "examples": [ - { - "value": "1191234" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 1, - "string_serialization": "{text}", - "multivalued": false, - "alias": "dna_seq_project", - "owner": "JgiMgInterface", - "domain_of": [ - "Biosample", - "JgiMgInterface" - ], - "slot_group": "jgi_metagenomics_section", - "range": "string", - "required": true, - "recommended": true - }, - "dna_seq_project_name": { - "name": "dna_seq_project_name", - "title": "DNA seq project name", - "comments": [ - "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." - ], - "examples": [ - { - "value": "JGI Pond metagenomics" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 2, - "string_serialization": "{text}", - "multivalued": false, - "alias": "dna_seq_project_name", - "owner": "JgiMgInterface", - "domain_of": [ - "Biosample", - "JgiMgInterface" - ], - "slot_group": "jgi_metagenomics_section", - "range": "string", - "required": true, - "recommended": true - }, - "dna_seq_project_pi": { - "name": "dna_seq_project_pi", - "title": "DNA seq project PI", - "comments": [ - "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." - ], - "examples": [ - { - "value": "Jane Johnson" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 17, - "string_serialization": "{text}", - "multivalued": false, - "alias": "dna_seq_project_pi", - "owner": "JgiMgInterface", - "domain_of": [ - "Biosample", - "JgiMgInterface" - ], - "slot_group": "jgi_metagenomics_section", - "range": "string", - "required": true, - "recommended": true - }, - "dna_volume": { - "name": "dna_volume", - "title": "DNA volume in ul", - "comments": [ - "Units must be in uL. Enter the numerical part only. Value must be 0-1000. This form accepts values < 25, but JGI may refuse to process them unless permission has been granted by a project manager" - ], - "examples": [ - { - "value": "25" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "string_serialization": "{float}", - "alias": "dna_volume", - "owner": "JgiMgInterface", - "domain_of": [ - "Biosample", - "JgiMgInterface" - ], - "slot_group": "jgi_metagenomics_section", - "range": "float", - "required": true, - "recommended": true, - "minimum_value": 0, - "maximum_value": 1000 - }, - "proposal_dna": { - "name": "proposal_dna", - "title": "DNA proposal ID", - "comments": [ - "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." - ], - "examples": [ - { - "value": "504000" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 19, - "string_serialization": "{text}", - "multivalued": false, - "alias": "proposal_dna", - "owner": "JgiMgInterface", - "domain_of": [ - "Biosample", - "JgiMgInterface" - ], - "slot_group": "jgi_metagenomics_section", - "range": "string", - "required": true, - "recommended": true - }, - "analysis_type": { - "name": "analysis_type", - "description": "Select all the data types associated or available for this biosample", - "title": "analysis/data type", - "examples": [ - { - "value": "metagenomics; metabolomics; proteomics" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:investigation_type" - ], - "rank": 3, - "multivalued": true, - "alias": "analysis_type", - "owner": "JgiMgInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "EmslInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface" - ], - "slot_group": "sample_id_section", - "range": "analysis_type_enum", - "required": true, - "recommended": true - }, - "samp_name": { - "name": "samp_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - } - }, - "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", - "title": "sample name", - "comments": [ - "It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." - ], - "examples": [ - { - "value": "Rock core CB1178(5-6) from NSW" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample name" - ], - "rank": 1, - "is_a": "investigation field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0001107", - "multivalued": false, - "identifier": true, - "alias": "samp_name", - "owner": "JgiMgInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "EmslInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true - }, - "source_mat_id": { - "name": "source_mat_id", - "description": "A globally unique identifier assigned to the biological sample.", - "title": "source material identifier", - "todos": [ - "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID.", - "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID." - ], - "notes": [ - "The source material IS the Globally Unique ID" - ], - "comments": [ - "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).", - "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/)." - ], - "examples": [ - { - "value": "IGSN:AU1243" - }, - { - "value": "UUID:24f1467a-40f4-11ed-b878-0242ac120002" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 2, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{text}:{text}", - "slot_uri": "MIXS:0000026", - "multivalued": false, - "alias": "source_mat_id", - "owner": "JgiMgInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "EmslInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" - } - }, - "rules": [ - { - "preconditions": { - "slot_conditions": { - "dna_cont_well": { - "name": "dna_cont_well", - "pattern": ".+" - } - } - }, - "postconditions": { - "slot_conditions": { - "dna_cont_type": { - "name": "dna_cont_type", - "equals_string": "plate" - } - } - }, - "description": "DNA samples shipped to JGI for metagenomic analysis in tubes can't have any value for their plate position.", - "title": "dna_well_requires_plate" - }, - { - "preconditions": { - "slot_conditions": { - "dna_cont_type": { - "name": "dna_cont_type", - "equals_string": "plate" - } - } - }, - "postconditions": { - "slot_conditions": { - "dna_cont_well": { - "name": "dna_cont_well", - "pattern": "^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$" - } - } - }, - "description": "DNA samples in plates must have a plate position that matches the regex. Note the requirement for an empty string in the tube case. Waiting for value_present validation to be added to runtime", - "title": "dna_plate_requires_well" - } - ] - }, - "JgiMtInterface": { - "name": "JgiMtInterface", - "description": "jgi_mt dh_interface", - "title": "JGI MT", - "from_schema": "https://example.com/nmdc_submission_schema", - "is_a": "DhInterface", - "mixins": [ - "DhMultiviewCommonColumnsMixin" - ], - "slots": [ - "dnase_rna", - "proposal_rna", - "rna_absorb1", - "rna_absorb2", - "rna_concentration", - "rna_cont_type", - "rna_cont_well", - "rna_container_id", - "rna_isolate_meth", - "rna_project_contact", - "rna_samp_id", - "rna_sample_format", - "rna_sample_name", - "rna_seq_project", - "rna_seq_project_name", - "rna_seq_project_pi", - "rna_volume", - "dnase_rna", - "proposal_rna", - "rna_absorb1", - "rna_absorb2", - "rna_concentration", - "rna_cont_type", - "rna_cont_well", - "rna_container_id", - "rna_isolate_meth", - "rna_project_contact", - "rna_samp_id", - "rna_sample_format", - "rna_sample_name", - "rna_seq_project", - "rna_seq_project_name", - "rna_seq_project_pi", - "rna_volume" - ], - "slot_usage": { - "dnase_rna": { - "name": "dnase_rna", - "title": "DNase treated", - "comments": [ - "Note DNase treatment is required for all RNA samples." - ], - "examples": [ - { - "value": "no" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 13, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "JgiMtInterface" - ], - "slot_group": "jgi_metatranscriptomics_section", - "range": "YesNoEnum", - "required": true, - "recommended": true - }, - "proposal_rna": { - "name": "proposal_rna", - "title": "RNA proposal ID", - "comments": [ - "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." - ], - "examples": [ - { - "value": "504000" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 19, - "string_serialization": "{text}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "JgiMtInterface" - ], - "slot_group": "jgi_metatranscriptomics_section", - "range": "string", - "required": true, - "recommended": true - }, - "rna_absorb1": { - "name": "rna_absorb1", - "description": "260/280 measurement of RNA sample purity", - "title": "RNA absorbance 260/280", - "comments": [ - "Recommended value is between 1 and 3." - ], - "examples": [ - { - "value": "2.02" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 7, - "is_a": "biomaterial_purity", - "string_serialization": "{float}", - "owner": "Biosample", - "domain_of": [ - "Biosample", - "JgiMtInterface" - ], - "slot_group": "jgi_metatranscriptomics_section", - "range": "float", - "recommended": true - }, - "rna_absorb2": { - "name": "rna_absorb2", - "description": "260/230 measurement of RNA sample purity", - "title": "RNA absorbance 260/230", - "comments": [ - "Recommended value is between 1 and 3." - ], - "examples": [ - { - "value": "2.02" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 8, - "is_a": "biomaterial_purity", - "string_serialization": "{float}", - "owner": "Biosample", - "domain_of": [ - "Biosample", - "JgiMtInterface" - ], - "slot_group": "jgi_metatranscriptomics_section", - "range": "float", - "recommended": true - }, - "rna_concentration": { - "name": "rna_concentration", - "title": "RNA concentration in ng/ul", - "comments": [ - "Units must be in ng/uL. Enter the numerical part only. Must be calculated using a fluorometric method. Acceptable values are 0-2000." - ], - "examples": [ - { - "value": "100" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "nmdc:nucleic_acid_concentration" - ], - "rank": 5, - "string_serialization": "{float}", - "owner": "Biosample", - "domain_of": [ - "Biosample", - "JgiMtInterface" - ], - "slot_group": "jgi_metatranscriptomics_section", - "range": "float", - "required": true, - "recommended": true, - "minimum_value": 0, - "maximum_value": 1000 - }, - "rna_cont_type": { - "name": "rna_cont_type", - "description": "Tube or plate (96-well)", - "title": "RNA container type", - "examples": [ - { - "value": "plate" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 10, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "JgiMtInterface" - ], - "slot_group": "jgi_metatranscriptomics_section", - "range": "JgiContTypeEnum", - "required": true, - "recommended": true - }, - "rna_cont_well": { - "name": "rna_cont_well", - "title": "RNA plate position", - "comments": [ - "Required when 'plate' is selected for container type.", - "Leave blank if the sample will be shipped in a tube.", - "JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass validation.", - "For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8)." - ], - "examples": [ - { - "value": "B2" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 11, - "string_serialization": "{96 well plate pos}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "JgiMtInterface" - ], - "slot_group": "jgi_metatranscriptomics_section", - "range": "string", - "recommended": true, - "pattern": "^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$" - }, - "rna_container_id": { - "name": "rna_container_id", - "title": "RNA container label", - "comments": [ - "Must be unique across all tubes and plates, and <20 characters. All samples in a plate should have the same plate label." - ], - "examples": [ - { - "value": "Pond_MT_041618" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 9, - "string_serialization": "{text < 20 characters}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "JgiMtInterface" - ], - "slot_group": "jgi_metatranscriptomics_section", - "range": "string", - "required": true, - "recommended": true, - "pattern": "^.{1,20}$" - }, - "rna_isolate_meth": { - "name": "rna_isolate_meth", - "description": "Describe the method/protocol/kit used to extract DNA/RNA.", - "title": "RNA isolation method", - "examples": [ - { - "value": "phenol/chloroform extraction" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 16, - "string_serialization": "{text}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "JgiMtInterface" - ], - "slot_group": "jgi_metatranscriptomics_section", - "range": "string", - "required": true, - "recommended": true - }, - "rna_project_contact": { - "name": "rna_project_contact", - "title": "RNA seq project contact", - "comments": [ - "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." - ], - "examples": [ - { - "value": "John Jones" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 18, - "string_serialization": "{text}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "JgiMtInterface" - ], - "slot_group": "jgi_metatranscriptomics_section", - "range": "string", - "required": true, - "recommended": true - }, - "rna_samp_id": { - "name": "rna_samp_id", - "title": "RNA sample ID", - "comments": [ - "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." - ], - "examples": [ - { - "value": "187654" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 3, - "string_serialization": "{text}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "JgiMtInterface" - ], - "slot_group": "jgi_metatranscriptomics_section", - "range": "string", - "required": true, - "recommended": true - }, - "rna_sample_format": { - "name": "rna_sample_format", - "description": "Solution in which the RNA sample has been suspended", - "title": "RNA sample format", - "examples": [ - { - "value": "Water" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 12, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "JgiMtInterface" - ], - "slot_group": "jgi_metatranscriptomics_section", - "range": "rna_sample_format_enum", - "required": true, - "recommended": true - }, - "rna_sample_name": { - "name": "rna_sample_name", - "description": "Give the RNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", - "title": "RNA sample name", - "examples": [ - { - "value": "JGI_pond_041618" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 4, - "string_serialization": "{text}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "JgiMtInterface" - ], - "slot_group": "jgi_metatranscriptomics_section", - "range": "string", - "required": true, - "recommended": true, - "minimum_value": 0, - "maximum_value": 2000 - }, - "rna_seq_project": { - "name": "rna_seq_project", - "title": "RNA seq project ID", - "comments": [ - "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." - ], - "examples": [ - { - "value": "1191234" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 1, - "string_serialization": "{text}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "JgiMtInterface" - ], - "slot_group": "jgi_metatranscriptomics_section", - "range": "string", - "required": true, - "recommended": true - }, - "rna_seq_project_name": { - "name": "rna_seq_project_name", - "title": "RNA seq project name", - "comments": [ - "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." - ], - "examples": [ - { - "value": "JGI Pond metatranscriptomics" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 2, - "string_serialization": "{text}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "JgiMtInterface" - ], - "slot_group": "jgi_metatranscriptomics_section", - "range": "string", - "required": true, - "recommended": true - }, - "rna_seq_project_pi": { - "name": "rna_seq_project_pi", - "title": "RNA seq project PI", - "comments": [ - "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." - ], - "examples": [ - { - "value": "Jane Johnson" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 17, - "string_serialization": "{text}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "JgiMtInterface" - ], - "slot_group": "jgi_metatranscriptomics_section", - "range": "string", - "required": true, - "recommended": true - }, - "rna_volume": { - "name": "rna_volume", - "title": "RNA volume in ul", - "comments": [ - "Units must be in uL. Enter the numerical part only. Value must be 0-1000. This form accepts values < 25, but JGI may refuse to process them unless permission has been granted by a project manager" - ], - "examples": [ - { - "value": "25" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "string_serialization": "{float}", - "owner": "Biosample", - "domain_of": [ - "Biosample", - "JgiMtInterface" - ], - "slot_group": "jgi_metatranscriptomics_section", - "range": "float", - "required": true, - "recommended": true, - "minimum_value": 0, - "maximum_value": 1000 - }, - "oxy_stat_samp": { - "name": "oxy_stat_samp", - "range": "OxyStatSampEnum" - } - }, - "attributes": { - "dnase_rna": { - "name": "dnase_rna", - "title": "DNase treated", - "comments": [ - "Note DNase treatment is required for all RNA samples." - ], - "examples": [ - { - "value": "no" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 13, - "alias": "dnase_rna", - "owner": "JgiMtInterface", - "domain_of": [ - "Biosample", - "JgiMtInterface" - ], - "slot_group": "jgi_metatranscriptomics_section", - "range": "YesNoEnum", - "required": true, - "recommended": true - }, - "proposal_rna": { - "name": "proposal_rna", - "title": "RNA proposal ID", - "comments": [ - "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." - ], - "examples": [ - { - "value": "504000" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 19, - "string_serialization": "{text}", - "multivalued": false, - "alias": "proposal_rna", - "owner": "JgiMtInterface", - "domain_of": [ - "Biosample", - "JgiMtInterface" - ], - "slot_group": "jgi_metatranscriptomics_section", - "range": "string", - "required": true, - "recommended": true - }, - "rna_absorb1": { - "name": "rna_absorb1", - "description": "260/280 measurement of RNA sample purity", - "title": "RNA absorbance 260/280", - "comments": [ - "Recommended value is between 1 and 3." - ], - "examples": [ - { - "value": "2.02" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 7, - "is_a": "biomaterial_purity", - "string_serialization": "{float}", - "alias": "rna_absorb1", - "owner": "JgiMtInterface", - "domain_of": [ - "Biosample", - "JgiMtInterface" - ], - "slot_group": "jgi_metatranscriptomics_section", - "range": "float", - "recommended": true - }, - "rna_absorb2": { - "name": "rna_absorb2", - "description": "260/230 measurement of RNA sample purity", - "title": "RNA absorbance 260/230", - "comments": [ - "Recommended value is between 1 and 3." - ], - "examples": [ - { - "value": "2.02" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 8, - "is_a": "biomaterial_purity", - "string_serialization": "{float}", - "alias": "rna_absorb2", - "owner": "JgiMtInterface", - "domain_of": [ - "Biosample", - "JgiMtInterface" - ], - "slot_group": "jgi_metatranscriptomics_section", - "range": "float", - "recommended": true - }, - "rna_concentration": { - "name": "rna_concentration", - "title": "RNA concentration in ng/ul", - "comments": [ - "Units must be in ng/uL. Enter the numerical part only. Must be calculated using a fluorometric method. Acceptable values are 0-2000." - ], - "examples": [ - { - "value": "100" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "nmdc:nucleic_acid_concentration" - ], - "rank": 5, - "string_serialization": "{float}", - "alias": "rna_concentration", - "owner": "JgiMtInterface", - "domain_of": [ - "Biosample", - "JgiMtInterface" - ], - "slot_group": "jgi_metatranscriptomics_section", - "range": "float", - "required": true, - "recommended": true, - "minimum_value": 0, - "maximum_value": 1000 - }, - "rna_cont_type": { - "name": "rna_cont_type", - "description": "Tube or plate (96-well)", - "title": "RNA container type", - "examples": [ - { - "value": "plate" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 10, - "alias": "rna_cont_type", - "owner": "JgiMtInterface", - "domain_of": [ - "Biosample", - "JgiMtInterface" - ], - "slot_group": "jgi_metatranscriptomics_section", - "range": "JgiContTypeEnum", - "required": true, - "recommended": true - }, - "rna_cont_well": { - "name": "rna_cont_well", - "title": "RNA plate position", - "comments": [ - "Required when 'plate' is selected for container type.", - "Leave blank if the sample will be shipped in a tube.", - "JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass validation.", - "For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8)." - ], - "examples": [ - { - "value": "B2" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 11, - "string_serialization": "{96 well plate pos}", - "multivalued": false, - "alias": "rna_cont_well", - "owner": "JgiMtInterface", - "domain_of": [ - "Biosample", - "JgiMtInterface" - ], - "slot_group": "jgi_metatranscriptomics_section", - "range": "string", - "recommended": true, - "pattern": "^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$" - }, - "rna_container_id": { - "name": "rna_container_id", - "title": "RNA container label", - "comments": [ - "Must be unique across all tubes and plates, and <20 characters. All samples in a plate should have the same plate label." - ], - "examples": [ - { - "value": "Pond_MT_041618" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 9, - "string_serialization": "{text < 20 characters}", - "multivalued": false, - "alias": "rna_container_id", - "owner": "JgiMtInterface", - "domain_of": [ - "Biosample", - "JgiMtInterface" - ], - "slot_group": "jgi_metatranscriptomics_section", - "range": "string", - "required": true, - "recommended": true, - "pattern": "^.{1,20}$" - }, - "rna_isolate_meth": { - "name": "rna_isolate_meth", - "description": "Describe the method/protocol/kit used to extract DNA/RNA.", - "title": "RNA isolation method", - "examples": [ - { - "value": "phenol/chloroform extraction" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 16, - "string_serialization": "{text}", - "multivalued": false, - "alias": "rna_isolate_meth", - "owner": "JgiMtInterface", - "domain_of": [ - "Biosample", - "JgiMtInterface" - ], - "slot_group": "jgi_metatranscriptomics_section", - "range": "string", - "required": true, - "recommended": true - }, - "rna_project_contact": { - "name": "rna_project_contact", - "title": "RNA seq project contact", - "comments": [ - "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." - ], - "examples": [ - { - "value": "John Jones" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 18, - "string_serialization": "{text}", - "multivalued": false, - "alias": "rna_project_contact", - "owner": "JgiMtInterface", - "domain_of": [ - "Biosample", - "JgiMtInterface" - ], - "slot_group": "jgi_metatranscriptomics_section", - "range": "string", - "required": true, - "recommended": true - }, - "rna_samp_id": { - "name": "rna_samp_id", - "title": "RNA sample ID", - "comments": [ - "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." - ], - "examples": [ - { - "value": "187654" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 3, - "string_serialization": "{text}", - "multivalued": false, - "alias": "rna_samp_id", - "owner": "JgiMtInterface", - "domain_of": [ - "Biosample", - "JgiMtInterface" - ], - "slot_group": "jgi_metatranscriptomics_section", - "range": "string", - "required": true, - "recommended": true - }, - "rna_sample_format": { - "name": "rna_sample_format", - "description": "Solution in which the RNA sample has been suspended", - "title": "RNA sample format", - "examples": [ - { - "value": "Water" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 12, - "alias": "rna_sample_format", - "owner": "JgiMtInterface", - "domain_of": [ - "Biosample", - "JgiMtInterface" - ], - "slot_group": "jgi_metatranscriptomics_section", - "range": "rna_sample_format_enum", - "required": true, - "recommended": true - }, - "rna_sample_name": { - "name": "rna_sample_name", - "description": "Give the RNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", - "title": "RNA sample name", - "examples": [ - { - "value": "JGI_pond_041618" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 4, - "string_serialization": "{text}", - "multivalued": false, - "alias": "rna_sample_name", - "owner": "JgiMtInterface", - "domain_of": [ - "Biosample", - "JgiMtInterface" - ], - "slot_group": "jgi_metatranscriptomics_section", - "range": "string", - "required": true, - "recommended": true, - "minimum_value": 0, - "maximum_value": 2000 - }, - "rna_seq_project": { - "name": "rna_seq_project", - "title": "RNA seq project ID", - "comments": [ - "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." - ], - "examples": [ - { - "value": "1191234" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 1, - "string_serialization": "{text}", - "multivalued": false, - "alias": "rna_seq_project", - "owner": "JgiMtInterface", - "domain_of": [ - "Biosample", - "JgiMtInterface" - ], - "slot_group": "jgi_metatranscriptomics_section", - "range": "string", - "required": true, - "recommended": true - }, - "rna_seq_project_name": { - "name": "rna_seq_project_name", - "title": "RNA seq project name", - "comments": [ - "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." - ], - "examples": [ - { - "value": "JGI Pond metatranscriptomics" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 2, - "string_serialization": "{text}", - "multivalued": false, - "alias": "rna_seq_project_name", - "owner": "JgiMtInterface", - "domain_of": [ - "Biosample", - "JgiMtInterface" - ], - "slot_group": "jgi_metatranscriptomics_section", - "range": "string", - "required": true, - "recommended": true - }, - "rna_seq_project_pi": { - "name": "rna_seq_project_pi", - "title": "RNA seq project PI", - "comments": [ - "Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled." - ], - "examples": [ - { - "value": "Jane Johnson" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 17, - "string_serialization": "{text}", - "multivalued": false, - "alias": "rna_seq_project_pi", - "owner": "JgiMtInterface", - "domain_of": [ - "Biosample", - "JgiMtInterface" - ], - "slot_group": "jgi_metatranscriptomics_section", - "range": "string", - "required": true, - "recommended": true - }, - "rna_volume": { - "name": "rna_volume", - "title": "RNA volume in ul", - "comments": [ - "Units must be in uL. Enter the numerical part only. Value must be 0-1000. This form accepts values < 25, but JGI may refuse to process them unless permission has been granted by a project manager" - ], - "examples": [ - { - "value": "25" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "string_serialization": "{float}", - "alias": "rna_volume", - "owner": "JgiMtInterface", - "domain_of": [ - "Biosample", - "JgiMtInterface" - ], - "slot_group": "jgi_metatranscriptomics_section", - "range": "float", - "required": true, - "recommended": true, - "minimum_value": 0, - "maximum_value": 1000 - }, - "analysis_type": { - "name": "analysis_type", - "description": "Select all the data types associated or available for this biosample", - "title": "analysis/data type", - "examples": [ - { - "value": "metagenomics; metabolomics; proteomics" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:investigation_type" - ], - "rank": 3, - "multivalued": true, - "alias": "analysis_type", - "owner": "JgiMtInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "EmslInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "JgiMgInterface" - ], - "slot_group": "sample_id_section", - "range": "analysis_type_enum", - "required": true, - "recommended": true - }, - "samp_name": { - "name": "samp_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - } - }, - "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", - "title": "sample name", - "comments": [ - "It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." - ], - "examples": [ - { - "value": "Rock core CB1178(5-6) from NSW" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample name" - ], - "rank": 1, - "is_a": "investigation field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0001107", - "multivalued": false, - "identifier": true, - "alias": "samp_name", - "owner": "JgiMtInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "EmslInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "JgiMgInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true - }, - "source_mat_id": { - "name": "source_mat_id", - "description": "A globally unique identifier assigned to the biological sample.", - "title": "source material identifier", - "todos": [ - "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID.", - "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID." - ], - "notes": [ - "The source material IS the Globally Unique ID" - ], - "comments": [ - "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).", - "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/)." - ], - "examples": [ - { - "value": "IGSN:AU1243" - }, - { - "value": "UUID:24f1467a-40f4-11ed-b878-0242ac120002" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 2, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{text}:{text}", - "slot_uri": "MIXS:0000026", - "multivalued": false, - "alias": "source_mat_id", - "owner": "JgiMtInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "EmslInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "JgiMgInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" - } - }, - "rules": [ - { - "preconditions": { - "slot_conditions": { - "rna_cont_well": { - "name": "rna_cont_well", - "pattern": ".+" - } - } - }, - "postconditions": { - "slot_conditions": { - "rna_cont_type": { - "name": "rna_cont_type", - "equals_string": "plate" - } - } - }, - "description": "RNA samples shipped to JGI for metagenomic analysis in tubes can't have any value for their plate position.", - "title": "rna_well_requires_plate" - }, - { - "preconditions": { - "slot_conditions": { - "rna_cont_type": { - "name": "rna_cont_type", - "equals_string": "plate" - } - } - }, - "postconditions": { - "slot_conditions": { - "rna_cont_well": { - "name": "rna_cont_well", - "pattern": "^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$" - } - } - }, - "description": "RNA samples in plates must have a plate position that matches the regex. Note the requirement for an empty string in the tube case. Waiting for value_present validation to be added to runtime", - "title": "rna_plate_requires_well" - } - ] - }, - "MiscEnvsInterface": { - "name": "MiscEnvsInterface", - "description": "misc_envs dh_interface", - "title": "Misc Envs", - "from_schema": "https://example.com/nmdc_submission_schema", - "is_a": "DhInterface", - "mixins": [ - "DhMultiviewCommonColumnsMixin" - ], - "slots": [ - "alkalinity", - "alt", - "ammonium", - "biomass", - "bromide", - "calcium", - "chem_administration", - "chloride", - "chlorophyll", - "collection_date", - "density", - "depth", - "diether_lipids", - "diss_carb_dioxide", - "diss_hydrogen", - "diss_inorg_carb", - "diss_org_nitro", - "diss_oxygen", - "ecosystem", - "ecosystem_category", - "ecosystem_subtype", - "ecosystem_type", - "elev", - "env_broad_scale", - "env_local_scale", - "env_medium", - "env_package", - "experimental_factor", - "geo_loc_name", - "horizon_meth", - "lat_lon", - "misc_param", - "nitrate", - "nitrite", - "nitro", - "org_carb", - "org_matter", - "org_nitro", - "organism_count", - "oxy_stat_samp", - "perturbation", - "ph", - "ph_meth", - "phosphate", - "phosplipid_fatt_acid", - "potassium", - "pressure", - "salinity", - "samp_collec_device", - "samp_collec_method", - "samp_mat_process", - "samp_size", - "samp_store_dur", - "samp_store_loc", - "samp_store_temp", - "sample_link", - "silicate", - "size_frac", - "sodium", - "specific_ecosystem", - "sulfate", - "sulfide", - "temp", - "water_current" - ], - "slot_usage": { - "alkalinity": { - "name": "alkalinity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milliequivalent per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate", - "title": "alkalinity", - "examples": [ - { - "value": "50 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "alkalinity" - ], - "rank": 1, - "is_a": "core field", - "slot_uri": "MIXS:0000421", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "alt": { - "name": "alt", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - } - }, - "description": "Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air", - "title": "altitude", - "examples": [ - { - "value": "100 meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "altitude" - ], - "rank": 26, - "is_a": "environment field", - "slot_uri": "MIXS:0000094", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HostAssociatedInterface", - "MiscEnvsInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "ammonium": { - "name": "ammonium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of ammonium in the sample", - "title": "ammonium", - "examples": [ - { - "value": "1.5 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "ammonium" - ], - "rank": 4, - "is_a": "core field", - "slot_uri": "MIXS:0000427", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "biomass": { - "name": "biomass", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "biomass type;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "ton, kilogram, gram" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements", - "title": "biomass", - "examples": [ - { - "value": "total;20 gram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "biomass" - ], - "rank": 6, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000174", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "bromide": { - "name": "bromide", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of bromide", - "title": "bromide", - "examples": [ - { - "value": "0.05 parts per million" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "bromide" - ], - "rank": 8, - "is_a": "core field", - "slot_uri": "MIXS:0000176", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "calcium": { - "name": "calcium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, micromole per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of calcium in the sample", - "title": "calcium", - "examples": [ - { - "value": "0.2 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "calcium" - ], - "rank": 9, - "is_a": "core field", - "slot_uri": "MIXS:0000432", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "chem_administration": { - "name": "chem_administration", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "CHEBI;timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", - "title": "chemical administration", - "examples": [ - { - "value": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22" - }, - { - "value": "agar [CHEBI:2509];2018-05" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "chemical administration" - ], - "rank": 17, - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]};{timestamp}", - "slot_uri": "MIXS:0000751", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" - }, - "chloride": { - "name": "chloride", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of chloride in the sample", - "title": "chloride", - "examples": [ - { - "value": "5000 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "chloride" - ], - "rank": 10, - "is_a": "core field", - "slot_uri": "MIXS:0000429", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "chlorophyll": { - "name": "chlorophyll", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per cubic meter, microgram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of chlorophyll", - "title": "chlorophyll", - "examples": [ - { - "value": "5 milligram per cubic meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "chlorophyll" - ], - "rank": 11, - "is_a": "core field", - "slot_uri": "MIXS:0000177", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "collection_date": { - "name": "collection_date", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "date and time" - } - }, - "description": "The date of sampling", - "title": "collection date", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", - "Use modified term (amended definition)" - ], - "examples": [ - { - "value": "2021-04-15" - }, - { - "value": "2021-04" - }, - { - "value": "2021" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "collection date" - ], - "rank": 3, - "is_a": "environment field", - "string_serialization": "{date, arbitrary precision}", - "slot_uri": "MIXS:0000011", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" - }, - "density": { - "name": "density", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram per cubic meter, gram per cubic centimeter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Density of the sample, which is its mass per unit volume (aka volumetric mass density)", - "title": "density", - "examples": [ - { - "value": "1000 kilogram per cubic meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "density" - ], - "rank": 12, - "is_a": "core field", - "slot_uri": "MIXS:0000435", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "depth": { - "name": "depth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - } - }, - "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", - "title": "depth, meters", - "notes": [ - "Use modified term" - ], - "comments": [ - "All depths must be reported in meters. Provide the numerical portion only." - ], - "examples": [ - { - "value": "0 - 0.1" - }, - { - "value": "1" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "depth" - ], - "rank": 9, - "is_a": "environment field", - "string_serialization": "{float}|{float}-{float}", - "slot_uri": "MIXS:0000018", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$" - }, - "diether_lipids": { - "name": "diether_lipids", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "diether lipid name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "nanogram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Concentration of diether lipids; can include multiple types of diether lipids", - "title": "diether lipids", - "examples": [ - { - "value": "0.2 nanogram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "diether lipids" - ], - "rank": 13, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000178", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "diss_carb_dioxide": { - "name": "diss_carb_dioxide", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample", - "title": "dissolved carbon dioxide", - "examples": [ - { - "value": "5 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved carbon dioxide" - ], - "rank": 14, - "is_a": "core field", - "slot_uri": "MIXS:0000436", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_hydrogen": { - "name": "diss_hydrogen", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved hydrogen", - "title": "dissolved hydrogen", - "examples": [ - { - "value": "0.3 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved hydrogen" - ], - "rank": 15, - "is_a": "core field", - "slot_uri": "MIXS:0000179", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_inorg_carb": { - "name": "diss_inorg_carb", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter", - "title": "dissolved inorganic carbon", - "examples": [ - { - "value": "2059 micromole per kilogram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved inorganic carbon" - ], - "rank": 16, - "is_a": "core field", - "slot_uri": "MIXS:0000434", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_org_nitro": { - "name": "diss_org_nitro", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2", - "title": "dissolved organic nitrogen", - "examples": [ - { - "value": "0.05 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved organic nitrogen" - ], - "rank": 18, - "is_a": "core field", - "slot_uri": "MIXS:0000162", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_oxygen": { - "name": "diss_oxygen", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per kilogram, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved oxygen", - "title": "dissolved oxygen", - "examples": [ - { - "value": "175 micromole per kilogram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved oxygen" - ], - "rank": 19, - "is_a": "core field", - "slot_uri": "MIXS:0000119", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "ecosystem": { - "name": "ecosystem", - "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", - "notes": [ - "range: string or EcosystemEnum? The enum could be dynamic or might be soil biased." - ], - "comments": [ - "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 9, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_category": { - "name": "ecosystem_category", - "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", - "notes": [ - "string or EcosystemCategoryEnum range?" - ], - "comments": [ - "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 10, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_subtype": { - "name": "ecosystem_subtype", - "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", - "notes": [ - "string or EcosystemSubtypeEnum range?" - ], - "comments": [ - "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 12, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_type": { - "name": "ecosystem_type", - "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", - "notes": [ - "string or EcosystemTypeEnum range?" - ], - "comments": [ - "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 11, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "elev": { - "name": "elev", - "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", - "title": "elevation, meters", - "comments": [ - "All elevations must be reported in meters. Provide the numerical portion only.", - "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." - ], - "examples": [ - { - "value": "225" - }, - { - "value": "0" - }, - { - "value": "1250" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "slot_uri": "MIXS:0000093", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "float", - "required": true - }, - "env_broad_scale": { - "name": "env_broad_scale", - "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", - "title": "broad-scale environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000012", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_local_scale": { - "name": "env_local_scale", - "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", - "title": "local environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "canopy [ENVO:00000047]" - }, - { - "value": "herb and fern layer [ENVO:01000337]" - }, - { - "value": "litter layer [ENVO:01000338]" - }, - { - "value": "understory [01000335]" - }, - { - "value": "shrub layer [ENVO:01000336]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 7, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000013", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_medium": { - "name": "env_medium", - "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", - "title": "environmental medium", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "soil [ENVO:00001998]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 8, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000014", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_package": { - "name": "env_package", - "description": "Select the MIxS enviromental package that best describes the environment from which your sample was collected.", - "title": "environmental package", - "examples": [ - { - "value": "soil" - } - ], - "in_subset": [ - "mixs extension" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "environmental package" - ], - "rank": 4, - "is_a": "attribute", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true - }, - "experimental_factor": { - "name": "experimental_factor", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text or EFO and/or OBI" - } - }, - "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", - "title": "experimental factor", - "examples": [ - { - "value": "time series design [EFO:EFO_0001779]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "experimental factor" - ], - "rank": 12, - "is_a": "investigation field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000008", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "geo_loc_name": { - "name": "geo_loc_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" - } - }, - "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", - "title": "geographic location (country and/or sea,region)", - "examples": [ - { - "value": "USA: Maryland, Bethesda" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "geographic location (country and/or sea,region)" - ], - "rank": 4, - "is_a": "environment field", - "string_serialization": "{text}: {text}, {text}", - "slot_uri": "MIXS:0000010", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" - }, - "horizon_meth": { - "name": "horizon_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining the horizon", - "title": "horizon method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "soil horizon method" - ], - "rank": 19, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000321", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "lat_lon": { - "name": "lat_lon", - "description": "This is currently a required field but it's not clear if this should be required for human hosts", - "title": "geographic location (latitude and longitude)", - "notes": [ - "required where?", - "This is currently a required field but it's not clear if this should be required for human hosts" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "is_a": "environment field", - "string_serialization": "{lat lon}", - "slot_uri": "MIXS:0000009", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" - }, - "misc_param": { - "name": "misc_param", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "parameter name;measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Any other measurement performed or parameter collected, that is not listed here", - "title": "miscellaneous parameter", - "examples": [ - { - "value": "Bicarbonate ion concentration;2075 micromole per kilogram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "miscellaneous parameter" - ], - "rank": 23, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000752", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "nitrate": { - "name": "nitrate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of nitrate in the sample", - "title": "nitrate", - "examples": [ - { - "value": "65 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "nitrate" - ], - "rank": 26, - "is_a": "core field", - "slot_uri": "MIXS:0000425", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "nitrite": { - "name": "nitrite", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of nitrite in the sample", - "title": "nitrite", - "examples": [ - { - "value": "0.5 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "nitrite" - ], - "rank": 27, - "is_a": "core field", - "slot_uri": "MIXS:0000426", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "nitro": { - "name": "nitro", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of nitrogen (total)", - "title": "nitrogen", - "examples": [ - { - "value": "4.2 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "nitrogen" - ], - "rank": 28, - "is_a": "core field", - "slot_uri": "MIXS:0000504", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "org_carb": { - "name": "org_carb", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of organic carbon", - "title": "organic carbon", - "examples": [ - { - "value": "1.5 microgram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "organic carbon" - ], - "rank": 29, - "is_a": "core field", - "slot_uri": "MIXS:0000508", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "org_matter": { - "name": "org_matter", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of organic matter", - "title": "organic matter", - "examples": [ - { - "value": "1.75 milligram per cubic meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "organic matter" - ], - "rank": 45, - "is_a": "core field", - "slot_uri": "MIXS:0000204", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "org_nitro": { - "name": "org_nitro", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of organic nitrogen", - "title": "organic nitrogen", - "examples": [ - { - "value": "4 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "organic nitrogen" - ], - "rank": 46, - "is_a": "core field", - "slot_uri": "MIXS:0000205", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "organism_count": { - "name": "organism_count", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "organism name;measurement value;enumeration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", - "title": "organism count", - "examples": [ - { - "value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "organism count" - ], - "rank": 30, - "is_a": "core field", - "slot_uri": "MIXS:0000103", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$" - }, - "oxy_stat_samp": { - "name": "oxy_stat_samp", - "description": "Oxygenation status of sample", - "title": "oxygenation status of sample", - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 25, - "is_a": "core field", - "slot_uri": "MIXS:0000753", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "OxyStatSampEnum" - }, - "perturbation": { - "name": "perturbation", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "perturbation type name;perturbation interval and duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types", - "title": "perturbation", - "examples": [ - { - "value": "antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "perturbation" - ], - "rank": 33, - "is_a": "core field", - "string_serialization": "{text};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000754", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "ph": { - "name": "ph", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid", - "title": "pH", - "notes": [ - "Use modified term" - ], - "examples": [ - { - "value": "7.2" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "pH" - ], - "rank": 27, - "is_a": "core field", - "string_serialization": "{float}", - "slot_uri": "MIXS:0001001", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "float", - "recommended": true, - "minimum_value": 0, - "maximum_value": 14 - }, - "ph_meth": { - "name": "ph_meth", - "description": "Reference or method used in determining ph", - "title": "pH method", - "comments": [ - "This can include a link to the instrument used or a citation for the method." - ], - "examples": [ - { - "value": "https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB" - }, - { - "value": "https://doi.org/10.2136/sssabookser5.3.c16" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 41, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0001106", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "phosphate": { - "name": "phosphate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of phosphate", - "title": "phosphate", - "examples": [ - { - "value": "0.7 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "phosphate" - ], - "rank": 53, - "is_a": "core field", - "slot_uri": "MIXS:0000505", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "phosplipid_fatt_acid": { - "name": "phosplipid_fatt_acid", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "phospholipid fatty acid name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mole per gram, mole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Concentration of phospholipid fatty acids; can include multiple values", - "title": "phospholipid fatty acid", - "examples": [ - { - "value": "2.98 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "phospholipid fatty acid" - ], - "rank": 36, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000181", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "potassium": { - "name": "potassium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of potassium in the sample", - "title": "potassium", - "examples": [ - { - "value": "463 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "potassium" - ], - "rank": 38, - "is_a": "core field", - "slot_uri": "MIXS:0000430", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "pressure": { - "name": "pressure", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "atmosphere" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Pressure to which the sample is subject to, in atmospheres", - "title": "pressure", - "examples": [ - { - "value": "50 atmosphere" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "pressure" - ], - "rank": 39, - "is_a": "core field", - "slot_uri": "MIXS:0000412", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "salinity": { - "name": "salinity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "practical salinity unit, percentage" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", - "title": "salinity", - "examples": [ - { - "value": "25 practical salinity unit" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "salinity" - ], - "rank": 54, - "is_a": "core field", - "slot_uri": "MIXS:0000183", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "samp_collec_device": { - "name": "samp_collec_device", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "device name" - } - }, - "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", - "title": "sample collection device", - "comments": [ - "Report dimensions and details when applicable" - ], - "examples": [ - { - "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection device" - ], - "rank": 14, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000002", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "samp_collec_method": { - "name": "samp_collec_method", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI,url , or text" - } - }, - "description": "The method employed for collecting the sample.", - "title": "sample collection method", - "comments": [ - "This can be a citation or description" - ], - "examples": [ - { - "value": "swabbing" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection method" - ], - "rank": 15, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{PMID}|{DOI}|{URL}|{text}", - "slot_uri": "MIXS:0001225", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_mat_process": { - "name": "samp_mat_process", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - } - }, - "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", - "title": "sample material processing", - "examples": [ - { - "value": "filtering of seawater" - }, - { - "value": "storing samples in ethanol" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample material processing" - ], - "rank": 12, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000016", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_size": { - "name": "samp_size", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millliter, gram, milligram, liter" - } - }, - "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", - "title": "amount or size of sample collected", - "comments": [ - "This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis." - ], - "examples": [ - { - "value": "5 grams" - }, - { - "value": "10 mL" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "amount or size of sample collected" - ], - "rank": 18, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float} {unit}", - "slot_uri": "MIXS:0000001", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" - }, - "samp_store_dur": { - "name": "samp_store_dur", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Duration for which the sample was stored", - "title": "sample storage duration", - "examples": [ - { - "value": "P1Y6M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage duration" - ], - "rank": 353, - "is_a": "core field", - "string_serialization": "{duration}", - "slot_uri": "MIXS:0000116", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_store_loc": { - "name": "samp_store_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "location name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Location at which sample was stored, usually name of a specific freezer/room", - "title": "sample storage location", - "examples": [ - { - "value": "Freezer no:5" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage location" - ], - "rank": 41, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000755", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_store_temp": { - "name": "samp_store_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Temperature at which the sample was stored (degrees are assumed)", - "title": "sample storage temperature", - "examples": [ - { - "value": "-80 Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage temperature" - ], - "rank": 7, - "is_a": "core field", - "slot_uri": "MIXS:0000110", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "sample_link": { - "name": "sample_link", - "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", - "title": "sample linkage", - "notes": [ - "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" - ], - "comments": [ - "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" - ], - "examples": [ - { - "value": "IGSN:DSJ0284" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "string_serialization": "{text}:{text}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface", - "SampIdNewTermsMixin" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true, - "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" - }, - "silicate": { - "name": "silicate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of silicate", - "title": "silicate", - "examples": [ - { - "value": "0.05 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "silicate" - ], - "rank": 43, - "is_a": "core field", - "slot_uri": "MIXS:0000184", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "size_frac": { - "name": "size_frac", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "filter size value range" - } - }, - "description": "Filtering pore size used in sample preparation", - "title": "size fraction selected", - "examples": [ - { - "value": "0-0.22 micrometer" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "size fraction selected" - ], - "rank": 285, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float}-{float} {unit}", - "slot_uri": "MIXS:0000017", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "sodium": { - "name": "sodium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Sodium concentration in the sample", - "title": "sodium", - "examples": [ - { - "value": "10.5 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sodium" - ], - "rank": 363, - "is_a": "core field", - "slot_uri": "MIXS:0000428", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "specific_ecosystem": { - "name": "specific_ecosystem", - "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", - "notes": [ - "string or SpecificEcosystemEnum range?" - ], - "comments": [ - "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 13, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "sulfate": { - "name": "sulfate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of sulfate in the sample", - "title": "sulfate", - "examples": [ - { - "value": "5 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sulfate" - ], - "rank": 44, - "is_a": "core field", - "slot_uri": "MIXS:0000423", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "sulfide": { - "name": "sulfide", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of sulfide in the sample", - "title": "sulfide", - "examples": [ - { - "value": "2 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sulfide" - ], - "rank": 371, - "is_a": "core field", - "slot_uri": "MIXS:0000424", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "temp": { - "name": "temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - } - }, - "description": "Temperature of the sample at the time of sampling.", - "title": "temperature", - "examples": [ - { - "value": "25 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "temperature" - ], - "rank": 37, - "is_a": "environment field", - "slot_uri": "MIXS:0000113", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "water_current": { - "name": "water_current", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "cubic meter per second, knots" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of magnitude and direction of flow within a fluid", - "title": "water current", - "examples": [ - { - "value": "10 cubic meter per second" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "water current" - ], - "rank": 236, - "is_a": "core field", - "slot_uri": "MIXS:0000203", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "MiscEnvsInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - } - }, - "attributes": { - "alkalinity": { - "name": "alkalinity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milliequivalent per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate", - "title": "alkalinity", - "examples": [ - { - "value": "50 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "alkalinity" - ], - "rank": 1, - "is_a": "core field", - "slot_uri": "MIXS:0000421", - "multivalued": false, - "alias": "alkalinity", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "alt": { - "name": "alt", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - } - }, - "description": "Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air", - "title": "altitude", - "examples": [ - { - "value": "100 meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "altitude" - ], - "rank": 26, - "is_a": "environment field", - "slot_uri": "MIXS:0000094", - "multivalued": false, - "alias": "alt", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HostAssociatedInterface", - "MiscEnvsInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "ammonium": { - "name": "ammonium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of ammonium in the sample", - "title": "ammonium", - "examples": [ - { - "value": "1.5 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "ammonium" - ], - "rank": 4, - "is_a": "core field", - "slot_uri": "MIXS:0000427", - "multivalued": false, - "alias": "ammonium", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "biomass": { - "name": "biomass", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "biomass type;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "ton, kilogram, gram" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements", - "title": "biomass", - "examples": [ - { - "value": "total;20 gram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "biomass" - ], - "rank": 6, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000174", - "multivalued": false, - "alias": "biomass", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "bromide": { - "name": "bromide", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of bromide", - "title": "bromide", - "examples": [ - { - "value": "0.05 parts per million" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "bromide" - ], - "rank": 8, - "is_a": "core field", - "slot_uri": "MIXS:0000176", - "multivalued": false, - "alias": "bromide", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "calcium": { - "name": "calcium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, micromole per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of calcium in the sample", - "title": "calcium", - "examples": [ - { - "value": "0.2 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "calcium" - ], - "rank": 9, - "is_a": "core field", - "slot_uri": "MIXS:0000432", - "multivalued": false, - "alias": "calcium", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "chem_administration": { - "name": "chem_administration", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "CHEBI;timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", - "title": "chemical administration", - "examples": [ - { - "value": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22" - }, - { - "value": "agar [CHEBI:2509];2018-05" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "chemical administration" - ], - "rank": 17, - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]};{timestamp}", - "slot_uri": "MIXS:0000751", - "multivalued": false, - "alias": "chem_administration", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" - }, - "chloride": { - "name": "chloride", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of chloride in the sample", - "title": "chloride", - "examples": [ - { - "value": "5000 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "chloride" - ], - "rank": 10, - "is_a": "core field", - "slot_uri": "MIXS:0000429", - "multivalued": false, - "alias": "chloride", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "chlorophyll": { - "name": "chlorophyll", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per cubic meter, microgram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of chlorophyll", - "title": "chlorophyll", - "examples": [ - { - "value": "5 milligram per cubic meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "chlorophyll" - ], - "rank": 11, - "is_a": "core field", - "slot_uri": "MIXS:0000177", - "multivalued": false, - "alias": "chlorophyll", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "collection_date": { - "name": "collection_date", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "date and time" - } - }, - "description": "The date of sampling", - "title": "collection date", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", - "Use modified term (amended definition)" - ], - "examples": [ - { - "value": "2021-04-15" - }, - { - "value": "2021-04" - }, - { - "value": "2021" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "collection date" - ], - "rank": 3, - "is_a": "environment field", - "string_serialization": "{date, arbitrary precision}", - "slot_uri": "MIXS:0000011", - "multivalued": false, - "alias": "collection_date", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" - }, - "density": { - "name": "density", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram per cubic meter, gram per cubic centimeter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Density of the sample, which is its mass per unit volume (aka volumetric mass density)", - "title": "density", - "examples": [ - { - "value": "1000 kilogram per cubic meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "density" - ], - "rank": 12, - "is_a": "core field", - "slot_uri": "MIXS:0000435", - "multivalued": false, - "alias": "density", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "depth": { - "name": "depth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - } - }, - "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", - "title": "depth, meters", - "notes": [ - "Use modified term" - ], - "comments": [ - "All depths must be reported in meters. Provide the numerical portion only." - ], - "examples": [ - { - "value": "0 - 0.1" - }, - { - "value": "1" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "depth" - ], - "rank": 9, - "is_a": "environment field", - "string_serialization": "{float}|{float}-{float}", - "slot_uri": "MIXS:0000018", - "multivalued": false, - "alias": "depth", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$" - }, - "diether_lipids": { - "name": "diether_lipids", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "diether lipid name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "nanogram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Concentration of diether lipids; can include multiple types of diether lipids", - "title": "diether lipids", - "examples": [ - { - "value": "0.2 nanogram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "diether lipids" - ], - "rank": 13, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000178", - "multivalued": false, - "alias": "diether_lipids", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "diss_carb_dioxide": { - "name": "diss_carb_dioxide", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample", - "title": "dissolved carbon dioxide", - "examples": [ - { - "value": "5 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved carbon dioxide" - ], - "rank": 14, - "is_a": "core field", - "slot_uri": "MIXS:0000436", - "multivalued": false, - "alias": "diss_carb_dioxide", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_hydrogen": { - "name": "diss_hydrogen", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved hydrogen", - "title": "dissolved hydrogen", - "examples": [ - { - "value": "0.3 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved hydrogen" - ], - "rank": 15, - "is_a": "core field", - "slot_uri": "MIXS:0000179", - "multivalued": false, - "alias": "diss_hydrogen", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_inorg_carb": { - "name": "diss_inorg_carb", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter", - "title": "dissolved inorganic carbon", - "examples": [ - { - "value": "2059 micromole per kilogram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved inorganic carbon" - ], - "rank": 16, - "is_a": "core field", - "slot_uri": "MIXS:0000434", - "multivalued": false, - "alias": "diss_inorg_carb", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_org_nitro": { - "name": "diss_org_nitro", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2", - "title": "dissolved organic nitrogen", - "examples": [ - { - "value": "0.05 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved organic nitrogen" - ], - "rank": 18, - "is_a": "core field", - "slot_uri": "MIXS:0000162", - "multivalued": false, - "alias": "diss_org_nitro", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_oxygen": { - "name": "diss_oxygen", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per kilogram, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved oxygen", - "title": "dissolved oxygen", - "examples": [ - { - "value": "175 micromole per kilogram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved oxygen" - ], - "rank": 19, - "is_a": "core field", - "slot_uri": "MIXS:0000119", - "multivalued": false, - "alias": "diss_oxygen", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "ecosystem": { - "name": "ecosystem", - "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", - "notes": [ - "range: string or EcosystemEnum? The enum could be dynamic or might be soil biased." - ], - "comments": [ - "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 9, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_category": { - "name": "ecosystem_category", - "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", - "notes": [ - "string or EcosystemCategoryEnum range?" - ], - "comments": [ - "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 10, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem_category", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_subtype": { - "name": "ecosystem_subtype", - "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", - "notes": [ - "string or EcosystemSubtypeEnum range?" - ], - "comments": [ - "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 12, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem_subtype", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_type": { - "name": "ecosystem_type", - "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", - "notes": [ - "string or EcosystemTypeEnum range?" - ], - "comments": [ - "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 11, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem_type", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "elev": { - "name": "elev", - "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", - "title": "elevation, meters", - "comments": [ - "All elevations must be reported in meters. Provide the numerical portion only.", - "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." - ], - "examples": [ - { - "value": "225" - }, - { - "value": "0" - }, - { - "value": "1250" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "slot_uri": "MIXS:0000093", - "multivalued": false, - "alias": "elev", - "owner": "MiscEnvsInterface", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "float", - "required": true - }, - "env_broad_scale": { - "name": "env_broad_scale", - "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", - "title": "broad-scale environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000012", - "multivalued": false, - "alias": "env_broad_scale", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_local_scale": { - "name": "env_local_scale", - "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", - "title": "local environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "canopy [ENVO:00000047]" - }, - { - "value": "herb and fern layer [ENVO:01000337]" - }, - { - "value": "litter layer [ENVO:01000338]" - }, - { - "value": "understory [01000335]" - }, - { - "value": "shrub layer [ENVO:01000336]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 7, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000013", - "multivalued": false, - "alias": "env_local_scale", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_medium": { - "name": "env_medium", - "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", - "title": "environmental medium", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "soil [ENVO:00001998]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 8, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000014", - "multivalued": false, - "alias": "env_medium", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_package": { - "name": "env_package", - "description": "Select the MIxS enviromental package that best describes the environment from which your sample was collected.", - "title": "environmental package", - "examples": [ - { - "value": "soil" - } - ], - "in_subset": [ - "mixs extension" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "environmental package" - ], - "rank": 4, - "is_a": "attribute", - "multivalued": false, - "alias": "env_package", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true - }, - "experimental_factor": { - "name": "experimental_factor", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text or EFO and/or OBI" - } - }, - "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", - "title": "experimental factor", - "examples": [ - { - "value": "time series design [EFO:EFO_0001779]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "experimental factor" - ], - "rank": 12, - "is_a": "investigation field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000008", - "multivalued": false, - "alias": "experimental_factor", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "geo_loc_name": { - "name": "geo_loc_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" - } - }, - "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", - "title": "geographic location (country and/or sea,region)", - "examples": [ - { - "value": "USA: Maryland, Bethesda" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "geographic location (country and/or sea,region)" - ], - "rank": 4, - "is_a": "environment field", - "string_serialization": "{text}: {text}, {text}", - "slot_uri": "MIXS:0000010", - "multivalued": false, - "alias": "geo_loc_name", - "owner": "MiscEnvsInterface", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - 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"title": "organic nitrogen", - "examples": [ - { - "value": "4 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "organic nitrogen" - ], - "rank": 46, - "is_a": "core field", - "slot_uri": "MIXS:0000205", - "multivalued": false, - "alias": "org_nitro", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "organism_count": { - "name": "organism_count", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "organism name;measurement value;enumeration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. 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These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", - "title": "salinity", - "examples": [ - { - "value": "25 practical salinity unit" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "salinity" - ], - "rank": 54, - "is_a": "core field", - "slot_uri": "MIXS:0000183", - "multivalued": false, - "alias": "salinity", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "samp_collec_device": { - "name": "samp_collec_device", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "device name" - } - }, - "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", - "title": "sample collection device", - "comments": [ - "Report dimensions and details when applicable" - ], - "examples": [ - { - "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection device" - ], - "rank": 14, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000002", - "multivalued": false, - "alias": "samp_collec_device", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "samp_collec_method": { - "name": "samp_collec_method", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI,url , or text" - } - }, - "description": "The method employed for collecting the sample.", - "title": "sample collection method", - "comments": [ - "This can be a citation or description" - ], - "examples": [ - { - "value": "swabbing" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection method" - ], - "rank": 15, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{PMID}|{DOI}|{URL}|{text}", - "slot_uri": "MIXS:0001225", - "multivalued": false, - "alias": "samp_collec_method", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_mat_process": { - "name": "samp_mat_process", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - } - }, - "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", - "title": "sample material processing", - "examples": [ - { - "value": "filtering of seawater" - }, - { - "value": "storing samples in ethanol" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample material processing" - ], - "rank": 12, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000016", - "multivalued": false, - "alias": "samp_mat_process", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_size": { - "name": "samp_size", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millliter, gram, milligram, liter" - } - }, - "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", - "title": "amount or size of sample collected", - "comments": [ - "This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis." - ], - "examples": [ - { - "value": "5 grams" - }, - { - "value": "10 mL" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "amount or size of sample collected" - ], - "rank": 18, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float} {unit}", - "slot_uri": "MIXS:0000001", - "multivalued": false, - "alias": "samp_size", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" - }, - "samp_store_dur": { - "name": "samp_store_dur", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Duration for which the sample was stored", - "title": "sample storage duration", - "examples": [ - { - "value": "P1Y6M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage duration" - ], - "rank": 353, - "is_a": "core field", - "string_serialization": "{duration}", - "slot_uri": "MIXS:0000116", - "multivalued": false, - "alias": "samp_store_dur", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_store_loc": { - "name": "samp_store_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "location name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Location at which sample was stored, usually name of a specific freezer/room", - "title": "sample storage location", - "examples": [ - { - "value": "Freezer no:5" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage location" - ], - "rank": 41, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000755", - "multivalued": false, - "alias": "samp_store_loc", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_store_temp": { - "name": "samp_store_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Temperature at which the sample was stored (degrees are assumed)", - "title": "sample storage temperature", - "examples": [ - { - "value": "-80 Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage temperature" - ], - "rank": 7, - "is_a": "core field", - "slot_uri": "MIXS:0000110", - "multivalued": false, - "alias": "samp_store_temp", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "sample_link": { - "name": "sample_link", - "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", - "title": "sample linkage", - "notes": [ - "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" - ], - "comments": [ - "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" - ], - "examples": [ - { - "value": "IGSN:DSJ0284" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "string_serialization": "{text}:{text}", - "multivalued": false, - "alias": "sample_link", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface", - "SampIdNewTermsMixin" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true, - "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" - }, - "silicate": { - "name": "silicate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of silicate", - "title": "silicate", - "examples": [ - { - "value": "0.05 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "silicate" - ], - "rank": 43, - "is_a": "core field", - "slot_uri": "MIXS:0000184", - "multivalued": false, - "alias": "silicate", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "size_frac": { - "name": "size_frac", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "filter size value range" - } - }, - "description": "Filtering pore size used in sample preparation", - "title": "size fraction selected", - "examples": [ - { - "value": "0-0.22 micrometer" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "size fraction selected" - ], - "rank": 285, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float}-{float} {unit}", - "slot_uri": "MIXS:0000017", - "multivalued": false, - "alias": "size_frac", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "sodium": { - "name": "sodium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Sodium concentration in the sample", - "title": "sodium", - "examples": [ - { - "value": "10.5 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sodium" - ], - "rank": 363, - "is_a": "core field", - "slot_uri": "MIXS:0000428", - "multivalued": false, - "alias": "sodium", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "specific_ecosystem": { - "name": "specific_ecosystem", - "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", - "notes": [ - "string or SpecificEcosystemEnum range?" - ], - "comments": [ - "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 13, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "specific_ecosystem", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "sulfate": { - "name": "sulfate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of sulfate in the sample", - "title": "sulfate", - "examples": [ - { - "value": "5 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sulfate" - ], - "rank": 44, - "is_a": "core field", - "slot_uri": "MIXS:0000423", - "multivalued": false, - "alias": "sulfate", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "sulfide": { - "name": "sulfide", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of sulfide in the sample", - "title": "sulfide", - "examples": [ - { - "value": "2 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sulfide" - ], - "rank": 371, - "is_a": "core field", - "slot_uri": "MIXS:0000424", - "multivalued": false, - "alias": "sulfide", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "temp": { - "name": "temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - } - }, - "description": "Temperature of the sample at the time of sampling.", - "title": "temperature", - "examples": [ - { - "value": "25 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "temperature" - ], - "rank": 37, - "is_a": "environment field", - "slot_uri": "MIXS:0000113", - "multivalued": false, - "alias": "temp", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "water_current": { - "name": "water_current", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "cubic meter per second, knots" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of magnitude and direction of flow within a fluid", - "title": "water current", - "examples": [ - { - "value": "10 cubic meter per second" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "water current" - ], - "rank": 236, - "is_a": "core field", - "slot_uri": "MIXS:0000203", - "multivalued": false, - "alias": "water_current", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "MiscEnvsInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "analysis_type": { - "name": "analysis_type", - "description": "Select all the data types associated or available for this biosample", - "title": "analysis/data type", - "examples": [ - { - "value": "metagenomics; metabolomics; proteomics" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:investigation_type" - ], - "rank": 3, - "multivalued": true, - "alias": "analysis_type", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "EmslInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "JgiMgInterface", - "JgiMtInterface" - ], - "slot_group": "sample_id_section", - "range": "analysis_type_enum", - "required": true, - "recommended": true - }, - "samp_name": { - "name": "samp_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - } - }, - "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", - "title": "sample name", - "comments": [ - "It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." - ], - "examples": [ - { - "value": "Rock core CB1178(5-6) from NSW" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample name" - ], - "rank": 1, - "is_a": "investigation field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0001107", - "multivalued": false, - "identifier": true, - "alias": "samp_name", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "EmslInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "JgiMgInterface", - "JgiMtInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true - }, - "source_mat_id": { - "name": "source_mat_id", - "description": "A globally unique identifier assigned to the biological sample.", - "title": "source material identifier", - "todos": [ - "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID.", - "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID." - ], - "notes": [ - "The source material IS the Globally Unique ID" - ], - "comments": [ - "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).", - "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/)." - ], - "examples": [ - { - "value": "IGSN:AU1243" - }, - { - "value": "UUID:24f1467a-40f4-11ed-b878-0242ac120002" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 2, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{text}:{text}", - "slot_uri": "MIXS:0000026", - "multivalued": false, - "alias": "source_mat_id", - "owner": "MiscEnvsInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "EmslInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "JgiMgInterface", - "JgiMtInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" - } - } - }, - "PlantAssociatedInterface": { - "name": "PlantAssociatedInterface", - "description": "plant_associated dh_interface", - "title": "Plant Associated", - "from_schema": "https://example.com/nmdc_submission_schema", - "is_a": "DhInterface", - "mixins": [ - "DhMultiviewCommonColumnsMixin", - "SampIdNewTermsMixin" - ], - "slots": [ - "air_temp_regm", - "ances_data", - "antibiotic_regm", - "biol_stat", - "biotic_regm", - "chem_administration", - "chem_mutagen", - "climate_environment", - "collection_date", - "cult_root_med", - "depth", - "ecosystem", - "ecosystem_category", - "ecosystem_subtype", - "ecosystem_type", - "elev", - "env_broad_scale", - "env_local_scale", - "env_medium", - "env_package", - "experimental_factor", - "fertilizer_regm", - "fungicide_regm", - "gaseous_environment", - "genetic_mod", - "geo_loc_name", - "gravity", - "growth_facil", - "growth_habit", - "growth_hormone_regm", - "herbicide_regm", - "horizon_meth", - "host_age", - "host_common_name", - "host_dry_mass", - "host_genotype", - "host_height", - "host_length", - "host_life_stage", - "host_phenotype", - "host_subspecf_genlin", - "host_symbiont", - "host_taxid", - "host_tot_mass", - "host_wet_mass", - "humidity_regm", - "lat_lon", - "light_regm", - "mechanical_damage", - "mineral_nutr_regm", - "misc_param", - "non_min_nutr_regm", - "organism_count", - "oxy_stat_samp", - "perturbation", - "pesticide_regm", - "ph_regm", - "plant_growth_med", - "plant_product", - "plant_sex", - "plant_struc", - "radiation_regm", - "rainfall_regm", - "root_cond", - "root_med_carbon", - "root_med_macronutr", - "root_med_micronutr", - "root_med_ph", - "root_med_regl", - "root_med_solid", - "root_med_suppl", - "salinity", - "salt_regm", - "samp_capt_status", - "samp_collec_device", - "samp_collec_method", - "samp_dis_stage", - "samp_mat_process", - "samp_size", - "samp_store_dur", - "samp_store_loc", - "samp_store_temp", - "sample_link", - "season_environment", - "size_frac", - "specific_ecosystem", - "standing_water_regm", - "temp", - "tiss_cult_growth_med", - "water_temp_regm", - "watering_regm" - ], - "slot_usage": { - "air_temp_regm": { - "name": "air_temp_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "temperature value;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens", - "title": "air temperature regimen", - "examples": [ - { - "value": "25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "air temperature regimen" - ], - "rank": 16, - "is_a": "core field", - "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000551", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface", - "SoilInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "ances_data": { - "name": "ances_data", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "free text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B)", - "title": "ancestral data", - "examples": [ - { - "value": "A/3*B" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "ancestral data" - ], - "rank": 237, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000247", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "antibiotic_regm": { - "name": "antibiotic_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "antibiotic name;antibiotic amount;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens", - "title": "antibiotic regimen", - "examples": [ - { - "value": "penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "antibiotic regimen" - ], - "rank": 238, - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000553", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "biol_stat": { - "name": "biol_stat", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The level of genome modification.", - "title": "biological status", - "examples": [ - { - "value": "natural" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "biological status" - ], - "rank": 239, - "is_a": "core field", - "slot_uri": "MIXS:0000858", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "biol_stat_enum" - }, - "biotic_regm": { - "name": "biotic_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "free text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi.", - "title": "biotic regimen", - "examples": [ - { - "value": "sample inoculated with Rhizobium spp. Culture" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "biotic regimen" - ], - "rank": 13, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0001038", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface", - "SoilInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "chem_administration": { - "name": "chem_administration", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "CHEBI;timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", - "title": "chemical administration", - "examples": [ - { - "value": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22" - }, - { - "value": "agar [CHEBI:2509];2018-05" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "chemical administration" - ], - "rank": 17, - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]};{timestamp}", - "slot_uri": "MIXS:0000751", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" - }, - "chem_mutagen": { - "name": "chem_mutagen", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "mutagen name;mutagen amount;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens", - "title": "chemical mutagen", - "examples": [ - { - "value": "nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "chemical mutagen" - ], - "rank": 240, - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000555", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "climate_environment": { - "name": "climate_environment", - "description": "Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates", - "title": "climate environment", - "todos": [ - "description says \"can include multiple climates\" but multivalued is set to false", - "add examples, i need to see some examples to add correctly formatted example.", - "description says \"can include multiple climates\" but multivalued is set to false", - "add examples, i need to see some examples to add correctly formatted example." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 19, - "is_a": "core field", - "string_serialization": "{text};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0001040", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface", - "SoilInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "collection_date": { - "name": "collection_date", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "date and time" - } - }, - "description": "The date of sampling", - "title": "collection date", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", - "Use modified term (amended definition)" - ], - "examples": [ - { - "value": "2021-04-15" - }, - { - "value": "2021-04" - }, - { - "value": "2021" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "collection date" - ], - "rank": 3, - "is_a": "environment field", - "string_serialization": "{date, arbitrary precision}", - "slot_uri": "MIXS:0000011", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" - }, - "cult_root_med": { - "name": "cult_root_med", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name, PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors.", - "title": "culture rooting medium", - "examples": [ - { - "value": "http://himedialabs.com/TD/PT158.pdf" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "culture rooting medium" - ], - "rank": 241, - "is_a": "core field", - "string_serialization": "{text}|{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0001041", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "depth": { - "name": "depth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - } - }, - "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", - "title": "depth, meters", - "notes": [ - "Use modified term" - ], - "comments": [ - "All depths must be reported in meters. Provide the numerical portion only." - ], - "examples": [ - { - "value": "0 - 0.1" - }, - { - "value": "1" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "depth" - ], - "rank": 9, - "is_a": "environment field", - "string_serialization": "{float}|{float}-{float}", - "slot_uri": "MIXS:0000018", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$" - }, - "ecosystem": { - "name": "ecosystem", - "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", - "notes": [ - "range: string or EcosystemEnum? The enum could be dynamic or might be soil biased." - ], - "comments": [ - "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 9, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_category": { - "name": "ecosystem_category", - "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", - "notes": [ - "string or EcosystemCategoryEnum range?" - ], - "comments": [ - "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 10, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_subtype": { - "name": "ecosystem_subtype", - "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", - "notes": [ - "string or EcosystemSubtypeEnum range?" - ], - "comments": [ - "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 12, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_type": { - "name": "ecosystem_type", - "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", - "notes": [ - "string or EcosystemTypeEnum range?" - ], - "comments": [ - "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 11, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "elev": { - "name": "elev", - "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", - "title": "elevation, meters", - "comments": [ - "All elevations must be reported in meters. Provide the numerical portion only.", - "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." - ], - "examples": [ - { - "value": "225" - }, - { - "value": "0" - }, - { - "value": "1250" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "slot_uri": "MIXS:0000093", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "float", - "required": true - }, - "env_broad_scale": { - "name": "env_broad_scale", - "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", - "title": "broad-scale environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000012", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_local_scale": { - "name": "env_local_scale", - "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", - "title": "local environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "canopy [ENVO:00000047]" - }, - { - "value": "herb and fern layer [ENVO:01000337]" - }, - { - "value": "litter layer [ENVO:01000338]" - }, - { - "value": "understory [01000335]" - }, - { - "value": "shrub layer [ENVO:01000336]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 7, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000013", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_medium": { - "name": "env_medium", - "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", - "title": "environmental medium", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "soil [ENVO:00001998]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 8, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000014", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_package": { - "name": "env_package", - "description": "Select the MIxS enviromental package that best describes the environment from which your sample was collected.", - "title": "environmental package", - "examples": [ - { - "value": "soil" - } - ], - "in_subset": [ - "mixs extension" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "environmental package" - ], - "rank": 4, - "is_a": "attribute", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true - }, - "experimental_factor": { - "name": "experimental_factor", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text or EFO and/or OBI" - } - }, - "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", - "title": "experimental factor", - "examples": [ - { - "value": "time series design [EFO:EFO_0001779]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "experimental factor" - ], - "rank": 12, - "is_a": "investigation field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000008", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "fertilizer_regm": { - "name": "fertilizer_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "fertilizer name;fertilizer amount;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, mole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens", - "title": "fertilizer regimen", - "examples": [ - { - "value": "urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "fertilizer regimen" - ], - "rank": 242, - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000556", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "fungicide_regm": { - "name": "fungicide_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "fungicide name;fungicide amount;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, mole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens", - "title": "fungicide regimen", - "examples": [ - { - "value": "bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "fungicide regimen" - ], - "rank": 243, - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000557", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "gaseous_environment": { - "name": "gaseous_environment", - "description": "Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens", - "title": "gaseous environment", - "todos": [ - "would like to see usage examples for this slot. Requiring micromole/L seems too limiting and doesn't match expected_value value", - "did I do this right? keep the example that's provided and add another? so as to not override", - "would like to see usage examples for this slot. Requiring micromole/L seems too limiting and doesn't match expected_value value", - "did I do this right? keep the example that's provided and add another? so as to not override" - ], - "examples": [ - { - "value": "CO2; 500ppm above ambient; constant" - }, - { - "value": "nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 20, - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000558", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface", - "SoilInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "genetic_mod": { - "name": "genetic_mod", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI,url or free text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection", - "title": "genetic modification", - "examples": [ - { - "value": "aox1A transgenic" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "genetic modification" - ], - "rank": 244, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}|{text}", - "slot_uri": "MIXS:0000859", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "geo_loc_name": { - "name": "geo_loc_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" - } - }, - "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", - "title": "geographic location (country and/or sea,region)", - "examples": [ - { - "value": "USA: Maryland, Bethesda" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "geographic location (country and/or sea,region)" - ], - "rank": 4, - "is_a": "environment field", - "string_serialization": "{text}: {text}, {text}", - "slot_uri": "MIXS:0000010", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" - }, - "gravity": { - "name": "gravity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "gravity factor value;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter per square second, g" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments", - "title": "gravity", - "examples": [ - { - "value": "12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "gravity" - ], - "rank": 245, - "is_a": "core field", - "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000559", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "growth_facil": { - "name": "growth_facil", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "free text or CO" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Type of facility/location where the sample was harvested; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field.", - "title": "growth facility", - "notes": [ - "Removed from description: Alternatively use Crop Ontology (CO) terms" - ], - "examples": [ - { - "value": "Growth chamber [CO_715:0000189]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "growth facility" - ], - "rank": 1, - "is_a": "core field", - "string_serialization": "{text}|{termLabel} {[termID]}", - "slot_uri": "MIXS:0001043", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface", - "SoilInterface" - ], - "slot_group": "mixs_modified_section", - "range": "GrowthFacilEnum", - "required": true - }, - "growth_habit": { - "name": "growth_habit", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Characteristic shape, appearance or growth form of a plant species", - "title": "growth habit", - "examples": [ - { - "value": "spreading" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "growth habit" - ], - "rank": 246, - "is_a": "core field", - "slot_uri": "MIXS:0001044", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "growth_habit_enum" - }, - "growth_hormone_regm": { - "name": "growth_hormone_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "growth hormone name;growth hormone amount;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, mole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens", - "title": "growth hormone regimen", - "examples": [ - { - "value": "abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "growth hormone regimen" - ], - "rank": 247, - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000560", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "herbicide_regm": { - "name": "herbicide_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "herbicide name;herbicide amount;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, mole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", - "title": "herbicide regimen", - "examples": [ - { - "value": "atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "herbicide regimen" - ], - "rank": 248, - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000561", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "horizon_meth": { - "name": "horizon_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining the horizon", - "title": "horizon method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "soil horizon method" - ], - "rank": 19, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000321", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "host_age": { - "name": "host_age", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "year, day, hour" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees", - "title": "host age", - "examples": [ - { - "value": "10 days" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host age" - ], - "rank": 249, - "is_a": "core field", - "slot_uri": "MIXS:0000255", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "host_common_name": { - "name": "host_common_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "common name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Common name of the host.", - "title": "host common name", - "examples": [ - { - "value": "human" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host common name" - ], - "rank": 250, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000248", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_dry_mass": { - "name": "host_dry_mass", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "kilogram, gram" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of dry mass", - "title": "host dry mass", - "examples": [ - { - "value": "500 gram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host dry mass" - ], - "rank": 251, - "is_a": "core field", - "slot_uri": "MIXS:0000257", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "host_genotype": { - "name": "host_genotype", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "genotype" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Observed genotype", - "title": "host genotype", - "examples": [ - { - "value": "C57BL/6" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host genotype" - ], - "rank": 252, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000365", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_height": { - "name": "host_height", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "centimeter, millimeter, meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The height of subject", - "title": "host height", - "examples": [ - { - "value": "0.1 meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host height" - ], - "rank": 253, - "is_a": "core field", - "slot_uri": "MIXS:0000264", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "host_length": { - "name": "host_length", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "centimeter, millimeter, meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The length of subject", - "title": "host length", - "examples": [ - { - "value": "1 meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host length" - ], - "rank": 254, - "is_a": "core field", - "slot_uri": "MIXS:0000256", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "host_life_stage": { - "name": "host_life_stage", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "stage" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Description of life stage of host", - "title": "host life stage", - "examples": [ - { - "value": "adult" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host life stage" - ], - "rank": 255, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000251", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_phenotype": { - "name": "host_phenotype", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PATO or HP" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP", - "title": "host phenotype", - "examples": [ - { - "value": "elongated [PATO:0001154]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host phenotype" - ], - "rank": 256, - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000874", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "host_subspecf_genlin": { - "name": "host_subspecf_genlin", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies, e.g. serovar, biotype, ecotype, variety, cultivar." - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about the genetic distinctness of the host organism below the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.", - "title": "host subspecific genetic lineage", - "examples": [ - { - "value": "serovar:Newport, variety:glabrum, cultivar: Red Delicious" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host subspecific genetic lineage" - ], - "rank": 257, - "is_a": "core field", - "string_serialization": "{rank name}:{text}", - "slot_uri": "MIXS:0001318", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_symbiont": { - "name": "host_symbiont", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "species name or common name" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host.", - "title": "observed host symbionts", - "examples": [ - { - "value": "flukeworms" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "observed host symbionts" - ], - "rank": 258, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0001298", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_taxid": { - "name": "host_taxid", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "NCBI taxon identifier" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "NCBI taxon id of the host, e.g. 9606", - "title": "host taxid", - "comments": [ - "Homo sapiens [NCBITaxon:9606] would be a reasonable has_raw_value" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host taxid" - ], - "rank": 259, - "is_a": "core field", - "slot_uri": "MIXS:0000250", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_tot_mass": { - "name": "host_tot_mass", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "kilogram, gram" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Total mass of the host at collection, the unit depends on host", - "title": "host total mass", - "examples": [ - { - "value": "2500 gram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host total mass" - ], - "rank": 260, - "is_a": "core field", - "slot_uri": "MIXS:0000263", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "host_wet_mass": { - "name": "host_wet_mass", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "kilogram, gram" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of wet mass", - "title": "host wet mass", - "examples": [ - { - "value": "1500 gram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host wet mass" - ], - "rank": 261, - "is_a": "core field", - "slot_uri": "MIXS:0000567", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "humidity_regm": { - "name": "humidity_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "humidity value;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram per cubic meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", - "title": "humidity regimen", - "examples": [ - { - "value": "25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "humidity regimen" - ], - "rank": 21, - "is_a": "core field", - "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000568", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface", - "SoilInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "lat_lon": { - "name": "lat_lon", - "description": "This is currently a required field but it's not clear if this should be required for human hosts", - "title": "geographic location (latitude and longitude)", - "notes": [ - "required where?", - "This is currently a required field but it's not clear if this should be required for human hosts" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "is_a": "environment field", - "string_serialization": "{lat lon}", - "slot_uri": "MIXS:0000009", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" - }, - "light_regm": { - "name": "light_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "exposure type;light intensity;light quality" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "lux; micrometer, nanometer, angstrom" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Information about treatment(s) involving exposure to light, including both light intensity and quality.", - "title": "light regimen", - "examples": [ - { - "value": "incandescant light;10 lux;450 nanometer" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "light regimen" - ], - "rank": 24, - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{float} {unit}", - "slot_uri": "MIXS:0000569", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface", - "SoilInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true, - "pattern": "^\\S+.*\\S+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" - }, - "mechanical_damage": { - "name": "mechanical_damage", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "damage type;body site" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about any mechanical damage exerted on the plant; can include multiple damages and sites", - "title": "mechanical damage", - "examples": [ - { - "value": "pruning;bark" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "mechanical damage" - ], - "rank": 262, - "is_a": "core field", - "string_serialization": "{text};{text}", - "slot_uri": "MIXS:0001052", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "mineral_nutr_regm": { - "name": "mineral_nutr_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "mineral nutrient name;mineral nutrient amount;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, mole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens", - "title": "mineral nutrient regimen", - "examples": [ - { - "value": "potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "mineral nutrient regimen" - ], - "rank": 263, - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000570", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "misc_param": { - "name": "misc_param", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "parameter name;measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Any other measurement performed or parameter collected, that is not listed here", - "title": "miscellaneous parameter", - "examples": [ - { - "value": "Bicarbonate ion concentration;2075 micromole per kilogram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "miscellaneous parameter" - ], - "rank": 23, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000752", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "non_min_nutr_regm": { - "name": "non_min_nutr_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "non-mineral nutrient name;non-mineral nutrient amount;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, mole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens", - "title": "non-mineral nutrient regimen", - "examples": [ - { - "value": "carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "non-mineral nutrient regimen" - ], - "rank": 264, - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000571", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "organism_count": { - "name": "organism_count", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "organism name;measurement value;enumeration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", - "title": "organism count", - "examples": [ - { - "value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "organism count" - ], - "rank": 30, - "is_a": "core field", - "slot_uri": "MIXS:0000103", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$" - }, - "oxy_stat_samp": { - "name": "oxy_stat_samp", - "description": "Oxygenation status of sample", - "title": "oxygenation status of sample", - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 25, - "is_a": "core field", - "slot_uri": "MIXS:0000753", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "OxyStatSampEnum" - }, - "perturbation": { - "name": "perturbation", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "perturbation type name;perturbation interval and duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types", - "title": "perturbation", - "examples": [ - { - "value": "antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "perturbation" - ], - "rank": 33, - "is_a": "core field", - "string_serialization": "{text};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000754", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "pesticide_regm": { - "name": "pesticide_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "pesticide name;pesticide amount;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, mole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens", - "title": "pesticide regimen", - "examples": [ - { - "value": "pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "pesticide regimen" - ], - "rank": 265, - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000573", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "ph_regm": { - "name": "ph_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value;treatment interval and duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen", - "title": "pH regimen", - "examples": [ - { - "value": "7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "pH regimen" - ], - "rank": 266, - "is_a": "core field", - "string_serialization": "{float};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0001056", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "plant_growth_med": { - "name": "plant_growth_med", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "EO or enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary", - "title": "plant growth medium", - "examples": [ - { - "value": "hydroponic plant culture media [EO:0007067]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "plant growth medium" - ], - "rank": 267, - "is_a": "core field", - "slot_uri": "MIXS:0001057", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "plant_product": { - "name": "plant_product", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "product name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Substance produced by the plant, where the sample was obtained from", - "title": "plant product", - "examples": [ - { - "value": "xylem sap [PO:0025539]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "plant product" - ], - "rank": 268, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0001058", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "plant_sex": { - "name": "plant_sex", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite.", - "title": "plant sex", - "examples": [ - { - "value": "Hermaphroditic" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "plant sex" - ], - "rank": 269, - "is_a": "core field", - "slot_uri": "MIXS:0001059", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "plant_sex_enum" - }, - "plant_struc": { - "name": "plant_struc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PO" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here.", - "title": "plant structure", - "examples": [ - { - "value": "epidermis [PO:0005679]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "plant structure" - ], - "rank": 270, - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0001060", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "radiation_regm": { - "name": "radiation_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "radiation type name;radiation amount;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "rad, gray" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens", - "title": "radiation regimen", - "examples": [ - { - "value": "gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "radiation regimen" - ], - "rank": 271, - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000575", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "rainfall_regm": { - "name": "rainfall_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millimeter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", - "title": "rainfall regimen", - "examples": [ - { - "value": "15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "rainfall regimen" - ], - "rank": 272, - "is_a": "core field", - "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000576", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "root_cond": { - "name": "root_cond", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI,url or free text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container.", - "title": "rooting conditions", - "examples": [ - { - "value": "http://himedialabs.com/TD/PT158.pdf" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "rooting conditions" - ], - "rank": 273, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}|{text}", - "slot_uri": "MIXS:0001061", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "root_med_carbon": { - "name": "root_med_carbon", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "carbon source name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Source of organic carbon in the culture rooting medium; e.g. sucrose.", - "title": "rooting medium carbon", - "examples": [ - { - "value": "sucrose" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "rooting medium carbon" - ], - "rank": 274, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000577", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" - }, - "root_med_macronutr": { - "name": "root_med_macronutr", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "macronutrient name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L).", - "title": "rooting medium macronutrients", - "examples": [ - { - "value": "KH2PO4;170¬†milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "rooting medium macronutrients" - ], - "rank": 275, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000578", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" - }, - "root_med_micronutr": { - "name": "root_med_micronutr", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "micronutrient name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L).", - "title": "rooting medium micronutrients", - "examples": [ - { - "value": "H3BO3;6.2¬†milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "rooting medium micronutrients" - ], - "rank": 276, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000579", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" - }, - "root_med_ph": { - "name": "root_med_ph", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "pH measurement of the culture rooting medium; e.g. 5.5.", - "title": "rooting medium pH", - "examples": [ - { - "value": "7.5" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "rooting medium pH" - ], - "rank": 277, - "is_a": "core field", - "slot_uri": "MIXS:0001062", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "root_med_regl": { - "name": "root_med_regl", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "regulator name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA.", - "title": "rooting medium regulators", - "examples": [ - { - "value": "abscisic acid;0.75 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "rooting medium regulators" - ], - "rank": 278, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000581", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" - }, - "root_med_solid": { - "name": "root_med_solid", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Specification of the solidifying agent in the culture rooting medium; e.g. agar.", - "title": "rooting medium solidifier", - "examples": [ - { - "value": "agar" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "rooting medium solidifier" - ], - "rank": 279, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0001063", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "root_med_suppl": { - "name": "root_med_suppl", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "supplement name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L).", - "title": "rooting medium organic supplements", - "examples": [ - { - "value": "nicotinic acid;0.5 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "rooting medium organic supplements" - ], - "rank": 280, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000580", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" - }, - "salinity": { - "name": "salinity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "practical salinity unit, percentage" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", - "title": "salinity", - "examples": [ - { - "value": "25 practical salinity unit" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "salinity" - ], - "rank": 54, - "is_a": "core field", - "slot_uri": "MIXS:0000183", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "salt_regm": { - "name": "salt_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "salt name;salt amount;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, microgram, mole per liter, gram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens", - "title": "salt regimen", - "examples": [ - { - "value": "NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "salt regimen" - ], - "rank": 281, - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000582", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_capt_status": { - "name": "samp_capt_status", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reason for the sample", - "title": "sample capture status", - "examples": [ - { - "value": "farm sample" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample capture status" - ], - "rank": 282, - "is_a": "core field", - "slot_uri": "MIXS:0000860", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "samp_capt_status_enum" - }, - "samp_collec_device": { - "name": "samp_collec_device", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "device name" - } - }, - "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", - "title": "sample collection device", - "comments": [ - "Report dimensions and details when applicable" - ], - "examples": [ - { - "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection device" - ], - "rank": 14, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000002", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "samp_collec_method": { - "name": "samp_collec_method", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI,url , or text" - } - }, - "description": "The method employed for collecting the sample.", - "title": "sample collection method", - "comments": [ - "This can be a citation or description" - ], - "examples": [ - { - "value": "swabbing" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection method" - ], - "rank": 15, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{PMID}|{DOI}|{URL}|{text}", - "slot_uri": "MIXS:0001225", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_dis_stage": { - "name": "samp_dis_stage", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen.", - "title": "sample disease stage", - "examples": [ - { - "value": "infection" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample disease stage" - ], - "rank": 283, - "is_a": "core field", - "slot_uri": "MIXS:0000249", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "samp_dis_stage_enum" - }, - "samp_mat_process": { - "name": "samp_mat_process", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - } - }, - "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", - "title": "sample material processing", - "examples": [ - { - "value": "filtering of seawater" - }, - { - "value": "storing samples in ethanol" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample material processing" - ], - "rank": 12, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000016", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_size": { - "name": "samp_size", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millliter, gram, milligram, liter" - } - }, - "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", - "title": "amount or size of sample collected", - "comments": [ - "This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis." - ], - "examples": [ - { - "value": "5 grams" - }, - { - "value": "10 mL" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "amount or size of sample collected" - ], - "rank": 18, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float} {unit}", - "slot_uri": "MIXS:0000001", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" - }, - "samp_store_dur": { - "name": "samp_store_dur", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Duration for which the sample was stored", - "title": "sample storage duration", - "examples": [ - { - "value": "P1Y6M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage duration" - ], - "rank": 353, - "is_a": "core field", - "string_serialization": "{duration}", - "slot_uri": "MIXS:0000116", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_store_loc": { - "name": "samp_store_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "location name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Location at which sample was stored, usually name of a specific freezer/room", - "title": "sample storage location", - "examples": [ - { - "value": "Freezer no:5" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage location" - ], - "rank": 41, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000755", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_store_temp": { - "name": "samp_store_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Temperature at which the sample was stored (degrees are assumed)", - "title": "sample storage temperature", - "examples": [ - { - "value": "-80 Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage temperature" - ], - "rank": 7, - "is_a": "core field", - "slot_uri": "MIXS:0000110", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "sample_link": { - "name": "sample_link", - "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", - "title": "sample linkage", - "notes": [ - "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" - ], - "comments": [ - "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" - ], - "examples": [ - { - "value": "IGSN:DSJ0284" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "string_serialization": "{text}:{text}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface", - "SampIdNewTermsMixin" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true, - "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" - }, - "season_environment": { - "name": "season_environment", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "seasonal environment name;treatment interval and duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment", - "title": "seasonal environment", - "examples": [ - { - "value": "rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "seasonal environment" - ], - "rank": 284, - "is_a": "core field", - "string_serialization": "{text};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0001068", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "size_frac": { - "name": "size_frac", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "filter size value range" - } - }, - "description": "Filtering pore size used in sample preparation", - "title": "size fraction selected", - "examples": [ - { - "value": "0-0.22 micrometer" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "size fraction selected" - ], - "rank": 285, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float}-{float} {unit}", - "slot_uri": "MIXS:0000017", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "specific_ecosystem": { - "name": "specific_ecosystem", - "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", - "notes": [ - "string or SpecificEcosystemEnum range?" - ], - "comments": [ - "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 13, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "standing_water_regm": { - "name": "standing_water_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "standing water type;treatment interval and duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", - "title": "standing water regimen", - "examples": [ - { - "value": "standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "standing water regimen" - ], - "rank": 286, - "is_a": "core field", - "string_serialization": "{text};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0001069", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "temp": { - "name": "temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - } - }, - "description": "Temperature of the sample at the time of sampling.", - "title": "temperature", - "examples": [ - { - "value": "25 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "temperature" - ], - "rank": 37, - "is_a": "environment field", - "slot_uri": "MIXS:0000113", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tiss_cult_growth_med": { - "name": "tiss_cult_growth_med", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI,url or free text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Description of plant tissue culture growth media used", - "title": "tissue culture growth media", - "examples": [ - { - "value": "https://link.springer.com/content/pdf/10.1007/BF02796489.pdf" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "tissue culture growth media" - ], - "rank": 287, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}|{text}", - "slot_uri": "MIXS:0001070", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "water_temp_regm": { - "name": "water_temp_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", - "title": "water temperature regimen", - "examples": [ - { - "value": "15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "water temperature regimen" - ], - "rank": 288, - "is_a": "core field", - "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000590", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "watering_regm": { - "name": "watering_regm", - "description": "Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", - "title": "watering regimen", - "examples": [ - { - "value": "1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - }, - { - "value": "75% water holding capacity; constant" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 25, - "is_a": "core field", - "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000591", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface", - "SoilInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - } - }, - "attributes": { - "air_temp_regm": { - "name": "air_temp_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "temperature value;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens", - "title": "air temperature regimen", - "examples": [ - { - "value": "25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "air temperature regimen" - ], - "rank": 16, - "is_a": "core field", - "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000551", - "multivalued": false, - "alias": "air_temp_regm", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface", - "SoilInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "ances_data": { - "name": "ances_data", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "free text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B)", - "title": "ancestral data", - "examples": [ - { - "value": "A/3*B" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "ancestral data" - ], - "rank": 237, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000247", - "multivalued": false, - "alias": "ances_data", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "antibiotic_regm": { - "name": "antibiotic_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "antibiotic name;antibiotic amount;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens", - "title": "antibiotic regimen", - "examples": [ - { - "value": "penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "antibiotic regimen" - ], - "rank": 238, - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000553", - "multivalued": false, - "alias": "antibiotic_regm", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "biol_stat": { - "name": "biol_stat", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The level of genome modification.", - "title": "biological status", - "examples": [ - { - "value": "natural" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "biological status" - ], - "rank": 239, - "is_a": "core field", - "slot_uri": "MIXS:0000858", - "multivalued": false, - "alias": "biol_stat", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "biol_stat_enum" - }, - "biotic_regm": { - "name": "biotic_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "free text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi.", - "title": "biotic regimen", - "examples": [ - { - "value": "sample inoculated with Rhizobium spp. Culture" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "biotic regimen" - ], - "rank": 13, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0001038", - "multivalued": false, - "alias": "biotic_regm", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface", - "SoilInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "chem_administration": { - "name": "chem_administration", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "CHEBI;timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", - "title": "chemical administration", - "examples": [ - { - "value": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22" - }, - { - "value": "agar [CHEBI:2509];2018-05" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "chemical administration" - ], - "rank": 17, - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]};{timestamp}", - "slot_uri": "MIXS:0000751", - "multivalued": false, - "alias": "chem_administration", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" - }, - "chem_mutagen": { - "name": "chem_mutagen", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "mutagen name;mutagen amount;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Treatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens", - "title": "chemical mutagen", - "examples": [ - { - "value": "nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "chemical mutagen" - ], - "rank": 240, - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000555", - "multivalued": false, - "alias": "chem_mutagen", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "climate_environment": { - "name": "climate_environment", - "description": "Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates", - "title": "climate environment", - "todos": [ - "description says \"can include multiple climates\" but multivalued is set to false", - "add examples, i need to see some examples to add correctly formatted example.", - "description says \"can include multiple climates\" but multivalued is set to false", - "add examples, i need to see some examples to add correctly formatted example." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 19, - "is_a": "core field", - "string_serialization": "{text};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0001040", - "multivalued": false, - "alias": "climate_environment", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface", - "SoilInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "collection_date": { - "name": "collection_date", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "date and time" - } - }, - "description": "The date of sampling", - "title": "collection date", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", - "Use modified term (amended definition)" - ], - "examples": [ - { - "value": "2021-04-15" - }, - { - "value": "2021-04" - }, - { - "value": "2021" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "collection date" - ], - "rank": 3, - "is_a": "environment field", - "string_serialization": "{date, arbitrary precision}", - "slot_uri": "MIXS:0000011", - "multivalued": false, - "alias": "collection_date", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" - }, - "cult_root_med": { - "name": "cult_root_med", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name, PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Name or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors.", - "title": "culture rooting medium", - "examples": [ - { - "value": "http://himedialabs.com/TD/PT158.pdf" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "culture rooting medium" - ], - "rank": 241, - "is_a": "core field", - "string_serialization": "{text}|{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0001041", - "multivalued": false, - "alias": "cult_root_med", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "depth": { - "name": "depth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - } - }, - "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", - "title": "depth, meters", - "notes": [ - "Use modified term" - ], - "comments": [ - "All depths must be reported in meters. Provide the numerical portion only." - ], - "examples": [ - { - "value": "0 - 0.1" - }, - { - "value": "1" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "depth" - ], - "rank": 9, - "is_a": "environment field", - "string_serialization": "{float}|{float}-{float}", - "slot_uri": "MIXS:0000018", - "multivalued": false, - "alias": "depth", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$" - }, - "ecosystem": { - "name": "ecosystem", - "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", - "notes": [ - "range: string or EcosystemEnum? The enum could be dynamic or might be soil biased." - ], - "comments": [ - "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 9, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_category": { - "name": "ecosystem_category", - "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", - "notes": [ - "string or EcosystemCategoryEnum range?" - ], - "comments": [ - "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 10, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem_category", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_subtype": { - "name": "ecosystem_subtype", - "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", - "notes": [ - "string or EcosystemSubtypeEnum range?" - ], - "comments": [ - "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 12, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem_subtype", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_type": { - "name": "ecosystem_type", - "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", - "notes": [ - "string or EcosystemTypeEnum range?" - ], - "comments": [ - "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 11, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem_type", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "elev": { - "name": "elev", - "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", - "title": "elevation, meters", - "comments": [ - "All elevations must be reported in meters. Provide the numerical portion only.", - "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." - ], - "examples": [ - { - "value": "225" - }, - { - "value": "0" - }, - { - "value": "1250" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "slot_uri": "MIXS:0000093", - "multivalued": false, - "alias": "elev", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "float", - "required": true - }, - "env_broad_scale": { - "name": "env_broad_scale", - "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", - "title": "broad-scale environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000012", - "multivalued": false, - "alias": "env_broad_scale", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_local_scale": { - "name": "env_local_scale", - "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", - "title": "local environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "canopy [ENVO:00000047]" - }, - { - "value": "herb and fern layer [ENVO:01000337]" - }, - { - "value": "litter layer [ENVO:01000338]" - }, - { - "value": "understory [01000335]" - }, - { - "value": "shrub layer [ENVO:01000336]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 7, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000013", - "multivalued": false, - "alias": "env_local_scale", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_medium": { - "name": "env_medium", - "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", - "title": "environmental medium", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "soil [ENVO:00001998]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 8, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000014", - "multivalued": false, - "alias": "env_medium", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_package": { - "name": "env_package", - "description": "Select the MIxS enviromental package that best describes the environment from which your sample was collected.", - "title": "environmental package", - "examples": [ - { - "value": "soil" - } - ], - "in_subset": [ - "mixs extension" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "environmental package" - ], - "rank": 4, - "is_a": "attribute", - "multivalued": false, - "alias": "env_package", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true - }, - "experimental_factor": { - "name": "experimental_factor", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text or EFO and/or OBI" - } - }, - "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", - "title": "experimental factor", - "examples": [ - { - "value": "time series design [EFO:EFO_0001779]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "experimental factor" - ], - "rank": 12, - "is_a": "investigation field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000008", - "multivalued": false, - "alias": "experimental_factor", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "fertilizer_regm": { - "name": "fertilizer_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "fertilizer name;fertilizer amount;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, mole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens", - "title": "fertilizer regimen", - "examples": [ - { - "value": "urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "fertilizer regimen" - ], - "rank": 242, - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000556", - "multivalued": false, - "alias": "fertilizer_regm", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "fungicide_regm": { - "name": "fungicide_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "fungicide name;fungicide amount;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, mole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens", - "title": "fungicide regimen", - "examples": [ - { - "value": "bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "fungicide regimen" - ], - "rank": 243, - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000557", - "multivalued": false, - "alias": "fungicide_regm", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "gaseous_environment": { - "name": "gaseous_environment", - "description": "Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens", - "title": "gaseous environment", - "todos": [ - "would like to see usage examples for this slot. Requiring micromole/L seems too limiting and doesn't match expected_value value", - "did I do this right? keep the example that's provided and add another? so as to not override", - "would like to see usage examples for this slot. Requiring micromole/L seems too limiting and doesn't match expected_value value", - "did I do this right? keep the example that's provided and add another? so as to not override" - ], - "examples": [ - { - "value": "CO2; 500ppm above ambient; constant" - }, - { - "value": "nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 20, - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000558", - "multivalued": false, - "alias": "gaseous_environment", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface", - "SoilInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "genetic_mod": { - "name": "genetic_mod", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI,url or free text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection", - "title": "genetic modification", - "examples": [ - { - "value": "aox1A transgenic" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "genetic modification" - ], - "rank": 244, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}|{text}", - "slot_uri": "MIXS:0000859", - "multivalued": false, - "alias": "genetic_mod", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "geo_loc_name": { - "name": "geo_loc_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" - } - }, - "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", - "title": "geographic location (country and/or sea,region)", - "examples": [ - { - "value": "USA: Maryland, Bethesda" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "geographic location (country and/or sea,region)" - ], - "rank": 4, - "is_a": "environment field", - "string_serialization": "{text}: {text}, {text}", - "slot_uri": "MIXS:0000010", - "multivalued": false, - "alias": "geo_loc_name", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" - }, - "gravity": { - "name": "gravity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "gravity factor value;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter per square second, g" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments", - "title": "gravity", - "examples": [ - { - "value": "12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "gravity" - ], - "rank": 245, - "is_a": "core field", - "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000559", - "multivalued": false, - "alias": "gravity", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "growth_facil": { - "name": "growth_facil", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "free text or CO" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Type of facility/location where the sample was harvested; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field.", - "title": "growth facility", - "notes": [ - "Removed from description: Alternatively use Crop Ontology (CO) terms" - ], - "examples": [ - { - "value": "Growth chamber [CO_715:0000189]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "growth facility" - ], - "rank": 1, - "is_a": "core field", - "string_serialization": "{text}|{termLabel} {[termID]}", - "slot_uri": "MIXS:0001043", - "multivalued": false, - "alias": "growth_facil", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface", - "SoilInterface" - ], - "slot_group": "mixs_modified_section", - "range": "GrowthFacilEnum", - "required": true - }, - "growth_habit": { - "name": "growth_habit", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Characteristic shape, appearance or growth form of a plant species", - "title": "growth habit", - "examples": [ - { - "value": "spreading" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "growth habit" - ], - "rank": 246, - "is_a": "core field", - "slot_uri": "MIXS:0001044", - "multivalued": false, - "alias": "growth_habit", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "growth_habit_enum" - }, - "growth_hormone_regm": { - "name": "growth_hormone_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "growth hormone name;growth hormone amount;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, mole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens", - "title": "growth hormone regimen", - "examples": [ - { - "value": "abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "growth hormone regimen" - ], - "rank": 247, - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000560", - "multivalued": false, - "alias": "growth_hormone_regm", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "herbicide_regm": { - "name": "herbicide_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "herbicide name;herbicide amount;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, mole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", - "title": "herbicide regimen", - "examples": [ - { - "value": "atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "herbicide regimen" - ], - "rank": 248, - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000561", - "multivalued": false, - "alias": "herbicide_regm", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "horizon_meth": { - "name": "horizon_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining the horizon", - "title": "horizon method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "soil horizon method" - ], - "rank": 19, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000321", - "multivalued": false, - "alias": "horizon_meth", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "host_age": { - "name": "host_age", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "year, day, hour" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees", - "title": "host age", - "examples": [ - { - "value": "10 days" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host age" - ], - "rank": 249, - "is_a": "core field", - "slot_uri": "MIXS:0000255", - "multivalued": false, - "alias": "host_age", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "host_common_name": { - "name": "host_common_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "common name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Common name of the host.", - "title": "host common name", - "examples": [ - { - "value": "human" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host common name" - ], - "rank": 250, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000248", - "multivalued": false, - "alias": "host_common_name", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_dry_mass": { - "name": "host_dry_mass", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "kilogram, gram" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of dry mass", - "title": "host dry mass", - "examples": [ - { - "value": "500 gram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host dry mass" - ], - "rank": 251, - "is_a": "core field", - "slot_uri": "MIXS:0000257", - "multivalued": false, - "alias": "host_dry_mass", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "host_genotype": { - "name": "host_genotype", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "genotype" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Observed genotype", - "title": "host genotype", - "examples": [ - { - "value": "C57BL/6" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host genotype" - ], - "rank": 252, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000365", - "multivalued": false, - "alias": "host_genotype", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_height": { - "name": "host_height", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "centimeter, millimeter, meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The height of subject", - "title": "host height", - "examples": [ - { - "value": "0.1 meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host height" - ], - "rank": 253, - "is_a": "core field", - "slot_uri": "MIXS:0000264", - "multivalued": false, - "alias": "host_height", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "host_length": { - "name": "host_length", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "centimeter, millimeter, meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The length of subject", - "title": "host length", - "examples": [ - { - "value": "1 meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host length" - ], - "rank": 254, - "is_a": "core field", - "slot_uri": "MIXS:0000256", - "multivalued": false, - "alias": "host_length", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "host_life_stage": { - "name": "host_life_stage", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "stage" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Description of life stage of host", - "title": "host life stage", - "examples": [ - { - "value": "adult" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host life stage" - ], - "rank": 255, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000251", - "multivalued": false, - "alias": "host_life_stage", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_phenotype": { - "name": "host_phenotype", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PATO or HP" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP", - "title": "host phenotype", - "examples": [ - { - "value": "elongated [PATO:0001154]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host phenotype" - ], - "rank": 256, - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000874", - "multivalued": false, - "alias": "host_phenotype", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "host_subspecf_genlin": { - "name": "host_subspecf_genlin", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies, e.g. serovar, biotype, ecotype, variety, cultivar." - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about the genetic distinctness of the host organism below the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.", - "title": "host subspecific genetic lineage", - "examples": [ - { - "value": "serovar:Newport, variety:glabrum, cultivar: Red Delicious" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host subspecific genetic lineage" - ], - "rank": 257, - "is_a": "core field", - "string_serialization": "{rank name}:{text}", - "slot_uri": "MIXS:0001318", - "multivalued": false, - "alias": "host_subspecf_genlin", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_symbiont": { - "name": "host_symbiont", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "species name or common name" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host.", - "title": "observed host symbionts", - "examples": [ - { - "value": "flukeworms" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "observed host symbionts" - ], - "rank": 258, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0001298", - "multivalued": false, - "alias": "host_symbiont", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_taxid": { - "name": "host_taxid", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "NCBI taxon identifier" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "NCBI taxon id of the host, e.g. 9606", - "title": "host taxid", - "comments": [ - "Homo sapiens [NCBITaxon:9606] would be a reasonable has_raw_value" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host taxid" - ], - "rank": 259, - "is_a": "core field", - "slot_uri": "MIXS:0000250", - "multivalued": false, - "alias": "host_taxid", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "host_tot_mass": { - "name": "host_tot_mass", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "kilogram, gram" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Total mass of the host at collection, the unit depends on host", - "title": "host total mass", - "examples": [ - { - "value": "2500 gram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host total mass" - ], - "rank": 260, - "is_a": "core field", - "slot_uri": "MIXS:0000263", - "multivalued": false, - "alias": "host_tot_mass", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "host_wet_mass": { - "name": "host_wet_mass", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "kilogram, gram" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of wet mass", - "title": "host wet mass", - "examples": [ - { - "value": "1500 gram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "host wet mass" - ], - "rank": 261, - "is_a": "core field", - "slot_uri": "MIXS:0000567", - "multivalued": false, - "alias": "host_wet_mass", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "humidity_regm": { - "name": "humidity_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "humidity value;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram per cubic meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", - "title": "humidity regimen", - "examples": [ - { - "value": "25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "humidity regimen" - ], - "rank": 21, - "is_a": "core field", - "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000568", - "multivalued": false, - "alias": "humidity_regm", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface", - "SoilInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "lat_lon": { - "name": "lat_lon", - "description": "This is currently a required field but it's not clear if this should be required for human hosts", - "title": "geographic location (latitude and longitude)", - "notes": [ - "required where?", - "This is currently a required field but it's not clear if this should be required for human hosts" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "is_a": "environment field", - "string_serialization": "{lat lon}", - "slot_uri": "MIXS:0000009", - "multivalued": false, - "alias": "lat_lon", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" - }, - "light_regm": { - "name": "light_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "exposure type;light intensity;light quality" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "lux; micrometer, nanometer, angstrom" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Information about treatment(s) involving exposure to light, including both light intensity and quality.", - "title": "light regimen", - "examples": [ - { - "value": "incandescant light;10 lux;450 nanometer" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "light regimen" - ], - "rank": 24, - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{float} {unit}", - "slot_uri": "MIXS:0000569", - "multivalued": false, - "alias": "light_regm", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface", - "SoilInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true, - "pattern": "^\\S+.*\\S+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" - }, - "mechanical_damage": { - "name": "mechanical_damage", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "damage type;body site" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about any mechanical damage exerted on the plant; can include multiple damages and sites", - "title": "mechanical damage", - "examples": [ - { - "value": "pruning;bark" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "mechanical damage" - ], - "rank": 262, - "is_a": "core field", - "string_serialization": "{text};{text}", - "slot_uri": "MIXS:0001052", - "multivalued": false, - "alias": "mechanical_damage", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "mineral_nutr_regm": { - "name": "mineral_nutr_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "mineral nutrient name;mineral nutrient amount;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, mole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens", - "title": "mineral nutrient regimen", - "examples": [ - { - "value": "potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "mineral nutrient regimen" - ], - "rank": 263, - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000570", - "multivalued": false, - "alias": "mineral_nutr_regm", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "misc_param": { - "name": "misc_param", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "parameter name;measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Any other measurement performed or parameter collected, that is not listed here", - "title": "miscellaneous parameter", - "examples": [ - { - "value": "Bicarbonate ion concentration;2075 micromole per kilogram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "miscellaneous parameter" - ], - "rank": 23, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000752", - "multivalued": false, - "alias": "misc_param", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "non_min_nutr_regm": { - "name": "non_min_nutr_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "non-mineral nutrient name;non-mineral nutrient amount;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, mole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens", - "title": "non-mineral nutrient regimen", - "examples": [ - { - "value": "carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "non-mineral nutrient regimen" - ], - "rank": 264, - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000571", - "multivalued": false, - "alias": "non_min_nutr_regm", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "organism_count": { - "name": "organism_count", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "organism name;measurement value;enumeration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", - "title": "organism count", - "examples": [ - { - "value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "organism count" - ], - "rank": 30, - "is_a": "core field", - "slot_uri": "MIXS:0000103", - "multivalued": false, - "alias": "organism_count", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$" - }, - "oxy_stat_samp": { - "name": "oxy_stat_samp", - "description": "Oxygenation status of sample", - "title": "oxygenation status of sample", - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 25, - "is_a": "core field", - "slot_uri": "MIXS:0000753", - "multivalued": false, - "alias": "oxy_stat_samp", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "OxyStatSampEnum" - }, - "perturbation": { - "name": "perturbation", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "perturbation type name;perturbation interval and duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types", - "title": "perturbation", - "examples": [ - { - "value": "antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "perturbation" - ], - "rank": 33, - "is_a": "core field", - "string_serialization": "{text};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000754", - "multivalued": false, - "alias": "perturbation", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "pesticide_regm": { - "name": "pesticide_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "pesticide name;pesticide amount;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, mole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens", - "title": "pesticide regimen", - "examples": [ - { - "value": "pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "pesticide regimen" - ], - "rank": 265, - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000573", - "multivalued": false, - "alias": "pesticide_regm", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "ph_regm": { - "name": "ph_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value;treatment interval and duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen", - "title": "pH regimen", - "examples": [ - { - "value": "7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "pH regimen" - ], - "rank": 266, - "is_a": "core field", - "string_serialization": "{float};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0001056", - "multivalued": false, - "alias": "ph_regm", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "plant_growth_med": { - "name": "plant_growth_med", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "EO or enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Specification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary", - "title": "plant growth medium", - "examples": [ - { - "value": "hydroponic plant culture media [EO:0007067]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "plant growth medium" - ], - "rank": 267, - "is_a": "core field", - "slot_uri": "MIXS:0001057", - "multivalued": false, - "alias": "plant_growth_med", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "plant_product": { - "name": "plant_product", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "product name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Substance produced by the plant, where the sample was obtained from", - "title": "plant product", - "examples": [ - { - "value": "xylem sap [PO:0025539]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "plant product" - ], - "rank": 268, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0001058", - "multivalued": false, - "alias": "plant_product", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "plant_sex": { - "name": "plant_sex", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite.", - "title": "plant sex", - "examples": [ - { - "value": "Hermaphroditic" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "plant sex" - ], - "rank": 269, - "is_a": "core field", - "slot_uri": "MIXS:0001059", - "multivalued": false, - "alias": "plant_sex", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "plant_sex_enum" - }, - "plant_struc": { - "name": "plant_struc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PO" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Name of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here.", - "title": "plant structure", - "examples": [ - { - "value": "epidermis [PO:0005679]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "plant structure" - ], - "rank": 270, - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0001060", - "multivalued": false, - "alias": "plant_struc", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "radiation_regm": { - "name": "radiation_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "radiation type name;radiation amount;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "rad, gray" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens", - "title": "radiation regimen", - "examples": [ - { - "value": "gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "radiation regimen" - ], - "rank": 271, - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000575", - "multivalued": false, - "alias": "radiation_regm", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "rainfall_regm": { - "name": "rainfall_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millimeter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", - "title": "rainfall regimen", - "examples": [ - { - "value": "15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "rainfall regimen" - ], - "rank": 272, - "is_a": "core field", - "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000576", - "multivalued": false, - "alias": "rainfall_regm", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "root_cond": { - "name": "root_cond", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI,url or free text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container.", - "title": "rooting conditions", - "examples": [ - { - "value": "http://himedialabs.com/TD/PT158.pdf" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "rooting conditions" - ], - "rank": 273, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}|{text}", - "slot_uri": "MIXS:0001061", - "multivalued": false, - "alias": "root_cond", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "root_med_carbon": { - "name": "root_med_carbon", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "carbon source name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Source of organic carbon in the culture rooting medium; e.g. sucrose.", - "title": "rooting medium carbon", - "examples": [ - { - "value": "sucrose" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "rooting medium carbon" - ], - "rank": 274, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000577", - "multivalued": false, - "alias": "root_med_carbon", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" - }, - "root_med_macronutr": { - "name": "root_med_macronutr", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "macronutrient name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L).", - "title": "rooting medium macronutrients", - "examples": [ - { - "value": "KH2PO4;170¬†milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "rooting medium macronutrients" - ], - "rank": 275, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000578", - "multivalued": false, - "alias": "root_med_macronutr", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" - }, - "root_med_micronutr": { - "name": "root_med_micronutr", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "micronutrient name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2¬†mg/L).", - "title": "rooting medium micronutrients", - "examples": [ - { - "value": "H3BO3;6.2¬†milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "rooting medium micronutrients" - ], - "rank": 276, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000579", - "multivalued": false, - "alias": "root_med_micronutr", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" - }, - "root_med_ph": { - "name": "root_med_ph", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "pH measurement of the culture rooting medium; e.g. 5.5.", - "title": "rooting medium pH", - "examples": [ - { - "value": "7.5" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "rooting medium pH" - ], - "rank": 277, - "is_a": "core field", - "slot_uri": "MIXS:0001062", - "multivalued": false, - "alias": "root_med_ph", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "root_med_regl": { - "name": "root_med_regl", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "regulator name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA.", - "title": "rooting medium regulators", - "examples": [ - { - "value": "abscisic acid;0.75 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "rooting medium regulators" - ], - "rank": 278, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000581", - "multivalued": false, - "alias": "root_med_regl", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" - }, - "root_med_solid": { - "name": "root_med_solid", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Specification of the solidifying agent in the culture rooting medium; e.g. agar.", - "title": "rooting medium solidifier", - "examples": [ - { - "value": "agar" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "rooting medium solidifier" - ], - "rank": 279, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0001063", - "multivalued": false, - "alias": "root_med_solid", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "root_med_suppl": { - "name": "root_med_suppl", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "supplement name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L).", - "title": "rooting medium organic supplements", - "examples": [ - { - "value": "nicotinic acid;0.5 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "rooting medium organic supplements" - ], - "rank": 280, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000580", - "multivalued": false, - "alias": "root_med_suppl", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" - }, - "salinity": { - "name": "salinity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "practical salinity unit, percentage" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", - "title": "salinity", - "examples": [ - { - "value": "25 practical salinity unit" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "salinity" - ], - "rank": 54, - "is_a": "core field", - "slot_uri": "MIXS:0000183", - "multivalued": false, - "alias": "salinity", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "salt_regm": { - "name": "salt_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "salt name;salt amount;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, microgram, mole per liter, gram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens", - "title": "salt regimen", - "examples": [ - { - "value": "NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "salt regimen" - ], - "rank": 281, - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000582", - "multivalued": false, - "alias": "salt_regm", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_capt_status": { - "name": "samp_capt_status", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reason for the sample", - "title": "sample capture status", - "examples": [ - { - "value": "farm sample" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample capture status" - ], - "rank": 282, - "is_a": "core field", - "slot_uri": "MIXS:0000860", - "multivalued": false, - "alias": "samp_capt_status", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "samp_capt_status_enum" - }, - "samp_collec_device": { - "name": "samp_collec_device", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "device name" - } - }, - "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", - "title": "sample collection device", - "comments": [ - "Report dimensions and details when applicable" - ], - "examples": [ - { - "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection device" - ], - "rank": 14, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000002", - "multivalued": false, - "alias": "samp_collec_device", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "samp_collec_method": { - "name": "samp_collec_method", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI,url , or text" - } - }, - "description": "The method employed for collecting the sample.", - "title": "sample collection method", - "comments": [ - "This can be a citation or description" - ], - "examples": [ - { - "value": "swabbing" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection method" - ], - "rank": 15, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{PMID}|{DOI}|{URL}|{text}", - "slot_uri": "MIXS:0001225", - "multivalued": false, - "alias": "samp_collec_method", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_dis_stage": { - "name": "samp_dis_stage", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen.", - "title": "sample disease stage", - "examples": [ - { - "value": "infection" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample disease stage" - ], - "rank": 283, - "is_a": "core field", - "slot_uri": "MIXS:0000249", - "multivalued": false, - "alias": "samp_dis_stage", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "HostAssociatedInterface", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "samp_dis_stage_enum" - }, - "samp_mat_process": { - "name": "samp_mat_process", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - } - }, - "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", - "title": "sample material processing", - "examples": [ - { - "value": "filtering of seawater" - }, - { - "value": "storing samples in ethanol" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample material processing" - ], - "rank": 12, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000016", - "multivalued": false, - "alias": "samp_mat_process", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_size": { - "name": "samp_size", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millliter, gram, milligram, liter" - } - }, - "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", - "title": "amount or size of sample collected", - "comments": [ - "This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis." - ], - "examples": [ - { - "value": "5 grams" - }, - { - "value": "10 mL" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "amount or size of sample collected" - ], - "rank": 18, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float} {unit}", - "slot_uri": "MIXS:0000001", - "multivalued": false, - "alias": "samp_size", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" - }, - "samp_store_dur": { - "name": "samp_store_dur", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Duration for which the sample was stored", - "title": "sample storage duration", - "examples": [ - { - "value": "P1Y6M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage duration" - ], - "rank": 353, - "is_a": "core field", - "string_serialization": "{duration}", - "slot_uri": "MIXS:0000116", - "multivalued": false, - "alias": "samp_store_dur", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_store_loc": { - "name": "samp_store_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "location name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Location at which sample was stored, usually name of a specific freezer/room", - "title": "sample storage location", - "examples": [ - { - "value": "Freezer no:5" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage location" - ], - "rank": 41, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000755", - "multivalued": false, - "alias": "samp_store_loc", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_store_temp": { - "name": "samp_store_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Temperature at which the sample was stored (degrees are assumed)", - "title": "sample storage temperature", - "examples": [ - { - "value": "-80 Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage temperature" - ], - "rank": 7, - "is_a": "core field", - "slot_uri": "MIXS:0000110", - "multivalued": false, - "alias": "samp_store_temp", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "sample_link": { - "name": "sample_link", - "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", - "title": "sample linkage", - "notes": [ - "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" - ], - "comments": [ - "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" - ], - "examples": [ - { - "value": "IGSN:DSJ0284" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "string_serialization": "{text}:{text}", - "multivalued": false, - "alias": "sample_link", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface", - "SampIdNewTermsMixin" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true, - "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" - }, - "season_environment": { - "name": "season_environment", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "seasonal environment name;treatment interval and duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Treatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment", - "title": "seasonal environment", - "examples": [ - { - "value": "rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "seasonal environment" - ], - "rank": 284, - "is_a": "core field", - "string_serialization": "{text};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0001068", - "multivalued": false, - "alias": "season_environment", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "size_frac": { - "name": "size_frac", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "filter size value range" - } - }, - "description": "Filtering pore size used in sample preparation", - "title": "size fraction selected", - "examples": [ - { - "value": "0-0.22 micrometer" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "size fraction selected" - ], - "rank": 285, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float}-{float} {unit}", - "slot_uri": "MIXS:0000017", - "multivalued": false, - "alias": "size_frac", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "specific_ecosystem": { - "name": "specific_ecosystem", - "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", - "notes": [ - "string or SpecificEcosystemEnum range?" - ], - "comments": [ - "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 13, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "specific_ecosystem", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "standing_water_regm": { - "name": "standing_water_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "standing water type;treatment interval and duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Treatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", - "title": "standing water regimen", - "examples": [ - { - "value": "standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "standing water regimen" - ], - "rank": 286, - "is_a": "core field", - "string_serialization": "{text};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0001069", - "multivalued": false, - "alias": "standing_water_regm", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "temp": { - "name": "temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - } - }, - "description": "Temperature of the sample at the time of sampling.", - "title": "temperature", - "examples": [ - { - "value": "25 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "temperature" - ], - "rank": 37, - "is_a": "environment field", - "slot_uri": "MIXS:0000113", - "multivalued": false, - "alias": "temp", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tiss_cult_growth_med": { - "name": "tiss_cult_growth_med", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI,url or free text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Description of plant tissue culture growth media used", - "title": "tissue culture growth media", - "examples": [ - { - "value": "https://link.springer.com/content/pdf/10.1007/BF02796489.pdf" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "tissue culture growth media" - ], - "rank": 287, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}|{text}", - "slot_uri": "MIXS:0001070", - "multivalued": false, - "alias": "tiss_cult_growth_med", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "water_temp_regm": { - "name": "water_temp_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", - "title": "water temperature regimen", - "examples": [ - { - "value": "15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "water temperature regimen" - ], - "rank": 288, - "is_a": "core field", - "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000590", - "multivalued": false, - "alias": "water_temp_regm", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "watering_regm": { - "name": "watering_regm", - "description": "Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", - "title": "watering regimen", - "examples": [ - { - "value": "1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - }, - { - "value": "75% water holding capacity; constant" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 25, - "is_a": "core field", - "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000591", - "multivalued": false, - "alias": "watering_regm", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface", - "SoilInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "analysis_type": { - "name": "analysis_type", - "description": "Select all the data types associated or available for this biosample", - "title": "analysis/data type", - "examples": [ - { - "value": "metagenomics; metabolomics; proteomics" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:investigation_type" - ], - "rank": 3, - "multivalued": true, - "alias": "analysis_type", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "EmslInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "JgiMgInterface", - "JgiMtInterface", - "MiscEnvsInterface" - ], - "slot_group": "sample_id_section", - "range": "analysis_type_enum", - "required": true, - "recommended": true - }, - "samp_name": { - "name": "samp_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - } - }, - "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", - "title": "sample name", - "comments": [ - "It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." - ], - "examples": [ - { - "value": "Rock core CB1178(5-6) from NSW" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample name" - ], - "rank": 1, - "is_a": "investigation field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0001107", - "multivalued": false, - "identifier": true, - "alias": "samp_name", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "EmslInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "JgiMgInterface", - "JgiMtInterface", - "MiscEnvsInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true - }, - "source_mat_id": { - "name": "source_mat_id", - "description": "A globally unique identifier assigned to the biological sample.", - "title": "source material identifier", - "todos": [ - "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID.", - "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID." - ], - "notes": [ - "The source material IS the Globally Unique ID" - ], - "comments": [ - "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).", - "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/)." - ], - "examples": [ - { - "value": "IGSN:AU1243" - }, - { - "value": "UUID:24f1467a-40f4-11ed-b878-0242ac120002" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 2, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{text}:{text}", - "slot_uri": "MIXS:0000026", - "multivalued": false, - "alias": "source_mat_id", - "owner": "PlantAssociatedInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "EmslInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "JgiMgInterface", - "JgiMtInterface", - "MiscEnvsInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" - } - } - }, - "SedimentInterface": { - "name": "SedimentInterface", - "description": "sediment dh_interface", - "title": "Sediment", - "from_schema": "https://example.com/nmdc_submission_schema", - "is_a": "DhInterface", - "mixins": [ - "DhMultiviewCommonColumnsMixin", - "SampIdNewTermsMixin" - ], - "slots": [ - "alkalinity", - "alkyl_diethers", - "aminopept_act", - "ammonium", - "bacteria_carb_prod", - "biomass", - "bishomohopanol", - "bromide", - "calcium", - "carb_nitro_ratio", - "chem_administration", - "chloride", - "chlorophyll", - "collection_date", - "density", - "depth", - "diether_lipids", - "diss_carb_dioxide", - "diss_hydrogen", - "diss_inorg_carb", - "diss_org_carb", - "diss_org_nitro", - "diss_oxygen", - "ecosystem", - "ecosystem_category", - "ecosystem_subtype", - "ecosystem_type", - "elev", - "env_broad_scale", - "env_local_scale", - "env_medium", - "env_package", - "experimental_factor", - "geo_loc_name", - "glucosidase_act", - "horizon_meth", - "lat_lon", - "magnesium", - "mean_frict_vel", - "mean_peak_frict_vel", - "methane", - "misc_param", - "n_alkanes", - "nitrate", - "nitrite", - "nitro", - "org_carb", - "org_matter", - "org_nitro", - "organism_count", - "oxy_stat_samp", - "part_org_carb", - "particle_class", - "perturbation", - "petroleum_hydrocarb", - "ph", - "ph_meth", - "phaeopigments", - "phosphate", - "phosplipid_fatt_acid", - "porosity", - "potassium", - "pressure", - "redox_potential", - "salinity", - "samp_collec_device", - "samp_collec_method", - "samp_mat_process", - "samp_size", - "samp_store_dur", - "samp_store_loc", - "samp_store_temp", - "sample_link", - "sediment_type", - "silicate", - "size_frac", - "sodium", - "specific_ecosystem", - "sulfate", - "sulfide", - "temp", - "tidal_stage", - "tot_carb", - "tot_depth_water_col", - "tot_nitro_content", - "tot_org_carb", - "turbidity", - "water_content" - ], - "slot_usage": { - "alkalinity": { - "name": "alkalinity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milliequivalent per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate", - "title": "alkalinity", - "examples": [ - { - "value": "50 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "alkalinity" - ], - "rank": 1, - "is_a": "core field", - "slot_uri": "MIXS:0000421", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "alkyl_diethers": { - "name": "alkyl_diethers", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of alkyl diethers", - "title": "alkyl diethers", - "examples": [ - { - "value": "0.005 mole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "alkyl diethers" - ], - "rank": 2, - "is_a": "core field", - "slot_uri": "MIXS:0000490", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "aminopept_act": { - "name": "aminopept_act", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mole per liter per hour" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of aminopeptidase activity", - "title": "aminopeptidase activity", - "examples": [ - { - "value": "0.269 mole per liter per hour" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "aminopeptidase activity" - ], - "rank": 3, - "is_a": "core field", - "slot_uri": "MIXS:0000172", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "ammonium": { - "name": "ammonium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of ammonium in the sample", - "title": "ammonium", - "examples": [ - { - "value": "1.5 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "ammonium" - ], - "rank": 4, - "is_a": "core field", - "slot_uri": "MIXS:0000427", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "bacteria_carb_prod": { - "name": "bacteria_carb_prod", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "nanogram per hour" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of bacterial carbon production", - "title": "bacterial carbon production", - "examples": [ - { - "value": "2.53 microgram per liter per hour" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "bacterial carbon production" - ], - "rank": 5, - "is_a": "core field", - "slot_uri": "MIXS:0000173", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "biomass": { - "name": "biomass", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "biomass type;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "ton, kilogram, gram" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements", - "title": "biomass", - "examples": [ - { - "value": "total;20 gram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "biomass" - ], - "rank": 6, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000174", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "bishomohopanol": { - "name": "bishomohopanol", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter, microgram per gram" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of bishomohopanol", - "title": "bishomohopanol", - "examples": [ - { - "value": "14 microgram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "bishomohopanol" - ], - "rank": 7, - "is_a": "core field", - "slot_uri": "MIXS:0000175", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "bromide": { - "name": "bromide", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of bromide", - "title": "bromide", - "examples": [ - { - "value": "0.05 parts per million" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "bromide" - ], - "rank": 8, - "is_a": "core field", - "slot_uri": "MIXS:0000176", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "calcium": { - "name": "calcium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, micromole per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of calcium in the sample", - "title": "calcium", - "examples": [ - { - "value": "0.2 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "calcium" - ], - "rank": 9, - "is_a": "core field", - "slot_uri": "MIXS:0000432", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "carb_nitro_ratio": { - "name": "carb_nitro_ratio", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Ratio of amount or concentrations of carbon to nitrogen", - "title": "carbon/nitrogen ratio", - "examples": [ - { - "value": "0.417361111" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "carbon/nitrogen ratio" - ], - "rank": 44, - "is_a": "core field", - "slot_uri": "MIXS:0000310", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "SoilInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "float", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "chem_administration": { - "name": "chem_administration", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "CHEBI;timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", - "title": "chemical administration", - "examples": [ - { - "value": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22" - }, - { - "value": "agar [CHEBI:2509];2018-05" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "chemical administration" - ], - "rank": 17, - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]};{timestamp}", - "slot_uri": "MIXS:0000751", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" - }, - "chloride": { - "name": "chloride", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of chloride in the sample", - "title": "chloride", - "examples": [ - { - "value": "5000 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "chloride" - ], - "rank": 10, - "is_a": "core field", - "slot_uri": "MIXS:0000429", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "chlorophyll": { - "name": "chlorophyll", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per cubic meter, microgram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of chlorophyll", - "title": "chlorophyll", - "examples": [ - { - "value": "5 milligram per cubic meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "chlorophyll" - ], - "rank": 11, - "is_a": "core field", - "slot_uri": "MIXS:0000177", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "collection_date": { - "name": "collection_date", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "date and time" - } - }, - "description": "The date of sampling", - "title": "collection date", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", - "Use modified term (amended definition)" - ], - "examples": [ - { - "value": "2021-04-15" - }, - { - "value": "2021-04" - }, - { - "value": "2021" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "collection date" - ], - "rank": 3, - "is_a": "environment field", - "string_serialization": "{date, arbitrary precision}", - "slot_uri": "MIXS:0000011", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" - }, - "density": { - "name": "density", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram per cubic meter, gram per cubic centimeter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Density of the sample, which is its mass per unit volume (aka volumetric mass density)", - "title": "density", - "examples": [ - { - "value": "1000 kilogram per cubic meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "density" - ], - "rank": 12, - "is_a": "core field", - "slot_uri": "MIXS:0000435", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "depth": { - "name": "depth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - } - }, - "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", - "title": "depth, meters", - "notes": [ - "Use modified term" - ], - "comments": [ - "All depths must be reported in meters. Provide the numerical portion only." - ], - "examples": [ - { - "value": "0 - 0.1" - }, - { - "value": "1" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "depth" - ], - "rank": 9, - "is_a": "environment field", - "string_serialization": "{float}-{float}", - "slot_uri": "MIXS:0000018", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?$" - }, - "diether_lipids": { - "name": "diether_lipids", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "diether lipid name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "nanogram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Concentration of diether lipids; can include multiple types of diether lipids", - "title": "diether lipids", - "examples": [ - { - "value": "0.2 nanogram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "diether lipids" - ], - "rank": 13, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000178", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "diss_carb_dioxide": { - "name": "diss_carb_dioxide", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample", - "title": "dissolved carbon dioxide", - "examples": [ - { - "value": "5 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved carbon dioxide" - ], - "rank": 14, - "is_a": "core field", - "slot_uri": "MIXS:0000436", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_hydrogen": { - "name": "diss_hydrogen", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved hydrogen", - "title": "dissolved hydrogen", - "examples": [ - { - "value": "0.3 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved hydrogen" - ], - "rank": 15, - "is_a": "core field", - "slot_uri": "MIXS:0000179", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_inorg_carb": { - "name": "diss_inorg_carb", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter", - "title": "dissolved inorganic carbon", - "examples": [ - { - "value": "2059 micromole per kilogram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved inorganic carbon" - ], - "rank": 16, - "is_a": "core field", - "slot_uri": "MIXS:0000434", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_org_carb": { - "name": "diss_org_carb", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid", - "title": "dissolved organic carbon", - "examples": [ - { - "value": "197 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved organic carbon" - ], - "rank": 17, - "is_a": "core field", - "slot_uri": "MIXS:0000433", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_org_nitro": { - "name": "diss_org_nitro", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2", - "title": "dissolved organic nitrogen", - "examples": [ - { - "value": "0.05 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved organic nitrogen" - ], - "rank": 18, - "is_a": "core field", - "slot_uri": "MIXS:0000162", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_oxygen": { - "name": "diss_oxygen", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per kilogram, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved oxygen", - "title": "dissolved oxygen", - "examples": [ - { - "value": "175 micromole per kilogram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved oxygen" - ], - "rank": 19, - "is_a": "core field", - "slot_uri": "MIXS:0000119", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "ecosystem": { - "name": "ecosystem", - "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", - "notes": [ - "range: string or EcosystemEnum? The enum could be dynamic or might be soil biased." - ], - "comments": [ - "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 9, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_category": { - "name": "ecosystem_category", - "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", - "notes": [ - "string or EcosystemCategoryEnum range?" - ], - "comments": [ - "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 10, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_subtype": { - "name": "ecosystem_subtype", - "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", - "notes": [ - "string or EcosystemSubtypeEnum range?" - ], - "comments": [ - "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 12, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_type": { - "name": "ecosystem_type", - "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", - "notes": [ - "string or EcosystemTypeEnum range?" - ], - "comments": [ - "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 11, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "elev": { - "name": "elev", - "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", - "title": "elevation, meters", - "comments": [ - "All elevations must be reported in meters. Provide the numerical portion only.", - "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." - ], - "examples": [ - { - "value": "225" - }, - { - "value": "0" - }, - { - "value": "1250" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "slot_uri": "MIXS:0000093", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "float", - "required": true - }, - "env_broad_scale": { - "name": "env_broad_scale", - "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", - "title": "broad-scale environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000012", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_local_scale": { - "name": "env_local_scale", - "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", - "title": "local environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "canopy [ENVO:00000047]" - }, - { - "value": "herb and fern layer [ENVO:01000337]" - }, - { - "value": "litter layer [ENVO:01000338]" - }, - { - "value": "understory [01000335]" - }, - { - "value": "shrub layer [ENVO:01000336]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 7, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000013", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_medium": { - "name": "env_medium", - "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", - "title": "environmental medium", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "soil [ENVO:00001998]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 8, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000014", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_package": { - "name": "env_package", - "description": "Select the MIxS enviromental package that best describes the environment from which your sample was collected.", - "title": "environmental package", - "examples": [ - { - "value": "soil" - } - ], - "in_subset": [ - "mixs extension" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "environmental package" - ], - "rank": 4, - "is_a": "attribute", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true - }, - "experimental_factor": { - "name": "experimental_factor", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text or EFO and/or OBI" - } - }, - "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", - "title": "experimental factor", - "examples": [ - { - "value": "time series design [EFO:EFO_0001779]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "experimental factor" - ], - "rank": 12, - "is_a": "investigation field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000008", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "geo_loc_name": { - "name": "geo_loc_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" - } - }, - "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", - "title": "geographic location (country and/or sea,region)", - "examples": [ - { - "value": "USA: Maryland, Bethesda" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "geographic location (country and/or sea,region)" - ], - "rank": 4, - "is_a": "environment field", - "string_serialization": "{text}: {text}, {text}", - "slot_uri": "MIXS:0000010", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" - }, - "glucosidase_act": { - "name": "glucosidase_act", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mol per liter per hour" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of glucosidase activity", - "title": "glucosidase activity", - "examples": [ - { - "value": "5 mol per liter per hour" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "glucosidase activity" - ], - "rank": 20, - "is_a": "core field", - "slot_uri": "MIXS:0000137", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "horizon_meth": { - "name": "horizon_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining the horizon", - "title": "horizon method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "soil horizon method" - ], - "rank": 19, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000321", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "lat_lon": { - "name": "lat_lon", - "description": "This is currently a required field but it's not clear if this should be required for human hosts", - "title": "geographic location (latitude and longitude)", - "notes": [ - "required where?", - "This is currently a required field but it's not clear if this should be required for human hosts" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "is_a": "environment field", - "string_serialization": "{lat lon}", - "slot_uri": "MIXS:0000009", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" - }, - "magnesium": { - "name": "magnesium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mole per liter, milligram per liter, parts per million, micromole per kilogram" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of magnesium in the sample", - "title": "magnesium", - "examples": [ - { - "value": "52.8 micromole per kilogram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "magnesium" - ], - "rank": 21, - "is_a": "core field", - "slot_uri": "MIXS:0000431", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "SedimentInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "mean_frict_vel": { - "name": "mean_frict_vel", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter per second" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of mean friction velocity", - "title": "mean friction velocity", - "examples": [ - { - "value": "0.5 meter per second" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "mean friction velocity" - ], - "rank": 22, - "is_a": "core field", - "slot_uri": "MIXS:0000498", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "mean_peak_frict_vel": { - "name": "mean_peak_frict_vel", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter per second" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of mean peak friction velocity", - "title": "mean peak friction velocity", - "examples": [ - { - "value": "1 meter per second" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "mean peak friction velocity" - ], - "rank": 23, - "is_a": "core field", - "slot_uri": "MIXS:0000502", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "methane": { - "name": "methane", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, parts per billion, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Methane (gas) amount or concentration at the time of sampling", - "title": "methane", - "examples": [ - { - "value": "1800 parts per billion" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "methane" - ], - "rank": 24, - "is_a": "core field", - "slot_uri": "MIXS:0000101", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "SedimentInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "misc_param": { - "name": "misc_param", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "parameter name;measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Any other measurement performed or parameter collected, that is not listed here", - "title": "miscellaneous parameter", - "examples": [ - { - "value": "Bicarbonate ion concentration;2075 micromole per kilogram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "miscellaneous parameter" - ], - "rank": 23, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000752", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "n_alkanes": { - "name": "n_alkanes", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "n-alkane name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Concentration of n-alkanes; can include multiple n-alkanes", - "title": "n-alkanes", - "examples": [ - { - "value": "n-hexadecane;100 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "n-alkanes" - ], - "rank": 25, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000503", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "nitrate": { - "name": "nitrate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of nitrate in the sample", - "title": "nitrate", - "examples": [ - { - "value": "65 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "nitrate" - ], - "rank": 26, - "is_a": "core field", - "slot_uri": "MIXS:0000425", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "nitrite": { - "name": "nitrite", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of nitrite in the sample", - "title": "nitrite", - "examples": [ - { - "value": "0.5 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "nitrite" - ], - "rank": 27, - "is_a": "core field", - "slot_uri": "MIXS:0000426", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "nitro": { - "name": "nitro", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of nitrogen (total)", - "title": "nitrogen", - "examples": [ - { - "value": "4.2 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "nitrogen" - ], - "rank": 28, - "is_a": "core field", - "slot_uri": "MIXS:0000504", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "org_carb": { - "name": "org_carb", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of organic carbon", - "title": "organic carbon", - "examples": [ - { - "value": "1.5 microgram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "organic carbon" - ], - "rank": 29, - "is_a": "core field", - "slot_uri": "MIXS:0000508", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "org_matter": { - "name": "org_matter", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of organic matter", - "title": "organic matter", - "examples": [ - { - "value": "1.75 milligram per cubic meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "organic matter" - ], - "rank": 45, - "is_a": "core field", - "slot_uri": "MIXS:0000204", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "org_nitro": { - "name": "org_nitro", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of organic nitrogen", - "title": "organic nitrogen", - "examples": [ - { - "value": "4 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "organic nitrogen" - ], - "rank": 46, - "is_a": "core field", - "slot_uri": "MIXS:0000205", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "organism_count": { - "name": "organism_count", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "organism name;measurement value;enumeration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", - "title": "organism count", - "examples": [ - { - "value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "organism count" - ], - "rank": 30, - "is_a": "core field", - "slot_uri": "MIXS:0000103", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$" - }, - "oxy_stat_samp": { - "name": "oxy_stat_samp", - "description": "Oxygenation status of sample", - "title": "oxygenation status of sample", - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 25, - "is_a": "core field", - "slot_uri": "MIXS:0000753", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "OxyStatSampEnum" - }, - "part_org_carb": { - "name": "part_org_carb", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of particulate organic carbon", - "title": "particulate organic carbon", - "examples": [ - { - "value": "1.92 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "particulate organic carbon" - ], - "rank": 31, - "is_a": "core field", - "slot_uri": "MIXS:0000515", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "particle_class": { - "name": "particle_class", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "particle name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micrometer" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Particles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values", - "title": "particle classification", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "particle classification" - ], - "rank": 32, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000206", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SedimentInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? 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While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", - "title": "salinity", - "examples": [ - { - "value": "25 practical salinity unit" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "salinity" - ], - "rank": 54, - "is_a": "core field", - "slot_uri": "MIXS:0000183", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "samp_collec_device": { - "name": "samp_collec_device", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "device name" - } - }, - "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", - "title": "sample collection device", - "comments": [ - "Report dimensions and details when applicable" - ], - "examples": [ - { - "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection device" - ], - "rank": 14, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000002", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "samp_collec_method": { - "name": "samp_collec_method", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI,url , or text" - } - }, - "description": "The method employed for collecting the sample.", - "title": "sample collection method", - "comments": [ - "This can be a citation or description" - ], - "examples": [ - { - "value": "swabbing" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection method" - ], - "rank": 15, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{PMID}|{DOI}|{URL}|{text}", - "slot_uri": "MIXS:0001225", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_mat_process": { - "name": "samp_mat_process", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - } - }, - "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", - "title": "sample material processing", - "examples": [ - { - "value": "filtering of seawater" - }, - { - "value": "storing samples in ethanol" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample material processing" - ], - "rank": 12, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000016", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_size": { - "name": "samp_size", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millliter, gram, milligram, liter" - } - }, - "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", - "title": "amount or size of sample collected", - "comments": [ - "This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis." - ], - "examples": [ - { - "value": "5 grams" - }, - { - "value": "10 mL" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "amount or size of sample collected" - ], - "rank": 18, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float} {unit}", - "slot_uri": "MIXS:0000001", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" - }, - "samp_store_dur": { - "name": "samp_store_dur", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Duration for which the sample was stored", - "title": "sample storage duration", - "examples": [ - { - "value": "P1Y6M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage duration" - ], - "rank": 353, - "is_a": "core field", - "string_serialization": "{duration}", - "slot_uri": "MIXS:0000116", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_store_loc": { - "name": "samp_store_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "location name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Location at which sample was stored, usually name of a specific freezer/room", - "title": "sample storage location", - "examples": [ - { - "value": "Freezer no:5" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage location" - ], - "rank": 41, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000755", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_store_temp": { - "name": "samp_store_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Temperature at which the sample was stored (degrees are assumed)", - "title": "sample storage temperature", - "examples": [ - { - "value": "-80 Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage temperature" - ], - "rank": 7, - "is_a": "core field", - "slot_uri": "MIXS:0000110", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "sample_link": { - "name": "sample_link", - "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", - "title": "sample linkage", - "notes": [ - "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" - ], - "comments": [ - "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" - ], - "examples": [ - { - "value": "IGSN:DSJ0284" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "string_serialization": "{text}:{text}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface", - "SampIdNewTermsMixin" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true, - "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" - }, - "sediment_type": { - "name": "sediment_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Information about the sediment type based on major constituents", - "title": "sediment type", - "examples": [ - { - "value": "biogenous" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sediment type" - ], - "rank": 42, - "is_a": "core field", - "slot_uri": "MIXS:0001078", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SedimentInterface" - ], - "slot_group": "mixs_core_section", - "range": "sediment_type_enum" - }, - "silicate": { - "name": "silicate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of silicate", - "title": "silicate", - "examples": [ - { - "value": "0.05 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "silicate" - ], - "rank": 43, - "is_a": "core field", - "slot_uri": "MIXS:0000184", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "size_frac": { - "name": "size_frac", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "filter size value range" - } - }, - "description": "Filtering pore size used in sample preparation", - "title": "size fraction selected", - "examples": [ - { - "value": "0-0.22 micrometer" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "size fraction selected" - ], - "rank": 285, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float}-{float} {unit}", - "slot_uri": "MIXS:0000017", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "sodium": { - "name": "sodium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Sodium concentration in the sample", - "title": "sodium", - "examples": [ - { - "value": "10.5 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sodium" - ], - "rank": 363, - "is_a": "core field", - "slot_uri": "MIXS:0000428", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "specific_ecosystem": { - "name": "specific_ecosystem", - "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", - "notes": [ - "string or SpecificEcosystemEnum range?" - ], - "comments": [ - "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 13, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "sulfate": { - "name": "sulfate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of sulfate in the sample", - "title": "sulfate", - "examples": [ - { - "value": "5 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sulfate" - ], - "rank": 44, - "is_a": "core field", - "slot_uri": "MIXS:0000423", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "sulfide": { - "name": "sulfide", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of sulfide in the sample", - "title": "sulfide", - "examples": [ - { - "value": "2 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sulfide" - ], - "rank": 371, - "is_a": "core field", - "slot_uri": "MIXS:0000424", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "temp": { - "name": "temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - } - }, - "description": "Temperature of the sample at the time of sampling.", - "title": "temperature", - "examples": [ - { - "value": "25 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "temperature" - ], - "rank": 37, - "is_a": "environment field", - "slot_uri": "MIXS:0000113", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tidal_stage": { - "name": "tidal_stage", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Stage of tide", - "title": "tidal stage", - "examples": [ - { - "value": "high tide" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "tidal stage" - ], - "rank": 45, - "is_a": "core field", - "slot_uri": "MIXS:0000750", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "tidal_stage_enum" - }, - "tot_carb": { - "name": "tot_carb", - "description": "Total carbon content", - "title": "total carbon", - "todos": [ - "is this inorganic and organic? both? could use some clarification.", - "ug/L doesn't seem like the right units. Should check this slots usage in databases and re-evaluate. I couldn't find any references that provided this data in this format", - "is this inorganic and organic? both? could use some clarification.", - "ug/L doesn't seem like the right units. Should check this slots usage in databases and re-evaluate. I couldn't find any references that provided this data in this format" - ], - "examples": [ - { - "value": "1 ug/L" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 47, - "is_a": "core field", - "slot_uri": "MIXS:0000525", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tot_depth_water_col": { - "name": "tot_depth_water_col", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of total depth of water column", - "title": "total depth of water column", - "examples": [ - { - "value": "500 meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "total depth of water column" - ], - "rank": 46, - "is_a": "core field", - "slot_uri": "MIXS:0000634", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tot_nitro_content": { - "name": "tot_nitro_content", - "description": "Total nitrogen content of the sample", - "title": "total nitrogen content", - "examples": [ - { - "value": "5 mg N/ L" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 48, - "is_a": "core field", - "slot_uri": "MIXS:0000530", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tot_org_carb": { - "name": "tot_org_carb", - "description": "Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content", - "title": "total organic carbon", - "todos": [ - "check description. How are they different?", - "check description. How are they different?" - ], - "examples": [ - { - "value": "5 mg N/ L" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 50, - "is_a": "core field", - "slot_uri": "MIXS:0000533", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "turbidity": { - "name": "turbidity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "formazin turbidity unit, formazin nephelometric units" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measure of the amount of cloudiness or haziness in water caused by individual particles", - "title": "turbidity", - "examples": [ - { - "value": "0.3 nephelometric turbidity units" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "turbidity" - ], - "rank": 47, - "is_a": "core field", - "slot_uri": "MIXS:0000191", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "water_content": { - "name": "water_content", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "string" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram per gram or cubic centimeter per cubic centimeter" - } - }, - "description": "Water content measurement", - "title": "water content", - "todos": [ - "value in preferred unit is too limiting. need to change this", - "check and correct validation so examples are accepted", - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "how to manage multiple water content methods?", - "value in preferred unit is too limiting. need to change this", - "check and correct validation so examples are accepted", - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "how to manage multiple water content methods?" - ], - "examples": [ - { - "value": "75%" - }, - { - "value": "75 %" - }, - { - "value": "0.75 g water/g dry soil" - }, - { - "value": "75% water holding capacity" - }, - { - "value": "1.1 g fresh weight/ dry weight" - }, - { - "value": "10% water filled pore space" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 39, - "is_a": "core field", - "string_serialization": "{float or pct} {unit}", - "slot_uri": "MIXS:0000185", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?%? \\S.+$" - } - }, - "attributes": { - "alkalinity": { - "name": "alkalinity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milliequivalent per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate", - "title": "alkalinity", - "examples": [ - { - "value": "50 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "alkalinity" - ], - "rank": 1, - "is_a": "core field", - "slot_uri": "MIXS:0000421", - "multivalued": false, - "alias": "alkalinity", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "alkyl_diethers": { - "name": "alkyl_diethers", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of alkyl diethers", - "title": "alkyl diethers", - "examples": [ - { - "value": "0.005 mole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "alkyl diethers" - ], - "rank": 2, - "is_a": "core field", - "slot_uri": "MIXS:0000490", - "multivalued": false, - "alias": "alkyl_diethers", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "aminopept_act": { - "name": "aminopept_act", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mole per liter per hour" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of aminopeptidase activity", - "title": "aminopeptidase activity", - "examples": [ - { - "value": "0.269 mole per liter per hour" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "aminopeptidase activity" - ], - "rank": 3, - "is_a": "core field", - "slot_uri": "MIXS:0000172", - "multivalued": false, - "alias": "aminopept_act", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "ammonium": { - "name": "ammonium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of ammonium in the sample", - "title": "ammonium", - "examples": [ - { - "value": "1.5 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "ammonium" - ], - "rank": 4, - "is_a": "core field", - "slot_uri": "MIXS:0000427", - "multivalued": false, - "alias": "ammonium", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "bacteria_carb_prod": { - "name": "bacteria_carb_prod", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "nanogram per hour" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of bacterial carbon production", - "title": "bacterial carbon production", - "examples": [ - { - "value": "2.53 microgram per liter per hour" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "bacterial carbon production" - ], - "rank": 5, - "is_a": "core field", - "slot_uri": "MIXS:0000173", - "multivalued": false, - "alias": "bacteria_carb_prod", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "biomass": { - "name": "biomass", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "biomass type;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "ton, kilogram, gram" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements", - "title": "biomass", - "examples": [ - { - "value": "total;20 gram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "biomass" - ], - "rank": 6, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000174", - "multivalued": false, - "alias": "biomass", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "bishomohopanol": { - "name": "bishomohopanol", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter, microgram per gram" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of bishomohopanol", - "title": "bishomohopanol", - "examples": [ - { - "value": "14 microgram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "bishomohopanol" - ], - "rank": 7, - "is_a": "core field", - "slot_uri": "MIXS:0000175", - "multivalued": false, - "alias": "bishomohopanol", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "bromide": { - "name": "bromide", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of bromide", - "title": "bromide", - "examples": [ - { - "value": "0.05 parts per million" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "bromide" - ], - "rank": 8, - "is_a": "core field", - "slot_uri": "MIXS:0000176", - "multivalued": false, - "alias": "bromide", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "calcium": { - "name": "calcium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, micromole per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of calcium in the sample", - "title": "calcium", - "examples": [ - { - "value": "0.2 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "calcium" - ], - "rank": 9, - "is_a": "core field", - "slot_uri": "MIXS:0000432", - "multivalued": false, - "alias": "calcium", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "carb_nitro_ratio": { - "name": "carb_nitro_ratio", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Ratio of amount or concentrations of carbon to nitrogen", - "title": "carbon/nitrogen ratio", - "examples": [ - { - "value": "0.417361111" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "carbon/nitrogen ratio" - ], - "rank": 44, - "is_a": "core field", - "slot_uri": "MIXS:0000310", - "multivalued": false, - "alias": "carb_nitro_ratio", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "SoilInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "float", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "chem_administration": { - "name": "chem_administration", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "CHEBI;timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. 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DH taking arb prec date only", - "Use modified term (amended definition)" - ], - "examples": [ - { - "value": "2021-04-15" - }, - { - "value": "2021-04" - }, - { - "value": "2021" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "collection date" - ], - "rank": 3, - "is_a": "environment field", - "string_serialization": "{date, arbitrary precision}", - "slot_uri": "MIXS:0000011", - "multivalued": false, - "alias": "collection_date", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" - }, - "density": { - "name": "density", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram per cubic meter, gram per cubic centimeter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Density of the sample, which is its mass per unit volume (aka volumetric mass density)", - "title": "density", - "examples": [ - { - "value": "1000 kilogram per cubic meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "density" - ], - "rank": 12, - "is_a": "core field", - "slot_uri": "MIXS:0000435", - "multivalued": false, - "alias": "density", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "depth": { - "name": "depth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - } - }, - "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. 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Provide the numerical portion only." - ], - "examples": [ - { - "value": "0 - 0.1" - }, - { - "value": "1" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "depth" - ], - "rank": 9, - "is_a": "environment field", - "string_serialization": "{float}-{float}", - "slot_uri": "MIXS:0000018", - "multivalued": false, - "alias": "depth", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?$" - }, - "diether_lipids": { - "name": "diether_lipids", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "diether lipid name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "nanogram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Concentration of diether lipids; can include multiple types of diether lipids", - "title": "diether lipids", - "examples": [ - { - "value": "0.2 nanogram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "diether lipids" - ], - "rank": 13, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000178", - "multivalued": false, - "alias": "diether_lipids", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "diss_carb_dioxide": { - "name": "diss_carb_dioxide", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample", - "title": "dissolved carbon dioxide", - "examples": [ - { - "value": "5 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved carbon dioxide" - ], - "rank": 14, - "is_a": "core field", - "slot_uri": "MIXS:0000436", - "multivalued": false, - "alias": "diss_carb_dioxide", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_hydrogen": { - "name": "diss_hydrogen", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved hydrogen", - "title": "dissolved hydrogen", - "examples": [ - { - "value": "0.3 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved hydrogen" - ], - "rank": 15, - "is_a": "core field", - "slot_uri": "MIXS:0000179", - "multivalued": false, - "alias": "diss_hydrogen", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_inorg_carb": { - "name": "diss_inorg_carb", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter", - "title": "dissolved inorganic carbon", - "examples": [ - { - "value": "2059 micromole per kilogram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved inorganic carbon" - ], - "rank": 16, - "is_a": "core field", - "slot_uri": "MIXS:0000434", - "multivalued": false, - "alias": "diss_inorg_carb", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_org_carb": { - "name": "diss_org_carb", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid", - "title": "dissolved organic carbon", - "examples": [ - { - "value": "197 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved organic carbon" - ], - "rank": 17, - "is_a": "core field", - "slot_uri": "MIXS:0000433", - "multivalued": false, - "alias": "diss_org_carb", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_org_nitro": { - "name": "diss_org_nitro", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2", - "title": "dissolved organic nitrogen", - "examples": [ - { - "value": "0.05 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved organic nitrogen" - ], - "rank": 18, - "is_a": "core field", - "slot_uri": "MIXS:0000162", - "multivalued": false, - "alias": "diss_org_nitro", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_oxygen": { - "name": "diss_oxygen", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per kilogram, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved oxygen", - "title": "dissolved oxygen", - "examples": [ - { - "value": "175 micromole per kilogram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved oxygen" - ], - "rank": 19, - "is_a": "core field", - "slot_uri": "MIXS:0000119", - "multivalued": false, - "alias": "diss_oxygen", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "ecosystem": { - "name": "ecosystem", - "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", - "notes": [ - "range: string or EcosystemEnum? The enum could be dynamic or might be soil biased." - ], - "comments": [ - "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 9, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_category": { - "name": "ecosystem_category", - "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", - "notes": [ - "string or EcosystemCategoryEnum range?" - ], - "comments": [ - "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 10, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem_category", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_subtype": { - "name": "ecosystem_subtype", - "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", - "notes": [ - "string or EcosystemSubtypeEnum range?" - ], - "comments": [ - "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 12, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem_subtype", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_type": { - "name": "ecosystem_type", - "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", - "notes": [ - "string or EcosystemTypeEnum range?" - ], - "comments": [ - "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 11, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem_type", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "elev": { - "name": "elev", - "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", - "title": "elevation, meters", - "comments": [ - "All elevations must be reported in meters. Provide the numerical portion only.", - "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." - ], - "examples": [ - { - "value": "225" - }, - { - "value": "0" - }, - { - "value": "1250" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "slot_uri": "MIXS:0000093", - "multivalued": false, - "alias": "elev", - "owner": "SedimentInterface", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "float", - "required": true - }, - "env_broad_scale": { - "name": "env_broad_scale", - "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", - "title": "broad-scale environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000012", - "multivalued": false, - "alias": "env_broad_scale", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_local_scale": { - "name": "env_local_scale", - "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", - "title": "local environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "canopy [ENVO:00000047]" - }, - { - "value": "herb and fern layer [ENVO:01000337]" - }, - { - "value": "litter layer [ENVO:01000338]" - }, - { - "value": "understory [01000335]" - }, - { - "value": "shrub layer [ENVO:01000336]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 7, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000013", - "multivalued": false, - "alias": "env_local_scale", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_medium": { - "name": "env_medium", - "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", - "title": "environmental medium", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "soil [ENVO:00001998]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 8, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000014", - "multivalued": false, - "alias": "env_medium", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_package": { - "name": "env_package", - "description": "Select the MIxS enviromental package that best describes the environment from which your sample was collected.", - "title": "environmental package", - "examples": [ - { - "value": "soil" - } - ], - "in_subset": [ - "mixs extension" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "environmental package" - ], - "rank": 4, - "is_a": "attribute", - "multivalued": false, - "alias": "env_package", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true - }, - "experimental_factor": { - "name": "experimental_factor", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text or EFO and/or OBI" - } - }, - "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", - "title": "experimental factor", - "examples": [ - { - "value": "time series design [EFO:EFO_0001779]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "experimental factor" - ], - "rank": 12, - "is_a": "investigation field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000008", - "multivalued": false, - "alias": "experimental_factor", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "geo_loc_name": { - "name": "geo_loc_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" - } - }, - "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", - "title": "geographic location (country and/or sea,region)", - "examples": [ - { - "value": "USA: Maryland, Bethesda" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "geographic location (country and/or sea,region)" - ], - "rank": 4, - "is_a": "environment field", - "string_serialization": "{text}: {text}, {text}", - "slot_uri": "MIXS:0000010", - "multivalued": false, - "alias": "geo_loc_name", - "owner": "SedimentInterface", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" - }, - "glucosidase_act": { - "name": "glucosidase_act", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mol per liter per hour" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of glucosidase activity", - "title": "glucosidase activity", - "examples": [ - { - "value": "5 mol per liter per hour" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "glucosidase activity" - ], - "rank": 20, - "is_a": "core field", - "slot_uri": "MIXS:0000137", - "multivalued": false, - "alias": "glucosidase_act", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - 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This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", - "title": "sample collection device", - "comments": [ - "Report dimensions and details when applicable" - ], - "examples": [ - { - "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection device" - ], - "rank": 14, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000002", - "multivalued": false, - "alias": "samp_collec_device", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "samp_collec_method": { - "name": "samp_collec_method", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI,url , or text" - } - }, - "description": "The method employed for collecting the sample.", - "title": "sample collection method", - "comments": [ - "This can be a citation or description" - ], - "examples": [ - { - "value": "swabbing" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection method" - ], - "rank": 15, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{PMID}|{DOI}|{URL}|{text}", - "slot_uri": "MIXS:0001225", - "multivalued": false, - "alias": "samp_collec_method", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_mat_process": { - "name": "samp_mat_process", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - } - }, - "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", - "title": "sample material processing", - "examples": [ - { - "value": "filtering of seawater" - }, - { - "value": "storing samples in ethanol" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample material processing" - ], - "rank": 12, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000016", - "multivalued": false, - "alias": "samp_mat_process", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_size": { - "name": "samp_size", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millliter, gram, milligram, liter" - } - }, - "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", - "title": "amount or size of sample collected", - "comments": [ - "This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis." - ], - "examples": [ - { - "value": "5 grams" - }, - { - "value": "10 mL" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "amount or size of sample collected" - ], - "rank": 18, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float} {unit}", - "slot_uri": "MIXS:0000001", - "multivalued": false, - "alias": "samp_size", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" - }, - "samp_store_dur": { - "name": "samp_store_dur", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Duration for which the sample was stored", - "title": "sample storage duration", - "examples": [ - { - "value": "P1Y6M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage duration" - ], - "rank": 353, - "is_a": "core field", - "string_serialization": "{duration}", - "slot_uri": "MIXS:0000116", - "multivalued": false, - "alias": "samp_store_dur", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_store_loc": { - "name": "samp_store_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "location name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Location at which sample was stored, usually name of a specific freezer/room", - "title": "sample storage location", - "examples": [ - { - "value": "Freezer no:5" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage location" - ], - "rank": 41, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000755", - "multivalued": false, - "alias": "samp_store_loc", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_store_temp": { - "name": "samp_store_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Temperature at which the sample was stored (degrees are assumed)", - "title": "sample storage temperature", - "examples": [ - { - "value": "-80 Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage temperature" - ], - "rank": 7, - "is_a": "core field", - "slot_uri": "MIXS:0000110", - "multivalued": false, - "alias": "samp_store_temp", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "sample_link": { - "name": "sample_link", - "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", - "title": "sample linkage", - "notes": [ - "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" - ], - "comments": [ - "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" - ], - "examples": [ - { - "value": "IGSN:DSJ0284" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "string_serialization": "{text}:{text}", - "multivalued": false, - "alias": "sample_link", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface", - "SampIdNewTermsMixin" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true, - "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" - }, - "sediment_type": { - "name": "sediment_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Information about the sediment type based on major constituents", - "title": "sediment type", - "examples": [ - { - "value": "biogenous" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sediment type" - ], - "rank": 42, - "is_a": "core field", - "slot_uri": "MIXS:0001078", - "multivalued": false, - "alias": "sediment_type", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "SedimentInterface" - ], - "slot_group": "mixs_core_section", - "range": "sediment_type_enum" - }, - "silicate": { - "name": "silicate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of silicate", - "title": "silicate", - "examples": [ - { - "value": "0.05 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "silicate" - ], - "rank": 43, - "is_a": "core field", - "slot_uri": "MIXS:0000184", - "multivalued": false, - "alias": "silicate", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "size_frac": { - "name": "size_frac", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "filter size value range" - } - }, - "description": "Filtering pore size used in sample preparation", - "title": "size fraction selected", - "examples": [ - { - "value": "0-0.22 micrometer" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "size fraction selected" - ], - "rank": 285, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float}-{float} {unit}", - "slot_uri": "MIXS:0000017", - "multivalued": false, - "alias": "size_frac", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "sodium": { - "name": "sodium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Sodium concentration in the sample", - "title": "sodium", - "examples": [ - { - "value": "10.5 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sodium" - ], - "rank": 363, - "is_a": "core field", - "slot_uri": "MIXS:0000428", - "multivalued": false, - "alias": "sodium", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "specific_ecosystem": { - "name": "specific_ecosystem", - "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", - "notes": [ - "string or SpecificEcosystemEnum range?" - ], - "comments": [ - "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 13, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "specific_ecosystem", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "sulfate": { - "name": "sulfate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of sulfate in the sample", - "title": "sulfate", - "examples": [ - { - "value": "5 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sulfate" - ], - "rank": 44, - "is_a": "core field", - "slot_uri": "MIXS:0000423", - "multivalued": false, - "alias": "sulfate", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "sulfide": { - "name": "sulfide", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of sulfide in the sample", - "title": "sulfide", - "examples": [ - { - "value": "2 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sulfide" - ], - "rank": 371, - "is_a": "core field", - "slot_uri": "MIXS:0000424", - "multivalued": false, - "alias": "sulfide", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "temp": { - "name": "temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - } - }, - "description": "Temperature of the sample at the time of sampling.", - "title": "temperature", - "examples": [ - { - "value": "25 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "temperature" - ], - "rank": 37, - "is_a": "environment field", - "slot_uri": "MIXS:0000113", - "multivalued": false, - "alias": "temp", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tidal_stage": { - "name": "tidal_stage", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Stage of tide", - "title": "tidal stage", - "examples": [ - { - "value": "high tide" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "tidal stage" - ], - "rank": 45, - "is_a": "core field", - "slot_uri": "MIXS:0000750", - "multivalued": false, - "alias": "tidal_stage", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "tidal_stage_enum" - }, - "tot_carb": { - "name": "tot_carb", - "description": "Total carbon content", - "title": "total carbon", - "todos": [ - "is this inorganic and organic? both? could use some clarification.", - "ug/L doesn't seem like the right units. Should check this slots usage in databases and re-evaluate. I couldn't find any references that provided this data in this format", - "is this inorganic and organic? both? could use some clarification.", - "ug/L doesn't seem like the right units. Should check this slots usage in databases and re-evaluate. I couldn't find any references that provided this data in this format" - ], - "examples": [ - { - "value": "1 ug/L" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 47, - "is_a": "core field", - "slot_uri": "MIXS:0000525", - "multivalued": false, - "alias": "tot_carb", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tot_depth_water_col": { - "name": "tot_depth_water_col", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of total depth of water column", - "title": "total depth of water column", - "examples": [ - { - "value": "500 meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "total depth of water column" - ], - "rank": 46, - "is_a": "core field", - "slot_uri": "MIXS:0000634", - "multivalued": false, - "alias": "tot_depth_water_col", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tot_nitro_content": { - "name": "tot_nitro_content", - "description": "Total nitrogen content of the sample", - "title": "total nitrogen content", - "examples": [ - { - "value": "5 mg N/ L" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 48, - "is_a": "core field", - "slot_uri": "MIXS:0000530", - "multivalued": false, - "alias": "tot_nitro_content", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tot_org_carb": { - "name": "tot_org_carb", - "description": "Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content", - "title": "total organic carbon", - "todos": [ - "check description. How are they different?", - "check description. How are they different?" - ], - "examples": [ - { - "value": "5 mg N/ L" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 50, - "is_a": "core field", - "slot_uri": "MIXS:0000533", - "multivalued": false, - "alias": "tot_org_carb", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "turbidity": { - "name": "turbidity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "formazin turbidity unit, formazin nephelometric units" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measure of the amount of cloudiness or haziness in water caused by individual particles", - "title": "turbidity", - "examples": [ - { - "value": "0.3 nephelometric turbidity units" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "turbidity" - ], - "rank": 47, - "is_a": "core field", - "slot_uri": "MIXS:0000191", - "multivalued": false, - "alias": "turbidity", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "water_content": { - "name": "water_content", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "string" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram per gram or cubic centimeter per cubic centimeter" - } - }, - "description": "Water content measurement", - "title": "water content", - "todos": [ - "value in preferred unit is too limiting. need to change this", - "check and correct validation so examples are accepted", - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "how to manage multiple water content methods?", - "value in preferred unit is too limiting. need to change this", - "check and correct validation so examples are accepted", - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "how to manage multiple water content methods?" - ], - "examples": [ - { - "value": "75%" - }, - { - "value": "75 %" - }, - { - "value": "0.75 g water/g dry soil" - }, - { - "value": "75% water holding capacity" - }, - { - "value": "1.1 g fresh weight/ dry weight" - }, - { - "value": "10% water filled pore space" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 39, - "is_a": "core field", - "string_serialization": "{float or pct} {unit}", - "slot_uri": "MIXS:0000185", - "multivalued": false, - "alias": "water_content", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?%? \\S.+$" - }, - "analysis_type": { - "name": "analysis_type", - "description": "Select all the data types associated or available for this biosample", - "title": "analysis/data type", - "examples": [ - { - "value": "metagenomics; metabolomics; proteomics" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:investigation_type" - ], - "rank": 3, - "multivalued": true, - "alias": "analysis_type", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "EmslInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "JgiMgInterface", - "JgiMtInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface" - ], - "slot_group": "sample_id_section", - "range": "analysis_type_enum", - "required": true, - "recommended": true - }, - "samp_name": { - "name": "samp_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - } - }, - "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", - "title": "sample name", - "comments": [ - "It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." - ], - "examples": [ - { - "value": "Rock core CB1178(5-6) from NSW" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample name" - ], - "rank": 1, - "is_a": "investigation field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0001107", - "multivalued": false, - "identifier": true, - "alias": "samp_name", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "EmslInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "JgiMgInterface", - "JgiMtInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true - }, - "source_mat_id": { - "name": "source_mat_id", - "description": "A globally unique identifier assigned to the biological sample.", - "title": "source material identifier", - "todos": [ - "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID.", - "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID." - ], - "notes": [ - "The source material IS the Globally Unique ID" - ], - "comments": [ - "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).", - "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/)." - ], - "examples": [ - { - "value": "IGSN:AU1243" - }, - { - "value": "UUID:24f1467a-40f4-11ed-b878-0242ac120002" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 2, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{text}:{text}", - "slot_uri": "MIXS:0000026", - "multivalued": false, - "alias": "source_mat_id", - "owner": "SedimentInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "EmslInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "JgiMgInterface", - "JgiMtInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" - } - } - }, - "SoilInterface": { - "name": "SoilInterface", - "description": "soil dh_interface", - "title": "Soil", - "from_schema": "https://example.com/nmdc_submission_schema", - "is_a": "DhInterface", - "mixins": [ - "DhMultiviewCommonColumnsMixin", - "SampIdNewTermsMixin", - "SoilMixsInspiredMixin" - ], - "slots": [ - "agrochem_addition", - "air_temp_regm", - "al_sat", - "al_sat_meth", - "ammonium_nitrogen", - "annual_precpt", - "annual_temp", - "biotic_regm", - "biotic_relationship", - "carb_nitro_ratio", - "chem_administration", - "climate_environment", - "collection_date", - "collection_date_inc", - "collection_time", - "collection_time_inc", - "crop_rotation", - "cur_land_use", - "cur_vegetation", - "cur_vegetation_meth", - "depth", - "drainage_class", - "ecosystem", - "ecosystem_category", - "ecosystem_subtype", - "ecosystem_type", - "elev", - "env_broad_scale", - "env_local_scale", - "env_medium", - "env_package", - "experimental_factor", - "experimental_factor_other", - "extreme_event", - "fao_class", - "filter_method", - "fire", - "flooding", - "gaseous_environment", - "geo_loc_name", - "growth_facil", - "heavy_metals", - "heavy_metals_meth", - "horizon_meth", - "humidity_regm", - "isotope_exposure", - "lat_lon", - "lbc_thirty", - "lbceq", - "light_regm", - "link_class_info", - "link_climate_info", - "local_class", - "local_class_meth", - "manganese", - "micro_biomass_c_meth", - "micro_biomass_c_meth", - "micro_biomass_meth", - "micro_biomass_n_meth", - "micro_biomass_n_meth", - "microbial_biomass", - "microbial_biomass_c", - "microbial_biomass_c", - "microbial_biomass_n", - "microbial_biomass_n", - "misc_param", - "nitrate_nitrogen", - "nitrite_nitrogen", - "non_microb_biomass", - "non_microb_biomass_method", - "org_matter", - "org_nitro", - "org_nitro_method", - "other_treatment", - "oxy_stat_samp", - "ph", - "ph_meth", - "phosphate", - "prev_land_use_meth", - "previous_land_use", - "profile_position", - "salinity", - "salinity_meth", - "samp_collec_device", - "samp_collec_method", - "samp_mat_process", - "samp_size", - "samp_store_temp", - "sample_link", - "season_precpt", - "season_temp", - "sieving", - "size_frac_low", - "size_frac_up", - "slope_aspect", - "slope_gradient", - "soil_horizon", - "soil_text_measure", - "soil_texture_meth", - "soil_type", - "soil_type_meth", - "specific_ecosystem", - "start_date_inc", - "start_time_inc", - "store_cond", - "temp", - "tillage", - "tot_carb", - "tot_nitro_cont_meth", - "tot_nitro_content", - "tot_org_c_meth", - "tot_org_carb", - "tot_phosp", - "water_cont_soil_meth", - "water_content", - "watering_regm", - "zinc" - ], - "slot_usage": { - "agrochem_addition": { - "name": "agrochem_addition", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "agrochemical name;agrochemical amount;timestamp" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, mole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Addition of fertilizers, pesticides, etc. - amount and time of applications", - "title": "history/agrochemical additions", - "examples": [ - { - "value": "roundup;5 milligram per liter;2018-06-21" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "history/agrochemical additions" - ], - "rank": 2, - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{timestamp}", - "slot_uri": "MIXS:0000639", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": ".*" - }, - "air_temp_regm": { - "name": "air_temp_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "temperature value;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens", - "title": "air temperature regimen", - "examples": [ - { - "value": "25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "air temperature regimen" - ], - "rank": 16, - "is_a": "core field", - "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000551", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface", - "SoilInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "al_sat": { - "name": "al_sat", - "description": "The relative abundance of aluminum in the sample", - "title": "aluminum saturation/ extreme unusual properties", - "todos": [ - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "Example & validation. Can we make rules that 27% & 27 % & 0.27 will validate?", - "I think it's weird the way GSC writes the title. I recommend this change. Thoughts? I would argue this isn't an extreme unusual property. It's just a biogeochemical measurement.", - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "Example & validation. Can we make rules that 27% & 27 % & 0.27 will validate?", - "I think it's weird the way GSC writes the title. I recommend this change. Thoughts? I would argue this isn't an extreme unusual property. It's just a biogeochemical measurement." - ], - "comments": [ - "Aluminum saturation is the percentage of the CEC occupies by aluminum. Like all cations, aluminum held by the cation exchange complex is in equilibrium with aluminum in the soil solution." - ], - "examples": [ - { - "value": "0.27" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 3, - "is_a": "core field", - "slot_uri": "MIXS:0000607", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "al_sat_meth": { - "name": "al_sat_meth", - "description": "Reference or method used in determining Aluminum saturation", - "title": "aluminum saturation method/ extreme unusual properties", - "todos": [ - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "I think it's weird the way GSC writes the title. I recommend this change. Thoughts?", - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "I think it's weird the way GSC writes the title. I recommend this change. Thoughts?" - ], - "comments": [ - "Required when aluminum saturation is provided." - ], - "examples": [ - { - "value": "https://doi.org/10.1371/journal.pone.0176357" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 4, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000324", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "ammonium_nitrogen": { - "name": "ammonium_nitrogen", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mg/kg" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of ammonium nitrogen in the sample", - "title": "ammonium nitrogen", - "examples": [ - { - "value": "2.3 mg/kg" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://www.ornl.gov/content/bio-scales-0" - ], - "aliases": [ - "ammonium_nitrogen", - "NH4-N" - ], - "rank": 1005, - "is_a": "attribute", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "annual_precpt": { - "name": "annual_precpt", - "description": "The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps.", - "title": "mean annual precipitation", - "todos": [ - "This is no longer matching the listed IRI from GSC, added example. When NMDC has its own slots, map this to the MIxS slot", - "This is no longer matching the listed IRI from GSC, added example. When NMDC has its own slots, map this to the MIxS slot" - ], - "examples": [ - { - "value": "8.94 inch" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "is_a": "core field", - "slot_uri": "MIXS:0000644", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "annual_temp": { - "name": "annual_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Mean annual temperature", - "title": "mean annual temperature", - "examples": [ - { - "value": "12.5 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "mean annual temperature" - ], - "rank": 6, - "is_a": "core field", - "slot_uri": "MIXS:0000642", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "biotic_regm": { - "name": "biotic_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "free text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi.", - "title": "biotic regimen", - "examples": [ - { - "value": "sample inoculated with Rhizobium spp. Culture" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "biotic regimen" - ], - "rank": 13, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0001038", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface", - "SoilInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "biotic_relationship": { - "name": "biotic_relationship", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - } - }, - "description": "Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object", - "title": "observed biotic relationship", - "examples": [ - { - "value": "free living" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "observed biotic relationship" - ], - "rank": 22, - "is_a": "nucleic acid sequence source field", - "slot_uri": "MIXS:0000028", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_modified_section", - "range": "biotic_relationship_enum" - }, - "carb_nitro_ratio": { - "name": "carb_nitro_ratio", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Ratio of amount or concentrations of carbon to nitrogen", - "title": "carbon/nitrogen ratio", - "examples": [ - { - "value": "0.417361111" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "carbon/nitrogen ratio" - ], - "rank": 44, - "is_a": "core field", - "slot_uri": "MIXS:0000310", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "SoilInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "float", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "chem_administration": { - "name": "chem_administration", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "CHEBI;timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", - "title": "chemical administration", - "examples": [ - { - "value": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22" - }, - { - "value": "agar [CHEBI:2509];2018-05" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "chemical administration" - ], - "rank": 17, - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]};{timestamp}", - "slot_uri": "MIXS:0000751", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" - }, - "climate_environment": { - "name": "climate_environment", - "description": "Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates", - "title": "climate environment", - "todos": [ - "description says \"can include multiple climates\" but multivalued is set to false", - "add examples, i need to see some examples to add correctly formatted example.", - "description says \"can include multiple climates\" but multivalued is set to false", - "add examples, i need to see some examples to add correctly formatted example." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 19, - "is_a": "core field", - "string_serialization": "{text};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0001040", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface", - "SoilInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "collection_date": { - "name": "collection_date", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "date and time" - } - }, - "description": "The date of sampling", - "title": "collection date", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", - "Use modified term (amended definition)" - ], - "examples": [ - { - "value": "2021-04-15" - }, - { - "value": "2021-04" - }, - { - "value": "2021" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "collection date" - ], - "rank": 3, - "is_a": "environment field", - "string_serialization": "{date, arbitrary precision}", - "slot_uri": "MIXS:0000011", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" - }, - "collection_date_inc": { - "name": "collection_date_inc", - "description": "Date the incubation was harvested/collected/ended. Only relevant for incubation samples.", - "title": "incubation collection date", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only" - ], - "comments": [ - "Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable." - ], - "examples": [ - { - "value": "2021-04-15, 2021-04 and 2021 are all acceptable." - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:collection_date" - ], - "rank": 2, - "string_serialization": "{date, arbitrary precision}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "recommended": true, - "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" - }, - "collection_time": { - "name": "collection_time", - "description": "The time of sampling, either as an instance (single point) or interval.", - "title": "collection time, GMT", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" - ], - "comments": [ - "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" - ], - "examples": [ - { - "value": "13:33 or 13:33:55" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:collection_date" - ], - "rank": 1, - "string_serialization": "{time, seconds optional}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "recommended": true, - "pattern": "^([01]?\\d|2[0-3]|24(?=:00?:00?$)):([0-5]\\d)(:([0-5]\\d))?$" - }, - "collection_time_inc": { - "name": "collection_time_inc", - "description": "Time the incubation was harvested/collected/ended. Only relevant for incubation samples.", - "title": "incubation collection time, GMT", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" - ], - "comments": [ - "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" - ], - "examples": [ - { - "value": "13:33 or 13:33:55" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:collection_date" - ], - "rank": 3, - "string_serialization": "{time, seconds optional}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "recommended": true, - "pattern": "^([01]?\\d|2[0-3]|24(?=:00?:00?$)):([0-5]\\d)(:([0-5]\\d))?$" - }, - "crop_rotation": { - "name": "crop_rotation", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "crop rotation status;schedule" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Whether or not crop is rotated, and if yes, rotation schedule", - "title": "history/crop rotation", - "examples": [ - { - "value": "yes;R2/2017-01-01/2018-12-31/P6M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "history/crop rotation" - ], - "rank": 7, - "is_a": "core field", - "string_serialization": "{boolean};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000318", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "cur_land_use": { - "name": "cur_land_use", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Present state of sample site", - "title": "current land use", - "examples": [ - { - "value": "conifers" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "current land use" - ], - "rank": 8, - "is_a": "core field", - "slot_uri": "MIXS:0001080", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "cur_land_use_enum" - }, - "cur_vegetation": { - "name": "cur_vegetation", - "description": "Vegetation classification from one or more standard classification systems, or agricultural crop", - "title": "current vegetation", - "todos": [ - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "Recommend changing this from text value to some king of ontology?", - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "Recommend changing this from text value to some kind of ontology?" - ], - "comments": [ - "Values provided here can be specific species of vegetation or vegetation regions", - "See for vegetation regions- https://education.nationalgeographic.org/resource/vegetation-region" - ], - "examples": [ - { - "value": "deciduous forest" - }, - { - "value": "forest" - }, - { - "value": "Bauhinia variegata" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 9, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000312", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "cur_vegetation_meth": { - "name": "cur_vegetation_meth", - "description": "Reference or method used in vegetation classification", - "title": "current vegetation method", - "todos": [ - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "I'm not sure this is a DOI, PMID, or URI. Should pool the community and find out how they accomplish this if provided.", - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "I'm not sure this is a DOI, PMID, or URI. Should pool the community and find out how they accomplish this if provided." - ], - "comments": [ - "Required when current vegetation is provided." - ], - "examples": [ - { - "value": "https://doi.org/10.1111/j.1654-109X.2011.01154.x" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 10, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000314", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "depth": { - "name": "depth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - } - }, - "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", - "title": "depth, meters", - "notes": [ - "Use modified term" - ], - "comments": [ - "All depths must be reported in meters. Provide the numerical portion only." - ], - "examples": [ - { - "value": "0 - 0.1" - }, - { - "value": "1" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "depth" - ], - "rank": 9, - "is_a": "environment field", - "string_serialization": "{float}-{float}", - "slot_uri": "MIXS:0000018", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?$" - }, - "drainage_class": { - "name": "drainage_class", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Drainage classification from a standard system such as the USDA system", - "title": "drainage classification", - "examples": [ - { - "value": "well" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "drainage classification" - ], - "rank": 11, - "is_a": "core field", - "slot_uri": "MIXS:0001085", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "drainage_class_enum" - }, - "ecosystem": { - "name": "ecosystem", - "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", - "notes": [ - "range: string or EcosystemEnum? The enum could be dynamic or might be soil biased." - ], - "comments": [ - "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 9, - "is_a": "gold_path_field", - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "EcosystemEnum", - "recommended": true - }, - "ecosystem_category": { - "name": "ecosystem_category", - "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", - "notes": [ - "string or EcosystemCategoryEnum range?" - ], - "comments": [ - "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 10, - "is_a": "gold_path_field", - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "EcosystemCategoryEnum", - "recommended": true - }, - "ecosystem_subtype": { - "name": "ecosystem_subtype", - "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", - "notes": [ - "string or EcosystemSubtypeEnum range?" - ], - "comments": [ - "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 12, - "is_a": "gold_path_field", - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "EcosystemSubtypeEnum", - "recommended": true - }, - "ecosystem_type": { - "name": "ecosystem_type", - "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", - "notes": [ - "string or EcosystemTypeEnum range?" - ], - "comments": [ - "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 11, - "is_a": "gold_path_field", - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "EcosystemTypeEnum", - "recommended": true - }, - "elev": { - "name": "elev", - "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", - "title": "elevation, meters", - "comments": [ - "All elevations must be reported in meters. Provide the numerical portion only.", - "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." - ], - "examples": [ - { - "value": "225" - }, - { - "value": "0" - }, - { - "value": "1250" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "slot_uri": "MIXS:0000093", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "float", - "required": true - }, - "env_broad_scale": { - "name": "env_broad_scale", - "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", - "title": "broad-scale environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000012", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "EnvBroadScaleSoilEnum", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_local_scale": { - "name": "env_local_scale", - "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", - "title": "local environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "canopy [ENVO:00000047]" - }, - { - "value": "herb and fern layer [ENVO:01000337]" - }, - { - "value": "litter layer [ENVO:01000338]" - }, - { - "value": "understory [01000335]" - }, - { - "value": "shrub layer [ENVO:01000336]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 7, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000013", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "EnvLocalScaleSoilEnum", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_medium": { - "name": "env_medium", - "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", - "title": "environmental medium", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "soil [ENVO:00001998]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 8, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000014", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "EnvMediumSoilEnum", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_package": { - "name": "env_package", - "description": "Select the MIxS enviromental package that best describes the environment from which your sample was collected.", - "title": "environmental package", - "examples": [ - { - "value": "soil" - } - ], - "in_subset": [ - "mixs extension" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "environmental package" - ], - "rank": 4, - "is_a": "attribute", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true - }, - "experimental_factor": { - "name": "experimental_factor", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text or EFO and/or OBI" - } - }, - "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", - "title": "experimental factor", - "examples": [ - { - "value": "time series design [EFO:0001779]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "experimental factor" - ], - "rank": 12, - "is_a": "investigation field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000008", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "experimental_factor_other": { - "name": "experimental_factor_other", - "description": "Other details about your sample that you feel can't be accurately represented in the available columns.", - "title": "experimental factor- other", - "comments": [ - "This slot accepts open-ended text about your sample.", - "We recommend using key:value pairs.", - "Provided pairs will be considered for inclusion as future slots/terms in this data collection template." - ], - "examples": [ - { - "value": "experimental treatment: value" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:experimental_factor|additional_info" - ], - "rank": 7, - "string_serialization": "{text}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "recommended": true - }, - "extreme_event": { - "name": "extreme_event", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "date, string" - } - }, - "description": "Unusual physical events that may have affected microbial populations", - "title": "history/extreme events", - "todos": [ - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot" - ], - "examples": [ - { - "value": "1980-05-18, volcanic eruption" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 13, - "is_a": "core field", - "slot_uri": "MIXS:0000320", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "fao_class": { - "name": "fao_class", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups", - "title": "soil_taxonomic/FAO classification", - "examples": [ - { - "value": "Luvisols" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "soil_taxonomic/FAO classification" - ], - "rank": 14, - "is_a": "core field", - "slot_uri": "MIXS:0001083", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "fao_class_enum" - }, - "filter_method": { - "name": "filter_method", - "description": "Type of filter used or how the sample was filtered", - "title": "filter method", - "comments": [ - "describe the filter or provide a catalog number and manufacturer" - ], - "examples": [ - { - "value": "C18" - }, - { - "value": "Basix PES, 13-100-106 FisherSci" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:filter_type" - ], - "rank": 6, - "string_serialization": "{text}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "recommended": true - }, - "fire": { - "name": "fire", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "date string" - } - }, - "description": "Historical and/or physical evidence of fire", - "title": "history/fire", - "todos": [ - "is \"to\" acceptable? Is there a better way to request that be written?", - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "is \"to\" acceptable? Is there a better way to request that be written?", - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot" - ], - "comments": [ - "Provide the date the fire occurred. If extended burning occurred provide the date range." - ], - "examples": [ - { - "value": "1871-10-10" - }, - { - "value": "1871-10-01 to 1871-10-31" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 15, - "is_a": "core field", - "slot_uri": "MIXS:0001086", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?(\\s+to\\s+[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?)?$" - }, - "flooding": { - "name": "flooding", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "date string" - } - }, - "description": "Historical and/or physical evidence of flooding", - "title": "history/flooding", - "todos": [ - "is \"to\" acceptable? Is there a better way to request that be written?", - "What about if the \"day\" isn't known? Is this ok?", - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "is \"to\" acceptable? Is there a better way to request that be written?", - "What about if the \"day\" isn't known? Is this ok?", - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot" - ], - "comments": [ - "Provide the date the flood occurred. If extended flooding occurred provide the date range." - ], - "examples": [ - { - "value": "1927-04-15" - }, - { - "value": "1927-04 to 1927-05" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 16, - "is_a": "core field", - "slot_uri": "MIXS:0000319", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "gaseous_environment": { - "name": "gaseous_environment", - "description": "Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens", - "title": "gaseous environment", - "todos": [ - "would like to see usage examples for this slot. Requiring micromole/L seems too limiting and doesn't match expected_value value", - "did I do this right? keep the example that's provided and add another? so as to not override", - "would like to see usage examples for this slot. Requiring micromole/L seems too limiting and doesn't match expected_value value", - "did I do this right? keep the example that's provided and add another? so as to not override" - ], - "examples": [ - { - "value": "CO2; 500ppm above ambient; constant" - }, - { - "value": "nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 20, - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000558", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface", - "SoilInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "geo_loc_name": { - "name": "geo_loc_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" - } - }, - "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", - "title": "geographic location (country and/or sea,region)", - "examples": [ - { - "value": "USA: Maryland, Bethesda" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "geographic location (country and/or sea,region)" - ], - "rank": 4, - "is_a": "environment field", - "string_serialization": "{text}: {text}, {text}", - "slot_uri": "MIXS:0000010", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" - }, - "growth_facil": { - "name": "growth_facil", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "free text or CO" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Type of facility/location where the sample was harvested; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field.", - "title": "growth facility", - "notes": [ - "Removed from description: Alternatively use Crop Ontology (CO) terms" - ], - "examples": [ - { - "value": "Growth chamber [CO_715:0000189]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "growth facility" - ], - "rank": 1, - "is_a": "core field", - "string_serialization": "{text}|{termLabel} {[termID]}", - "slot_uri": "MIXS:0001043", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface", - "SoilInterface" - ], - "slot_group": "mixs_modified_section", - "range": "GrowthFacilEnum", - "required": true - }, - "heavy_metals": { - "name": "heavy_metals", - "description": "Heavy metals present in the sample and their concentrations.", - "title": "heavy metals/ extreme unusual properties", - "todos": [ - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "Example & validation. Can we make rules that 27% & 27 % & 0.27 will validate?", - "I think it's weird the way GSC writes the title. I recommend this change. Thoughts? I would argue this isn't an extreme unusual property. It's just a biogeochemical measurement.", - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "Example & validation. Can we make rules that 27% & 27 % & 0.27 will validate?", - "I think it's weird the way GSC writes the title. I recommend this change. Thoughts? I would argue this isn't an extreme unusual property. It's just a biogeochemical measurement." - ], - "notes": [ - "Changed to multi-valued. In MIxS, you add another column to denote multiple heavy metals. We don't have that ability in the submission portal.", - "Changed to multi-valued. In MIxS, you add another column to denote multiple heavy metals. We don't have that ability in the submission portal." - ], - "comments": [ - "For multiple heavy metals and concentrations, separate by ;" - ], - "examples": [ - { - "value": "mercury 0.09 micrograms per gram" - }, - { - "value": "mercury 0.09 ug/g; chromium 0.03 ug/g" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 17, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000652", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "heavy_metals_meth": { - "name": "heavy_metals_meth", - "description": "Reference or method used in determining heavy metals", - "title": "heavy metals method/ extreme unusual properties", - "todos": [ - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot" - ], - "comments": [ - "Required when heavy metals are provided", - "If different methods are used for multiple metals, indicate the metal and method. Separate metals by ;" - ], - "examples": [ - { - "value": "https://doi.org/10.3390/ijms9040434" - }, - { - "value": "mercury https://doi.org/10.1007/BF01056090; chromium https://doi.org/10.1007/s00216-006-0322-8" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 18, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000343", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "horizon_meth": { - "name": "horizon_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining the horizon", - "title": "soil horizon method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "soil horizon method" - ], - "rank": 19, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000321", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "humidity_regm": { - "name": "humidity_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "humidity value;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram per cubic meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", - "title": "humidity regimen", - "examples": [ - { - "value": "25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "humidity regimen" - ], - "rank": 21, - "is_a": "core field", - "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000568", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface", - "SoilInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "isotope_exposure": { - "name": "isotope_exposure", - "description": "List isotope exposure or addition applied to your sample.", - "title": "isotope exposure/addition", - "todos": [ - "Can we make the H218O correctly super and subscripted?" - ], - "comments": [ - "This is required when your experimental design includes the use of isotopically labeled compounds" - ], - "examples": [ - { - "value": "13C glucose" - }, - { - "value": "H218O" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:chem_administration" - ], - "rank": 16, - "string_serialization": "{termLabel} {[termID]}; {timestamp}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "recommended": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]; ([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" - }, - "lat_lon": { - "name": "lat_lon", - "description": "This is currently a required field but it's not clear if this should be required for human hosts", - "title": "geographic location (latitude and longitude)", - "notes": [ - "required where?", - "This is currently a required field but it's not clear if this should be required for human hosts" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "is_a": "environment field", - "string_serialization": "{lat lon}", - "slot_uri": "MIXS:0000009", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" - }, - "lbc_thirty": { - "name": "lbc_thirty", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "ppm CaCO3/pH" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "lime buffer capacity, determined after 30 minute incubation", - "title": "lime buffer capacity (at 30 minutes)", - "comments": [ - "This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one pH unit" - ], - "examples": [ - { - "value": "543 mg/kg" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://www.ornl.gov/content/bio-scales-0", - "https://secure.caes.uga.edu/extension/publications/files/pdf/C%20874_5.PDF" - ], - "aliases": [ - "lbc_thirty", - "lbc30", - "lime buffer capacity (at 30 minutes)" - ], - "rank": 1001, - "is_a": "attribute", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "lbceq": { - "name": "lbceq", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "ppm CaCO3/pH" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "lime buffer capacity, determined at equilibrium after 5 day incubation", - "title": "lime buffer capacity (after 5 day incubation)", - "comments": [ - "This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one pH unit" - ], - "examples": [ - { - "value": "1575 mg/kg" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://www.ornl.gov/content/bio-scales-0" - ], - "aliases": [ - "lbceq", - "lime buffer capacity (at 5-day equilibrium)" - ], - "rank": 1002, - "is_a": "attribute", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "light_regm": { - "name": "light_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "exposure type;light intensity;light quality" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "lux; micrometer, nanometer, angstrom" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Information about treatment(s) involving exposure to light, including both light intensity and quality.", - "title": "light regimen", - "examples": [ - { - "value": "incandescant light;10 lux;450 nanometer" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "light regimen" - ], - "rank": 24, - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{float} {unit}", - "slot_uri": "MIXS:0000569", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface", - "SoilInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true, - "pattern": "^\\S+.*\\S+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" - }, - "link_class_info": { - "name": "link_class_info", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Link to digitized soil maps or other soil classification information", - "title": "link to classification information", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "link to classification information" - ], - "rank": 20, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000329", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "link_climate_info": { - "name": "link_climate_info", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Link to climate resource", - "title": "link to climate information", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "link to climate information" - ], - "rank": 21, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000328", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "local_class": { - "name": "local_class", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "local classification name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Soil classification based on local soil classification system", - "title": "soil_taxonomic/local classification", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "soil_taxonomic/local classification" - ], - "rank": 22, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000330", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "local_class_meth": { - "name": "local_class_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining the local soil classification", - "title": "soil_taxonomic/local classification method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "soil_taxonomic/local classification method" - ], - "rank": 24, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000331", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "manganese": { - "name": "manganese", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mg/kg (ppm)" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of manganese in the sample", - "title": "manganese", - "examples": [ - { - "value": "24.7 mg/kg" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://www.ornl.gov/content/bio-scales-0" - ], - "aliases": [ - "manganese" - ], - "rank": 1003, - "is_a": "attribute", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "micro_biomass_c_meth": { - "name": "micro_biomass_c_meth", - "description": "Reference or method used in determining microbial biomass carbon", - "title": "microbial biomass carbon method", - "todos": [ - "How should we separate values? | or ;? lets be consistent" - ], - "comments": [ - "required if \"microbial_biomass_c\" is provided" - ], - "examples": [ - { - "value": "https://doi.org/10.1016/0038-0717(87)90052-6" - }, - { - "value": "https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:micro_biomass_meth" - ], - "rank": 1004, - "string_serialization": "{PMID}|{DOI}|{URL}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "recommended": true - }, - "micro_biomass_meth": { - "name": "micro_biomass_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining microbial biomass", - "title": "microbial biomass method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "microbial biomass method" - ], - "rank": 43, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000339", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "micro_biomass_n_meth": { - "name": "micro_biomass_n_meth", - "description": "Reference or method used in determining microbial biomass nitrogen", - "title": "microbial biomass nitrogen method", - "comments": [ - "required if \"microbial_biomass_n\" is provided" - ], - "examples": [ - { - "value": "https://doi.org/10.1016/0038-0717(87)90052-6" - }, - { - "value": "https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:micro_biomass_meth" - ], - "rank": 1004, - "string_serialization": "{PMID}|{DOI}|{URL}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string" - }, - "microbial_biomass": { - "name": "microbial_biomass", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "ton, kilogram, gram per kilogram soil" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units", - "title": "microbial biomass", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "microbial biomass" - ], - "rank": 42, - "is_a": "core field", - "slot_uri": "MIXS:0000650", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "microbial_biomass_c": { - "name": "microbial_biomass_c", - "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.", - "title": "microbial biomass carbon", - "comments": [ - "If you provide this, correction factors used for conversion to the final units and method are required" - ], - "examples": [ - { - "value": "0.05 ug C/g dry soil" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:microbial_biomass" - ], - "rank": 1004, - "string_serialization": "{float} {unit}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" - }, - "microbial_biomass_n": { - "name": "microbial_biomass_n", - "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.", - "title": "microbial biomass nitrogen", - "comments": [ - "If you provide this, correction factors used for conversion to the final units and method are required" - ], - "examples": [ - { - "value": "0.05 ug N/g dry soil" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:microbial_biomass" - ], - "rank": 1004, - "string_serialization": "{float} {unit}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" - }, - "misc_param": { - "name": "misc_param", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "parameter name;measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Any other measurement performed or parameter collected, that is not listed here", - "title": "miscellaneous parameter", - "examples": [ - { - "value": "Bicarbonate ion concentration;2075 micromole per kilogram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "miscellaneous parameter" - ], - "rank": 23, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000752", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "nitrate_nitrogen": { - "name": "nitrate_nitrogen", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mg/kg" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of nitrate nitrogen in the sample", - "title": "nitrate_nitrogen", - "comments": [ - "often below some specified limit of detection" - ], - "examples": [ - { - "value": "0.29 mg/kg" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://www.ornl.gov/content/bio-scales-0" - ], - "aliases": [ - "nitrate_nitrogen", - "NO3-N" - ], - "rank": 1006, - "is_a": "attribute", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "nitrite_nitrogen": { - "name": "nitrite_nitrogen", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mg/kg" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of nitrite nitrogen in the sample", - "title": "nitrite_nitrogen", - "examples": [ - { - "value": "1.2 mg/kg" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://www.ornl.gov/content/bio-scales-0" - ], - "aliases": [ - "nitrite_nitrogen", - "NO2-N" - ], - "rank": 1007, - "is_a": "attribute", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "non_microb_biomass": { - "name": "non_microb_biomass", - "description": "Amount of biomass; should include the name for the part of biomass measured, e.g.insect, plant, total. Can include multiple measurements separated by ;", - "title": "non-microbial biomass", - "examples": [ - { - "value": "insect 0.23 ug; plant 1g" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:biomass|microbial_biomass" - ], - "rank": 8, - "string_serialization": "{text};{float} {unit}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" - }, - "non_microb_biomass_method": { - "name": "non_microb_biomass_method", - "description": "Reference or method used in determining biomass", - "title": "non-microbial biomass method", - "comments": [ - "required if \"non-microbial biomass\" is provided" - ], - "examples": [ - { - "value": "https://doi.org/10.1038/s41467-021-26181-3" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:microbial_biomass" - ], - "rank": 9, - "string_serialization": "{PMID}|{DOI}|{URL}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string" - }, - "org_matter": { - "name": "org_matter", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of organic matter", - "title": "organic matter", - "examples": [ - { - "value": "1.75 milligram per cubic meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "organic matter" - ], - "rank": 45, - "is_a": "core field", - "slot_uri": "MIXS:0000204", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "org_nitro": { - "name": "org_nitro", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of organic nitrogen", - "title": "organic nitrogen", - "examples": [ - { - "value": "4 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "organic nitrogen" - ], - "rank": 46, - "is_a": "core field", - "slot_uri": "MIXS:0000205", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "org_nitro_method": { - "name": "org_nitro_method", - "description": "Method used for obtaining organic nitrogen", - "title": "organic nitrogen method", - "comments": [ - "required if \"org_nitro\" is provided" - ], - "examples": [ - { - "value": "https://doi.org/10.1016/0038-0717(85)90144-0" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:org_nitro|tot_nitro_cont_meth" - ], - "rank": 14, - "string_serialization": "{PMID}|{DOI}|{URL}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string" - }, - "other_treatment": { - "name": "other_treatment", - "description": "Other treatments applied to your samples that are not applicable to the provided fields", - "title": "other treatments", - "comments": [ - "This is an open text field to provide any treatments that cannot be captured in the provided slots." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:additional_info" - ], - "rank": 15, - "string_serialization": "{text}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "recommended": true - }, - "oxy_stat_samp": { - "name": "oxy_stat_samp", - "description": "Oxygenation status of sample", - "title": "oxygenation status of sample", - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 25, - "is_a": "core field", - "slot_uri": "MIXS:0000753", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "OxyStatSampEnum" - }, - "ph": { - "name": "ph", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid", - "title": "pH", - "notes": [ - "Use modified term" - ], - "examples": [ - { - "value": "7.2" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "pH" - ], - "rank": 27, - "is_a": "core field", - "string_serialization": "{float}", - "slot_uri": "MIXS:0001001", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "float", - "recommended": true, - "minimum_value": 0, - "maximum_value": 14 - }, - "ph_meth": { - "name": "ph_meth", - "description": "Reference or method used in determining ph", - "title": "pH method", - "comments": [ - "This can include a link to the instrument used or a citation for the method." - ], - "examples": [ - { - "value": "https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB" - }, - { - "value": "https://doi.org/10.2136/sssabookser5.3.c16" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 41, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0001106", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "phosphate": { - "name": "phosphate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of phosphate", - "title": "phosphate", - "examples": [ - { - "value": "0.7 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "phosphate" - ], - "rank": 53, - "is_a": "core field", - "slot_uri": "MIXS:0000505", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "prev_land_use_meth": { - "name": "prev_land_use_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining previous land use and dates", - "title": "history/previous land use method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "history/previous land use method" - ], - "rank": 26, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000316", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "previous_land_use": { - "name": "previous_land_use", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "land use name;date" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Previous land use and dates", - "title": "history/previous land use", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "history/previous land use" - ], - "rank": 27, - "is_a": "core field", - "string_serialization": "{text};{timestamp}", - "slot_uri": "MIXS:0000315", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^\\S+.*\\S+;([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" - }, - "profile_position": { - "name": "profile_position", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas", - "title": "profile position", - "examples": [ - { - "value": "summit" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "profile position" - ], - "rank": 28, - "is_a": "core field", - "slot_uri": "MIXS:0001084", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "profile_position_enum" - }, - "salinity": { - "name": "salinity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "practical salinity unit, percentage" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", - "title": "salinity", - "examples": [ - { - "value": "25 practical salinity unit" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "salinity" - ], - "rank": 54, - "is_a": "core field", - "slot_uri": "MIXS:0000183", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "salinity_meth": { - "name": "salinity_meth", - "description": "Reference or method used in determining salinity", - "title": "salinity method", - "examples": [ - { - "value": "https://doi.org/10.1007/978-1-61779-986-0_28" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 55, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000341", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "samp_collec_device": { - "name": "samp_collec_device", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "device name" - } - }, - "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", - "title": "sample collection device", - "comments": [ - "Report dimensions and details when applicable" - ], - "examples": [ - { - "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection device" - ], - "rank": 14, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000002", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "samp_collec_method": { - "name": "samp_collec_method", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI,url , or text" - } - }, - "description": "The method employed for collecting the sample.", - "title": "sample collection method", - "comments": [ - "This can be a citation or description" - ], - "examples": [ - { - "value": "swabbing" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection method" - ], - "rank": 15, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{PMID}|{DOI}|{URL}|{text}", - "slot_uri": "MIXS:0001225", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_mat_process": { - "name": "samp_mat_process", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - } - }, - "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", - "title": "sample material processing", - "examples": [ - { - "value": "filtering of seawater" - }, - { - "value": "storing samples in ethanol" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample material processing" - ], - "rank": 12, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000016", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_size": { - "name": "samp_size", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millliter, gram, milligram, liter" - } - }, - "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", - "title": "amount or size of sample collected", - "comments": [ - "This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis." - ], - "examples": [ - { - "value": "5 grams" - }, - { - "value": "10 mL" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "amount or size of sample collected" - ], - "rank": 18, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float} {unit}", - "slot_uri": "MIXS:0000001", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" - }, - "samp_store_temp": { - "name": "samp_store_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Temperature at which the sample was stored (degrees are assumed)", - "title": "sample storage temperature", - "examples": [ - { - "value": "-80 Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage temperature" - ], - "rank": 7, - "is_a": "core field", - "slot_uri": "MIXS:0000110", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "sample_link": { - "name": "sample_link", - "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", - "title": "sample linkage", - "notes": [ - "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" - ], - "comments": [ - "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" - ], - "examples": [ - { - "value": "IGSN:DSJ0284" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "string_serialization": "{text}:{text}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface", - "SampIdNewTermsMixin" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true, - "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" - }, - "season_precpt": { - "name": "season_precpt", - "description": "The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps.", - "title": "average seasonal precipitation", - "todos": [ - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "check validation & examples. always mm? so value only? Or value + unit", - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "check validation & examples. always mm? so value only? Or value + unit" - ], - "notes": [ - "mean and average are the same thing, but it seems like bad practice to not be consistent. Changed mean to average", - "mean and average are the same thing, but it seems like bad practice to not be consistent. Changed mean to average" - ], - "comments": [ - "Seasons are defined as spring (March, April, May), summer (June, July, August), autumn (September, October, November) and winter (December, January, February)." - ], - "examples": [ - { - "value": "0.4 inch" - }, - { - "value": "10.16 mm" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 29, - "is_a": "core field", - "slot_uri": "MIXS:0000645", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "season_temp": { - "name": "season_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Mean seasonal temperature", - "title": "mean seasonal temperature", - "examples": [ - { - "value": "18 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "mean seasonal temperature" - ], - "rank": 30, - "is_a": "core field", - "slot_uri": "MIXS:0000643", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "sieving": { - "name": "sieving", - "description": "Collection design of pooled samples and/or sieve size and amount of sample sieved", - "title": "composite design/sieving", - "todos": [ - "check validation and examples", - "check validation and examples" - ], - "comments": [ - "Describe how samples were composited or sieved.", - "Use 'sample link' to indicate which samples were combined." - ], - "examples": [ - { - "value": "combined 2 cores" - }, - { - "value": "4mm sieved" - }, - { - "value": "4 mm sieved and homogenized" - }, - { - "value": "50 g" - }, - { - "value": "5 cores" - }, - { - "value": "2 mm sieved" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 8, - "is_a": "core field", - "string_serialization": "{{text}|{float} {unit}};{float} {unit}", - "slot_uri": "MIXS:0000322", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "size_frac_low": { - "name": "size_frac_low", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micrometer" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample", - "title": "size-fraction lower threshold", - "examples": [ - { - "value": "0.2 micrometer" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "size-fraction lower threshold" - ], - "rank": 10, - "is_a": "core field", - "slot_uri": "MIXS:0000735", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "size_frac_up": { - "name": "size_frac_up", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micrometer" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample", - "title": "size-fraction upper threshold", - "examples": [ - { - "value": "20 micrometer" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "size-fraction upper threshold" - ], - "rank": 11, - "is_a": "core field", - "slot_uri": "MIXS:0000736", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "slope_aspect": { - "name": "slope_aspect", - "description": "The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees). - This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration.", - "title": "slope aspect", - "todos": [ - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot" - ], - "comments": [ - "Aspect is the orientation of slope, measured clockwise in degrees from 0 to 360, where 0 is north-facing, 90 is east-facing, 180 is south-facing, and 270 is west-facing." - ], - "examples": [ - { - "value": "35" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 1, - "is_a": "core field", - "slot_uri": "MIXS:0000647", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "slope_gradient": { - "name": "slope_gradient", - "description": "Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer", - "title": "slope gradient", - "todos": [ - "Slope is a percent. How does the validation work? Check to correct examples", - "Slope is a percent. How does the validation work? Check to correct examples" - ], - "examples": [ - { - "value": "10%" - }, - { - "value": "10 %" - }, - { - "value": "0.1" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 31, - "is_a": "core field", - "slot_uri": "MIXS:0000646", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "soil_horizon": { - "name": "soil_horizon", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath", - "title": "soil horizon", - "examples": [ - { - "value": "A horizon" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "soil horizon" - ], - "rank": 32, - "is_a": "core field", - "slot_uri": "MIXS:0001082", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "soil_horizon_enum" - }, - "soil_text_measure": { - "name": "soil_text_measure", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional.", - "title": "soil texture measurement", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "soil texture measurement" - ], - "rank": 33, - "is_a": "core field", - "slot_uri": "MIXS:0000335", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "soil_texture_meth": { - "name": "soil_texture_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining soil texture", - "title": "soil texture method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "soil texture method" - ], - "rank": 34, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000336", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "soil_type": { - "name": "soil_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "ENVO_00001998" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes.", - "title": "soil type", - "examples": [ - { - "value": "plinthosol [ENVO:00002250]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "soil type" - ], - "rank": 35, - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000332", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "soil_type_meth": { - "name": "soil_type_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining soil series name or other lower-level classification", - "title": "soil type method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "soil type method" - ], - "rank": 36, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000334", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "specific_ecosystem": { - "name": "specific_ecosystem", - "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", - "notes": [ - "string or SpecificEcosystemEnum range?" - ], - "comments": [ - "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 13, - "is_a": "gold_path_field", - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "SpecificEcosystemEnum", - "recommended": true - }, - "start_date_inc": { - "name": "start_date_inc", - "description": "Date the incubation was started. Only relevant for incubation samples.", - "title": "incubation start date", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only" - ], - "comments": [ - "Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable." - ], - "examples": [ - { - "value": "2021-04-15, 2021-04 and 2021 are all acceptable." - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:collection_date" - ], - "rank": 4, - "string_serialization": "{date, arbitrary precision}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "recommended": true, - "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" - }, - "start_time_inc": { - "name": "start_time_inc", - "description": "Time the incubation was started. Only relevant for incubation samples.", - "title": "incubation start time, GMT", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" - ], - "comments": [ - "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" - ], - "examples": [ - { - "value": "13:33 or 13:33:55" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:collection_date" - ], - "rank": 5, - "string_serialization": "{time, seconds optional}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "recommended": true, - "pattern": "^([01]?\\d|2[0-3]|24(?=:00?:00?$)):([0-5]\\d)(:([0-5]\\d))?$" - }, - "store_cond": { - "name": "store_cond", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "storage condition type;duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Explain how the soil sample is stored (fresh/frozen/other).", - "title": "storage conditions", - "examples": [ - { - "value": "-20 degree Celsius freezer;P2Y10D" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "storage conditions" - ], - "rank": 2, - "is_a": "core field", - "string_serialization": "{text};{duration}", - "slot_uri": "MIXS:0000327", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_modified_section", - "range": "StoreCondEnum", - "required": true - }, - "temp": { - "name": "temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - } - }, - "description": "Temperature of the sample at the time of sampling.", - "title": "temperature", - "examples": [ - { - "value": "25 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "temperature" - ], - "rank": 37, - "is_a": "environment field", - "slot_uri": "MIXS:0000113", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tillage": { - "name": "tillage", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Note method(s) used for tilling", - "title": "history/tillage", - "examples": [ - { - "value": "chisel" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "history/tillage" - ], - "rank": 38, - "is_a": "core field", - "slot_uri": "MIXS:0001081", - "multivalued": true, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "tillage_enum" - }, - "tot_carb": { - "name": "tot_carb", - "description": "Total carbon content", - "title": "total carbon", - "todos": [ - "is this inorganic and organic? both? could use some clarification.", - "ug/L doesn't seem like the right units. Should check this slots usage in databases and re-evaluate. I couldn't find any references that provided this data in this format", - "is this inorganic and organic? both? could use some clarification.", - "ug/L doesn't seem like the right units. Should check this slots usage in databases and re-evaluate. I couldn't find any references that provided this data in this format" - ], - "examples": [ - { - "value": "1 ug/L" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 47, - "is_a": "core field", - "slot_uri": "MIXS:0000525", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tot_nitro_cont_meth": { - "name": "tot_nitro_cont_meth", - "description": "Reference or method used in determining the total nitrogen", - "title": "total nitrogen content method", - "examples": [ - { - "value": "https://doi.org/10.2134/agronmonogr9.2.c32" - }, - { - "value": "https://acsess.onlinelibrary.wiley.com/doi/full/10.2136/sssaj2009.0389?casa_token=bm0pYIUdNMgAAAAA%3AOWVRR0STHaOe-afTcTdxn5m1hM8n2ltM0wY-b1iYpYdD9dhwppk5j3LvC2IO5yhOIvyLVeQz4NZRCZo" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 49, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000338", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "tot_nitro_content": { - "name": "tot_nitro_content", - "description": "Total nitrogen content of the sample", - "title": "total nitrogen content", - "examples": [ - { - "value": "5 mg N/ L" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 48, - "is_a": "core field", - "slot_uri": "MIXS:0000530", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tot_org_c_meth": { - "name": "tot_org_c_meth", - "description": "Reference or method used in determining total organic carbon", - "title": "total organic carbon method", - "examples": [ - { - "value": "https://doi.org/10.1080/07352680902776556" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 51, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000337", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "tot_org_carb": { - "name": "tot_org_carb", - "description": "Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content", - "title": "total organic carbon", - "todos": [ - "check description. How are they different?", - "check description. How are they different?" - ], - "examples": [ - { - "value": "5 mg N/ L" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 50, - "is_a": "core field", - "slot_uri": "MIXS:0000533", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tot_phosp": { - "name": "tot_phosp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus", - "title": "total phosphorus", - "examples": [ - { - "value": "0.03 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "total phosphorus" - ], - "rank": 52, - "is_a": "core field", - "slot_uri": "MIXS:0000117", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "water_cont_soil_meth": { - "name": "water_cont_soil_meth", - "description": "Reference or method used in determining the water content of soil", - "title": "water content method", - "todos": [ - "Why is it soil water content method in the name but not the title? Is this slot used in other samples?", - "Soil water content can be measure MANY ways and often, multiple ways are used in one experiment (gravimetric water content and water holding capacity and water filled pore space, to name a few).", - "Should this be multi valued? How to we manage and validate this?", - "Why is it soil water content method in the name but not the title? Is this slot used in other samples?", - "Soil water content can be measure MANY ways and often, multiple ways are used in one experiment (gravimetric water content and water holding capacity and water filled pore space, to name a few).", - "Should this be multi valued? How to we manage and validate this?" - ], - "comments": [ - "Required if providing water content" - ], - "examples": [ - { - "value": "J. Nat. Prod. Plant Resour., 2012, 2 (4):500-503" - }, - { - "value": "https://dec.alaska.gov/applications/spar/webcalc/definitions.htm" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 40, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000323", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "water_content": { - "name": "water_content", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "string" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram per gram or cubic centimeter per cubic centimeter" - } - }, - "description": "Water content measurement", - "title": "water content", - "todos": [ - "value in preferred unit is too limiting. need to change this", - "check and correct validation so examples are accepted", - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "how to manage multiple water content methods?", - "value in preferred unit is too limiting. need to change this", - "check and correct validation so examples are accepted", - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "how to manage multiple water content methods?" - ], - "examples": [ - { - "value": "75%" - }, - { - "value": "75 %" - }, - { - "value": "0.75 g water/g dry soil" - }, - { - "value": "75% water holding capacity" - }, - { - "value": "1.1 g fresh weight/ dry weight" - }, - { - "value": "10% water filled pore space" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 39, - "is_a": "core field", - "string_serialization": "{float or pct} {unit}", - "slot_uri": "MIXS:0000185", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?%? \\S.+$" - }, - "watering_regm": { - "name": "watering_regm", - "description": "Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", - "title": "watering regimen", - "examples": [ - { - "value": "1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - }, - { - "value": "75% water holding capacity; constant" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 25, - "is_a": "core field", - "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000591", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface", - "SoilInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "zinc": { - "name": "zinc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mg/kg (ppm)" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of zinc in the sample", - "title": "zinc", - "examples": [ - { - "value": "2.5 mg/kg" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://www.ornl.gov/content/bio-scales-0" - ], - "aliases": [ - "zinc" - ], - "rank": 1004, - "is_a": "attribute", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "organism_count": { - "name": "organism_count", - "multivalued": false, - "range": "string", - "pattern": "^(\\S+.*\\S+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+.*\\S+;(qPCR|ATP|MPN|other)\\|)*(\\S+.*\\S+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+.*\\S+;(qPCR|ATP|MPN|other))$" - } - }, - "attributes": { - "agrochem_addition": { - "name": "agrochem_addition", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "agrochemical name;agrochemical amount;timestamp" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, mole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Addition of fertilizers, pesticides, etc. - amount and time of applications", - "title": "history/agrochemical additions", - "examples": [ - { - "value": "roundup;5 milligram per liter;2018-06-21" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "history/agrochemical additions" - ], - "rank": 2, - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{timestamp}", - "slot_uri": "MIXS:0000639", - "multivalued": false, - "alias": "agrochem_addition", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": ".*" - }, - "air_temp_regm": { - "name": "air_temp_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "temperature value;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens", - "title": "air temperature regimen", - "examples": [ - { - "value": "25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "air temperature regimen" - ], - "rank": 16, - "is_a": "core field", - "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000551", - "multivalued": false, - "alias": "air_temp_regm", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface", - "SoilInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "al_sat": { - "name": "al_sat", - "description": "The relative abundance of aluminum in the sample", - "title": "aluminum saturation/ extreme unusual properties", - "todos": [ - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "Example & validation. Can we make rules that 27% & 27 % & 0.27 will validate?", - "I think it's weird the way GSC writes the title. I recommend this change. Thoughts? I would argue this isn't an extreme unusual property. It's just a biogeochemical measurement.", - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "Example & validation. Can we make rules that 27% & 27 % & 0.27 will validate?", - "I think it's weird the way GSC writes the title. I recommend this change. Thoughts? I would argue this isn't an extreme unusual property. It's just a biogeochemical measurement." - ], - "comments": [ - "Aluminum saturation is the percentage of the CEC occupies by aluminum. Like all cations, aluminum held by the cation exchange complex is in equilibrium with aluminum in the soil solution." - ], - "examples": [ - { - "value": "0.27" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 3, - "is_a": "core field", - "slot_uri": "MIXS:0000607", - "multivalued": false, - "alias": "al_sat", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "al_sat_meth": { - "name": "al_sat_meth", - "description": "Reference or method used in determining Aluminum saturation", - "title": "aluminum saturation method/ extreme unusual properties", - "todos": [ - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "I think it's weird the way GSC writes the title. I recommend this change. Thoughts?", - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "I think it's weird the way GSC writes the title. I recommend this change. Thoughts?" - ], - "comments": [ - "Required when aluminum saturation is provided." - ], - "examples": [ - { - "value": "https://doi.org/10.1371/journal.pone.0176357" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 4, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000324", - "multivalued": false, - "alias": "al_sat_meth", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "ammonium_nitrogen": { - "name": "ammonium_nitrogen", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mg/kg" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of ammonium nitrogen in the sample", - "title": "ammonium nitrogen", - "examples": [ - { - "value": "2.3 mg/kg" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://www.ornl.gov/content/bio-scales-0" - ], - "aliases": [ - "ammonium_nitrogen", - "NH4-N" - ], - "rank": 1005, - "is_a": "attribute", - "multivalued": false, - "alias": "ammonium_nitrogen", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "annual_precpt": { - "name": "annual_precpt", - "description": "The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps.", - "title": "mean annual precipitation", - "todos": [ - "This is no longer matching the listed IRI from GSC, added example. When NMDC has its own slots, map this to the MIxS slot", - "This is no longer matching the listed IRI from GSC, added example. When NMDC has its own slots, map this to the MIxS slot" - ], - "examples": [ - { - "value": "8.94 inch" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "is_a": "core field", - "slot_uri": "MIXS:0000644", - "multivalued": false, - "alias": "annual_precpt", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "annual_temp": { - "name": "annual_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Mean annual temperature", - "title": "mean annual temperature", - "examples": [ - { - "value": "12.5 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "mean annual temperature" - ], - "rank": 6, - "is_a": "core field", - "slot_uri": "MIXS:0000642", - "multivalued": false, - "alias": "annual_temp", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "biotic_regm": { - "name": "biotic_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "free text" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi.", - "title": "biotic regimen", - "examples": [ - { - "value": "sample inoculated with Rhizobium spp. Culture" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "biotic regimen" - ], - "rank": 13, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0001038", - "multivalued": false, - "alias": "biotic_regm", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface", - "SoilInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "biotic_relationship": { - "name": "biotic_relationship", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - } - }, - "description": "Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object", - "title": "observed biotic relationship", - "examples": [ - { - "value": "free living" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "observed biotic relationship" - ], - "rank": 22, - "is_a": "nucleic acid sequence source field", - "slot_uri": "MIXS:0000028", - "multivalued": false, - "alias": "biotic_relationship", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_modified_section", - "range": "biotic_relationship_enum" - }, - "carb_nitro_ratio": { - "name": "carb_nitro_ratio", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Ratio of amount or concentrations of carbon to nitrogen", - "title": "carbon/nitrogen ratio", - "examples": [ - { - "value": "0.417361111" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "carbon/nitrogen ratio" - ], - "rank": 44, - "is_a": "core field", - "slot_uri": "MIXS:0000310", - "multivalued": false, - "alias": "carb_nitro_ratio", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "SoilInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "float", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "chem_administration": { - "name": "chem_administration", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "CHEBI;timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", - "title": "chemical administration", - "examples": [ - { - "value": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22" - }, - { - "value": "agar [CHEBI:2509];2018-05" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "chemical administration" - ], - "rank": 17, - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]};{timestamp}", - "slot_uri": "MIXS:0000751", - "multivalued": false, - "alias": "chem_administration", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" - }, - "climate_environment": { - "name": "climate_environment", - "description": "Treatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates", - "title": "climate environment", - "todos": [ - "description says \"can include multiple climates\" but multivalued is set to false", - "add examples, i need to see some examples to add correctly formatted example.", - "description says \"can include multiple climates\" but multivalued is set to false", - "add examples, i need to see some examples to add correctly formatted example." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 19, - "is_a": "core field", - "string_serialization": "{text};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0001040", - "multivalued": false, - "alias": "climate_environment", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface", - "SoilInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "collection_date": { - "name": "collection_date", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "date and time" - } - }, - "description": "The date of sampling", - "title": "collection date", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", - "Use modified term (amended definition)" - ], - "examples": [ - { - "value": "2021-04-15" - }, - { - "value": "2021-04" - }, - { - "value": "2021" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "collection date" - ], - "rank": 3, - "is_a": "environment field", - "string_serialization": "{date, arbitrary precision}", - "slot_uri": "MIXS:0000011", - "multivalued": false, - "alias": "collection_date", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" - }, - "collection_date_inc": { - "name": "collection_date_inc", - "description": "Date the incubation was harvested/collected/ended. Only relevant for incubation samples.", - "title": "incubation collection date", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only" - ], - "comments": [ - "Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable." - ], - "examples": [ - { - "value": "2021-04-15, 2021-04 and 2021 are all acceptable." - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:collection_date" - ], - "rank": 2, - "string_serialization": "{date, arbitrary precision}", - "multivalued": false, - "alias": "collection_date_inc", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "recommended": true, - "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" - }, - "collection_time": { - "name": "collection_time", - "description": "The time of sampling, either as an instance (single point) or interval.", - "title": "collection time, GMT", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" - ], - "comments": [ - "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" - ], - "examples": [ - { - "value": "13:33 or 13:33:55" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:collection_date" - ], - "rank": 1, - "string_serialization": "{time, seconds optional}", - "multivalued": false, - "alias": "collection_time", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "recommended": true, - "pattern": "^([01]?\\d|2[0-3]|24(?=:00?:00?$)):([0-5]\\d)(:([0-5]\\d))?$" - }, - "collection_time_inc": { - "name": "collection_time_inc", - "description": "Time the incubation was harvested/collected/ended. Only relevant for incubation samples.", - "title": "incubation collection time, GMT", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" - ], - "comments": [ - "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" - ], - "examples": [ - { - "value": "13:33 or 13:33:55" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:collection_date" - ], - "rank": 3, - "string_serialization": "{time, seconds optional}", - "multivalued": false, - "alias": "collection_time_inc", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "recommended": true, - "pattern": "^([01]?\\d|2[0-3]|24(?=:00?:00?$)):([0-5]\\d)(:([0-5]\\d))?$" - }, - "crop_rotation": { - "name": "crop_rotation", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "crop rotation status;schedule" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Whether or not crop is rotated, and if yes, rotation schedule", - "title": "history/crop rotation", - "examples": [ - { - "value": "yes;R2/2017-01-01/2018-12-31/P6M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "history/crop rotation" - ], - "rank": 7, - "is_a": "core field", - "string_serialization": "{boolean};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000318", - "multivalued": false, - "alias": "crop_rotation", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "cur_land_use": { - "name": "cur_land_use", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Present state of sample site", - "title": "current land use", - "examples": [ - { - "value": "conifers" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "current land use" - ], - "rank": 8, - "is_a": "core field", - "slot_uri": "MIXS:0001080", - "multivalued": false, - "alias": "cur_land_use", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "cur_land_use_enum" - }, - "cur_vegetation": { - "name": "cur_vegetation", - "description": "Vegetation classification from one or more standard classification systems, or agricultural crop", - "title": "current vegetation", - "todos": [ - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "Recommend changing this from text value to some king of ontology?", - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "Recommend changing this from text value to some kind of ontology?" - ], - "comments": [ - "Values provided here can be specific species of vegetation or vegetation regions", - "See for vegetation regions- https://education.nationalgeographic.org/resource/vegetation-region" - ], - "examples": [ - { - "value": "deciduous forest" - }, - { - "value": "forest" - }, - { - "value": "Bauhinia variegata" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 9, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000312", - "multivalued": false, - "alias": "cur_vegetation", - "owner": "SoilInterface", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "cur_vegetation_meth": { - "name": "cur_vegetation_meth", - "description": "Reference or method used in vegetation classification", - "title": "current vegetation method", - "todos": [ - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "I'm not sure this is a DOI, PMID, or URI. Should pool the community and find out how they accomplish this if provided.", - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "I'm not sure this is a DOI, PMID, or URI. Should pool the community and find out how they accomplish this if provided." - ], - "comments": [ - "Required when current vegetation is provided." - ], - "examples": [ - { - "value": "https://doi.org/10.1111/j.1654-109X.2011.01154.x" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 10, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000314", - "multivalued": false, - "alias": "cur_vegetation_meth", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "depth": { - "name": "depth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - } - }, - "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", - "title": "depth, meters", - "notes": [ - "Use modified term" - ], - "comments": [ - "All depths must be reported in meters. Provide the numerical portion only." - ], - "examples": [ - { - "value": "0 - 0.1" - }, - { - "value": "1" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "depth" - ], - "rank": 9, - "is_a": "environment field", - "string_serialization": "{float}-{float}", - "slot_uri": "MIXS:0000018", - "multivalued": false, - "alias": "depth", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?$" - }, - "drainage_class": { - "name": "drainage_class", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Drainage classification from a standard system such as the USDA system", - "title": "drainage classification", - "examples": [ - { - "value": "well" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "drainage classification" - ], - "rank": 11, - "is_a": "core field", - "slot_uri": "MIXS:0001085", - "multivalued": false, - "alias": "drainage_class", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "drainage_class_enum" - }, - "ecosystem": { - "name": "ecosystem", - "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", - "notes": [ - "range: string or EcosystemEnum? The enum could be dynamic or might be soil biased." - ], - "comments": [ - "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 9, - "is_a": "gold_path_field", - "alias": "ecosystem", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "EcosystemEnum", - "recommended": true - }, - "ecosystem_category": { - "name": "ecosystem_category", - "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", - "notes": [ - "string or EcosystemCategoryEnum range?" - ], - "comments": [ - "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 10, - "is_a": "gold_path_field", - "alias": "ecosystem_category", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "EcosystemCategoryEnum", - "recommended": true - }, - "ecosystem_subtype": { - "name": "ecosystem_subtype", - "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", - "notes": [ - "string or EcosystemSubtypeEnum range?" - ], - "comments": [ - "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 12, - "is_a": "gold_path_field", - "alias": "ecosystem_subtype", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "EcosystemSubtypeEnum", - "recommended": true - }, - "ecosystem_type": { - "name": "ecosystem_type", - "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", - "notes": [ - "string or EcosystemTypeEnum range?" - ], - "comments": [ - "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 11, - "is_a": "gold_path_field", - "alias": "ecosystem_type", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "EcosystemTypeEnum", - "recommended": true - }, - "elev": { - "name": "elev", - "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", - "title": "elevation, meters", - "comments": [ - "All elevations must be reported in meters. Provide the numerical portion only.", - "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." - ], - "examples": [ - { - "value": "225" - }, - { - "value": "0" - }, - { - "value": "1250" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "slot_uri": "MIXS:0000093", - "multivalued": false, - "alias": "elev", - "owner": "SoilInterface", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "float", - "required": true - }, - "env_broad_scale": { - "name": "env_broad_scale", - "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", - "title": "broad-scale environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000012", - "multivalued": false, - "alias": "env_broad_scale", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "EnvBroadScaleSoilEnum", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_local_scale": { - "name": "env_local_scale", - "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", - "title": "local environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "canopy [ENVO:00000047]" - }, - { - "value": "herb and fern layer [ENVO:01000337]" - }, - { - "value": "litter layer [ENVO:01000338]" - }, - { - "value": "understory [01000335]" - }, - { - "value": "shrub layer [ENVO:01000336]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 7, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000013", - "multivalued": false, - "alias": "env_local_scale", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "EnvLocalScaleSoilEnum", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_medium": { - "name": "env_medium", - "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", - "title": "environmental medium", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "soil [ENVO:00001998]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 8, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000014", - "multivalued": false, - "alias": "env_medium", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "EnvMediumSoilEnum", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_package": { - "name": "env_package", - "description": "Select the MIxS enviromental package that best describes the environment from which your sample was collected.", - "title": "environmental package", - "examples": [ - { - "value": "soil" - } - ], - "in_subset": [ - "mixs extension" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "environmental package" - ], - "rank": 4, - "is_a": "attribute", - "multivalued": false, - "alias": "env_package", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true - }, - "experimental_factor": { - "name": "experimental_factor", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text or EFO and/or OBI" - } - }, - "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", - "title": "experimental factor", - "examples": [ - { - "value": "time series design [EFO:0001779]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "experimental factor" - ], - "rank": 12, - "is_a": "investigation field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000008", - "multivalued": false, - "alias": "experimental_factor", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "experimental_factor_other": { - "name": "experimental_factor_other", - "description": "Other details about your sample that you feel can't be accurately represented in the available columns.", - "title": "experimental factor- other", - "comments": [ - "This slot accepts open-ended text about your sample.", - "We recommend using key:value pairs.", - "Provided pairs will be considered for inclusion as future slots/terms in this data collection template." - ], - "examples": [ - { - "value": "experimental treatment: value" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:experimental_factor|additional_info" - ], - "rank": 7, - "string_serialization": "{text}", - "multivalued": false, - "alias": "experimental_factor_other", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "recommended": true - }, - "extreme_event": { - "name": "extreme_event", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "date, string" - } - }, - "description": "Unusual physical events that may have affected microbial populations", - "title": "history/extreme events", - "todos": [ - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot" - ], - "examples": [ - { - "value": "1980-05-18, volcanic eruption" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 13, - "is_a": "core field", - "slot_uri": "MIXS:0000320", - "multivalued": false, - "alias": "extreme_event", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "fao_class": { - "name": "fao_class", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Soil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups", - "title": "soil_taxonomic/FAO classification", - "examples": [ - { - "value": "Luvisols" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "soil_taxonomic/FAO classification" - ], - "rank": 14, - "is_a": "core field", - "slot_uri": "MIXS:0001083", - "multivalued": false, - "alias": "fao_class", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "fao_class_enum" - }, - "filter_method": { - "name": "filter_method", - "description": "Type of filter used or how the sample was filtered", - "title": "filter method", - "comments": [ - "describe the filter or provide a catalog number and manufacturer" - ], - "examples": [ - { - "value": "C18" - }, - { - "value": "Basix PES, 13-100-106 FisherSci" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:filter_type" - ], - "rank": 6, - "string_serialization": "{text}", - "multivalued": false, - "alias": "filter_method", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "recommended": true - }, - "fire": { - "name": "fire", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "date string" - } - }, - "description": "Historical and/or physical evidence of fire", - "title": "history/fire", - "todos": [ - "is \"to\" acceptable? Is there a better way to request that be written?", - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "is \"to\" acceptable? Is there a better way to request that be written?", - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot" - ], - "comments": [ - "Provide the date the fire occurred. If extended burning occurred provide the date range." - ], - "examples": [ - { - "value": "1871-10-10" - }, - { - "value": "1871-10-01 to 1871-10-31" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 15, - "is_a": "core field", - "slot_uri": "MIXS:0001086", - "multivalued": false, - "alias": "fire", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?(\\s+to\\s+[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?)?$" - }, - "flooding": { - "name": "flooding", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "date string" - } - }, - "description": "Historical and/or physical evidence of flooding", - "title": "history/flooding", - "todos": [ - "is \"to\" acceptable? Is there a better way to request that be written?", - "What about if the \"day\" isn't known? Is this ok?", - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "is \"to\" acceptable? Is there a better way to request that be written?", - "What about if the \"day\" isn't known? Is this ok?", - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot" - ], - "comments": [ - "Provide the date the flood occurred. If extended flooding occurred provide the date range." - ], - "examples": [ - { - "value": "1927-04-15" - }, - { - "value": "1927-04 to 1927-05" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 16, - "is_a": "core field", - "slot_uri": "MIXS:0000319", - "multivalued": false, - "alias": "flooding", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "gaseous_environment": { - "name": "gaseous_environment", - "description": "Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens", - "title": "gaseous environment", - "todos": [ - "would like to see usage examples for this slot. Requiring micromole/L seems too limiting and doesn't match expected_value value", - "did I do this right? keep the example that's provided and add another? so as to not override", - "would like to see usage examples for this slot. Requiring micromole/L seems too limiting and doesn't match expected_value value", - "did I do this right? keep the example that's provided and add another? so as to not override" - ], - "examples": [ - { - "value": "CO2; 500ppm above ambient; constant" - }, - { - "value": "nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 20, - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000558", - "multivalued": false, - "alias": "gaseous_environment", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface", - "SoilInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "geo_loc_name": { - "name": "geo_loc_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" - } - }, - "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", - "title": "geographic location (country and/or sea,region)", - "examples": [ - { - "value": "USA: Maryland, Bethesda" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "geographic location (country and/or sea,region)" - ], - "rank": 4, - "is_a": "environment field", - "string_serialization": "{text}: {text}, {text}", - "slot_uri": "MIXS:0000010", - "multivalued": false, - "alias": "geo_loc_name", - "owner": "SoilInterface", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" - }, - "growth_facil": { - "name": "growth_facil", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "free text or CO" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Type of facility/location where the sample was harvested; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field.", - "title": "growth facility", - "notes": [ - "Removed from description: Alternatively use Crop Ontology (CO) terms" - ], - "examples": [ - { - "value": "Growth chamber [CO_715:0000189]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "growth facility" - ], - "rank": 1, - "is_a": "core field", - "string_serialization": "{text}|{termLabel} {[termID]}", - "slot_uri": "MIXS:0001043", - "multivalued": false, - "alias": "growth_facil", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface", - "SoilInterface" - ], - "slot_group": "mixs_modified_section", - "range": "GrowthFacilEnum", - "required": true - }, - "heavy_metals": { - "name": "heavy_metals", - "description": "Heavy metals present in the sample and their concentrations.", - "title": "heavy metals/ extreme unusual properties", - "todos": [ - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "Example & validation. Can we make rules that 27% & 27 % & 0.27 will validate?", - "I think it's weird the way GSC writes the title. I recommend this change. Thoughts? I would argue this isn't an extreme unusual property. It's just a biogeochemical measurement.", - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "Example & validation. Can we make rules that 27% & 27 % & 0.27 will validate?", - "I think it's weird the way GSC writes the title. I recommend this change. Thoughts? I would argue this isn't an extreme unusual property. It's just a biogeochemical measurement." - ], - "notes": [ - "Changed to multi-valued. In MIxS, you add another column to denote multiple heavy metals. We don't have that ability in the submission portal.", - "Changed to multi-valued. In MIxS, you add another column to denote multiple heavy metals. We don't have that ability in the submission portal." - ], - "comments": [ - "For multiple heavy metals and concentrations, separate by ;" - ], - "examples": [ - { - "value": "mercury 0.09 micrograms per gram" - }, - { - "value": "mercury 0.09 ug/g; chromium 0.03 ug/g" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 17, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000652", - "multivalued": false, - "alias": "heavy_metals", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "heavy_metals_meth": { - "name": "heavy_metals_meth", - "description": "Reference or method used in determining heavy metals", - "title": "heavy metals method/ extreme unusual properties", - "todos": [ - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot" - ], - "comments": [ - "Required when heavy metals are provided", - "If different methods are used for multiple metals, indicate the metal and method. Separate metals by ;" - ], - "examples": [ - { - "value": "https://doi.org/10.3390/ijms9040434" - }, - { - "value": "mercury https://doi.org/10.1007/BF01056090; chromium https://doi.org/10.1007/s00216-006-0322-8" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 18, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000343", - "multivalued": false, - "alias": "heavy_metals_meth", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "horizon_meth": { - "name": "horizon_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining the horizon", - "title": "soil horizon method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "soil horizon method" - ], - "rank": 19, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000321", - "multivalued": false, - "alias": "horizon_meth", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "humidity_regm": { - "name": "humidity_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "humidity value;treatment interval and duration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram per cubic meter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Information about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", - "title": "humidity regimen", - "examples": [ - { - "value": "25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "humidity regimen" - ], - "rank": 21, - "is_a": "core field", - "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000568", - "multivalued": false, - "alias": "humidity_regm", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface", - "SoilInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "isotope_exposure": { - "name": "isotope_exposure", - "description": "List isotope exposure or addition applied to your sample.", - "title": "isotope exposure/addition", - "todos": [ - "Can we make the H218O correctly super and subscripted?" - ], - "comments": [ - "This is required when your experimental design includes the use of isotopically labeled compounds" - ], - "examples": [ - { - "value": "13C glucose" - }, - { - "value": "H218O" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:chem_administration" - ], - "rank": 16, - "string_serialization": "{termLabel} {[termID]}; {timestamp}", - "multivalued": false, - "alias": "isotope_exposure", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "recommended": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]; ([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" - }, - "lat_lon": { - "name": "lat_lon", - "description": "This is currently a required field but it's not clear if this should be required for human hosts", - "title": "geographic location (latitude and longitude)", - "notes": [ - "required where?", - "This is currently a required field but it's not clear if this should be required for human hosts" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "is_a": "environment field", - "string_serialization": "{lat lon}", - "slot_uri": "MIXS:0000009", - "multivalued": false, - "alias": "lat_lon", - "owner": "SoilInterface", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" - }, - "lbc_thirty": { - "name": "lbc_thirty", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "ppm CaCO3/pH" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "lime buffer capacity, determined after 30 minute incubation", - "title": "lime buffer capacity (at 30 minutes)", - "comments": [ - "This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one pH unit" - ], - "examples": [ - { - "value": "543 mg/kg" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://www.ornl.gov/content/bio-scales-0", - "https://secure.caes.uga.edu/extension/publications/files/pdf/C%20874_5.PDF" - ], - "aliases": [ - "lbc_thirty", - "lbc30", - "lime buffer capacity (at 30 minutes)" - ], - "rank": 1001, - "is_a": "attribute", - "multivalued": false, - "alias": "lbc_thirty", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "lbceq": { - "name": "lbceq", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "ppm CaCO3/pH" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "lime buffer capacity, determined at equilibrium after 5 day incubation", - "title": "lime buffer capacity (after 5 day incubation)", - "comments": [ - "This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one pH unit" - ], - "examples": [ - { - "value": "1575 mg/kg" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://www.ornl.gov/content/bio-scales-0" - ], - "aliases": [ - "lbceq", - "lime buffer capacity (at 5-day equilibrium)" - ], - "rank": 1002, - "is_a": "attribute", - "multivalued": false, - "alias": "lbceq", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "light_regm": { - "name": "light_regm", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "exposure type;light intensity;light quality" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "lux; micrometer, nanometer, angstrom" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Information about treatment(s) involving exposure to light, including both light intensity and quality.", - "title": "light regimen", - "examples": [ - { - "value": "incandescant light;10 lux;450 nanometer" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "light regimen" - ], - "rank": 24, - "is_a": "core field", - "string_serialization": "{text};{float} {unit};{float} {unit}", - "slot_uri": "MIXS:0000569", - "multivalued": false, - "alias": "light_regm", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface", - "SoilInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true, - "pattern": "^\\S+.*\\S+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" - }, - "link_class_info": { - "name": "link_class_info", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Link to digitized soil maps or other soil classification information", - "title": "link to classification information", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "link to classification information" - ], - "rank": 20, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000329", - "multivalued": false, - "alias": "link_class_info", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "link_climate_info": { - "name": "link_climate_info", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Link to climate resource", - "title": "link to climate information", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "link to climate information" - ], - "rank": 21, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000328", - "multivalued": false, - "alias": "link_climate_info", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "local_class": { - "name": "local_class", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "local classification name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Soil classification based on local soil classification system", - "title": "soil_taxonomic/local classification", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "soil_taxonomic/local classification" - ], - "rank": 22, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000330", - "multivalued": false, - "alias": "local_class", - "owner": "SoilInterface", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "local_class_meth": { - "name": "local_class_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining the local soil classification", - "title": "soil_taxonomic/local classification method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "soil_taxonomic/local classification method" - ], - "rank": 24, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000331", - "multivalued": false, - "alias": "local_class_meth", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "manganese": { - "name": "manganese", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mg/kg (ppm)" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of manganese in the sample", - "title": "manganese", - "examples": [ - { - "value": "24.7 mg/kg" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://www.ornl.gov/content/bio-scales-0" - ], - "aliases": [ - "manganese" - ], - "rank": 1003, - "is_a": "attribute", - "multivalued": false, - "alias": "manganese", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "micro_biomass_c_meth": { - "name": "micro_biomass_c_meth", - "description": "Reference or method used in determining microbial biomass carbon", - "title": "microbial biomass carbon method", - "todos": [ - "How should we separate values? | or ;? lets be consistent" - ], - "comments": [ - "required if \"microbial_biomass_c\" is provided" - ], - "examples": [ - { - "value": "https://doi.org/10.1016/0038-0717(87)90052-6" - }, - { - "value": "https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:micro_biomass_meth" - ], - "rank": 1004, - "string_serialization": "{PMID}|{DOI}|{URL}", - "multivalued": false, - "alias": "micro_biomass_c_meth", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "recommended": true - }, - "micro_biomass_meth": { - "name": "micro_biomass_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining microbial biomass", - "title": "microbial biomass method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "microbial biomass method" - ], - "rank": 43, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000339", - "multivalued": false, - "alias": "micro_biomass_meth", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "micro_biomass_n_meth": { - "name": "micro_biomass_n_meth", - "description": "Reference or method used in determining microbial biomass nitrogen", - "title": "microbial biomass nitrogen method", - "comments": [ - "required if \"microbial_biomass_n\" is provided" - ], - "examples": [ - { - "value": "https://doi.org/10.1016/0038-0717(87)90052-6" - }, - { - "value": "https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:micro_biomass_meth" - ], - "rank": 1004, - "string_serialization": "{PMID}|{DOI}|{URL}", - "multivalued": false, - "alias": "micro_biomass_n_meth", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string" - }, - "microbial_biomass": { - "name": "microbial_biomass", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "ton, kilogram, gram per kilogram soil" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units", - "title": "microbial biomass", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "microbial biomass" - ], - "rank": 42, - "is_a": "core field", - "slot_uri": "MIXS:0000650", - "multivalued": false, - "alias": "microbial_biomass", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "microbial_biomass_c": { - "name": "microbial_biomass_c", - "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.", - "title": "microbial biomass carbon", - "comments": [ - "If you provide this, correction factors used for conversion to the final units and method are required" - ], - "examples": [ - { - "value": "0.05 ug C/g dry soil" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:microbial_biomass" - ], - "rank": 1004, - "string_serialization": "{float} {unit}", - "multivalued": false, - "alias": "microbial_biomass_c", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" - }, - "microbial_biomass_n": { - "name": "microbial_biomass_n", - "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.", - "title": "microbial biomass nitrogen", - "comments": [ - "If you provide this, correction factors used for conversion to the final units and method are required" - ], - "examples": [ - { - "value": "0.05 ug N/g dry soil" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:microbial_biomass" - ], - "rank": 1004, - "string_serialization": "{float} {unit}", - "multivalued": false, - "alias": "microbial_biomass_n", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" - }, - "misc_param": { - "name": "misc_param", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "parameter name;measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Any other measurement performed or parameter collected, that is not listed here", - "title": "miscellaneous parameter", - "examples": [ - { - "value": "Bicarbonate ion concentration;2075 micromole per kilogram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "miscellaneous parameter" - ], - "rank": 23, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000752", - "multivalued": false, - "alias": "misc_param", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "nitrate_nitrogen": { - "name": "nitrate_nitrogen", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mg/kg" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of nitrate nitrogen in the sample", - "title": "nitrate_nitrogen", - "comments": [ - "often below some specified limit of detection" - ], - "examples": [ - { - "value": "0.29 mg/kg" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://www.ornl.gov/content/bio-scales-0" - ], - "aliases": [ - "nitrate_nitrogen", - "NO3-N" - ], - "rank": 1006, - "is_a": "attribute", - "multivalued": false, - "alias": "nitrate_nitrogen", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "nitrite_nitrogen": { - "name": "nitrite_nitrogen", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mg/kg" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of nitrite nitrogen in the sample", - "title": "nitrite_nitrogen", - "examples": [ - { - "value": "1.2 mg/kg" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://www.ornl.gov/content/bio-scales-0" - ], - "aliases": [ - "nitrite_nitrogen", - "NO2-N" - ], - "rank": 1007, - "is_a": "attribute", - "multivalued": false, - "alias": "nitrite_nitrogen", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "non_microb_biomass": { - "name": "non_microb_biomass", - "description": "Amount of biomass; should include the name for the part of biomass measured, e.g.insect, plant, total. Can include multiple measurements separated by ;", - "title": "non-microbial biomass", - "examples": [ - { - "value": "insect 0.23 ug; plant 1g" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:biomass|microbial_biomass" - ], - "rank": 8, - "string_serialization": "{text};{float} {unit}", - "multivalued": false, - "alias": "non_microb_biomass", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" - }, - "non_microb_biomass_method": { - "name": "non_microb_biomass_method", - "description": "Reference or method used in determining biomass", - "title": "non-microbial biomass method", - "comments": [ - "required if \"non-microbial biomass\" is provided" - ], - "examples": [ - { - "value": "https://doi.org/10.1038/s41467-021-26181-3" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:microbial_biomass" - ], - "rank": 9, - "string_serialization": "{PMID}|{DOI}|{URL}", - "multivalued": false, - "alias": "non_microb_biomass_method", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string" - }, - "org_matter": { - "name": "org_matter", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of organic matter", - "title": "organic matter", - "examples": [ - { - "value": "1.75 milligram per cubic meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "organic matter" - ], - "rank": 45, - "is_a": "core field", - "slot_uri": "MIXS:0000204", - "multivalued": false, - "alias": "org_matter", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "org_nitro": { - "name": "org_nitro", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of organic nitrogen", - "title": "organic nitrogen", - "examples": [ - { - "value": "4 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "organic nitrogen" - ], - "rank": 46, - "is_a": "core field", - "slot_uri": "MIXS:0000205", - "multivalued": false, - "alias": "org_nitro", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "org_nitro_method": { - "name": "org_nitro_method", - "description": "Method used for obtaining organic nitrogen", - "title": "organic nitrogen method", - "comments": [ - "required if \"org_nitro\" is provided" - ], - "examples": [ - { - "value": "https://doi.org/10.1016/0038-0717(85)90144-0" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:org_nitro|tot_nitro_cont_meth" - ], - "rank": 14, - "string_serialization": "{PMID}|{DOI}|{URL}", - "multivalued": false, - "alias": "org_nitro_method", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string" - }, - "other_treatment": { - "name": "other_treatment", - "description": "Other treatments applied to your samples that are not applicable to the provided fields", - "title": "other treatments", - "comments": [ - "This is an open text field to provide any treatments that cannot be captured in the provided slots." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:additional_info" - ], - "rank": 15, - "string_serialization": "{text}", - "multivalued": false, - "alias": "other_treatment", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "recommended": true - }, - "oxy_stat_samp": { - "name": "oxy_stat_samp", - "description": "Oxygenation status of sample", - "title": "oxygenation status of sample", - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 25, - "is_a": "core field", - "slot_uri": "MIXS:0000753", - "multivalued": false, - "alias": "oxy_stat_samp", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "OxyStatSampEnum" - }, - "ph": { - "name": "ph", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid", - "title": "pH", - "notes": [ - "Use modified term" - ], - "examples": [ - { - "value": "7.2" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "pH" - ], - "rank": 27, - "is_a": "core field", - "string_serialization": "{float}", - "slot_uri": "MIXS:0001001", - "multivalued": false, - "alias": "ph", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "float", - "recommended": true, - "minimum_value": 0, - "maximum_value": 14 - }, - "ph_meth": { - "name": "ph_meth", - "description": "Reference or method used in determining ph", - "title": "pH method", - "comments": [ - "This can include a link to the instrument used or a citation for the method." - ], - "examples": [ - { - "value": "https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB" - }, - { - "value": "https://doi.org/10.2136/sssabookser5.3.c16" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 41, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0001106", - "multivalued": false, - "alias": "ph_meth", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "phosphate": { - "name": "phosphate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of phosphate", - "title": "phosphate", - "examples": [ - { - "value": "0.7 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "phosphate" - ], - "rank": 53, - "is_a": "core field", - "slot_uri": "MIXS:0000505", - "multivalued": false, - "alias": "phosphate", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "prev_land_use_meth": { - "name": "prev_land_use_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining previous land use and dates", - "title": "history/previous land use method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "history/previous land use method" - ], - "rank": 26, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000316", - "multivalued": false, - "alias": "prev_land_use_meth", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "previous_land_use": { - "name": "previous_land_use", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "land use name;date" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Previous land use and dates", - "title": "history/previous land use", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "history/previous land use" - ], - "rank": 27, - "is_a": "core field", - "string_serialization": "{text};{timestamp}", - "slot_uri": "MIXS:0000315", - "multivalued": false, - "alias": "previous_land_use", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^\\S+.*\\S+;([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" - }, - "profile_position": { - "name": "profile_position", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas", - "title": "profile position", - "examples": [ - { - "value": "summit" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "profile position" - ], - "rank": 28, - "is_a": "core field", - "slot_uri": "MIXS:0001084", - "multivalued": false, - "alias": "profile_position", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "profile_position_enum" - }, - "salinity": { - "name": "salinity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "practical salinity unit, percentage" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", - "title": "salinity", - "examples": [ - { - "value": "25 practical salinity unit" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "salinity" - ], - "rank": 54, - "is_a": "core field", - "slot_uri": "MIXS:0000183", - "multivalued": false, - "alias": "salinity", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "salinity_meth": { - "name": "salinity_meth", - "description": "Reference or method used in determining salinity", - "title": "salinity method", - "examples": [ - { - "value": "https://doi.org/10.1007/978-1-61779-986-0_28" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 55, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000341", - "multivalued": false, - "alias": "salinity_meth", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "samp_collec_device": { - "name": "samp_collec_device", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "device name" - } - }, - "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", - "title": "sample collection device", - "comments": [ - "Report dimensions and details when applicable" - ], - "examples": [ - { - "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection device" - ], - "rank": 14, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000002", - "multivalued": false, - "alias": "samp_collec_device", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "samp_collec_method": { - "name": "samp_collec_method", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI,url , or text" - } - }, - "description": "The method employed for collecting the sample.", - "title": "sample collection method", - "comments": [ - "This can be a citation or description" - ], - "examples": [ - { - "value": "swabbing" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection method" - ], - "rank": 15, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{PMID}|{DOI}|{URL}|{text}", - "slot_uri": "MIXS:0001225", - "multivalued": false, - "alias": "samp_collec_method", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_mat_process": { - "name": "samp_mat_process", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - } - }, - "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", - "title": "sample material processing", - "examples": [ - { - "value": "filtering of seawater" - }, - { - "value": "storing samples in ethanol" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample material processing" - ], - "rank": 12, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000016", - "multivalued": false, - "alias": "samp_mat_process", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_size": { - "name": "samp_size", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millliter, gram, milligram, liter" - } - }, - "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", - "title": "amount or size of sample collected", - "comments": [ - "This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis." - ], - "examples": [ - { - "value": "5 grams" - }, - { - "value": "10 mL" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "amount or size of sample collected" - ], - "rank": 18, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float} {unit}", - "slot_uri": "MIXS:0000001", - "multivalued": false, - "alias": "samp_size", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" - }, - "samp_store_temp": { - "name": "samp_store_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Temperature at which the sample was stored (degrees are assumed)", - "title": "sample storage temperature", - "examples": [ - { - "value": "-80 Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage temperature" - ], - "rank": 7, - "is_a": "core field", - "slot_uri": "MIXS:0000110", - "multivalued": false, - "alias": "samp_store_temp", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "sample_link": { - "name": "sample_link", - "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", - "title": "sample linkage", - "notes": [ - "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" - ], - "comments": [ - "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" - ], - "examples": [ - { - "value": "IGSN:DSJ0284" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "string_serialization": "{text}:{text}", - "multivalued": false, - "alias": "sample_link", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface", - "SampIdNewTermsMixin" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true, - "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" - }, - "season_precpt": { - "name": "season_precpt", - "description": "The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps.", - "title": "average seasonal precipitation", - "todos": [ - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "check validation & examples. always mm? so value only? Or value + unit", - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "check validation & examples. always mm? so value only? Or value + unit" - ], - "notes": [ - "mean and average are the same thing, but it seems like bad practice to not be consistent. Changed mean to average", - "mean and average are the same thing, but it seems like bad practice to not be consistent. Changed mean to average" - ], - "comments": [ - "Seasons are defined as spring (March, April, May), summer (June, July, August), autumn (September, October, November) and winter (December, January, February)." - ], - "examples": [ - { - "value": "0.4 inch" - }, - { - "value": "10.16 mm" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 29, - "is_a": "core field", - "slot_uri": "MIXS:0000645", - "multivalued": false, - "alias": "season_precpt", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "season_temp": { - "name": "season_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Mean seasonal temperature", - "title": "mean seasonal temperature", - "examples": [ - { - "value": "18 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "mean seasonal temperature" - ], - "rank": 30, - "is_a": "core field", - "slot_uri": "MIXS:0000643", - "multivalued": false, - "alias": "season_temp", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "sieving": { - "name": "sieving", - "description": "Collection design of pooled samples and/or sieve size and amount of sample sieved", - "title": "composite design/sieving", - "todos": [ - "check validation and examples", - "check validation and examples" - ], - "comments": [ - "Describe how samples were composited or sieved.", - "Use 'sample link' to indicate which samples were combined." - ], - "examples": [ - { - "value": "combined 2 cores" - }, - { - "value": "4mm sieved" - }, - { - "value": "4 mm sieved and homogenized" - }, - { - "value": "50 g" - }, - { - "value": "5 cores" - }, - { - "value": "2 mm sieved" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 8, - "is_a": "core field", - "string_serialization": "{{text}|{float} {unit}};{float} {unit}", - "slot_uri": "MIXS:0000322", - "multivalued": false, - "alias": "sieving", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "size_frac_low": { - "name": "size_frac_low", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micrometer" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample", - "title": "size-fraction lower threshold", - "examples": [ - { - "value": "0.2 micrometer" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "size-fraction lower threshold" - ], - "rank": 10, - "is_a": "core field", - "slot_uri": "MIXS:0000735", - "multivalued": false, - "alias": "size_frac_low", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "size_frac_up": { - "name": "size_frac_up", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micrometer" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample", - "title": "size-fraction upper threshold", - "examples": [ - { - "value": "20 micrometer" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "size-fraction upper threshold" - ], - "rank": 11, - "is_a": "core field", - "slot_uri": "MIXS:0000736", - "multivalued": false, - "alias": "size_frac_up", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "slope_aspect": { - "name": "slope_aspect", - "description": "The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees). - This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration.", - "title": "slope aspect", - "todos": [ - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot" - ], - "comments": [ - "Aspect is the orientation of slope, measured clockwise in degrees from 0 to 360, where 0 is north-facing, 90 is east-facing, 180 is south-facing, and 270 is west-facing." - ], - "examples": [ - { - "value": "35" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 1, - "is_a": "core field", - "slot_uri": "MIXS:0000647", - "multivalued": false, - "alias": "slope_aspect", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "slope_gradient": { - "name": "slope_gradient", - "description": "Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer", - "title": "slope gradient", - "todos": [ - "Slope is a percent. How does the validation work? Check to correct examples", - "Slope is a percent. How does the validation work? Check to correct examples" - ], - "examples": [ - { - "value": "10%" - }, - { - "value": "10 %" - }, - { - "value": "0.1" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 31, - "is_a": "core field", - "slot_uri": "MIXS:0000646", - "multivalued": false, - "alias": "slope_gradient", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "soil_horizon": { - "name": "soil_horizon", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath", - "title": "soil horizon", - "examples": [ - { - "value": "A horizon" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "soil horizon" - ], - "rank": 32, - "is_a": "core field", - "slot_uri": "MIXS:0001082", - "multivalued": false, - "alias": "soil_horizon", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "soil_horizon_enum" - }, - "soil_text_measure": { - "name": "soil_text_measure", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional.", - "title": "soil texture measurement", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "soil texture measurement" - ], - "rank": 33, - "is_a": "core field", - "slot_uri": "MIXS:0000335", - "multivalued": false, - "alias": "soil_text_measure", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "soil_texture_meth": { - "name": "soil_texture_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining soil texture", - "title": "soil texture method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "soil texture method" - ], - "rank": 34, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000336", - "multivalued": false, - "alias": "soil_texture_meth", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "soil_type": { - "name": "soil_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "ENVO_00001998" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Description of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes.", - "title": "soil type", - "examples": [ - { - "value": "plinthosol [ENVO:00002250]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "soil type" - ], - "rank": 35, - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000332", - "multivalued": false, - "alias": "soil_type", - "owner": "SoilInterface", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "soil_type_meth": { - "name": "soil_type_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining soil series name or other lower-level classification", - "title": "soil type method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "soil type method" - ], - "rank": 36, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000334", - "multivalued": false, - "alias": "soil_type_meth", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "specific_ecosystem": { - "name": "specific_ecosystem", - "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", - "notes": [ - "string or SpecificEcosystemEnum range?" - ], - "comments": [ - "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 13, - "is_a": "gold_path_field", - "alias": "specific_ecosystem", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "SpecificEcosystemEnum", - "recommended": true - }, - "start_date_inc": { - "name": "start_date_inc", - "description": "Date the incubation was started. Only relevant for incubation samples.", - "title": "incubation start date", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only" - ], - "comments": [ - "Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable." - ], - "examples": [ - { - "value": "2021-04-15, 2021-04 and 2021 are all acceptable." - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:collection_date" - ], - "rank": 4, - "string_serialization": "{date, arbitrary precision}", - "multivalued": false, - "alias": "start_date_inc", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "recommended": true, - "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" - }, - "start_time_inc": { - "name": "start_time_inc", - "description": "Time the incubation was started. Only relevant for incubation samples.", - "title": "incubation start time, GMT", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" - ], - "comments": [ - "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" - ], - "examples": [ - { - "value": "13:33 or 13:33:55" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:collection_date" - ], - "rank": 5, - "string_serialization": "{time, seconds optional}", - "multivalued": false, - "alias": "start_time_inc", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "recommended": true, - "pattern": "^([01]?\\d|2[0-3]|24(?=:00?:00?$)):([0-5]\\d)(:([0-5]\\d))?$" - }, - "store_cond": { - "name": "store_cond", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "storage condition type;duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Explain how the soil sample is stored (fresh/frozen/other).", - "title": "storage conditions", - "examples": [ - { - "value": "-20 degree Celsius freezer;P2Y10D" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "storage conditions" - ], - "rank": 2, - "is_a": "core field", - "string_serialization": "{text};{duration}", - "slot_uri": "MIXS:0000327", - "multivalued": false, - "alias": "store_cond", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_modified_section", - "range": "StoreCondEnum", - "required": true - }, - "temp": { - "name": "temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - } - }, - "description": "Temperature of the sample at the time of sampling.", - "title": "temperature", - "examples": [ - { - "value": "25 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "temperature" - ], - "rank": 37, - "is_a": "environment field", - "slot_uri": "MIXS:0000113", - "multivalued": false, - "alias": "temp", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tillage": { - "name": "tillage", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "enumeration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Note method(s) used for tilling", - "title": "history/tillage", - "examples": [ - { - "value": "chisel" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "history/tillage" - ], - "rank": 38, - "is_a": "core field", - "slot_uri": "MIXS:0001081", - "multivalued": true, - "alias": "tillage", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "tillage_enum" - }, - "tot_carb": { - "name": "tot_carb", - "description": "Total carbon content", - "title": "total carbon", - "todos": [ - "is this inorganic and organic? both? could use some clarification.", - "ug/L doesn't seem like the right units. Should check this slots usage in databases and re-evaluate. I couldn't find any references that provided this data in this format", - "is this inorganic and organic? both? could use some clarification.", - "ug/L doesn't seem like the right units. Should check this slots usage in databases and re-evaluate. I couldn't find any references that provided this data in this format" - ], - "examples": [ - { - "value": "1 ug/L" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 47, - "is_a": "core field", - "slot_uri": "MIXS:0000525", - "multivalued": false, - "alias": "tot_carb", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tot_nitro_cont_meth": { - "name": "tot_nitro_cont_meth", - "description": "Reference or method used in determining the total nitrogen", - "title": "total nitrogen content method", - "examples": [ - { - "value": "https://doi.org/10.2134/agronmonogr9.2.c32" - }, - { - "value": "https://acsess.onlinelibrary.wiley.com/doi/full/10.2136/sssaj2009.0389?casa_token=bm0pYIUdNMgAAAAA%3AOWVRR0STHaOe-afTcTdxn5m1hM8n2ltM0wY-b1iYpYdD9dhwppk5j3LvC2IO5yhOIvyLVeQz4NZRCZo" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 49, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000338", - "multivalued": false, - "alias": "tot_nitro_cont_meth", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "tot_nitro_content": { - "name": "tot_nitro_content", - "description": "Total nitrogen content of the sample", - "title": "total nitrogen content", - "examples": [ - { - "value": "5 mg N/ L" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 48, - "is_a": "core field", - "slot_uri": "MIXS:0000530", - "multivalued": false, - "alias": "tot_nitro_content", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tot_org_c_meth": { - "name": "tot_org_c_meth", - "description": "Reference or method used in determining total organic carbon", - "title": "total organic carbon method", - "examples": [ - { - "value": "https://doi.org/10.1080/07352680902776556" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 51, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000337", - "multivalued": false, - "alias": "tot_org_c_meth", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "tot_org_carb": { - "name": "tot_org_carb", - "description": "Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content", - "title": "total organic carbon", - "todos": [ - "check description. How are they different?", - "check description. How are they different?" - ], - "examples": [ - { - "value": "5 mg N/ L" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 50, - "is_a": "core field", - "slot_uri": "MIXS:0000533", - "multivalued": false, - "alias": "tot_org_carb", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tot_phosp": { - "name": "tot_phosp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus", - "title": "total phosphorus", - "examples": [ - { - "value": "0.03 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "total phosphorus" - ], - "rank": 52, - "is_a": "core field", - "slot_uri": "MIXS:0000117", - "multivalued": false, - "alias": "tot_phosp", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "water_cont_soil_meth": { - "name": "water_cont_soil_meth", - "description": "Reference or method used in determining the water content of soil", - "title": "water content method", - "todos": [ - "Why is it soil water content method in the name but not the title? Is this slot used in other samples?", - "Soil water content can be measure MANY ways and often, multiple ways are used in one experiment (gravimetric water content and water holding capacity and water filled pore space, to name a few).", - "Should this be multi valued? How to we manage and validate this?", - "Why is it soil water content method in the name but not the title? Is this slot used in other samples?", - "Soil water content can be measure MANY ways and often, multiple ways are used in one experiment (gravimetric water content and water holding capacity and water filled pore space, to name a few).", - "Should this be multi valued? How to we manage and validate this?" - ], - "comments": [ - "Required if providing water content" - ], - "examples": [ - { - "value": "J. Nat. Prod. Plant Resour., 2012, 2 (4):500-503" - }, - { - "value": "https://dec.alaska.gov/applications/spar/webcalc/definitions.htm" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 40, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000323", - "multivalued": false, - "alias": "water_cont_soil_meth", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "water_content": { - "name": "water_content", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "string" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram per gram or cubic centimeter per cubic centimeter" - } - }, - "description": "Water content measurement", - "title": "water content", - "todos": [ - "value in preferred unit is too limiting. need to change this", - "check and correct validation so examples are accepted", - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "how to manage multiple water content methods?", - "value in preferred unit is too limiting. need to change this", - "check and correct validation so examples are accepted", - "This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot", - "how to manage multiple water content methods?" - ], - "examples": [ - { - "value": "75%" - }, - { - "value": "75 %" - }, - { - "value": "0.75 g water/g dry soil" - }, - { - "value": "75% water holding capacity" - }, - { - "value": "1.1 g fresh weight/ dry weight" - }, - { - "value": "10% water filled pore space" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 39, - "is_a": "core field", - "string_serialization": "{float or pct} {unit}", - "slot_uri": "MIXS:0000185", - "multivalued": false, - "alias": "water_content", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "SoilInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?%? \\S.+$" - }, - "watering_regm": { - "name": "watering_regm", - "description": "Information about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", - "title": "watering regimen", - "examples": [ - { - "value": "1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" - }, - { - "value": "75% water holding capacity; constant" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 25, - "is_a": "core field", - "string_serialization": "{float} {unit};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000591", - "multivalued": false, - "alias": "watering_regm", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "PlantAssociatedInterface", - "SoilInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "zinc": { - "name": "zinc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mg/kg (ppm)" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of zinc in the sample", - "title": "zinc", - "examples": [ - { - "value": "2.5 mg/kg" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://www.ornl.gov/content/bio-scales-0" - ], - "aliases": [ - "zinc" - ], - "rank": 1004, - "is_a": "attribute", - "multivalued": false, - "alias": "zinc", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "SoilInterface" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "analysis_type": { - "name": "analysis_type", - "description": "Select all the data types associated or available for this biosample", - "title": "analysis/data type", - "examples": [ - { - "value": "metagenomics; metabolomics; proteomics" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:investigation_type" - ], - "rank": 3, - "multivalued": true, - "alias": "analysis_type", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "EmslInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "JgiMgInterface", - "JgiMtInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface" - ], - "slot_group": "sample_id_section", - "range": "analysis_type_enum", - "required": true, - "recommended": true - }, - "samp_name": { - "name": "samp_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - } - }, - "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", - "title": "sample name", - "comments": [ - "It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." - ], - "examples": [ - { - "value": "Rock core CB1178(5-6) from NSW" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample name" - ], - "rank": 1, - "is_a": "investigation field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0001107", - "multivalued": false, - "identifier": true, - "alias": "samp_name", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "EmslInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "JgiMgInterface", - "JgiMtInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true - }, - "source_mat_id": { - "name": "source_mat_id", - "description": "A globally unique identifier assigned to the biological sample.", - "title": "source material identifier", - "todos": [ - "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID.", - "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID." - ], - "notes": [ - "The source material IS the Globally Unique ID" - ], - "comments": [ - "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).", - "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/)." - ], - "examples": [ - { - "value": "IGSN:AU1243" - }, - { - "value": "UUID:24f1467a-40f4-11ed-b878-0242ac120002" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 2, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{text}:{text}", - "slot_uri": "MIXS:0000026", - "multivalued": false, - "alias": "source_mat_id", - "owner": "SoilInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "EmslInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "JgiMgInterface", - "JgiMtInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" - } - } - }, - "WastewaterSludgeInterface": { - "name": "WastewaterSludgeInterface", - "description": "wastewater_sludge dh_interface", - "title": "Wastewater Sludge", - "from_schema": "https://example.com/nmdc_submission_schema", - "is_a": "DhInterface", - "mixins": [ - "DhMultiviewCommonColumnsMixin", - "SampIdNewTermsMixin" - ], - "slots": [ - "alkalinity", - "biochem_oxygen_dem", - "chem_administration", - "chem_oxygen_dem", - "collection_date", - "depth", - "ecosystem", - "ecosystem_category", - "ecosystem_subtype", - "ecosystem_type", - "efficiency_percent", - "elev", - "emulsions", - "env_broad_scale", - "env_local_scale", - "env_medium", - "env_package", - "experimental_factor", - "gaseous_substances", - "geo_loc_name", - "horizon_meth", - "indust_eff_percent", - "inorg_particles", - "lat_lon", - "misc_param", - "nitrate", - "org_particles", - "organism_count", - "oxy_stat_samp", - "perturbation", - "ph", - "ph_meth", - "phosphate", - "pre_treatment", - "primary_treatment", - "reactor_type", - "salinity", - "samp_collec_device", - "samp_collec_method", - "samp_mat_process", - "samp_size", - "samp_store_dur", - "samp_store_loc", - "samp_store_temp", - "sample_link", - "secondary_treatment", - "sewage_type", - "size_frac", - "sludge_retent_time", - "sodium", - "soluble_inorg_mat", - "soluble_org_mat", - "specific_ecosystem", - "suspend_solids", - "temp", - "tertiary_treatment", - "tot_nitro", - "tot_phosphate", - "wastewater_type" - ], - "slot_usage": { - "alkalinity": { - "name": "alkalinity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milliequivalent per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate", - "title": "alkalinity", - "examples": [ - { - "value": "50 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "alkalinity" - ], - "rank": 1, - "is_a": "core field", - "slot_uri": "MIXS:0000421", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "biochem_oxygen_dem": { - "name": "biochem_oxygen_dem", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period", - "title": "biochemical oxygen demand", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "biochemical oxygen demand" - ], - "rank": 296, - "is_a": "core field", - "slot_uri": "MIXS:0000653", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "WastewaterSludgeInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "chem_administration": { - "name": "chem_administration", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "CHEBI;timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", - "title": "chemical administration", - "examples": [ - { - "value": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22" - }, - { - "value": "agar [CHEBI:2509];2018-05" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "chemical administration" - ], - "rank": 17, - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]};{timestamp}", - "slot_uri": "MIXS:0000751", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" - }, - "chem_oxygen_dem": { - "name": "chem_oxygen_dem", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite", - "title": "chemical oxygen demand", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "chemical oxygen demand" - ], - "rank": 301, - "is_a": "core field", - "slot_uri": "MIXS:0000656", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "WastewaterSludgeInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "collection_date": { - "name": "collection_date", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "date and time" - } - }, - "description": "The date of sampling", - "title": "collection date", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", - "Use modified term (amended definition)" - ], - "examples": [ - { - "value": "2021-04-15" - }, - { - "value": "2021-04" - }, - { - "value": "2021" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "collection date" - ], - "rank": 3, - "is_a": "environment field", - "string_serialization": "{date, arbitrary precision}", - "slot_uri": "MIXS:0000011", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" - }, - "depth": { - "name": "depth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - } - }, - "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", - "title": "depth, meters", - "notes": [ - "Use modified term" - ], - "comments": [ - "All depths must be reported in meters. Provide the numerical portion only." - ], - "examples": [ - { - "value": "0 - 0.1" - }, - { - "value": "1" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "depth" - ], - "rank": 9, - "is_a": "environment field", - "string_serialization": "{float}|{float}-{float}", - "slot_uri": "MIXS:0000018", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$" - }, - "ecosystem": { - "name": "ecosystem", - "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", - "notes": [ - "range: string or EcosystemEnum? The enum could be dynamic or might be soil biased." - ], - "comments": [ - "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 9, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_category": { - "name": "ecosystem_category", - "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", - "notes": [ - "string or EcosystemCategoryEnum range?" - ], - "comments": [ - "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 10, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_subtype": { - "name": "ecosystem_subtype", - "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", - "notes": [ - "string or EcosystemSubtypeEnum range?" - ], - "comments": [ - "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 12, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_type": { - "name": "ecosystem_type", - "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", - "notes": [ - "string or EcosystemTypeEnum range?" - ], - "comments": [ - "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 11, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "efficiency_percent": { - "name": "efficiency_percent", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Percentage of volatile solids removed from the anaerobic digestor", - "title": "efficiency percent", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "efficiency percent" - ], - "rank": 307, - "is_a": "core field", - "slot_uri": "MIXS:0000657", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "WastewaterSludgeInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "elev": { - "name": "elev", - "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", - "title": "elevation, meters", - "comments": [ - "All elevations must be reported in meters. Provide the numerical portion only.", - "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." - ], - "examples": [ - { - "value": "225" - }, - { - "value": "0" - }, - { - "value": "1250" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "slot_uri": "MIXS:0000093", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "float", - "required": true - }, - "emulsions": { - "name": "emulsions", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "emulsion name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types", - "title": "emulsions", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "emulsions" - ], - "rank": 308, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000660", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "WastewaterSludgeInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "env_broad_scale": { - "name": "env_broad_scale", - "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", - "title": "broad-scale environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000012", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_local_scale": { - "name": "env_local_scale", - "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", - "title": "local environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "canopy [ENVO:00000047]" - }, - { - "value": "herb and fern layer [ENVO:01000337]" - }, - { - "value": "litter layer [ENVO:01000338]" - }, - { - "value": "understory [01000335]" - }, - { - "value": "shrub layer [ENVO:01000336]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 7, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000013", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_medium": { - "name": "env_medium", - "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", - "title": "environmental medium", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "soil [ENVO:00001998]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 8, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000014", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_package": { - "name": "env_package", - "description": "Select the MIxS enviromental package that best describes the environment from which your sample was collected.", - "title": "environmental package", - "examples": [ - { - "value": "soil" - } - ], - "in_subset": [ - "mixs extension" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "environmental package" - ], - "rank": 4, - "is_a": "attribute", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true - }, - "experimental_factor": { - "name": "experimental_factor", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text or EFO and/or OBI" - } - }, - "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", - "title": "experimental factor", - "examples": [ - { - "value": "time series design [EFO:EFO_0001779]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "experimental factor" - ], - "rank": 12, - "is_a": "investigation field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000008", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "gaseous_substances": { - "name": "gaseous_substances", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "gaseous substance name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances", - "title": "gaseous substances", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "gaseous substances" - ], - "rank": 311, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000661", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "WastewaterSludgeInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "geo_loc_name": { - "name": "geo_loc_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" - } - }, - "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", - "title": "geographic location (country and/or sea,region)", - "examples": [ - { - "value": "USA: Maryland, Bethesda" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "geographic location (country and/or sea,region)" - ], - "rank": 4, - "is_a": "environment field", - "string_serialization": "{text}: {text}, {text}", - "slot_uri": "MIXS:0000010", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" - }, - "horizon_meth": { - "name": "horizon_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining the horizon", - "title": "horizon method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "soil horizon method" - ], - "rank": 19, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000321", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "indust_eff_percent": { - "name": "indust_eff_percent", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "percentage" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Percentage of industrial effluents received by wastewater treatment plant", - "title": "industrial effluent percent", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "industrial effluent percent" - ], - "rank": 332, - "is_a": "core field", - "slot_uri": "MIXS:0000662", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "WastewaterSludgeInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "inorg_particles": { - "name": "inorg_particles", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "inorganic particle name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles", - "title": "inorganic particles", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "inorganic particles" - ], - "rank": 333, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000664", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "WastewaterSludgeInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "lat_lon": { - "name": "lat_lon", - "description": "This is currently a required field but it's not clear if this should be required for human hosts", - "title": "geographic location (latitude and longitude)", - "notes": [ - "required where?", - "This is currently a required field but it's not clear if this should be required for human hosts" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "is_a": "environment field", - "string_serialization": "{lat lon}", - "slot_uri": "MIXS:0000009", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" - }, - "misc_param": { - "name": "misc_param", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "parameter name;measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Any other measurement performed or parameter collected, that is not listed here", - "title": "miscellaneous parameter", - "examples": [ - { - "value": "Bicarbonate ion concentration;2075 micromole per kilogram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "miscellaneous parameter" - ], - "rank": 23, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000752", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "nitrate": { - "name": "nitrate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of nitrate in the sample", - "title": "nitrate", - "examples": [ - { - "value": "65 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "nitrate" - ], - "rank": 26, - "is_a": "core field", - "slot_uri": "MIXS:0000425", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "org_particles": { - "name": "org_particles", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "particle name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc.", - "title": "organic particles", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "organic particles" - ], - "rank": 338, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000665", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "WastewaterSludgeInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "organism_count": { - "name": "organism_count", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "organism name;measurement value;enumeration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", - "title": "organism count", - "examples": [ - { - "value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "organism count" - ], - "rank": 30, - "is_a": "core field", - "slot_uri": "MIXS:0000103", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$" - }, - "oxy_stat_samp": { - "name": "oxy_stat_samp", - "description": "Oxygenation status of sample", - "title": "oxygenation status of sample", - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 25, - "is_a": "core field", - "slot_uri": "MIXS:0000753", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "OxyStatSampEnum" - }, - "perturbation": { - "name": "perturbation", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "perturbation type name;perturbation interval and duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types", - "title": "perturbation", - "examples": [ - { - "value": "antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "perturbation" - ], - "rank": 33, - "is_a": "core field", - "string_serialization": "{text};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000754", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "ph": { - "name": "ph", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid", - "title": "pH", - "notes": [ - "Use modified term" - ], - "examples": [ - { - "value": "7.2" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "pH" - ], - "rank": 27, - "is_a": "core field", - "string_serialization": "{float}", - "slot_uri": "MIXS:0001001", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "float", - "recommended": true, - "minimum_value": 0, - "maximum_value": 14 - }, - "ph_meth": { - "name": "ph_meth", - "description": "Reference or method used in determining ph", - "title": "pH method", - "comments": [ - "This can include a link to the instrument used or a citation for the method." - ], - "examples": [ - { - "value": "https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB" - }, - { - "value": "https://doi.org/10.2136/sssabookser5.3.c16" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 41, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0001106", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "phosphate": { - "name": "phosphate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of phosphate", - "title": "phosphate", - "examples": [ - { - "value": "0.7 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "phosphate" - ], - "rank": 53, - "is_a": "core field", - "slot_uri": "MIXS:0000505", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "pre_treatment": { - "name": "pre_treatment", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "pre-treatment type" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The process of pre-treatment removes materials that can be easily collected from the raw wastewater", - "title": "pre-treatment", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "pre-treatment" - ], - "rank": 342, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000348", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "WastewaterSludgeInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "primary_treatment": { - "name": "primary_treatment", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "primary treatment type" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed", - "title": "primary treatment", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "primary treatment" - ], - "rank": 343, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000349", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "WastewaterSludgeInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "reactor_type": { - "name": "reactor_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "reactor type name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage", - "title": "reactor type", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "reactor type" - ], - "rank": 346, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000350", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "WastewaterSludgeInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "salinity": { - "name": "salinity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "practical salinity unit, percentage" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", - "title": "salinity", - "examples": [ - { - "value": "25 practical salinity unit" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "salinity" - ], - "rank": 54, - "is_a": "core field", - "slot_uri": "MIXS:0000183", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "samp_collec_device": { - "name": "samp_collec_device", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "device name" - } - }, - "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", - "title": "sample collection device", - "comments": [ - "Report dimensions and details when applicable" - ], - "examples": [ - { - "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection device" - ], - "rank": 14, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000002", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "samp_collec_method": { - "name": "samp_collec_method", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI,url , or text" - } - }, - "description": "The method employed for collecting the sample.", - "title": "sample collection method", - "comments": [ - "This can be a citation or description" - ], - "examples": [ - { - "value": "swabbing" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection method" - ], - "rank": 15, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{PMID}|{DOI}|{URL}|{text}", - "slot_uri": "MIXS:0001225", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_mat_process": { - "name": "samp_mat_process", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - } - }, - "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", - "title": "sample material processing", - "examples": [ - { - "value": "filtering of seawater" - }, - { - "value": "storing samples in ethanol" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample material processing" - ], - "rank": 12, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000016", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_size": { - "name": "samp_size", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millliter, gram, milligram, liter" - } - }, - "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", - "title": "amount or size of sample collected", - "comments": [ - "This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis." - ], - "examples": [ - { - "value": "5 grams" - }, - { - "value": "10 mL" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "amount or size of sample collected" - ], - "rank": 18, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float} {unit}", - "slot_uri": "MIXS:0000001", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" - }, - "samp_store_dur": { - "name": "samp_store_dur", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Duration for which the sample was stored", - "title": "sample storage duration", - "examples": [ - { - "value": "P1Y6M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage duration" - ], - "rank": 353, - "is_a": "core field", - "string_serialization": "{duration}", - "slot_uri": "MIXS:0000116", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_store_loc": { - "name": "samp_store_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "location name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Location at which sample was stored, usually name of a specific freezer/room", - "title": "sample storage location", - "examples": [ - { - "value": "Freezer no:5" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage location" - ], - "rank": 41, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000755", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_store_temp": { - "name": "samp_store_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Temperature at which the sample was stored (degrees are assumed)", - "title": "sample storage temperature", - "examples": [ - { - "value": "-80 Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage temperature" - ], - "rank": 7, - "is_a": "core field", - "slot_uri": "MIXS:0000110", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "sample_link": { - "name": "sample_link", - "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", - "title": "sample linkage", - "notes": [ - "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" - ], - "comments": [ - "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" - ], - "examples": [ - { - "value": "IGSN:DSJ0284" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "string_serialization": "{text}:{text}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface", - "SampIdNewTermsMixin" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true, - "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" - }, - "secondary_treatment": { - "name": "secondary_treatment", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "secondary treatment type" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The process for substantially degrading the biological content of the sewage", - "title": "secondary treatment", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "secondary treatment" - ], - "rank": 360, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000351", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "WastewaterSludgeInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "sewage_type": { - "name": "sewage_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "sewage type name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Type of wastewater treatment plant as municipial or industrial", - "title": "sewage type", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sewage type" - ], - "rank": 361, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000215", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "WastewaterSludgeInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "size_frac": { - "name": "size_frac", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "filter size value range" - } - }, - "description": "Filtering pore size used in sample preparation", - "title": "size fraction selected", - "examples": [ - { - "value": "0-0.22 micrometer" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "size fraction selected" - ], - "rank": 285, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float}-{float} {unit}", - "slot_uri": "MIXS:0000017", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "sludge_retent_time": { - "name": "sludge_retent_time", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "hours" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The time activated sludge remains in reactor", - "title": "sludge retention time", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sludge retention time" - ], - "rank": 362, - "is_a": "core field", - "slot_uri": "MIXS:0000669", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "WastewaterSludgeInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "sodium": { - "name": "sodium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Sodium concentration in the sample", - "title": "sodium", - "examples": [ - { - "value": "10.5 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sodium" - ], - "rank": 363, - "is_a": "core field", - "slot_uri": "MIXS:0000428", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "soluble_inorg_mat": { - "name": "soluble_inorg_mat", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "soluble inorganic material name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, microgram, mole per liter, gram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc.", - "title": "soluble inorganic material", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "soluble inorganic material" - ], - "rank": 364, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000672", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "WastewaterSludgeInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "soluble_org_mat": { - "name": "soluble_org_mat", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "soluble organic material name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, microgram, mole per liter, gram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc.", - "title": "soluble organic material", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "soluble organic material" - ], - "rank": 365, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000673", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "WastewaterSludgeInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "specific_ecosystem": { - "name": "specific_ecosystem", - "description": "Specific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.", - "notes": [ - "string or SpecificEcosystemEnum range?" - ], - "comments": [ - "Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 13, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "suspend_solids": { - "name": "suspend_solids", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "suspended solid name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, microgram, milligram per liter, mole per liter, gram per liter, part per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances", - "title": "suspended solids", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "suspended solids" - ], - "rank": 372, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000150", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "WastewaterSludgeInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "temp": { - "name": "temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - } - }, - "description": "Temperature of the sample at the time of sampling.", - "title": "temperature", - "examples": [ - { - "value": "25 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "temperature" - ], - "rank": 37, - "is_a": "environment field", - "slot_uri": "MIXS:0000113", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tertiary_treatment": { - "name": "tertiary_treatment", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "tertiary treatment type" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment", - "title": "tertiary treatment", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "tertiary treatment" - ], - "rank": 374, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000352", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "WastewaterSludgeInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "tot_nitro": { - "name": "tot_nitro", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter, micromole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen", - "title": "total nitrogen concentration", - "examples": [ - { - "value": "50 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "total nitrogen concentration" - ], - "rank": 377, - "is_a": "core field", - "slot_uri": "MIXS:0000102", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tot_phosphate": { - "name": "tot_phosphate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter, micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Total amount or concentration of phosphate", - "title": "total phosphate", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "total phosphate" - ], - "rank": 378, - "is_a": "core field", - "slot_uri": "MIXS:0000689", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "WastewaterSludgeInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "wastewater_type": { - "name": "wastewater_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "wastewater type name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The origin of wastewater such as human waste, rainfall, storm drains, etc.", - "title": "wastewater type", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "wastewater type" - ], - "rank": 385, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000353", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "WastewaterSludgeInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - } - }, - "attributes": { - "alkalinity": { - "name": "alkalinity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milliequivalent per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate", - "title": "alkalinity", - "examples": [ - { - "value": "50 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "alkalinity" - ], - "rank": 1, - "is_a": "core field", - "slot_uri": "MIXS:0000421", - "multivalued": false, - "alias": "alkalinity", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "biochem_oxygen_dem": { - "name": "biochem_oxygen_dem", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Amount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period", - "title": "biochemical oxygen demand", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "biochemical oxygen demand" - ], - "rank": 296, - "is_a": "core field", - "slot_uri": "MIXS:0000653", - "multivalued": false, - "alias": "biochem_oxygen_dem", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "WastewaterSludgeInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "chem_administration": { - "name": "chem_administration", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "CHEBI;timestamp" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi", - "title": "chemical administration", - "examples": [ - { - "value": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22" - }, - { - "value": "agar [CHEBI:2509];2018-05" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "chemical administration" - ], - "rank": 17, - "is_a": "core field", - "string_serialization": "{termLabel} {[termID]};{timestamp}", - "slot_uri": "MIXS:0000751", - "multivalued": false, - "alias": "chem_administration", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\];([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" - }, - "chem_oxygen_dem": { - "name": "chem_oxygen_dem", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "A measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite", - "title": "chemical oxygen demand", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "chemical oxygen demand" - ], - "rank": 301, - "is_a": "core field", - "slot_uri": "MIXS:0000656", - "multivalued": false, - "alias": "chem_oxygen_dem", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "WastewaterSludgeInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "collection_date": { - "name": "collection_date", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "date and time" - } - }, - "description": "The date of sampling", - "title": "collection date", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only", - "Use modified term (amended definition)" - ], - "examples": [ - { - "value": "2021-04-15" - }, - { - "value": "2021-04" - }, - { - "value": "2021" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "collection date" - ], - "rank": 3, - "is_a": "environment field", - "string_serialization": "{date, arbitrary precision}", - "slot_uri": "MIXS:0000011", - "multivalued": false, - "alias": "collection_date", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" - }, - "depth": { - "name": "depth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - } - }, - "description": "The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.", - "title": "depth, meters", - "notes": [ - "Use modified term" - ], - "comments": [ - "All depths must be reported in meters. Provide the numerical portion only." - ], - "examples": [ - { - "value": "0 - 0.1" - }, - { - "value": "1" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "depth" - ], - "rank": 9, - "is_a": "environment field", - "string_serialization": "{float}|{float}-{float}", - "slot_uri": "MIXS:0000018", - "multivalued": false, - "alias": "depth", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?(\\s*-\\s*[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)?$" - }, - "ecosystem": { - "name": "ecosystem", - "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", - "notes": [ - "range: string or EcosystemEnum? The enum could be dynamic or might be soil biased." - ], - "comments": [ - "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 9, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_category": { - "name": "ecosystem_category", - "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", - "notes": [ - "string or EcosystemCategoryEnum range?" - ], - "comments": [ - "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 10, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem_category", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_subtype": { - "name": "ecosystem_subtype", - "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", - "notes": [ - "string or EcosystemSubtypeEnum range?" - ], - "comments": [ - "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 12, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem_subtype", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_type": { - "name": "ecosystem_type", - "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", - "notes": [ - "string or EcosystemTypeEnum range?" - ], - "comments": [ - "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 11, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem_type", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "efficiency_percent": { - "name": "efficiency_percent", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Percentage of volatile solids removed from the anaerobic digestor", - "title": "efficiency percent", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "efficiency percent" - ], - "rank": 307, - "is_a": "core field", - "slot_uri": "MIXS:0000657", - "multivalued": false, - "alias": "efficiency_percent", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "WastewaterSludgeInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "elev": { - "name": "elev", - "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", - "title": "elevation, meters", - "comments": [ - "All elevations must be reported in meters. Provide the numerical portion only.", - "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." - ], - "examples": [ - { - "value": "225" - }, - { - "value": "0" - }, - { - "value": "1250" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "slot_uri": "MIXS:0000093", - "multivalued": false, - "alias": "elev", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "float", - "required": true - }, - "emulsions": { - "name": "emulsions", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "emulsion name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types", - "title": "emulsions", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "emulsions" - ], - "rank": 308, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000660", - "multivalued": false, - "alias": "emulsions", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "WastewaterSludgeInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "env_broad_scale": { - "name": "env_broad_scale", - "description": "In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html", - "title": "broad-scale environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000012", - "multivalued": false, - "alias": "env_broad_scale", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_local_scale": { - "name": "env_local_scale", - "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", - "title": "local environmental context", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "canopy [ENVO:00000047]" - }, - { - "value": "herb and fern layer [ENVO:01000337]" - }, - { - "value": "litter layer [ENVO:01000338]" - }, - { - "value": "understory [01000335]" - }, - { - "value": "shrub layer [ENVO:01000336]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 7, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000013", - "multivalued": false, - "alias": "env_local_scale", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_medium": { - "name": "env_medium", - "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", - "title": "environmental medium", - "notes": [ - "range changed to enumeration late in makefile, so this is modified (but \"sample ID\" anyway)" - ], - "examples": [ - { - "value": "soil [ENVO:00001998]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 8, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000014", - "multivalued": false, - "alias": "env_medium", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_package": { - "name": "env_package", - "description": "Select the MIxS enviromental package that best describes the environment from which your sample was collected.", - "title": "environmental package", - "examples": [ - { - "value": "soil" - } - ], - "in_subset": [ - "mixs extension" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "environmental package" - ], - "rank": 4, - "is_a": "attribute", - "multivalued": false, - "alias": "env_package", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true - }, - "experimental_factor": { - "name": "experimental_factor", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text or EFO and/or OBI" - } - }, - "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", - "title": "experimental factor", - "examples": [ - { - "value": "time series design [EFO:EFO_0001779]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "experimental factor" - ], - "rank": 12, - "is_a": "investigation field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000008", - "multivalued": false, - "alias": "experimental_factor", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "gaseous_substances": { - "name": "gaseous_substances", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "gaseous substance name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances", - "title": "gaseous substances", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "gaseous substances" - ], - "rank": 311, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000661", - "multivalued": false, - "alias": "gaseous_substances", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "WastewaterSludgeInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "geo_loc_name": { - "name": "geo_loc_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" - } - }, - "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", - "title": "geographic location (country and/or sea,region)", - "examples": [ - { - "value": "USA: Maryland, Bethesda" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "geographic location (country and/or sea,region)" - ], - "rank": 4, - "is_a": "environment field", - "string_serialization": "{text}: {text}, {text}", - "slot_uri": "MIXS:0000010", - "multivalued": false, - "alias": "geo_loc_name", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" - }, - "horizon_meth": { - "name": "horizon_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining the horizon", - "title": "horizon method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "soil horizon method" - ], - "rank": 19, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000321", - "multivalued": false, - "alias": "horizon_meth", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "indust_eff_percent": { - "name": "indust_eff_percent", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "percentage" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Percentage of industrial effluents received by wastewater treatment plant", - "title": "industrial effluent percent", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "industrial effluent percent" - ], - "rank": 332, - "is_a": "core field", - "slot_uri": "MIXS:0000662", - "multivalued": false, - "alias": "indust_eff_percent", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "WastewaterSludgeInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "inorg_particles": { - "name": "inorg_particles", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "inorganic particle name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles", - "title": "inorganic particles", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "inorganic particles" - ], - "rank": 333, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000664", - "multivalued": false, - "alias": "inorg_particles", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "WastewaterSludgeInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "lat_lon": { - "name": "lat_lon", - "description": "This is currently a required field but it's not clear if this should be required for human hosts", - "title": "geographic location (latitude and longitude)", - "notes": [ - "required where?", - "This is currently a required field but it's not clear if this should be required for human hosts" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "is_a": "environment field", - "string_serialization": "{lat lon}", - "slot_uri": "MIXS:0000009", - "multivalued": false, - "alias": "lat_lon", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" - }, - "misc_param": { - "name": "misc_param", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "parameter name;measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Any other measurement performed or parameter collected, that is not listed here", - "title": "miscellaneous parameter", - "examples": [ - { - "value": "Bicarbonate ion concentration;2075 micromole per kilogram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "miscellaneous parameter" - ], - "rank": 23, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000752", - "multivalued": false, - "alias": "misc_param", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "nitrate": { - "name": "nitrate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of nitrate in the sample", - "title": "nitrate", - "examples": [ - { - "value": "65 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "nitrate" - ], - "rank": 26, - "is_a": "core field", - "slot_uri": "MIXS:0000425", - "multivalued": false, - "alias": "nitrate", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "org_particles": { - "name": "org_particles", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "particle name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc.", - "title": "organic particles", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "organic particles" - ], - "rank": 338, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000665", - "multivalued": false, - "alias": "org_particles", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "WastewaterSludgeInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "organism_count": { - "name": "organism_count", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "organism name;measurement value;enumeration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)", - "title": "organism count", - "examples": [ - { - "value": "total prokaryotes;3.5e7 cells per milliliter;qPCR" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "organism count" - ], - "rank": 30, - "is_a": "core field", - "slot_uri": "MIXS:0000103", - "multivalued": false, - "alias": "organism_count", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([-+]?[0-9]*\\.?[0-9]+ +\\S.*\\|)*([-+]?[0-9]*\\.?[0-9]+ +\\S.*)$" - }, - "oxy_stat_samp": { - "name": "oxy_stat_samp", - "description": "Oxygenation status of sample", - "title": "oxygenation status of sample", - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 25, - "is_a": "core field", - "slot_uri": "MIXS:0000753", - "multivalued": false, - "alias": "oxy_stat_samp", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "OxyStatSampEnum" - }, - "perturbation": { - "name": "perturbation", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "perturbation type name;perturbation interval and duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types", - "title": "perturbation", - "examples": [ - { - "value": "antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "perturbation" - ], - "rank": 33, - "is_a": "core field", - "string_serialization": "{text};{Rn/start_time/end_time/duration}", - "slot_uri": "MIXS:0000754", - "multivalued": false, - "alias": "perturbation", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "ph": { - "name": "ph", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid", - "title": "pH", - "notes": [ - "Use modified term" - ], - "examples": [ - { - "value": "7.2" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "pH" - ], - "rank": 27, - "is_a": "core field", - "string_serialization": "{float}", - "slot_uri": "MIXS:0001001", - "multivalued": false, - "alias": "ph", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "float", - "recommended": true, - "minimum_value": 0, - "maximum_value": 14 - }, - "ph_meth": { - "name": "ph_meth", - "description": "Reference or method used in determining ph", - "title": "pH method", - "comments": [ - "This can include a link to the instrument used or a citation for the method." - ], - "examples": [ - { - "value": "https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB" - }, - { - "value": "https://doi.org/10.2136/sssabookser5.3.c16" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 41, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0001106", - "multivalued": false, - "alias": "ph_meth", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "phosphate": { - "name": "phosphate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of phosphate", - "title": "phosphate", - "examples": [ - { - "value": "0.7 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "phosphate" - ], - "rank": 53, - "is_a": "core field", - "slot_uri": "MIXS:0000505", - "multivalued": false, - "alias": "phosphate", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "pre_treatment": { - "name": "pre_treatment", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "pre-treatment type" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The process of pre-treatment removes materials that can be easily collected from the raw wastewater", - "title": "pre-treatment", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "pre-treatment" - ], - "rank": 342, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000348", - "multivalued": false, - "alias": "pre_treatment", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "WastewaterSludgeInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "primary_treatment": { - "name": "primary_treatment", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "primary treatment type" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed", - "title": "primary treatment", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "primary treatment" - ], - "rank": 343, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000349", - "multivalued": false, - "alias": "primary_treatment", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "WastewaterSludgeInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "reactor_type": { - "name": "reactor_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "reactor type name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Anaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage", - "title": "reactor type", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "reactor type" - ], - "rank": 346, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000350", - "multivalued": false, - "alias": "reactor_type", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "WastewaterSludgeInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "salinity": { - "name": "salinity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "practical salinity unit, percentage" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", - "title": "salinity", - "examples": [ - { - "value": "25 practical salinity unit" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "salinity" - ], - "rank": 54, - "is_a": "core field", - "slot_uri": "MIXS:0000183", - "multivalued": false, - "alias": "salinity", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "samp_collec_device": { - "name": "samp_collec_device", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "device name" - } - }, - "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", - "title": "sample collection device", - "comments": [ - "Report dimensions and details when applicable" - ], - "examples": [ - { - "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection device" - ], - "rank": 14, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000002", - "multivalued": false, - "alias": "samp_collec_device", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "recommended": true - }, - "samp_collec_method": { - "name": "samp_collec_method", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI,url , or text" - } - }, - "description": "The method employed for collecting the sample.", - "title": "sample collection method", - "comments": [ - "This can be a citation or description" - ], - "examples": [ - { - "value": "swabbing" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection method" - ], - "rank": 15, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{PMID}|{DOI}|{URL}|{text}", - "slot_uri": "MIXS:0001225", - "multivalued": false, - "alias": "samp_collec_method", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_mat_process": { - "name": "samp_mat_process", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - } - }, - "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", - "title": "sample material processing", - "examples": [ - { - "value": "filtering of seawater" - }, - { - "value": "storing samples in ethanol" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample material processing" - ], - "rank": 12, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000016", - "multivalued": false, - "alias": "samp_mat_process", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_size": { - "name": "samp_size", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millliter, gram, milligram, liter" - } - }, - "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", - "title": "amount or size of sample collected", - "comments": [ - "This refers to the TOTAL amount of sample collected from the experiment. 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This is relevant when a sample or other material was used to generate the new sample.", - "title": "sample linkage", - "notes": [ - "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" - ], - "comments": [ - "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" - ], - "examples": [ - { - "value": "IGSN:DSJ0284" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "string_serialization": "{text}:{text}", - "multivalued": false, - "alias": "sample_link", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface", - "SampIdNewTermsMixin" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true, - "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" - }, - "secondary_treatment": { - "name": "secondary_treatment", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "secondary treatment type" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The process for substantially degrading the biological content of the sewage", - "title": "secondary treatment", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "secondary treatment" - ], - "rank": 360, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000351", - "multivalued": false, - "alias": "secondary_treatment", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "WastewaterSludgeInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "sewage_type": { - "name": "sewage_type", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "sewage type name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Type of wastewater treatment plant as municipial or industrial", - "title": "sewage type", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sewage type" - ], - "rank": 361, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000215", - "multivalued": false, - "alias": "sewage_type", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "WastewaterSludgeInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "size_frac": { - "name": "size_frac", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "filter size value range" - } - }, - "description": "Filtering pore size used in sample preparation", - "title": "size fraction selected", - "examples": [ - { - "value": "0-0.22 micrometer" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "size fraction selected" - ], - "rank": 285, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float}-{float} {unit}", - "slot_uri": "MIXS:0000017", - "multivalued": false, - "alias": "size_frac", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "sludge_retent_time": { - "name": "sludge_retent_time", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "hours" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The time activated sludge remains in reactor", - "title": "sludge retention time", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sludge retention time" - ], - "rank": 362, - "is_a": "core field", - "slot_uri": "MIXS:0000669", - "multivalued": false, - "alias": "sludge_retent_time", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "WastewaterSludgeInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "sodium": { - "name": "sodium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Sodium concentration in the sample", - "title": "sodium", - "examples": [ - { - "value": "10.5 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sodium" - ], - "rank": 363, - "is_a": "core field", - "slot_uri": "MIXS:0000428", - "multivalued": false, - "alias": "sodium", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "soluble_inorg_mat": { - "name": "soluble_inorg_mat", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "soluble inorganic material name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "gram, microgram, mole per liter, gram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc.", - "title": "soluble inorganic material", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "soluble inorganic material" - ], - "rank": 364, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000672", - "multivalued": false, - "alias": "soluble_inorg_mat", - "owner": "WastewaterSludgeInterface", - "domain_of": [ - "Biosample", - "WastewaterSludgeInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? 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Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. 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"pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_inorg_nitro": { - "name": "diss_inorg_nitro", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter, micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved inorganic nitrogen", - "title": "dissolved inorganic nitrogen", - "examples": [ - { - "value": "761 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved inorganic nitrogen" - ], - "rank": 223, - "is_a": "core field", - "slot_uri": "MIXS:0000698", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_inorg_phosp": { - "name": "diss_inorg_phosp", - "annotations": { - 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"value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid", - "title": "dissolved organic carbon", - "examples": [ - { - "value": "197 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved organic carbon" - ], - "rank": 17, - "is_a": "core field", - "slot_uri": "MIXS:0000433", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_org_nitro": { - "name": "diss_org_nitro", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2", - "title": "dissolved organic nitrogen", - "examples": [ - { - "value": "0.05 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved organic nitrogen" - ], - "rank": 18, - "is_a": "core field", - "slot_uri": "MIXS:0000162", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_oxygen": { - "name": "diss_oxygen", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per kilogram, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved oxygen", - "title": "dissolved oxygen", - "examples": [ - { - "value": "175 micromole per kilogram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved oxygen" - ], - "rank": 19, - "is_a": "core field", - "slot_uri": "MIXS:0000119", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "down_par": { - "name": "down_par", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microEinstein per square meter per second, microEinstein per square centimeter per second" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Visible waveband radiance and irradiance measurements in the water column", - "title": "downward PAR", - "examples": [ - { - "value": "28.71 microEinstein per square meter per second" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "downward PAR" - ], - "rank": 225, - "is_a": "core field", - "slot_uri": "MIXS:0000703", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "ecosystem": { - "name": "ecosystem", - "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", - "comments": [ - "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 9, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_category": { - "name": "ecosystem_category", - "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", - "comments": [ - "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 10, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_subtype": { - "name": "ecosystem_subtype", - "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", - "comments": [ - "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 12, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_type": { - "name": "ecosystem_type", - "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", - "comments": [ - "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 11, - "is_a": "gold_path_field", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "elev": { - "name": "elev", - "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", - "title": "elevation, meters", - "comments": [ - "All elevations must be reported in meters. Provide the numerical portion only.", - "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." - ], - "examples": [ - { - "value": "100" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "slot_uri": "MIXS:0000093", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "float" - }, - "env_broad_scale": { - "name": "env_broad_scale", - "description": "Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS", - "title": "broad-scale environmental context", - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000012", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_local_scale": { - "name": "env_local_scale", - "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", - "title": "local environmental context", - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 7, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000013", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_medium": { - "name": "env_medium", - "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", - "title": "environmental medium", - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 8, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000014", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_package": { - "name": "env_package", - "description": "Select the MIxS enviromental package that best describes the environment from which your sample was collected.", - "title": "environmental package", - "examples": [ - { - "value": "soil" - } - ], - "in_subset": [ - "mixs extension" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "environmental package" - ], - "rank": 4, - "is_a": "attribute", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true - }, - "experimental_factor": { - "name": "experimental_factor", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text or EFO and/or OBI" - } - }, - "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", - "title": "experimental factor", - "examples": [ - { - "value": "time series design [EFO:0001779]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "experimental factor" - ], - "rank": 12, - "is_a": "investigation field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000008", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "fluor": { - "name": "fluor", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram chlorophyll a per cubic meter, volts" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Raw or converted fluorescence of water", - "title": "fluorescence", - "examples": [ - { - "value": "2.5 volts" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "fluorescence" - ], - "rank": 226, - "is_a": "core field", - "slot_uri": "MIXS:0000704", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "geo_loc_name": { - "name": "geo_loc_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" - } - }, - "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", - "title": "geographic location (country and/or sea,region)", - "examples": [ - { - "value": "USA: Maryland, Bethesda" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "geographic location (country and/or sea,region)" - ], - "rank": 4, - "is_a": "environment field", - "string_serialization": "{term}: {term}, {text}", - "slot_uri": "MIXS:0000010", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true - }, - "glucosidase_act": { - "name": "glucosidase_act", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mol per liter per hour" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of glucosidase activity", - "title": "glucosidase activity", - "examples": [ - { - "value": "5 mol per liter per hour" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "glucosidase activity" - ], - "rank": 20, - "is_a": "core field", - "slot_uri": "MIXS:0000137", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "horizon_meth": { - "name": "horizon_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining the horizon", - "title": "soil horizon method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "soil horizon method" - ], - "rank": 19, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000321", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "lat_lon": { - "name": "lat_lon", - "description": "This is currently a required field but it's not clear if this should be required for human hosts", - "title": "geographic location (latitude and longitude)", - "notes": [ - "required where?" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "is_a": "environment field", - "string_serialization": "{float} {float}", - "slot_uri": "MIXS:0000009", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? 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"title": "organic matter", - "examples": [ - { - "value": "1.75 milligram per cubic meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "organic matter" - ], - "rank": 45, - "is_a": "core field", - "slot_uri": "MIXS:0000204", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "org_nitro": { - "name": "org_nitro", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of organic nitrogen", - "title": "organic nitrogen", - "examples": [ - { - "value": "4 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "organic nitrogen" - ], - "rank": 46, - "is_a": "core field", - "slot_uri": "MIXS:0000205", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "organism_count": { - "name": "organism_count", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "organism name;measurement value;enumeration" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. 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can include multiple phaeopigments", - "title": "phaeopigments", - "examples": [ - { - "value": "2.5 milligram per cubic meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "phaeopigments" - ], - "rank": 35, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000180", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? 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[^;\\t\\r\\x0A]+)$" - }, - "phosphate": { - "name": "phosphate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of phosphate", - "title": "phosphate", - "examples": [ - { - "value": "0.7 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "phosphate" - ], - "rank": 53, - "is_a": "core field", - "slot_uri": "MIXS:0000505", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "phosplipid_fatt_acid": { - "name": "phosplipid_fatt_acid", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "phospholipid fatty acid name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mole per gram, mole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Concentration of phospholipid fatty acids; can include multiple values", - "title": "phospholipid fatty acid", - "examples": [ - { - "value": "2.98 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "phospholipid fatty acid" - ], - "rank": 36, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000181", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "photon_flux": { - "name": "photon_flux", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "number of photons per second per unit area" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of photon flux", - "title": "photon flux", - "examples": [ - { - "value": "3.926 micromole photons per second per square meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "photon flux" - ], - "rank": 229, - "is_a": "core field", - "slot_uri": "MIXS:0000725", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "potassium": { - "name": "potassium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of potassium in the sample", - "title": "potassium", - "examples": [ - { - "value": "463 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "potassium" - ], - "rank": 38, - "is_a": "core field", - "slot_uri": "MIXS:0000430", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "pressure": { - "name": "pressure", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "atmosphere" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Pressure to which the sample is subject to, in atmospheres", - "title": "pressure", - "examples": [ - { - "value": "50 atmosphere" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "pressure" - ], - "rank": 39, - "is_a": "core field", - "slot_uri": "MIXS:0000412", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "primary_prod": { - "name": "primary_prod", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per cubic meter per day, gram per square meter per day" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of primary production, generally measured as isotope uptake", - "title": "primary production", - "examples": [ - { - "value": "100 milligram per cubic meter per day" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "primary production" - ], - "rank": 230, - "is_a": "core field", - "slot_uri": "MIXS:0000728", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "redox_potential": { - "name": "redox_potential", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millivolt" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential", - "title": "redox potential", - "examples": [ - { - "value": "300 millivolt" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "redox potential" - ], - "rank": 40, - "is_a": "core field", - "slot_uri": "MIXS:0000182", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "salinity": { - "name": "salinity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "practical salinity unit, percentage" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", - "title": "salinity", - "examples": [ - { - "value": "25 practical salinity unit" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "salinity" - ], - "rank": 54, - "is_a": "core field", - "slot_uri": "MIXS:0000183", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "samp_collec_device": { - "name": "samp_collec_device", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "device name" - } - }, - "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", - "title": "sample collection device", - "examples": [ - { - "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection device" - ], - "rank": 14, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000002", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_collec_method": { - "name": "samp_collec_method", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI,url , or text" - } - }, - "description": "The method employed for collecting the sample.", - "title": "sample collection method", - "examples": [ - { - "value": "swabbing" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection method" - ], - "rank": 15, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{PMID}|{DOI}|{URL}|{text}", - "slot_uri": "MIXS:0001225", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_mat_process": { - "name": "samp_mat_process", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - } - }, - "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", - "title": "sample material processing", - "examples": [ - { - "value": "filtering of seawater" - }, - { - "value": "storing samples in ethanol" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample material processing" - ], - "rank": 12, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000016", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_size": { - "name": "samp_size", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millliter, gram, milligram, liter" - } - }, - "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", - "title": "amount or size of sample collected", - "examples": [ - { - "value": "5 liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "amount or size of sample collected" - ], - "rank": 18, - "is_a": "nucleic acid sequence source field", - "slot_uri": "MIXS:0000001", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "samp_store_dur": { - "name": "samp_store_dur", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Duration for which the sample was stored", - "title": "sample storage duration", - "examples": [ - { - "value": "P1Y6M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage duration" - ], - "rank": 353, - "is_a": "core field", - "string_serialization": "{duration}", - "slot_uri": "MIXS:0000116", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_store_loc": { - "name": "samp_store_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "location name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Location at which sample was stored, usually name of a specific freezer/room", - "title": "sample storage location", - "examples": [ - { - "value": "Freezer no:5" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage location" - ], - "rank": 41, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000755", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_store_temp": { - "name": "samp_store_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Temperature at which sample was stored, e.g. -80 degree Celsius", - "title": "sample storage temperature", - "examples": [ - { - "value": "-80 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage temperature" - ], - "rank": 7, - "is_a": "core field", - "slot_uri": "MIXS:0000110", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "sample_link": { - "name": "sample_link", - "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", - "title": "sample linkage", - "notes": [ - "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" - ], - "comments": [ - "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" - ], - "examples": [ - { - "value": "IGSN:DSJ0284" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "string_serialization": "{text}:{text}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface", - "SampIdNewTermsMixin" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true, - "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" - }, - "silicate": { - "name": "silicate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of silicate", - "title": "silicate", - "examples": [ - { - "value": "0.05 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "silicate" - ], - "rank": 43, - "is_a": "core field", - "slot_uri": "MIXS:0000184", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "size_frac": { - "name": "size_frac", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "filter size value range" - } - }, - "description": "Filtering pore size used in sample preparation", - "title": "size fraction selected", - "examples": [ - { - "value": "0-0.22 micrometer" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "size fraction selected" - ], - "rank": 285, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float}-{float} {unit}", - "slot_uri": "MIXS:0000017", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "size_frac_low": { - "name": "size_frac_low", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micrometer" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Refers to the mesh/pore size used to pre-filter/pre-sort the sample. 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"pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_inorg_phosp": { - "name": "diss_inorg_phosp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter, milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved inorganic phosphorus in the sample", - "title": "dissolved inorganic phosphorus", - "examples": [ - { - "value": "56.5 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved inorganic phosphorus" - ], - "rank": 224, - "is_a": "core field", - "slot_uri": "MIXS:0000106", - "multivalued": false, - "alias": "diss_inorg_phosp", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_org_carb": { - "name": "diss_org_carb", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid", - "title": "dissolved organic carbon", - "examples": [ - { - "value": "197 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved organic carbon" - ], - "rank": 17, - "is_a": "core field", - "slot_uri": "MIXS:0000433", - "multivalued": false, - "alias": "diss_org_carb", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_org_nitro": { - "name": "diss_org_nitro", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2", - "title": "dissolved organic nitrogen", - "examples": [ - { - "value": "0.05 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved organic nitrogen" - ], - "rank": 18, - "is_a": "core field", - "slot_uri": "MIXS:0000162", - "multivalued": false, - "alias": "diss_org_nitro", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "diss_oxygen": { - "name": "diss_oxygen", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per kilogram, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of dissolved oxygen", - "title": "dissolved oxygen", - "examples": [ - { - "value": "175 micromole per kilogram" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "dissolved oxygen" - ], - "rank": 19, - "is_a": "core field", - "slot_uri": "MIXS:0000119", - "multivalued": false, - "alias": "diss_oxygen", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "down_par": { - "name": "down_par", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microEinstein per square meter per second, microEinstein per square centimeter per second" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Visible waveband radiance and irradiance measurements in the water column", - "title": "downward PAR", - "examples": [ - { - "value": "28.71 microEinstein per square meter per second" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "downward PAR" - ], - "rank": 225, - "is_a": "core field", - "slot_uri": "MIXS:0000703", - "multivalued": false, - "alias": "down_par", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "ecosystem": { - "name": "ecosystem", - "description": "An ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.", - "comments": [ - "The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 9, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_category": { - "name": "ecosystem_category", - "description": "Ecosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.", - "comments": [ - "The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 10, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem_category", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_subtype": { - "name": "ecosystem_subtype", - "description": "Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.", - "comments": [ - "Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 12, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem_subtype", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "ecosystem_type": { - "name": "ecosystem_type", - "description": "Ecosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.", - "comments": [ - "The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "https://gold.jgi.doe.gov/help" - ], - "rank": 11, - "is_a": "gold_path_field", - "multivalued": false, - "alias": "ecosystem_type", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "Study", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true - }, - "elev": { - "name": "elev", - "description": "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.", - "title": "elevation, meters", - "comments": [ - "All elevations must be reported in meters. Provide the numerical portion only.", - "Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates, if needed, to help estimate the elevation based on latitude and longitude coordinates." - ], - "examples": [ - { - "value": "100" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "slot_uri": "MIXS:0000093", - "multivalued": false, - "alias": "elev", - "owner": "WaterInterface", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "float" - }, - "env_broad_scale": { - "name": "env_broad_scale", - "description": "Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS", - "title": "broad-scale environmental context", - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 6, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000012", - "multivalued": false, - "alias": "env_broad_scale", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_local_scale": { - "name": "env_local_scale", - "description": "Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.", - "title": "local environmental context", - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 7, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000013", - "multivalued": false, - "alias": "env_local_scale", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_medium": { - "name": "env_medium", - "description": "Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).", - "title": "environmental medium", - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 8, - "is_a": "environment field", - "string_serialization": "{termLabel} {[termID]}", - "slot_uri": "MIXS:0000014", - "multivalued": false, - "alias": "env_medium", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]$" - }, - "env_package": { - "name": "env_package", - "description": "Select the MIxS enviromental package that best describes the environment from which your sample was collected.", - "title": "environmental package", - "examples": [ - { - "value": "soil" - } - ], - "in_subset": [ - "mixs extension" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "environmental package" - ], - "rank": 4, - "is_a": "attribute", - "multivalued": false, - "alias": "env_package", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true - }, - "experimental_factor": { - "name": "experimental_factor", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text or EFO and/or OBI" - } - }, - "description": "Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI", - "title": "experimental factor", - "examples": [ - { - "value": "time series design [EFO:0001779]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "experimental factor" - ], - "rank": 12, - "is_a": "investigation field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000008", - "multivalued": false, - "alias": "experimental_factor", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "fluor": { - "name": "fluor", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram chlorophyll a per cubic meter, volts" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Raw or converted fluorescence of water", - "title": "fluorescence", - "examples": [ - { - "value": "2.5 volts" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "fluorescence" - ], - "rank": 226, - "is_a": "core field", - "slot_uri": "MIXS:0000704", - "multivalued": false, - "alias": "fluor", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "geo_loc_name": { - "name": "geo_loc_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "country or sea name (INSDC or GAZ): region(GAZ), specific location name" - } - }, - "description": "The geographical origin of the sample as defined by the country or sea name followed by specific region name.", - "title": "geographic location (country and/or sea,region)", - "examples": [ - { - "value": "USA: Maryland, Bethesda" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "geographic location (country and/or sea,region)" - ], - "rank": 4, - "is_a": "environment field", - "string_serialization": "{term}: {term}, {text}", - "slot_uri": "MIXS:0000010", - "multivalued": false, - "alias": "geo_loc_name", - "owner": "WaterInterface", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "required": true - }, - "glucosidase_act": { - "name": "glucosidase_act", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mol per liter per hour" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of glucosidase activity", - "title": "glucosidase activity", - "examples": [ - { - "value": "5 mol per liter per hour" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "glucosidase activity" - ], - "rank": 20, - "is_a": "core field", - "slot_uri": "MIXS:0000137", - "multivalued": false, - "alias": "glucosidase_act", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "horizon_meth": { - "name": "horizon_meth", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI or url" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Reference or method used in determining the horizon", - "title": "soil horizon method", - "examples": [ - { - "value": "" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "soil horizon method" - ], - "rank": 19, - "is_a": "core field", - "string_serialization": "{PMID}|{DOI}|{URL}", - "slot_uri": "MIXS:0000321", - "multivalued": false, - "alias": "horizon_meth", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string" - }, - "lat_lon": { - "name": "lat_lon", - "description": "This is currently a required field but it's not clear if this should be required for human hosts", - "title": "geographic location (latitude and longitude)", - "notes": [ - "required where?" - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "is_a": "environment field", - "string_serialization": "{float} {float}", - "slot_uri": "MIXS:0000009", - "multivalued": false, - "alias": "lat_lon", - "owner": "WaterInterface", - "domain_of": [ - "FieldResearchSite", - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? 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[^;\\t\\r\\x0A]+)$" - }, - "phosphate": { - "name": "phosphate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of phosphate", - "title": "phosphate", - "examples": [ - { - "value": "0.7 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "phosphate" - ], - "rank": 53, - "is_a": "core field", - "slot_uri": "MIXS:0000505", - "multivalued": false, - "alias": "phosphate", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "phosplipid_fatt_acid": { - "name": "phosplipid_fatt_acid", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "phospholipid fatty acid name;measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "mole per gram, mole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "m" - } - }, - "description": "Concentration of phospholipid fatty acids; can include multiple values", - "title": "phospholipid fatty acid", - "examples": [ - { - "value": "2.98 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "phospholipid fatty acid" - ], - "rank": 36, - "is_a": "core field", - "string_serialization": "{text};{float} {unit}", - "slot_uri": "MIXS:0000181", - "multivalued": false, - "alias": "phosplipid_fatt_acid", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+\\|)*([^;\\t\\r\\x0A]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A]+)$" - }, - "photon_flux": { - "name": "photon_flux", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "number of photons per second per unit area" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of photon flux", - "title": "photon flux", - "examples": [ - { - "value": "3.926 micromole photons per second per square meter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "photon flux" - ], - "rank": 229, - "is_a": "core field", - "slot_uri": "MIXS:0000725", - "multivalued": false, - "alias": "photon_flux", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "potassium": { - "name": "potassium", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per liter, parts per million" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of potassium in the sample", - "title": "potassium", - "examples": [ - { - "value": "463 milligram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "potassium" - ], - "rank": 38, - "is_a": "core field", - "slot_uri": "MIXS:0000430", - "multivalued": false, - "alias": "potassium", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "pressure": { - "name": "pressure", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "atmosphere" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Pressure to which the sample is subject to, in atmospheres", - "title": "pressure", - "examples": [ - { - "value": "50 atmosphere" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "pressure" - ], - "rank": 39, - "is_a": "core field", - "slot_uri": "MIXS:0000412", - "multivalued": false, - "alias": "pressure", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "primary_prod": { - "name": "primary_prod", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "milligram per cubic meter per day, gram per square meter per day" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of primary production, generally measured as isotope uptake", - "title": "primary production", - "examples": [ - { - "value": "100 milligram per cubic meter per day" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "primary production" - ], - "rank": 230, - "is_a": "core field", - "slot_uri": "MIXS:0000728", - "multivalued": false, - "alias": "primary_prod", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "redox_potential": { - "name": "redox_potential", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millivolt" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential", - "title": "redox potential", - "examples": [ - { - "value": "300 millivolt" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "redox potential" - ], - "rank": 40, - "is_a": "core field", - "slot_uri": "MIXS:0000182", - "multivalued": false, - "alias": "redox_potential", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "salinity": { - "name": "salinity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "practical salinity unit, percentage" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.", - "title": "salinity", - "examples": [ - { - "value": "25 practical salinity unit" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "salinity" - ], - "rank": 54, - "is_a": "core field", - "slot_uri": "MIXS:0000183", - "multivalued": false, - "alias": "salinity", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "samp_collec_device": { - "name": "samp_collec_device", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "device name" - } - }, - "description": "The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).", - "title": "sample collection device", - "examples": [ - { - "value": "swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection device" - ], - "rank": 14, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{termLabel} {[termID]}|{text}", - "slot_uri": "MIXS:0000002", - "multivalued": false, - "alias": "samp_collec_device", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_collec_method": { - "name": "samp_collec_method", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "PMID,DOI,url , or text" - } - }, - "description": "The method employed for collecting the sample.", - "title": "sample collection method", - "examples": [ - { - "value": "swabbing" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample collection method" - ], - "rank": 15, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{PMID}|{DOI}|{URL}|{text}", - "slot_uri": "MIXS:0001225", - "multivalued": false, - "alias": "samp_collec_method", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_mat_process": { - "name": "samp_mat_process", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - } - }, - "description": "A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.", - "title": "sample material processing", - "examples": [ - { - "value": "filtering of seawater" - }, - { - "value": "storing samples in ethanol" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample material processing" - ], - "rank": 12, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000016", - "multivalued": false, - "alias": "samp_mat_process", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string" - }, - "samp_size": { - "name": "samp_size", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "millliter, gram, milligram, liter" - } - }, - "description": "The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.", - "title": "amount or size of sample collected", - "examples": [ - { - "value": "5 liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "amount or size of sample collected" - ], - "rank": 18, - "is_a": "nucleic acid sequence source field", - "slot_uri": "MIXS:0000001", - "multivalued": false, - "alias": "samp_size", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "samp_store_dur": { - "name": "samp_store_dur", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "duration" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Duration for which the sample was stored", - "title": "sample storage duration", - "examples": [ - { - "value": "P1Y6M" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage duration" - ], - "rank": 353, - "is_a": "core field", - "string_serialization": "{duration}", - "slot_uri": "MIXS:0000116", - "multivalued": false, - "alias": "samp_store_dur", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_store_loc": { - "name": "samp_store_loc", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "location name" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Location at which sample was stored, usually name of a specific freezer/room", - "title": "sample storage location", - "examples": [ - { - "value": "Freezer no:5" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage location" - ], - "rank": 41, - "is_a": "core field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0000755", - "multivalued": false, - "alias": "samp_store_loc", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "samp_store_temp": { - "name": "samp_store_temp", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "degree Celsius" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Temperature at which sample was stored, e.g. -80 degree Celsius", - "title": "sample storage temperature", - "examples": [ - { - "value": "-80 degree Celsius" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample storage temperature" - ], - "rank": 7, - "is_a": "core field", - "slot_uri": "MIXS:0000110", - "multivalued": false, - "alias": "samp_store_temp", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "sample_link": { - "name": "sample_link", - "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", - "title": "sample linkage", - "notes": [ - "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and \"placeholder\" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" - ], - "comments": [ - "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" - ], - "examples": [ - { - "value": "IGSN:DSJ0284" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 5, - "string_serialization": "{text}:{text}", - "multivalued": false, - "alias": "sample_link", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface", - "SampIdNewTermsMixin" - ], - "slot_group": "sample_id_section", - "range": "string", - "recommended": true, - "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" - }, - "silicate": { - "name": "silicate", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Concentration of silicate", - "title": "silicate", - "examples": [ - { - "value": "0.05 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "silicate" - ], - "rank": 43, - "is_a": "core field", - "slot_uri": "MIXS:0000184", - "multivalued": false, - "alias": "silicate", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "MiscEnvsInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "size_frac": { - "name": "size_frac", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "filter size value range" - } - }, - "description": "Filtering pore size used in sample preparation", - "title": "size fraction selected", - "examples": [ - { - "value": "0-0.22 micrometer" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "size fraction selected" - ], - "rank": 285, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{float}-{float} {unit}", - "slot_uri": "MIXS:0000017", - "multivalued": false, - "alias": "size_frac", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string" - }, - "size_frac_low": { - "name": "size_frac_low", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micrometer" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample", - "title": "size-fraction lower threshold", - "examples": [ - { - "value": "0.2 micrometer" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "size-fraction lower threshold" - ], - "rank": 10, - "is_a": "core field", - "slot_uri": "MIXS:0000735", - "multivalued": false, - "alias": "size_frac_low", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "SoilInterface", - "WaterInterface" - ], - "slot_group": "mixs_modified_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "size_frac_up": { - "name": "size_frac_up", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "micrometer" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Refers to the mesh/pore size used to retain the sample. 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"is_a": "core field", - "slot_uri": "MIXS:0000634", - "multivalued": false, - "alias": "tot_depth_water_col", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tot_diss_nitro": { - "name": "tot_diss_nitro", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen", - "title": "total dissolved nitrogen", - "examples": [ - { - "value": "40 microgram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "total dissolved nitrogen" - ], - "rank": 233, - "is_a": "core field", - "slot_uri": "MIXS:0000744", - "multivalued": false, - "alias": "tot_diss_nitro", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tot_inorg_nitro": { - "name": "tot_inorg_nitro", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Total inorganic nitrogen content", - "title": "total inorganic nitrogen", - "examples": [ - { - "value": "40 microgram per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "total inorganic nitrogen" - ], - "rank": 234, - "is_a": "core field", - "slot_uri": "MIXS:0000745", - "multivalued": false, - "alias": "tot_inorg_nitro", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tot_nitro": { - "name": "tot_nitro", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter, micromole per liter, milligram per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen", - "title": "total nitrogen concentration", - "examples": [ - { - "value": "50 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "total nitrogen concentration" - ], - "rank": 377, - "is_a": "core field", - "slot_uri": "MIXS:0000102", - "multivalued": false, - "alias": "tot_nitro", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "tot_part_carb": { - "name": "tot_part_carb", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "microgram per liter, micromole per liter" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Total particulate carbon content", - "title": "total particulate carbon", - "examples": [ - { - "value": "35 micromole per liter" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "total particulate carbon" - ], - "rank": 235, - "is_a": "core field", - "slot_uri": "MIXS:0000747", - "multivalued": false, - "alias": "tot_part_carb", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "turbidity": { - "name": "turbidity", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "formazin turbidity unit, formazin nephelometric units" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measure of the amount of cloudiness or haziness in water caused by individual particles", - "title": "turbidity", - "examples": [ - { - "value": "0.3 nephelometric turbidity units" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "turbidity" - ], - "rank": 47, - "is_a": "core field", - "slot_uri": "MIXS:0000191", - "multivalued": false, - "alias": "turbidity", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "BiofilmInterface", - "SedimentInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "water_current": { - "name": "water_current", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "measurement value" - }, - "preferred_unit": { - "tag": "preferred_unit", - "value": "cubic meter per second, knots" - }, - "occurrence": { - "tag": "occurrence", - "value": "1" - } - }, - "description": "Measurement of magnitude and direction of flow within a fluid", - "title": "water current", - "examples": [ - { - "value": "10 cubic meter per second" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "water current" - ], - "rank": 236, - "is_a": "core field", - "slot_uri": "MIXS:0000203", - "multivalued": false, - "alias": "water_current", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "MiscEnvsInterface", - "WaterInterface" - ], - "slot_group": "mixs_core_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$" - }, - "analysis_type": { - "name": "analysis_type", - "description": "Select all the data types associated or available for this biosample", - "title": "analysis/data type", - "examples": [ - { - "value": "metagenomics; metabolomics; proteomics" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:investigation_type" - ], - "rank": 3, - "multivalued": true, - "alias": "analysis_type", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "EmslInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "JgiMgInterface", - "JgiMtInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface" - ], - "slot_group": "sample_id_section", - "range": "analysis_type_enum", - "required": true, - "recommended": true - }, - "samp_name": { - "name": "samp_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - } - }, - "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", - "title": "sample name", - "comments": [ - "It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." - ], - "examples": [ - { - "value": "Rock core CB1178(5-6) from NSW" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample name" - ], - "rank": 1, - "is_a": "investigation field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0001107", - "multivalued": false, - "identifier": true, - "alias": "samp_name", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "EmslInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "JgiMgInterface", - "JgiMtInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true - }, - "source_mat_id": { - "name": "source_mat_id", - "description": "A globally unique identifier assigned to the biological sample.", - "title": "source material identifier", - "todos": [ - "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID.", - "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID." - ], - "notes": [ - "The source material IS the Globally Unique ID" - ], - "comments": [ - "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).", - "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/)." - ], - "examples": [ - { - "value": "IGSN:AU1243" - }, - { - "value": "UUID:24f1467a-40f4-11ed-b878-0242ac120002" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 2, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{text}:{text}", - "slot_uri": "MIXS:0000026", - "multivalued": false, - "alias": "source_mat_id", - "owner": "WaterInterface", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "EmslInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "JgiMgInterface", - "JgiMtInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" - } - } - }, - "DhMultiviewCommonColumnsMixin": { - "name": "DhMultiviewCommonColumnsMixin", - "description": "Mixin with DhMutliviewCommon Columns", - "title": "Dh Mutliview Common Columns", - "from_schema": "https://example.com/nmdc_submission_schema", - "mixin": true, - "slots": [ - "analysis_type", - "samp_name", - "source_mat_id" - ], - "slot_usage": { - "analysis_type": { - "name": "analysis_type", - "description": "Select all the data types associated or available for this biosample", - "title": "analysis/data type", - "examples": [ - { - "value": "metagenomics; metabolomics; proteomics" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:investigation_type" - ], - "rank": 3, - "multivalued": true, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "EmslInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "JgiMgInterface", - "JgiMtInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "analysis_type_enum", - "required": true, - "recommended": true - }, - "samp_name": { - "name": "samp_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - } - }, - "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", - "title": "sample name", - "comments": [ - "It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." - ], - "examples": [ - { - "value": "Rock core CB1178(5-6) from NSW" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample name" - ], - "rank": 1, - "is_a": "investigation field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0001107", - "multivalued": false, - "identifier": true, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "EmslInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "JgiMgInterface", - "JgiMtInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true - }, - "source_mat_id": { - "name": "source_mat_id", - "description": "A globally unique identifier assigned to the biological sample.", - "title": "source material identifier", - "todos": [ - "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID.", - "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID." - ], - "notes": [ - "The source material IS the Globally Unique ID" - ], - "comments": [ - "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).", - "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/)." - ], - "examples": [ - { - "value": "IGSN:AU1243" - }, - { - "value": "UUID:24f1467a-40f4-11ed-b878-0242ac120002" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 2, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{text}:{text}", - "slot_uri": "MIXS:0000026", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "EmslInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "JgiMgInterface", - "JgiMtInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" - }, - "oxy_stat_samp": { - "name": "oxy_stat_samp", - "range": "OxyStatSampEnum" - } - }, - "attributes": { - "analysis_type": { - "name": "analysis_type", - "description": "Select all the data types associated or available for this biosample", - "title": "analysis/data type", - "examples": [ - { - "value": "metagenomics; metabolomics; proteomics" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:investigation_type" - ], - "rank": 3, - "multivalued": true, - "alias": "analysis_type", - "owner": "DhMultiviewCommonColumnsMixin", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "EmslInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "JgiMgInterface", - "JgiMtInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "analysis_type_enum", - "required": true, - "recommended": true - }, - "samp_name": { - "name": "samp_name", - "annotations": { - "expected_value": { - "tag": "expected_value", - "value": "text" - } - }, - "description": "A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples.", - "title": "sample name", - "comments": [ - "It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." - ], - "examples": [ - { - "value": "Rock core CB1178(5-6) from NSW" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "aliases": [ - "sample name" - ], - "rank": 1, - "is_a": "investigation field", - "string_serialization": "{text}", - "slot_uri": "MIXS:0001107", - "multivalued": false, - "identifier": true, - "alias": "samp_name", - "owner": "DhMultiviewCommonColumnsMixin", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "EmslInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "JgiMgInterface", - "JgiMtInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "required": true - }, - "source_mat_id": { - "name": "source_mat_id", - "description": "A globally unique identifier assigned to the biological sample.", - "title": "source material identifier", - "todos": [ - "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID.", - "Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID." - ], - "notes": [ - "The source material IS the Globally Unique ID" - ], - "comments": [ - "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).", - "Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/)." - ], - "examples": [ - { - "value": "IGSN:AU1243" - }, - { - "value": "UUID:24f1467a-40f4-11ed-b878-0242ac120002" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "rank": 2, - "is_a": "nucleic acid sequence source field", - "string_serialization": "{text}:{text}", - "slot_uri": "MIXS:0000026", - "multivalued": false, - "alias": "source_mat_id", - "owner": "DhMultiviewCommonColumnsMixin", - "domain_of": [ - "Biosample", - "DhMultiviewCommonColumnsMixin", - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "EmslInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "JgiMgInterface", - "JgiMtInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface" - ], - "slot_group": "sample_id_section", - "range": "string", - "pattern": "[^\\:\\n\\r]+\\:[^\\:\\n\\r]+" - } - } - }, - "SampIdNewTermsMixin": { - "name": "SampIdNewTermsMixin", - "description": "Mixin with SampIdNew Terms", - "title": "SampId New Terms", - "from_schema": "https://example.com/nmdc_submission_schema", - "mixin": true, - "slots": [ - "sample_link" - ], - "attributes": { - "sample_link": { - "name": "sample_link", - "description": "A unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.", - "title": "sample linkage", - "comments": [ - "This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample)" - ], - "examples": [ - { - "value": "IGSN:DSJ0284" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "rank": 5, - "string_serialization": "{text}:{text}", - "multivalued": false, - "alias": "sample_link", - "owner": "SampIdNewTermsMixin", - "domain_of": [ - "AirInterface", - "BiofilmInterface", - "BuiltEnvInterface", - "HcrCoresInterface", - "HcrFluidsSwabsInterface", - "HostAssociatedInterface", - "MiscEnvsInterface", - "PlantAssociatedInterface", - "SedimentInterface", - "SoilInterface", - "WastewaterSludgeInterface", - "WaterInterface", - "SampIdNewTermsMixin" - ], - "slot_group": "Sample ID", - "range": "string", - "recommended": true - } - } - }, - "SoilMixsInspiredMixin": { - "name": "SoilMixsInspiredMixin", - "description": "Mixin with SoilMixsInspired Terms", - "title": "Soil MIxS Inspired Mixin", - "from_schema": "https://example.com/nmdc_submission_schema", - "mixin": true, - "slots": [ - "collection_date_inc", - "collection_time", - "collection_time_inc", - "experimental_factor_other", - "filter_method", - "isotope_exposure", - "micro_biomass_c_meth", - "micro_biomass_n_meth", - "microbial_biomass_c", - "microbial_biomass_n", - "non_microb_biomass", - "non_microb_biomass_method", - "org_nitro_method", - "other_treatment", - "start_date_inc", - "start_time_inc", - "collection_date_inc", - "collection_time", - "collection_time_inc", - "experimental_factor_other", - "filter_method", - "isotope_exposure", - "micro_biomass_c_meth", - "micro_biomass_n_meth", - "microbial_biomass_c", - "microbial_biomass_n", - "non_microb_biomass", - "non_microb_biomass_method", - "org_nitro_method", - "other_treatment", - "start_date_inc", - "start_time_inc" - ], - "slot_usage": { - "collection_date_inc": { - "name": "collection_date_inc", - "description": "Date the incubation was harvested/collected/ended. Only relevant for incubation samples.", - "title": "incubation collection date", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only" - ], - "comments": [ - "Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable." - ], - "examples": [ - { - "value": "2021-04-15, 2021-04 and 2021 are all acceptable." - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:collection_date" - ], - "rank": 2, - "string_serialization": "{date, arbitrary precision}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "recommended": true, - "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" - }, - "collection_time": { - "name": "collection_time", - "description": "The time of sampling, either as an instance (single point) or interval.", - "title": "collection time, GMT", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" - ], - "comments": [ - "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" - ], - "examples": [ - { - "value": "13:33 or 13:33:55" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:collection_date" - ], - "rank": 1, - "string_serialization": "{time, seconds optional}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "recommended": true, - "pattern": "^([01]?\\d|2[0-3]|24(?=:00?:00?$)):([0-5]\\d)(:([0-5]\\d))?$" - }, - "collection_time_inc": { - "name": "collection_time_inc", - "description": "Time the incubation was harvested/collected/ended. Only relevant for incubation samples.", - "title": "incubation collection time, GMT", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" - ], - "comments": [ - "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" - ], - "examples": [ - { - "value": "13:33 or 13:33:55" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:collection_date" - ], - "rank": 3, - "string_serialization": "{time, seconds optional}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "recommended": true, - "pattern": "^([01]?\\d|2[0-3]|24(?=:00?:00?$)):([0-5]\\d)(:([0-5]\\d))?$" - }, - "experimental_factor_other": { - "name": "experimental_factor_other", - "description": "Other details about your sample that you feel can't be accurately represented in the available columns.", - "title": "experimental factor- other", - "comments": [ - "This slot accepts open-ended text about your sample.", - "We recommend using key:value pairs.", - "Provided pairs will be considered for inclusion as future slots/terms in this data collection template." - ], - "examples": [ - { - "value": "experimental treatment: value" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:experimental_factor|additional_info" - ], - "rank": 7, - "string_serialization": "{text}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "recommended": true - }, - "filter_method": { - "name": "filter_method", - "description": "Type of filter used or how the sample was filtered", - "title": "filter method", - "comments": [ - "describe the filter or provide a catalog number and manufacturer" - ], - "examples": [ - { - "value": "C18" - }, - { - "value": "Basix PES, 13-100-106 FisherSci" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:filter_type" - ], - "rank": 6, - "string_serialization": "{text}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "recommended": true - }, - "isotope_exposure": { - "name": "isotope_exposure", - "description": "List isotope exposure or addition applied to your sample.", - "title": "isotope exposure/addition", - "todos": [ - "Can we make the H218O correctly super and subscripted?" - ], - "comments": [ - "This is required when your experimental design includes the use of isotopically labeled compounds" - ], - "examples": [ - { - "value": "13C glucose" - }, - { - "value": "H218O" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:chem_administration" - ], - "rank": 16, - "string_serialization": "{termLabel} {[termID]}; {timestamp}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "recommended": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]; ([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" - }, - "micro_biomass_c_meth": { - "name": "micro_biomass_c_meth", - "description": "Reference or method used in determining microbial biomass carbon", - "title": "microbial biomass carbon method", - "todos": [ - "How should we separate values? | or ;? lets be consistent" - ], - "comments": [ - "required if \"microbial_biomass_c\" is provided" - ], - "examples": [ - { - "value": "https://doi.org/10.1016/0038-0717(87)90052-6" - }, - { - "value": "https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:micro_biomass_meth" - ], - "rank": 1004, - "string_serialization": "{PMID}|{DOI}|{URL}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "recommended": true - }, - "micro_biomass_n_meth": { - "name": "micro_biomass_n_meth", - "description": "Reference or method used in determining microbial biomass nitrogen", - "title": "microbial biomass nitrogen method", - "comments": [ - "required if \"microbial_biomass_n\" is provided" - ], - "examples": [ - { - "value": "https://doi.org/10.1016/0038-0717(87)90052-6" - }, - { - "value": "https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:micro_biomass_meth" - ], - "rank": 1004, - "string_serialization": "{PMID}|{DOI}|{URL}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string" - }, - "microbial_biomass_c": { - "name": "microbial_biomass_c", - "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.", - "title": "microbial biomass carbon", - "comments": [ - "If you provide this, correction factors used for conversion to the final units and method are required" - ], - "examples": [ - { - "value": "0.05 ug C/g dry soil" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:microbial_biomass" - ], - "rank": 1004, - "string_serialization": "{float} {unit}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" - }, - "microbial_biomass_n": { - "name": "microbial_biomass_n", - "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.", - "title": "microbial biomass nitrogen", - "comments": [ - "If you provide this, correction factors used for conversion to the final units and method are required" - ], - "examples": [ - { - "value": "0.05 ug N/g dry soil" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:microbial_biomass" - ], - "rank": 1004, - "string_serialization": "{float} {unit}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" - }, - "non_microb_biomass": { - "name": "non_microb_biomass", - "description": "Amount of biomass; should include the name for the part of biomass measured, e.g.insect, plant, total. Can include multiple measurements separated by ;", - "title": "non-microbial biomass", - "examples": [ - { - "value": "insect 0.23 ug; plant 1g" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:biomass|microbial_biomass" - ], - "rank": 8, - "string_serialization": "{text};{float} {unit}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" - }, - "non_microb_biomass_method": { - "name": "non_microb_biomass_method", - "description": "Reference or method used in determining biomass", - "title": "non-microbial biomass method", - "comments": [ - "required if \"non-microbial biomass\" is provided" - ], - "examples": [ - { - "value": "https://doi.org/10.1038/s41467-021-26181-3" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:microbial_biomass" - ], - "rank": 9, - "string_serialization": "{PMID}|{DOI}|{URL}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string" - }, - "org_nitro_method": { - "name": "org_nitro_method", - "description": "Method used for obtaining organic nitrogen", - "title": "organic nitrogen method", - "comments": [ - "required if \"org_nitro\" is provided" - ], - "examples": [ - { - "value": "https://doi.org/10.1016/0038-0717(85)90144-0" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:org_nitro|tot_nitro_cont_meth" - ], - "rank": 14, - "string_serialization": "{PMID}|{DOI}|{URL}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string" - }, - "other_treatment": { - "name": "other_treatment", - "description": "Other treatments applied to your samples that are not applicable to the provided fields", - "title": "other treatments", - "comments": [ - "This is an open text field to provide any treatments that cannot be captured in the provided slots." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:additional_info" - ], - "rank": 15, - "string_serialization": "{text}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "recommended": true - }, - "start_date_inc": { - "name": "start_date_inc", - "description": "Date the incubation was started. 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Only relevant for incubation samples.", - "title": "incubation start time, GMT", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" - ], - "comments": [ - "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" - ], - "examples": [ - { - "value": "13:33 or 13:33:55" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:collection_date" - ], - "rank": 5, - "string_serialization": "{time, seconds optional}", - "multivalued": false, - "owner": "Biosample", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "recommended": true, - "pattern": "^([01]?\\d|2[0-3]|24(?=:00?:00?$)):([0-5]\\d)(:([0-5]\\d))?$" - } - }, - "attributes": { - "collection_date_inc": { - "name": "collection_date_inc", - "description": "Date the incubation was harvested/collected/ended. Only relevant for incubation samples.", - "title": "incubation collection date", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only" - ], - "comments": [ - "Date should be formatted as YYYY(-MM(-DD)). 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DH taking seconds optional time only" - ], - "comments": [ - "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" - ], - "examples": [ - { - "value": "13:33 or 13:33:55" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:collection_date" - ], - "rank": 1, - "string_serialization": "{time, seconds optional}", - "multivalued": false, - "alias": "collection_time", - "owner": "SoilMixsInspiredMixin", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "recommended": true, - "pattern": "^([01]?\\d|2[0-3]|24(?=:00?:00?$)):([0-5]\\d)(:([0-5]\\d))?$" - }, - "collection_time_inc": { - "name": "collection_time_inc", - "description": "Time the incubation was harvested/collected/ended. Only relevant for incubation samples.", - "title": "incubation collection time, GMT", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" - ], - "comments": [ - "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" - ], - "examples": [ - { - "value": "13:33 or 13:33:55" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:collection_date" - ], - "rank": 3, - "string_serialization": "{time, seconds optional}", - "multivalued": false, - "alias": "collection_time_inc", - "owner": "SoilMixsInspiredMixin", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "recommended": true, - "pattern": "^([01]?\\d|2[0-3]|24(?=:00?:00?$)):([0-5]\\d)(:([0-5]\\d))?$" - }, - "experimental_factor_other": { - "name": "experimental_factor_other", - "description": "Other details about your sample that you feel can't be accurately represented in the available columns.", - "title": "experimental factor- other", - "comments": [ - "This slot accepts open-ended text about your sample.", - "We recommend using key:value pairs.", - "Provided pairs will be considered for inclusion as future slots/terms in this data collection template." - ], - "examples": [ - { - "value": "experimental treatment: value" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:experimental_factor|additional_info" - ], - "rank": 7, - "string_serialization": "{text}", - "multivalued": false, - "alias": "experimental_factor_other", - "owner": "SoilMixsInspiredMixin", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "recommended": true - }, - "filter_method": { - "name": "filter_method", - "description": "Type of filter used or how the sample was filtered", - "title": "filter method", - "comments": [ - "describe the filter or provide a catalog number and manufacturer" - ], - "examples": [ - { - "value": "C18" - }, - { - "value": "Basix PES, 13-100-106 FisherSci" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:filter_type" - ], - "rank": 6, - "string_serialization": "{text}", - "multivalued": false, - "alias": "filter_method", - "owner": "SoilMixsInspiredMixin", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "recommended": true - }, - "isotope_exposure": { - "name": "isotope_exposure", - "description": "List isotope exposure or addition applied to your sample.", - "title": "isotope exposure/addition", - "todos": [ - "Can we make the H218O correctly super and subscripted?" - ], - "comments": [ - "This is required when your experimental design includes the use of isotopically labeled compounds" - ], - "examples": [ - { - "value": "13C glucose" - }, - { - "value": "H218O" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:chem_administration" - ], - "rank": 16, - "string_serialization": "{termLabel} {[termID]}; {timestamp}", - "multivalued": false, - "alias": "isotope_exposure", - "owner": "SoilMixsInspiredMixin", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "recommended": true, - "pattern": "^\\S+.*\\S+ \\[[a-zA-Z]{2,}:\\d+\\]; ([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" - }, - "micro_biomass_c_meth": { - "name": "micro_biomass_c_meth", - "description": "Reference or method used in determining microbial biomass carbon", - "title": "microbial biomass carbon method", - "todos": [ - "How should we separate values? | or ;? lets be consistent" - ], - "comments": [ - "required if \"microbial_biomass_c\" is provided" - ], - "examples": [ - { - "value": "https://doi.org/10.1016/0038-0717(87)90052-6" - }, - { - "value": "https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:micro_biomass_meth" - ], - "rank": 1004, - "string_serialization": "{PMID}|{DOI}|{URL}", - "multivalued": false, - "alias": "micro_biomass_c_meth", - "owner": "SoilMixsInspiredMixin", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "recommended": true - }, - "micro_biomass_n_meth": { - "name": "micro_biomass_n_meth", - "description": "Reference or method used in determining microbial biomass nitrogen", - "title": "microbial biomass nitrogen method", - "comments": [ - "required if \"microbial_biomass_n\" is provided" - ], - "examples": [ - { - "value": "https://doi.org/10.1016/0038-0717(87)90052-6" - }, - { - "value": "https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:micro_biomass_meth" - ], - "rank": 1004, - "string_serialization": "{PMID}|{DOI}|{URL}", - "multivalued": false, - "alias": "micro_biomass_n_meth", - "owner": "SoilMixsInspiredMixin", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string" - }, - "microbial_biomass_c": { - "name": "microbial_biomass_c", - "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.", - "title": "microbial biomass carbon", - "comments": [ - "If you provide this, correction factors used for conversion to the final units and method are required" - ], - "examples": [ - { - "value": "0.05 ug C/g dry soil" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:microbial_biomass" - ], - "rank": 1004, - "string_serialization": "{float} {unit}", - "multivalued": false, - "alias": "microbial_biomass_c", - "owner": "SoilMixsInspiredMixin", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" - }, - "microbial_biomass_n": { - "name": "microbial_biomass_n", - "description": "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.", - "title": "microbial biomass nitrogen", - "comments": [ - "If you provide this, correction factors used for conversion to the final units and method are required" - ], - "examples": [ - { - "value": "0.05 ug N/g dry soil" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:microbial_biomass" - ], - "rank": 1004, - "string_serialization": "{float} {unit}", - "multivalued": false, - "alias": "microbial_biomass_n", - "owner": "SoilMixsInspiredMixin", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? \\S+$" - }, - "non_microb_biomass": { - "name": "non_microb_biomass", - "description": "Amount of biomass; should include the name for the part of biomass measured, e.g.insect, plant, total. Can include multiple measurements separated by ;", - "title": "non-microbial biomass", - "examples": [ - { - "value": "insect 0.23 ug; plant 1g" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:biomass|microbial_biomass" - ], - "rank": 8, - "string_serialization": "{text};{float} {unit}", - "multivalued": false, - "alias": "non_microb_biomass", - "owner": "SoilMixsInspiredMixin", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "pattern": "^[^;\\t\\r\\x0A\\|]+;[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [^;\\t\\r\\x0A\\|]+$" - }, - "non_microb_biomass_method": { - "name": "non_microb_biomass_method", - "description": "Reference or method used in determining biomass", - "title": "non-microbial biomass method", - "comments": [ - "required if \"non-microbial biomass\" is provided" - ], - "examples": [ - { - "value": "https://doi.org/10.1038/s41467-021-26181-3" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:microbial_biomass" - ], - "rank": 9, - "string_serialization": "{PMID}|{DOI}|{URL}", - "multivalued": false, - "alias": "non_microb_biomass_method", - "owner": "SoilMixsInspiredMixin", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string" - }, - "org_nitro_method": { - "name": "org_nitro_method", - "description": "Method used for obtaining organic nitrogen", - "title": "organic nitrogen method", - "comments": [ - "required if \"org_nitro\" is provided" - ], - "examples": [ - { - "value": "https://doi.org/10.1016/0038-0717(85)90144-0" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:org_nitro|tot_nitro_cont_meth" - ], - "rank": 14, - "string_serialization": "{PMID}|{DOI}|{URL}", - "multivalued": false, - "alias": "org_nitro_method", - "owner": "SoilMixsInspiredMixin", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string" - }, - "other_treatment": { - "name": "other_treatment", - "description": "Other treatments applied to your samples that are not applicable to the provided fields", - "title": "other treatments", - "comments": [ - "This is an open text field to provide any treatments that cannot be captured in the provided slots." - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:additional_info" - ], - "rank": 15, - "string_serialization": "{text}", - "multivalued": false, - "alias": "other_treatment", - "owner": "SoilMixsInspiredMixin", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "recommended": true - }, - "start_date_inc": { - "name": "start_date_inc", - "description": "Date the incubation was started. Only relevant for incubation samples.", - "title": "incubation start date", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only" - ], - "comments": [ - "Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable." - ], - "examples": [ - { - "value": "2021-04-15, 2021-04 and 2021 are all acceptable." - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:collection_date" - ], - "rank": 4, - "string_serialization": "{date, arbitrary precision}", - "multivalued": false, - "alias": "start_date_inc", - "owner": "SoilMixsInspiredMixin", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "recommended": true, - "pattern": "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?$" - }, - "start_time_inc": { - "name": "start_time_inc", - "description": "Time the incubation was started. Only relevant for incubation samples.", - "title": "incubation start time, GMT", - "notes": [ - "MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only" - ], - "comments": [ - "Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter" - ], - "examples": [ - { - "value": "13:33 or 13:33:55" - } - ], - "from_schema": "https://w3id.org/nmdc/nmdc", - "see_also": [ - "MIxS:collection_date" - ], - "rank": 5, - "string_serialization": "{time, seconds optional}", - "multivalued": false, - "alias": "start_time_inc", - "owner": "SoilMixsInspiredMixin", - "domain_of": [ - "Biosample", - "SoilInterface", - "SoilMixsInspiredMixin" - ], - "slot_group": "mixs_inspired_section", - "range": "string", - "recommended": true, - "pattern": "^([01]?\\d|2[0-3]|24(?=:00?:00?$)):([0-5]\\d)(:([0-5]\\d))?$" - } - } - }, - "DhInterface": { - "name": "DhInterface", - "description": "One DataHarmonizer interface, for the specified combination of a checklist, enviornmental_package, and various standards, user facilities or analysis types", - "title": "Dh Root Interface", - "from_schema": "https://example.com/nmdc_submission_schema" - }, - "SampleData": { - "name": "SampleData", - "description": "represents data produced by the DataHarmonizer tabs of the submission portal", - "title": "SampleData", - "from_schema": "https://example.com/nmdc_submission_schema", - "slots": [ - "air_data", - "biofilm_data", - "built_env_data", - "host_associated_data", - "plant_associated_data", - "sediment_data", - "soil_data", - "wastewater_sludge_data", - "water_data", - "emsl_data", - "jgi_mg_data", - "jgi_mt_data" - ], - "attributes": { - "air_data": { - "name": "air_data", - "description": "aggregation slot relating air data collections to a SampleData container", - "from_schema": "https://example.com/nmdc_submission_schema", - "multivalued": true, - "alias": "air_data", - "owner": "SampleData", - "domain_of": [ - "SampleData" - ], - "range": "AirInterface", - "inlined": true, - "inlined_as_list": true - }, - "biofilm_data": { - "name": "biofilm_data", - "description": "aggregation slot relating biofilm data collections to a SampleData container", - "from_schema": "https://example.com/nmdc_submission_schema", - "multivalued": true, - "alias": "biofilm_data", - "owner": "SampleData", - "domain_of": [ - "SampleData" - ], - "range": "BiofilmInterface", - "inlined": true, - "inlined_as_list": true - }, - "built_env_data": { - "name": "built_env_data", - "description": "aggregation slot relating built_env data collections to a SampleData container", - "from_schema": "https://example.com/nmdc_submission_schema", - "multivalued": true, - "alias": "built_env_data", - "owner": "SampleData", - "domain_of": [ - "SampleData" - ], - "range": "BuiltEnvInterface", - "inlined": true, - "inlined_as_list": true - }, - "host_associated_data": { - "name": "host_associated_data", - "description": "aggregation slot relating host_associated data collections to a SampleData container", - "from_schema": "https://example.com/nmdc_submission_schema", - "multivalued": true, - "alias": "host_associated_data", - "owner": "SampleData", - "domain_of": [ - "SampleData" - ], - "range": "HostAssociatedInterface", - "inlined": true, - "inlined_as_list": true - }, - "plant_associated_data": { - "name": "plant_associated_data", - "description": "aggregation slot relating plant_associated data collections to a SampleData container", - "from_schema": "https://example.com/nmdc_submission_schema", - "multivalued": true, - "alias": "plant_associated_data", - "owner": "SampleData", - "domain_of": [ - "SampleData" - ], - "range": "PlantAssociatedInterface", - "inlined": true, - "inlined_as_list": true - }, - "sediment_data": { - "name": "sediment_data", - "description": "aggregation slot relating sediment data collections to a SampleData container", - "from_schema": "https://example.com/nmdc_submission_schema", - "multivalued": true, - "alias": "sediment_data", - "owner": "SampleData", - "domain_of": [ - "SampleData" - ], - "range": "SedimentInterface", - "inlined": true, - "inlined_as_list": true - }, - "soil_data": { - "name": "soil_data", - "description": "aggregation slot relating soil data collections to a SampleData container", - "from_schema": "https://example.com/nmdc_submission_schema", - "multivalued": true, - "alias": "soil_data", - "owner": "SampleData", - "domain_of": [ - "SampleData" - ], - "range": "SoilInterface", - "inlined": true, - "inlined_as_list": true - }, - "wastewater_sludge_data": { - "name": "wastewater_sludge_data", - "description": "aggregation slot relating wastewater_sludge data collections to a SampleData container", - "from_schema": "https://example.com/nmdc_submission_schema", - "multivalued": true, - "alias": "wastewater_sludge_data", - "owner": "SampleData", - "domain_of": [ - "SampleData" - ], - "range": "WastewaterSludgeInterface", - "inlined": true, - "inlined_as_list": true - }, - "water_data": { - "name": "water_data", - "description": "aggregation slot relating water data collections to a SampleData container", - "from_schema": "https://example.com/nmdc_submission_schema", - "multivalued": true, - "alias": "water_data", - "owner": "SampleData", - "domain_of": [ - "SampleData" - ], - "range": "WaterInterface", - "inlined": true, - "inlined_as_list": true - }, - "emsl_data": { - "name": "emsl_data", - "description": "aggregation slot relating emsl data collections to a SampleData container", - "from_schema": "https://example.com/nmdc_submission_schema", - "multivalued": true, - "alias": "emsl_data", - "owner": "SampleData", - "domain_of": [ - "SampleData" - ], - "range": "EmslInterface", - "inlined": true, - "inlined_as_list": true - }, - "jgi_mg_data": { - "name": "jgi_mg_data", - "description": "aggregation slot relating jgi_mg data collections to a SampleData container", - "from_schema": "https://example.com/nmdc_submission_schema", - "multivalued": true, - "alias": "jgi_mg_data", - "owner": "SampleData", - "domain_of": [ - "SampleData" - ], - "range": "JgiMgInterface", - "inlined": true, - "inlined_as_list": true - }, - "jgi_mt_data": { - "name": "jgi_mt_data", - "description": "aggregation slot relating jgi_mt data collections to a SampleData container", - "from_schema": "https://example.com/nmdc_submission_schema", - "multivalued": true, - "alias": "jgi_mt_data", - "owner": "SampleData", - "domain_of": [ - "SampleData" - ], - "range": "JgiMtInterface", - "inlined": true, - "inlined_as_list": true - } - }, - "tree_root": true - }, - "NamedThing": { - "name": "NamedThing", - "description": "a databased entity or concept/class", - "from_schema": "https://example.com/nmdc_submission_schema", - "abstract": true, - "slots": [ - "id", - "name", - "description", - "alternative_identifiers" - ], - "attributes": { - "id": { - "name": "id", - "description": "A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI", - "notes": [ - "abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?", - "a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters will be accepted", - "typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked via per-class id slot usage assertions", - "minting authority shoulders should probably be enumerated and checked in the pattern" - ], - "examples": [ - { - "value": "nmdc:mgmag-00-x012.1_7_c1", - "description": "https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248" - } - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "identifier": true, - "alias": "id", - "owner": "NamedThing", - "domain_of": [ - "NamedThing" - ], - "range": "uriorcurie", - "required": true, - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$" - }, - "name": { - "name": "name", - "description": "A human readable label for an entity", - "from_schema": "https://example.com/nmdc_submission_schema", - "multivalued": false, - "alias": "name", - "owner": "NamedThing", - "domain_of": [ - "NamedThing" - ], - "range": "string" - }, - "description": { - "name": "description", - "description": "a human-readable description of a thing", - "from_schema": "https://example.com/nmdc_submission_schema", - "slot_uri": "dcterms:description", - "multivalued": false, - "alias": "description", - "owner": "NamedThing", - "domain_of": [ - "NamedThing" - ], - "range": "string" - }, - "alternative_identifiers": { - "name": "alternative_identifiers", - "description": "A list of alternative identifiers for the entity.", - "from_schema": "https://example.com/nmdc_submission_schema", - "multivalued": true, - "alias": "alternative_identifiers", - "owner": "NamedThing", - "domain_of": [ - "NamedThing" - ], - "range": "uriorcurie", - "pattern": "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$" - } - } - } - }, - "source_file": "src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml", - "@type": "SchemaDefinition" -} diff --git a/project/jsonschema/nmdc_submission_schema.schema.json b/project/jsonschema/nmdc_submission_schema.schema.json index 7aa63116..41b89017 100644 --- a/project/jsonschema/nmdc_submission_schema.schema.json +++ b/project/jsonschema/nmdc_submission_schema.schema.json @@ -99,10 +99,6 @@ "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$", "type": "string" }, - "horizon_meth": { - "description": "Reference or method used in determining the horizon", - "type": "string" - }, "humidity": { "description": "Amount of water vapour in the air, at the time of sampling", "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", @@ -455,10 +451,6 @@ "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", "type": "string" }, - "horizon_meth": { - "description": "Reference or method used in determining the horizon", - "type": "string" - }, "lat_lon": { "description": "This is currently a required field but it's not clear if this should be required for human hosts", "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$", @@ -1171,10 +1163,6 @@ "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", "type": "string" }, - "horizon_meth": { - "description": "Reference or method used in determining the horizon", - "type": "string" - }, "indoor_space": { "$ref": "#/$defs/IndoorSpaceEnum", "description": "A distinguishable space within a structure, the purpose for which discrete areas of a building is used" @@ -2712,10 +2700,6 @@ "description": "Original temperature of the hydrocarbon resource", "type": "string" }, - "horizon_meth": { - "description": "Reference or method used in determining the horizon", - "type": "string" - }, "lat_lon": { "description": "This is currently a required field but it's not clear if this should be required for human hosts", "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$", @@ -3254,10 +3238,6 @@ "description": "Original temperature of the hydrocarbon resource", "type": "string" }, - "horizon_meth": { - "description": "Reference or method used in determining the horizon", - "type": "string" - }, "iw_bt_date_well": { "description": "Injection water breakthrough date per well following a secondary and/or tertiary recovery", "type": "string" @@ -3718,10 +3698,6 @@ "description": "Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used", "type": "string" }, - "horizon_meth": { - "description": "Reference or method used in determining the horizon", - "type": "string" - }, "host_age": { "description": "Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees", "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", @@ -4505,10 +4481,6 @@ "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$", "type": "string" }, - "horizon_meth": { - "description": "Reference or method used in determining the horizon", - "type": "string" - }, "lat_lon": { "description": "This is currently a required field but it's not clear if this should be required for human hosts", "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$", @@ -4860,10 +4832,6 @@ "description": "Information about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens", "type": "string" }, - "horizon_meth": { - "description": "Reference or method used in determining the horizon", - "type": "string" - }, "host_age": { "description": "Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees", "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", @@ -5711,10 +5679,6 @@ "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", "type": "string" }, - "horizon_meth": { - "description": "Reference or method used in determining the horizon", - "type": "string" - }, "lat_lon": { "description": "This is currently a required field but it's not clear if this should be required for human hosts", "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$", @@ -7016,10 +6980,6 @@ "pattern": "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$", "type": "string" }, - "horizon_meth": { - "description": "Reference or method used in determining the horizon", - "type": "string" - }, "indust_eff_percent": { "description": "Percentage of industrial effluents received by wastewater treatment plant", "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", @@ -7455,10 +7415,6 @@ "pattern": "^[-+]?[0-9]*\\.?[0-9]+ +\\S.*$", "type": "string" }, - "horizon_meth": { - "description": "Reference or method used in determining the horizon", - "type": "string" - }, "lat_lon": { "description": "This is currently a required field but it's not clear if this should be required for human hosts", "pattern": "^[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)? [-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?$", diff --git a/project/owl/nmdc_submission_schema.owl.ttl b/project/owl/nmdc_submission_schema.owl.ttl index ca560848..98a12acc 100644 --- a/project/owl/nmdc_submission_schema.owl.ttl +++ b/project/owl/nmdc_submission_schema.owl.ttl @@ -607,52 +607,48 @@ nmdc_sub_schema:HcrCoresInterface a owl:Class, dcterms:title "Hcr Cores" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000424 ], + owl:onClass nmdc_sub_schema:DeposEnvEnum ; + owl:onProperty MIXS:0000992 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000393 ], + owl:onProperty MIXS:0000300 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000009 ], + owl:onProperty MIXS:0000429 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000998 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:Double ; - owl:onProperty MIXS:0001001 ], + owl:onProperty MIXS:0000120 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000425 ], + owl:onProperty MIXS:0000296 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000300 ], + owl:onProperty MIXS:0000303 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000409 ], + owl:onProperty MIXS:0000395 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000127 ], + owl:onProperty MIXS:0000011 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem_type ], + owl:onProperty MIXS:0000321 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000395 ], + owl:onProperty MIXS:0000438 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000423 ], + owl:onProperty nmdc_sub_schema:ecosystem ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; @@ -660,119 +656,119 @@ nmdc_sub_schema:HcrCoresInterface a owl:Class, [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000426 ], + owl:onProperty MIXS:0000131 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000155 ], + owl:onProperty MIXS:0001106 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:DeposEnvEnum ; - owl:onProperty MIXS:0000992 ], + owl:onClass nmdc_sub_schema:LithologyEnum ; + owl:onProperty MIXS:0000990 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000133 ], + owl:onProperty MIXS:0000155 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:OxyStatSampEnum ; - owl:onProperty MIXS:0000753 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000013 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000153 ], + owl:onProperty MIXS:0000427 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onProperty MIXS:0000150 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000156 ], + owl:onClass nmdc_sub_schema:OxyStatSampEnum ; + owl:onProperty MIXS:0000753 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem_category ], + owl:onProperty MIXS:0000397 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000001 ], + owl:onClass nmdc_sub_schema:SrGeolAgeEnum ; + owl:onProperty MIXS:0000997 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000116 ], + owl:onProperty MIXS:0000431 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem_subtype ], + owl:onProperty MIXS:0000404 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000397 ], + owl:onProperty MIXS:0000127 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000117 ], + owl:onProperty MIXS:0000393 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000405 ], + owl:onProperty nmdc_sub_schema:ecosystem_category ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000157 ], + owl:onProperty MIXS:0000410 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000404 ], + owl:onClass nmdc_sub_schema:Double ; + owl:onProperty MIXS:0001001 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000026 ], + owl:onProperty MIXS:0000110 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000412 ], + owl:onProperty MIXS:0000430 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000152 ], + owl:onProperty MIXS:0000154 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000012 ], + owl:onProperty MIXS:0000183 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000106 ], + owl:onProperty MIXS:0000408 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000434 ], + owl:onProperty MIXS:0000017 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000427 ], + owl:onProperty MIXS:0000139 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000290 ], + owl:onProperty nmdc_sub_schema:specific_ecosystem ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000211 ], + owl:onProperty MIXS:0000751 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000428 ], + owl:onProperty MIXS:0000406 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000303 ], + owl:onProperty MIXS:0000211 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000431 ], + owl:onProperty MIXS:0000135 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; @@ -780,253 +776,257 @@ nmdc_sub_schema:HcrCoresInterface a owl:Class, [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem ], + owl:onProperty MIXS:0000425 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000433 ], + owl:onProperty MIXS:0001225 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000110 ], + owl:onClass nmdc_sub_schema:HcrEnum ; + owl:onProperty MIXS:0000988 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000150 ], + owl:onProperty nmdc_sub_schema:ecosystem_subtype ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:HcrEnum ; - owl:onProperty MIXS:0000988 ], + owl:onClass nmdc_sub_schema:HcrGeolAgeEnum ; + owl:onProperty MIXS:0000993 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000011 ], + owl:onProperty MIXS:0000297 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000296 ], + owl:onProperty MIXS:0000298 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000126 ], + owl:onClass nmdc_sub_schema:SrKerogTypeEnum ; + owl:onProperty MIXS:0000994 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000410 ], + owl:onProperty MIXS:0000412 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000430 ], + owl:onProperty MIXS:0000009 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000102 ], + owl:onProperty MIXS:0000426 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000421 ], + owl:onProperty MIXS:0000290 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000755 ], + owl:onProperty MIXS:0001107 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000154 ], + owl:onClass nmdc_sub_schema:SrLithologyEnum ; + owl:onProperty MIXS:0000995 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000298 ], + owl:onProperty MIXS:0000002 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:env_package ], - [ a owl:Class ; - owl:intersectionOf ( [ a owl:Restriction ; - owl:allValuesFrom nmdc_sub_schema:AnalysisTypeEnum ; - owl:onProperty ] [ a owl:Restriction ; - owl:onProperty ; - owl:someValuesFrom nmdc_sub_schema:AnalysisTypeEnum ] ) ], + owl:onProperty MIXS:0000001 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:HcrGeolAgeEnum ; - owl:onProperty MIXS:0000993 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000405 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000406 ], + owl:onProperty MIXS:0000424 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000752 ], + owl:onProperty MIXS:0000134 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:SrDepEnvEnum ; - owl:onProperty MIXS:0000996 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000291 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000135 ], + owl:onProperty MIXS:0000436 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000002 ], + owl:onProperty MIXS:0000157 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000093 ], + owl:onProperty MIXS:0000156 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000120 ], + owl:onProperty MIXS:0000026 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000010 ], + owl:onProperty MIXS:0000434 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:LithologyEnum ; - owl:onProperty MIXS:0000990 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000133 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001106 ], + owl:onProperty MIXS:0000117 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000291 ], + owl:onProperty MIXS:0000998 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000436 ], + owl:onProperty MIXS:0000010 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001107 ], + owl:onProperty MIXS:0000423 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:SrGeolAgeEnum ; - owl:onProperty MIXS:0000997 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000433 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000419 ], + owl:onProperty MIXS:0000755 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000008 ], + owl:onProperty MIXS:0000126 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000751 ], + owl:onProperty MIXS:0000428 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000408 ], + owl:onProperty nmdc_sub_schema:ecosystem_type ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000432 ], + owl:onProperty MIXS:0000435 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000016 ], + owl:onProperty MIXS:0000752 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000394 ], + owl:onProperty MIXS:0000409 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000438 ], + owl:onProperty MIXS:0000012 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001225 ], + owl:onProperty nmdc_sub_schema:env_package ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000103 ], + owl:onProperty MIXS:0000105 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000013 ], + owl:onProperty MIXS:0000407 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000099 ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000105 ], + owl:onProperty MIXS:0000099 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:specific_ecosystem ], + owl:onClass nmdc_sub_schema:SrDepEnvEnum ; + owl:onProperty MIXS:0000996 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000413 ], + owl:onProperty MIXS:0000152 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:SampSubtypeEnum ; - owl:onProperty MIXS:0000999 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000116 ], + [ a owl:Class ; + owl:intersectionOf ( [ a owl:Restriction ; + owl:allValuesFrom nmdc_sub_schema:AnalysisTypeEnum ; + owl:onProperty ] [ a owl:Restriction ; + owl:onProperty ; + owl:someValuesFrom nmdc_sub_schema:AnalysisTypeEnum ] ) ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000131 ], + owl:onProperty MIXS:0000016 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000139 ], + owl:onProperty MIXS:0000413 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000435 ], + owl:onProperty MIXS:0000008 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000297 ], + owl:onClass nmdc_sub_schema:HcProducedEnum ; + owl:onProperty MIXS:0000989 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000014 ], + owl:onProperty MIXS:0000093 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000321 ], + owl:onProperty MIXS:0000106 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:SrLithologyEnum ; - owl:onProperty MIXS:0000995 ], + owl:onClass nmdc_sub_schema:SampSubtypeEnum ; + owl:onProperty MIXS:0000999 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:SrKerogTypeEnum ; - owl:onProperty MIXS:0000994 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000432 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:HcProducedEnum ; - owl:onProperty MIXS:0000989 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000394 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000134 ], + owl:onProperty MIXS:0000102 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000017 ], + owl:onProperty MIXS:0000421 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000429 ], + owl:onProperty MIXS:0000419 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000407 ], + owl:onProperty MIXS:0000103 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000183 ], + owl:onProperty MIXS:0000153 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000014 ], nmdc_sub_schema:DhInterface, nmdc_sub_schema:DhMultiviewCommonColumnsMixin ; skos:definition "hcr_cores dh_interface" . @@ -1038,139 +1038,139 @@ nmdc_sub_schema:HcrFluidsSwabsInterface a owl:Class, rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem_category ], + owl:onProperty MIXS:0000419 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:env_package ], + owl:onProperty MIXS:0000099 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000397 ], + owl:onProperty MIXS:0000429 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000017 ], + owl:onProperty MIXS:0000134 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000183 ], + owl:onProperty MIXS:0000410 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000393 ], + owl:onProperty MIXS:0000139 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000154 ], + owl:onProperty MIXS:0000407 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000755 ], + owl:onProperty MIXS:0000126 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000456 ], + owl:onProperty MIXS:0000425 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000136 ], + owl:onProperty MIXS:0000454 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:Double ; - owl:onProperty MIXS:0001001 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000428 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000433 ], + owl:onProperty MIXS:0000110 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000156 ], + owl:onProperty MIXS:0000153 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000093 ], + owl:onProperty MIXS:0001011 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000434 ], + owl:onProperty MIXS:0000008 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000463 ], + owl:onProperty MIXS:0000002 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000410 ], + owl:onClass nmdc_sub_schema:DeposEnvEnum ; + owl:onProperty MIXS:0000992 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000099 ], + owl:onProperty MIXS:0000436 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000113 ], + owl:onClass nmdc_sub_schema:SampCollectPointEnum ; + owl:onProperty MIXS:0001015 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000407 ], + owl:onClass nmdc_sub_schema:LithologyEnum ; + owl:onProperty MIXS:0000990 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001008 ], + owl:onProperty MIXS:0000113 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000419 ], + owl:onProperty MIXS:0000755 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000454 ], + owl:onProperty MIXS:0000432 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000751 ], + owl:onProperty nmdc_sub_schema:ecosystem_subtype ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000155 ], + owl:onClass nmdc_sub_schema:HcrGeolAgeEnum ; + owl:onProperty MIXS:0000993 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000431 ], + owl:onProperty MIXS:0000183 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000406 ], + owl:onProperty MIXS:0000116 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000424 ], + owl:onClass nmdc_sub_schema:OxyStatSampEnum ; + owl:onProperty MIXS:0000753 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000018 ], + owl:onProperty MIXS:0001106 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000408 ], + owl:onProperty MIXS:0000136 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000291 ], + owl:onClass nmdc_sub_schema:Double ; + owl:onProperty MIXS:0001001 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000110 ], + owl:onProperty nmdc_sub_schema:env_package ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000412 ], + owl:onProperty MIXS:0000456 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem_type ], + owl:onProperty MIXS:0000154 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; @@ -1178,139 +1178,141 @@ nmdc_sub_schema:HcrFluidsSwabsInterface a owl:Class, [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000013 ], + owl:onProperty MIXS:0001225 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001107 ], + owl:onProperty MIXS:0000297 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000120 ], + owl:onProperty MIXS:0000026 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000321 ], + owl:onProperty MIXS:0000102 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001106 ], + owl:onProperty MIXS:0000424 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000296 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:SampSubtypeEnum ; - owl:onProperty MIXS:0000999 ], + owl:onProperty nmdc_sub_schema:ecosystem_type ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000016 ], + owl:onProperty MIXS:0000105 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001011 ], + owl:onProperty MIXS:0000303 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000150 ], + owl:onProperty MIXS:0000155 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000008 ], + owl:onProperty MIXS:0000452 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000300 ], + owl:onProperty MIXS:0000135 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000012 ], + owl:onProperty MIXS:0000093 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000297 ], + owl:onProperty MIXS:0000395 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000430 ], + owl:onProperty MIXS:0000014 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000453 ], + owl:onProperty nmdc_sub_schema:ecosystem_category ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000135 ], + owl:onProperty MIXS:0000152 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000421 ], + owl:onProperty MIXS:0000457 ], + [ a owl:Class ; + owl:intersectionOf ( [ a owl:Restriction ; + owl:allValuesFrom nmdc_sub_schema:AnalysisTypeEnum ; + owl:onProperty ] [ a owl:Restriction ; + owl:onProperty ; + owl:someValuesFrom nmdc_sub_schema:AnalysisTypeEnum ] ) ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001010 ], + owl:onProperty MIXS:0000397 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000426 ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:HcProducedEnum ; - owl:onProperty MIXS:0000989 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000434 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001012 ], + owl:onProperty MIXS:0000463 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000303 ], + owl:onProperty MIXS:0000009 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:HcrEnum ; - owl:onProperty MIXS:0000988 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0001107 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000452 ], + owl:onProperty MIXS:0000431 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000001 ], + owl:onProperty MIXS:0000438 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000134 ], + owl:onProperty MIXS:0000157 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000002 ], + owl:onProperty MIXS:0000421 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000010 ], + owl:onProperty MIXS:0000150 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000752 ], + owl:onProperty MIXS:0000300 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000152 ], + owl:onProperty MIXS:0000423 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000998 ], + owl:onProperty MIXS:0000408 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000157 ], + owl:onProperty MIXS:0000296 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000423 ], + owl:onProperty MIXS:0001008 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; @@ -1318,73 +1320,59 @@ nmdc_sub_schema:HcrFluidsSwabsInterface a owl:Class, [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000435 ], + owl:onProperty MIXS:0000016 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000106 ], - [ a owl:Class ; - owl:intersectionOf ( [ a owl:Restriction ; - owl:allValuesFrom nmdc_sub_schema:AnalysisTypeEnum ; - owl:onProperty ] [ a owl:Restriction ; - owl:onProperty ; - owl:someValuesFrom nmdc_sub_schema:AnalysisTypeEnum ] ) ], + owl:onProperty MIXS:0000427 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000011 ], + owl:onClass nmdc_sub_schema:SampSubtypeEnum ; + owl:onProperty MIXS:0000999 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000394 ], + owl:onProperty MIXS:0000291 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001009 ], + owl:onProperty MIXS:0000406 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000457 ], + owl:onProperty nmdc_sub_schema:specific_ecosystem ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000131 ], + owl:onProperty MIXS:0000011 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000438 ], + owl:onProperty MIXS:0000010 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000102 ], + owl:onProperty MIXS:0000455 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000290 ], + owl:onProperty MIXS:0000998 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000395 ], + owl:onProperty MIXS:0000106 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001225 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:DeposEnvEnum ; - owl:onProperty MIXS:0000992 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:OxyStatSampEnum ; - owl:onProperty MIXS:0000753 ], + owl:onProperty MIXS:0000298 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:SampCollectPointEnum ; - owl:onProperty MIXS:0001015 ], + owl:onClass nmdc_sub_schema:HcProducedEnum ; + owl:onProperty MIXS:0000989 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000127 ], + owl:onProperty MIXS:0000430 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; @@ -1392,91 +1380,103 @@ nmdc_sub_schema:HcrFluidsSwabsInterface a owl:Class, [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000126 ], + owl:onProperty MIXS:0000018 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000432 ], + owl:onProperty MIXS:0000290 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:specific_ecosystem ], + owl:onProperty MIXS:0001010 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000455 ], + owl:onProperty MIXS:0000393 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000133 ], + owl:onProperty MIXS:0000412 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000116 ], + owl:onProperty MIXS:0000426 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000153 ], + owl:onProperty MIXS:0000751 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:HcrGeolAgeEnum ; - owl:onProperty MIXS:0000993 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000752 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000298 ], + owl:onProperty MIXS:0000435 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000026 ], + owl:onProperty MIXS:0000433 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000425 ], + owl:onProperty MIXS:0000001 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000139 ], + owl:onProperty MIXS:0000321 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000105 ], + owl:onClass nmdc_sub_schema:HcrEnum ; + owl:onProperty MIXS:0000988 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000428 ], + owl:onProperty MIXS:0000131 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem_subtype ], + owl:onProperty MIXS:0000017 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000427 ], + owl:onProperty MIXS:0000133 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:LithologyEnum ; - owl:onProperty MIXS:0000990 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000013 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000009 ], + owl:onProperty MIXS:0000156 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000436 ], + owl:onProperty MIXS:0000120 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onProperty MIXS:0000127 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000014 ], + owl:onProperty MIXS:0000012 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000429 ], + owl:onProperty MIXS:0000453 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0001012 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000394 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0001009 ], nmdc_sub_schema:DhInterface, nmdc_sub_schema:DhMultiviewCommonColumnsMixin ; skos:definition "hcr_fluids_swabs dh_interface" . @@ -1496,141 +1496,141 @@ nmdc_sub_schema:MiscEnvsInterface a owl:Class, rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000119 ], + owl:onProperty nmdc_sub_schema:ecosystem_subtype ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000010 ], + owl:onProperty nmdc_sub_schema:specific_ecosystem ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000181 ], + owl:onProperty MIXS:0000751 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000754 ], + owl:onProperty MIXS:0000179 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000184 ], + owl:onProperty MIXS:0000093 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000008 ], + owl:onProperty MIXS:0000434 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000752 ], + owl:onProperty nmdc_sub_schema:ecosystem_type ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000179 ], + owl:onProperty MIXS:0000113 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000012 ], + owl:onProperty MIXS:0000008 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000435 ], + owl:onProperty MIXS:0000204 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000017 ], + owl:onProperty MIXS:0000203 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000412 ], + owl:onProperty MIXS:0000427 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000176 ], + owl:onProperty MIXS:0000178 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000755 ], + owl:onProperty MIXS:0000094 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem_type ], - [ a owl:Class ; - owl:intersectionOf ( [ a owl:Restriction ; - owl:allValuesFrom nmdc_sub_schema:AnalysisTypeEnum ; - owl:onProperty ] [ a owl:Restriction ; - owl:onProperty ; - owl:someValuesFrom nmdc_sub_schema:AnalysisTypeEnum ] ) ], + owl:onProperty MIXS:0000184 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:Double ; - owl:onProperty MIXS:0001001 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000013 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000429 ], + owl:onProperty MIXS:0000010 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000424 ], + owl:onProperty MIXS:0000436 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000505 ], + owl:onProperty MIXS:0000176 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000009 ], + owl:onProperty MIXS:0000014 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000426 ], + owl:onProperty MIXS:0000754 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem_subtype ], + owl:onProperty MIXS:0000103 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000436 ], + owl:onProperty MIXS:0000430 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001225 ], + owl:onProperty MIXS:0000423 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000026 ], + owl:onProperty MIXS:0000119 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000428 ], + owl:onProperty MIXS:0000429 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000203 ], + owl:onProperty MIXS:0001106 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000016 ], + owl:onProperty nmdc_sub_schema:ecosystem ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000116 ], + owl:onProperty MIXS:0001107 ], + [ a owl:Class ; + owl:intersectionOf ( [ a owl:Restriction ; + owl:allValuesFrom nmdc_sub_schema:AnalysisTypeEnum ; + owl:onProperty ] [ a owl:Restriction ; + owl:onProperty ; + owl:someValuesFrom nmdc_sub_schema:AnalysisTypeEnum ] ) ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000434 ], + owl:onProperty MIXS:0000001 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000110 ], + owl:onClass nmdc_sub_schema:OxyStatSampEnum ; + owl:onProperty MIXS:0000753 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000321 ], + owl:onProperty MIXS:0000116 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000205 ], + owl:onProperty nmdc_sub_schema:ecosystem_category ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; @@ -1638,47 +1638,51 @@ nmdc_sub_schema:MiscEnvsInterface a owl:Class, [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000011 ], + owl:onProperty MIXS:0000426 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000178 ], + owl:onProperty MIXS:0000177 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000001 ], + owl:onProperty MIXS:0000755 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass nmdc_sub_schema:Double ; + owl:onProperty MIXS:0001001 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000018 ], + owl:onProperty MIXS:0000017 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001107 ], + owl:onProperty MIXS:0000016 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000093 ], + owl:onProperty MIXS:0000321 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000103 ], + owl:onProperty MIXS:0000428 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000113 ], + owl:onProperty MIXS:0000183 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000002 ], + owl:onProperty MIXS:0000011 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000177 ], + owl:onProperty MIXS:0000181 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000423 ], + owl:onProperty MIXS:0000018 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; @@ -1686,7 +1690,7 @@ nmdc_sub_schema:MiscEnvsInterface a owl:Class, [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000013 ], + owl:onProperty MIXS:0000425 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; @@ -1694,75 +1698,71 @@ nmdc_sub_schema:MiscEnvsInterface a owl:Class, [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000751 ], + owl:onProperty nmdc_sub_schema:env_package ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000425 ], + owl:onProperty MIXS:0000412 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001106 ], + owl:onProperty MIXS:0000110 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000162 ], + owl:onProperty MIXS:0000002 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000430 ], + owl:onProperty MIXS:0000505 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:env_package ], + owl:onProperty MIXS:0000162 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000432 ], + owl:onProperty MIXS:0000435 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000183 ], + owl:onProperty MIXS:0000752 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000204 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:OxyStatSampEnum ; - owl:onProperty MIXS:0000753 ], + owl:onProperty MIXS:0000009 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000094 ], + owl:onProperty MIXS:0000504 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000014 ], + owl:onProperty MIXS:0000026 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000427 ], + owl:onProperty MIXS:0000424 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000504 ], + owl:onProperty MIXS:0000432 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem_category ], + owl:onProperty MIXS:0001225 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onProperty MIXS:0000012 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:specific_ecosystem ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem ], + owl:onProperty MIXS:0000205 ], nmdc_sub_schema:DhInterface, nmdc_sub_schema:DhMultiviewCommonColumnsMixin ; skos:definition "misc_envs dh_interface" . @@ -1774,17 +1774,17 @@ nmdc_sub_schema:NamedThing a owl:Class, owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; owl:onProperty dcterms:description ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass nmdc_sub_schema:String ; + owl:onProperty nmdc_sub_schema:name ], [ a owl:Restriction ; owl:allValuesFrom nmdc_sub_schema:Uriorcurie ; owl:onProperty nmdc_sub_schema:alternative_identifiers ], [ a owl:Restriction ; owl:onClass nmdc_sub_schema:Uriorcurie ; owl:onProperty nmdc_sub_schema:id ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:name ] ; + owl:qualifiedCardinality 1 ] ; skos:definition "a databased entity or concept/class" . nmdc_sub_schema:SampleData a owl:Class, @@ -1794,39 +1794,39 @@ nmdc_sub_schema:SampleData a owl:Class, rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom nmdc_sub_schema:SedimentInterface ; owl:onProperty nmdc_sub_schema:sediment_data ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc_sub_schema:WaterInterface ; - owl:onProperty nmdc_sub_schema:water_data ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc_sub_schema:BiofilmInterface ; - owl:onProperty nmdc_sub_schema:biofilm_data ], [ a owl:Restriction ; owl:allValuesFrom nmdc_sub_schema:AirInterface ; owl:onProperty nmdc_sub_schema:air_data ], [ a owl:Restriction ; - owl:allValuesFrom nmdc_sub_schema:WastewaterSludgeInterface ; - owl:onProperty nmdc_sub_schema:wastewater_sludge_data ], + owl:allValuesFrom nmdc_sub_schema:EmslInterface ; + owl:onProperty nmdc_sub_schema:emsl_data ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc_sub_schema:JgiMtInterface ; + owl:onProperty nmdc_sub_schema:jgi_mt_data ], [ a owl:Restriction ; owl:allValuesFrom nmdc_sub_schema:SoilInterface ; owl:onProperty nmdc_sub_schema:soil_data ], [ a owl:Restriction ; owl:allValuesFrom nmdc_sub_schema:JgiMgInterface ; owl:onProperty nmdc_sub_schema:jgi_mg_data ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc_sub_schema:EmslInterface ; - owl:onProperty nmdc_sub_schema:emsl_data ], [ a owl:Restriction ; owl:allValuesFrom nmdc_sub_schema:HostAssociatedInterface ; owl:onProperty nmdc_sub_schema:host_associated_data ], [ a owl:Restriction ; - owl:allValuesFrom nmdc_sub_schema:PlantAssociatedInterface ; - owl:onProperty nmdc_sub_schema:plant_associated_data ], + owl:allValuesFrom nmdc_sub_schema:WaterInterface ; + owl:onProperty nmdc_sub_schema:water_data ], [ a owl:Restriction ; - owl:allValuesFrom nmdc_sub_schema:JgiMtInterface ; - owl:onProperty nmdc_sub_schema:jgi_mt_data ], + owl:allValuesFrom nmdc_sub_schema:BiofilmInterface ; + owl:onProperty nmdc_sub_schema:biofilm_data ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc_sub_schema:WastewaterSludgeInterface ; + owl:onProperty nmdc_sub_schema:wastewater_sludge_data ], [ a owl:Restriction ; owl:allValuesFrom nmdc_sub_schema:BuiltEnvInterface ; - owl:onProperty nmdc_sub_schema:built_env_data ] ; + owl:onProperty nmdc_sub_schema:built_env_data ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc_sub_schema:PlantAssociatedInterface ; + owl:onProperty nmdc_sub_schema:plant_associated_data ] ; skos:definition "represents data produced by the DataHarmonizer tabs of the submission portal" . nmdc_sub_schema:air_data a owl:ObjectProperty, @@ -2062,37 +2062,31 @@ nmdc_sub_schema:AirInterface a owl:Class, rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001107 ], + owl:onProperty MIXS:0000011 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000097 ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000112 ], - [ a owl:Class ; - owl:intersectionOf ( [ a owl:Restriction ; - owl:allValuesFrom nmdc_sub_schema:AnalysisTypeEnum ; - owl:onProperty ] [ a owl:Restriction ; - owl:onProperty ; - owl:someValuesFrom nmdc_sub_schema:AnalysisTypeEnum ] ) ], + owl:onProperty MIXS:0000098 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000116 ], + owl:onProperty nmdc_sub_schema:ecosystem ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000001 ], + owl:onProperty MIXS:0000010 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:specific_ecosystem ], + owl:onProperty MIXS:0000012 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000752 ], + owl:onProperty MIXS:0000118 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; @@ -2100,99 +2094,105 @@ nmdc_sub_schema:AirInterface a owl:Class, [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000118 ], + owl:onProperty MIXS:0000110 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000026 ], + owl:onProperty MIXS:0000115 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000101 ], + owl:onProperty MIXS:0000016 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000107 ], + owl:onProperty MIXS:0000112 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001225 ], + owl:onClass nmdc_sub_schema:OxyStatSampEnum ; + owl:onProperty MIXS:0000753 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem ], + owl:onProperty MIXS:0000096 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000017 ], + owl:onProperty MIXS:0000756 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000103 ], + owl:onProperty MIXS:0000094 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000754 ], + owl:onProperty MIXS:0000014 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000114 ], + owl:onProperty MIXS:0000001 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000104 ], + owl:onProperty MIXS:0000103 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000755 ], + owl:onProperty MIXS:0000183 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000113 ], + owl:onProperty MIXS:0000097 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000183 ], + owl:onProperty MIXS:0000009 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000110 ], + owl:onProperty nmdc_sub_schema:env_package ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000012 ], + owl:onProperty MIXS:0000113 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000002 ], + owl:onProperty MIXS:0000107 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000094 ], + owl:onProperty MIXS:0000755 ], + [ a owl:Class ; + owl:intersectionOf ( [ a owl:Restriction ; + owl:allValuesFrom nmdc_sub_schema:AnalysisTypeEnum ; + owl:onProperty ] [ a owl:Restriction ; + owl:onProperty ; + owl:someValuesFrom nmdc_sub_schema:AnalysisTypeEnum ] ) ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000096 ], + owl:onProperty MIXS:0000026 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000093 ], + owl:onProperty MIXS:0001225 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem_subtype ], + owl:onProperty MIXS:0000752 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000009 ], + owl:onProperty MIXS:0000754 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem_type ], + owl:onProperty MIXS:0000101 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000016 ], + owl:onProperty MIXS:0000108 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; @@ -2200,11 +2200,11 @@ nmdc_sub_schema:AirInterface a owl:Class, [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000010 ], + owl:onProperty MIXS:0000751 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem_category ], + owl:onProperty MIXS:0000002 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; @@ -2212,55 +2212,55 @@ nmdc_sub_schema:AirInterface a owl:Class, [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000014 ], + owl:onProperty MIXS:0000114 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000098 ], + owl:onProperty nmdc_sub_schema:ecosystem_category ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000115 ], + owl:onProperty MIXS:0001107 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000013 ], + owl:onProperty MIXS:0000104 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000751 ], + owl:onProperty nmdc_sub_schema:ecosystem_type ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000108 ], + owl:onProperty nmdc_sub_schema:specific_ecosystem ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000756 ], + owl:onProperty MIXS:0000013 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onProperty MIXS:0000100 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000100 ], + owl:onProperty nmdc_sub_schema:ecosystem_subtype ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:OxyStatSampEnum ; - owl:onProperty MIXS:0000753 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000008 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:env_package ], + owl:onProperty MIXS:0000116 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000008 ], + owl:onProperty MIXS:0000017 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000011 ], + owl:onProperty MIXS:0000093 ], nmdc_sub_schema:DhInterface, nmdc_sub_schema:DhMultiviewCommonColumnsMixin, nmdc_sub_schema:SampIdNewTermsMixin ; @@ -2285,349 +2285,349 @@ nmdc_sub_schema:BiofilmInterface a owl:Class, rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:env_package ], + owl:onProperty MIXS:0000755 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000103 ], + owl:onProperty MIXS:0000432 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000173 ], + owl:onProperty MIXS:0000110 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000182 ], + owl:onProperty MIXS:0000412 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000754 ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onProperty MIXS:0000013 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000498 ], + owl:onProperty MIXS:0000014 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000183 ], + owl:onProperty MIXS:0000436 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000014 ], + owl:onProperty MIXS:0000011 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000116 ], + owl:onProperty MIXS:0000533 ], + [ a owl:Class ; + owl:intersectionOf ( [ a owl:Restriction ; + owl:allValuesFrom nmdc_sub_schema:AnalysisTypeEnum ; + owl:onProperty ] [ a owl:Restriction ; + owl:onProperty ; + owl:someValuesFrom nmdc_sub_schema:AnalysisTypeEnum ] ) ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000525 ], + owl:onProperty MIXS:0000431 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000180 ], + owl:onProperty MIXS:0000754 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000516 ], + owl:onProperty MIXS:0000424 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000008 ], + owl:onProperty MIXS:0000026 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000017 ], + owl:onProperty MIXS:0000525 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem_subtype ], + owl:onProperty MIXS:0000001 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000412 ], + owl:onProperty nmdc_sub_schema:env_package ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000533 ], + owl:onProperty MIXS:0000428 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000101 ], + owl:onProperty MIXS:0000530 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000321 ], + owl:onProperty nmdc_sub_schema:ecosystem ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000002 ], + owl:onProperty MIXS:0000172 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000205 ], + owl:onProperty MIXS:0000010 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000011 ], + owl:onProperty MIXS:0000179 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000016 ], + owl:onProperty MIXS:0000204 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000178 ], + owl:onProperty MIXS:0000017 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000504 ], + owl:onProperty MIXS:0000094 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000018 ], + owl:onProperty MIXS:0001225 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000428 ], + owl:onProperty nmdc_sub_schema:ecosystem_category ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000204 ], + owl:onProperty MIXS:0000310 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000191 ], + owl:onProperty MIXS:0000119 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000172 ], + owl:onProperty MIXS:0000093 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000176 ], + owl:onProperty MIXS:0000116 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000310 ], + owl:onProperty MIXS:0000016 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000426 ], + owl:onProperty MIXS:0000205 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem ], + owl:onProperty MIXS:0000433 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000430 ], + owl:onProperty MIXS:0000498 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000009 ], + owl:onProperty MIXS:0000427 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000010 ], + owl:onProperty MIXS:0000101 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000001 ], + owl:onProperty MIXS:0000177 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000436 ], + owl:onClass nmdc_sub_schema:OxyStatSampEnum ; + owl:onProperty MIXS:0000753 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000432 ], + owl:onProperty MIXS:0000113 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem_type ], + owl:onProperty MIXS:0000191 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000181 ], + owl:onProperty MIXS:0000178 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:OxyStatSampEnum ; - owl:onProperty MIXS:0000753 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000180 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000179 ], + owl:onProperty MIXS:0000751 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000175 ], + owl:onProperty MIXS:0000137 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000424 ], + owl:onProperty MIXS:0000009 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000490 ], + owl:onProperty nmdc_sub_schema:specific_ecosystem ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000423 ], + owl:onProperty MIXS:0000508 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000503 ], + owl:onProperty MIXS:0000515 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000421 ], + owl:onProperty MIXS:0000173 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000013 ], + owl:onProperty MIXS:0000182 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000752 ], + owl:onProperty nmdc_sub_schema:ecosystem_subtype ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000119 ], + owl:onProperty MIXS:0000430 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001225 ], + owl:onClass nmdc_sub_schema:Double ; + owl:onProperty MIXS:0001001 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000185 ], + owl:onProperty MIXS:0000423 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000012 ], + owl:onProperty MIXS:0000176 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000093 ], + owl:onProperty MIXS:0000184 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000184 ], + owl:onProperty MIXS:0000175 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000427 ], + owl:onProperty MIXS:0000321 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000508 ], + owl:onProperty MIXS:0000490 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000162 ], + owl:onProperty MIXS:0000505 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000431 ], + owl:onProperty MIXS:0000503 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000113 ], + owl:onProperty MIXS:0001106 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000502 ], + owl:onProperty MIXS:0000752 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000177 ], - [ a owl:Class ; - owl:intersectionOf ( [ a owl:Restriction ; - owl:allValuesFrom nmdc_sub_schema:AnalysisTypeEnum ; - owl:onProperty ] [ a owl:Restriction ; - owl:onProperty ; - owl:someValuesFrom nmdc_sub_schema:AnalysisTypeEnum ] ) ], + owl:onProperty MIXS:0000012 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000751 ], + owl:onProperty MIXS:0000181 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000094 ], + owl:onProperty MIXS:0000162 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:specific_ecosystem ], + owl:onProperty MIXS:0000502 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000174 ], + owl:onProperty MIXS:0000002 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000433 ], + owl:onProperty MIXS:0000103 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000110 ], + owl:onProperty MIXS:0000429 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001107 ], + owl:onProperty MIXS:0000426 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000505 ], + owl:onProperty MIXS:0000183 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem_category ], + owl:onProperty MIXS:0000174 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000425 ], + owl:onProperty MIXS:0000421 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000434 ], + owl:onProperty MIXS:0000008 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000530 ], + owl:onProperty MIXS:0000434 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000755 ], + owl:onProperty MIXS:0000516 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000515 ], + owl:onProperty MIXS:0000504 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001106 ], + owl:onProperty nmdc_sub_schema:ecosystem_type ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000429 ], + owl:onProperty MIXS:0000185 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000137 ], + owl:onProperty MIXS:0000425 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000026 ], + owl:onProperty MIXS:0001107 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:Double ; - owl:onProperty MIXS:0001001 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000018 ], nmdc_sub_schema:DhInterface, nmdc_sub_schema:DhMultiviewCommonColumnsMixin, nmdc_sub_schema:SampIdNewTermsMixin ; @@ -2820,735 +2820,735 @@ nmdc_sub_schema:BuiltEnvInterface a owl:Class, rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000786 ], + owl:onProperty MIXS:0000218 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000721 ], + owl:onClass nmdc_sub_schema:RoomCondtEnum ; + owl:onProperty MIXS:0000822 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000143 ], + owl:onProperty MIXS:0000802 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000223 ], + owl:onProperty MIXS:0000196 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:SeasonUseEnum ; - owl:onProperty MIXS:0000830 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:SpecificEnum ; - owl:onProperty MIXS:0000836 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000228 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000781 ], + owl:onClass nmdc_sub_schema:ExtWallOrientEnum ; + owl:onProperty MIXS:0000817 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:OxyStatSampEnum ; - owl:onProperty MIXS:0000753 ], + owl:onClass nmdc_sub_schema:WeekdayEnum ; + owl:onProperty MIXS:0000848 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:QuadPosEnum ; - owl:onProperty MIXS:0000820 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000812 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem ], + owl:onProperty MIXS:0000124 ], [ a owl:Restriction ; - owl:allValuesFrom nmdc_sub_schema:LightTypeEnum ; - owl:onProperty MIXS:0000769 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass nmdc_sub_schema:CeilTextureEnum ; + owl:onProperty MIXS:0000783 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000812 ], + owl:onProperty MIXS:0000214 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000010 ], - [ a owl:Class ; - owl:intersectionOf ( [ a owl:Restriction ; - owl:allValuesFrom nmdc_sub_schema:AnalysisTypeEnum ; - owl:onProperty ] [ a owl:Restriction ; - owl:onProperty ; - owl:someValuesFrom nmdc_sub_schema:AnalysisTypeEnum ] ) ], + owl:onProperty MIXS:0000122 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem_category ], + owl:onProperty MIXS:0001107 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:ExtWindowOrientEnum ; - owl:onProperty MIXS:0000818 ], + owl:onClass nmdc_sub_schema:ArchStrucEnum ; + owl:onProperty MIXS:0000774 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000833 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:RoomCondtEnum ; - owl:onProperty MIXS:0000822 ], + owl:onProperty MIXS:0000012 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000220 ], + owl:onProperty MIXS:0000194 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onProperty MIXS:0000195 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000166 ], + owl:onProperty nmdc_sub_schema:ecosystem_type ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:DoorTypeEnum ; - owl:onProperty MIXS:0000794 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000148 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:WindowLocEnum ; - owl:onProperty MIXS:0000852 ], + owl:onClass nmdc_sub_schema:SpecificEnum ; + owl:onProperty MIXS:0000836 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000017 ], + owl:onProperty MIXS:0000094 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000233 ], + owl:onProperty MIXS:0000772 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000013 ], + owl:onProperty MIXS:0000773 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:CeilTypeEnum ; - owl:onProperty MIXS:0000784 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000143 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000094 ], + owl:onProperty MIXS:0000093 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:WindowCondEnum ; - owl:onProperty MIXS:0000849 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000224 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:WallConstTypeEnum ; - owl:onProperty MIXS:0000841 ], + owl:onClass nmdc_sub_schema:DoorTypeEnum ; + owl:onProperty MIXS:0000794 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:FloorWaterMoldEnum ; - owl:onProperty MIXS:0000805 ], + owl:onClass nmdc_sub_schema:MechStrucEnum ; + owl:onProperty MIXS:0000815 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:OccupDocumentEnum ; - owl:onProperty MIXS:0000816 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000776 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:CeilTextureEnum ; - owl:onProperty MIXS:0000783 ], + owl:onClass nmdc_sub_schema:WaterFeatTypeEnum ; + owl:onProperty MIXS:0000847 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000103 ], + owl:onClass nmdc_sub_schema:WindowTypeEnum ; + owl:onProperty MIXS:0000856 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000829 ], + owl:onProperty MIXS:0000321 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000800 ], + owl:onProperty MIXS:0000168 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:WindowCoverEnum ; - owl:onProperty MIXS:0000850 ], + owl:onClass nmdc_sub_schema:BuildingSettingEnum ; + owl:onProperty MIXS:0000768 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000782 ], + owl:onProperty MIXS:0000128 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000785 ], + owl:onProperty MIXS:0000244 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000198 ], + owl:onProperty MIXS:0000793 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000227 ], + owl:onClass nmdc_sub_schema:RoomSampPosEnum ; + owl:onProperty MIXS:0000824 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:DoorTypeWoodEnum ; - owl:onProperty MIXS:0000797 ], + owl:onClass nmdc_sub_schema:RoomTypeEnum ; + owl:onProperty MIXS:0000825 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000188 ], + owl:onClass nmdc_sub_schema:FurnitureEnum ; + owl:onProperty MIXS:0000807 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000142 ], + owl:onClass nmdc_sub_schema:FloorStrucEnum ; + owl:onProperty MIXS:0000806 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000238 ], + owl:onProperty MIXS:0000103 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000242 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:RoomLocEnum ; - owl:onProperty MIXS:0000823 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:ExtWallOrientEnum ; - owl:onProperty MIXS:0000817 ], + owl:onProperty MIXS:0000855 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000193 ], + owl:onClass nmdc_sub_schema:BuildDocsEnum ; + owl:onProperty MIXS:0000787 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000093 ], + owl:onProperty MIXS:0000814 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000192 ], + owl:onProperty MIXS:0000220 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:FloorStrucEnum ; - owl:onProperty MIXS:0000806 ], + owl:onClass nmdc_sub_schema:WindowHorizPosEnum ; + owl:onProperty MIXS:0000851 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000225 ], + owl:onProperty MIXS:0000113 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000216 ], + owl:onProperty MIXS:0000123 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:GenderRestroomEnum ; - owl:onProperty MIXS:0000808 ], + owl:onClass nmdc_sub_schema:DrawingsEnum ; + owl:onProperty MIXS:0000798 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000196 ], + owl:onProperty MIXS:0000014 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:IndoorSpaceEnum ; - owl:onProperty MIXS:0000763 ], + owl:onClass nmdc_sub_schema:DoorLocEnum ; + owl:onProperty MIXS:0000790 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000776 ], + owl:onProperty MIXS:0000227 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:TrainStatLocEnum ; - owl:onProperty MIXS:0000838 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000158 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:CeilFinishMatEnum ; - owl:onProperty MIXS:0000780 ], + owl:onClass nmdc_sub_schema:RoomConnectedEnum ; + owl:onProperty MIXS:0000826 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000814 ], + owl:onProperty MIXS:0000010 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000008 ], + owl:onClass nmdc_sub_schema:Double ; + owl:onProperty MIXS:0000771 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000128 ], + owl:onProperty MIXS:0000188 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000217 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:SampFloorEnum ; - owl:onProperty MIXS:0000828 ], + owl:onProperty MIXS:0000775 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001107 ], + owl:onProperty MIXS:0000829 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:FloorCondEnum ; - owl:onProperty MIXS:0000803 ], + owl:onClass nmdc_sub_schema:DoorDirectEnum ; + owl:onProperty MIXS:0000789 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem_type ], + owl:onProperty MIXS:0000167 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000819 ], + owl:onProperty MIXS:0000231 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000219 ], + owl:onClass nmdc_sub_schema:TrainLineEnum ; + owl:onProperty MIXS:0000837 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000124 ], + owl:onProperty MIXS:0000166 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000194 ], + owl:onProperty MIXS:0000223 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:IntWallCondEnum ; - owl:onProperty MIXS:0000813 ], + owl:onClass nmdc_sub_schema:DoorMoveEnum ; + owl:onProperty MIXS:0000792 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:ArchStrucEnum ; - owl:onProperty MIXS:0000774 ], + owl:onClass nmdc_sub_schema:TrainStopLocEnum ; + owl:onProperty MIXS:0000839 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000802 ], + owl:onProperty MIXS:0000193 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000014 ], + owl:onClass nmdc_sub_schema:QuadPosEnum ; + owl:onProperty MIXS:0000820 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:RelSampLocEnum ; - owl:onProperty MIXS:0000821 ], + owl:onClass nmdc_sub_schema:VisMediaEnum ; + owl:onProperty MIXS:0000840 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass nmdc_sub_schema:WallLocEnum ; + owl:onProperty MIXS:0000843 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000018 ], + owl:onProperty MIXS:0000217 ], [ a owl:Restriction ; owl:allValuesFrom nmdc_sub_schema:FilterTypeEnum ; owl:onProperty MIXS:0000765 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:DoorMatEnum ; - owl:onProperty MIXS:0000791 ], + owl:onClass nmdc_sub_schema:SeasonUseEnum ; + owl:onProperty MIXS:0000830 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000224 ], + owl:onProperty MIXS:0000232 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000158 ], + owl:onProperty MIXS:0000236 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:SampWeatherEnum ; - owl:onProperty MIXS:0000827 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000142 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:Integer ; - owl:onProperty MIXS:0000237 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000229 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:TrainLineEnum ; - owl:onProperty MIXS:0000837 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000141 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000793 ], + owl:onProperty MIXS:0000226 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000141 ], + owl:onProperty nmdc_sub_schema:env_package ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:BuildDocsEnum ; - owl:onProperty MIXS:0000787 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000245 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:BuildingSettingEnum ; - owl:onProperty MIXS:0000768 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000129 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000012 ], + owl:onProperty MIXS:0000169 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:FloorFinishMatEnum ; - owl:onProperty MIXS:0000804 ], + owl:onClass nmdc_sub_schema:GenderRestroomEnum ; + owl:onProperty MIXS:0000808 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:specific_ecosystem ], + owl:onProperty MIXS:0000125 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:DoorMoveEnum ; - owl:onProperty MIXS:0000792 ], + owl:onClass nmdc_sub_schema:WindowCoverEnum ; + owl:onProperty MIXS:0000850 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000011 ], + owl:onProperty MIXS:0000799 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000113 ], + owl:onProperty MIXS:0000170 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:WallSurfTreatmentEnum ; - owl:onProperty MIXS:0000845 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000017 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000164 ], + owl:onProperty MIXS:0000854 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000799 ], + owl:onProperty MIXS:0000164 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000125 ], + owl:onProperty MIXS:0000833 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:DoorCondEnum ; - owl:onProperty MIXS:0000788 ], + owl:onClass nmdc_sub_schema:CeilTypeEnum ; + owl:onProperty MIXS:0000784 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000770 ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc_sub_schema:SubstructureTypeEnum ; - owl:onProperty MIXS:0000767 ], + owl:onClass nmdc_sub_schema:WallConstTypeEnum ; + owl:onProperty MIXS:0000841 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000145 ], + owl:onProperty MIXS:0000013 ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc_sub_schema:SurfAirContEnum ; + owl:onProperty MIXS:0000759 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:ShadingDeviceTypeEnum ; - owl:onProperty MIXS:0000835 ], + owl:onClass nmdc_sub_schema:WindowCondEnum ; + owl:onProperty MIXS:0000849 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000129 ], + owl:onClass nmdc_sub_schema:ExtWindowOrientEnum ; + owl:onProperty MIXS:0000818 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000195 ], + owl:onProperty MIXS:0000786 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem_subtype ], + owl:onProperty MIXS:0000234 ], [ a owl:Restriction ; - owl:allValuesFrom nmdc_sub_schema:HeatCoolTypeEnum ; - owl:onProperty MIXS:0000766 ], + owl:allValuesFrom nmdc_sub_schema:BuildOccupTypeEnum ; + owl:onProperty MIXS:0000761 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:Double ; - owl:onProperty MIXS:0000771 ], + owl:onClass nmdc_sub_schema:OxyStatSampEnum ; + owl:onProperty MIXS:0000753 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000097 ], + owl:onClass nmdc_sub_schema:WindowVertPosEnum ; + owl:onProperty MIXS:0000857 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000226 ], + owl:onClass nmdc_sub_schema:DoorMatEnum ; + owl:onProperty MIXS:0000791 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000245 ], + owl:onProperty MIXS:0000782 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000148 ], + owl:onClass nmdc_sub_schema:WallTextureEnum ; + owl:onProperty MIXS:0000846 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000168 ], + owl:onClass nmdc_sub_schema:WallSurfTreatmentEnum ; + owl:onProperty MIXS:0000845 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000773 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:IndoorSurfEnum ; - owl:onProperty MIXS:0000764 ], + owl:onProperty MIXS:0000777 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:Integer ; - owl:onProperty MIXS:0000235 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000145 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000144 ], + owl:onClass nmdc_sub_schema:SampWeatherEnum ; + owl:onProperty MIXS:0000827 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:WindowMatEnum ; - owl:onProperty MIXS:0000853 ], + owl:onClass nmdc_sub_schema:RelSampLocEnum ; + owl:onProperty MIXS:0000821 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:ShadingDeviceCondEnum ; - owl:onProperty MIXS:0000831 ], + owl:onClass nmdc_sub_schema:DoorCompTypeEnum ; + owl:onProperty MIXS:0000795 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000777 ], + owl:onProperty MIXS:0000121 ], + [ a owl:Class ; + owl:intersectionOf ( [ a owl:Restriction ; + owl:allValuesFrom nmdc_sub_schema:AnalysisTypeEnum ; + owl:onProperty ] [ a owl:Restriction ; + owl:onProperty ; + owl:someValuesFrom nmdc_sub_schema:AnalysisTypeEnum ] ) ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:FurnitureEnum ; - owl:onProperty MIXS:0000807 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty nmdc_sub_schema:ecosystem_category ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:TrainStopLocEnum ; - owl:onProperty MIXS:0000839 ], + owl:allValuesFrom nmdc_sub_schema:LightTypeEnum ; + owl:onProperty MIXS:0000769 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:DoorCompTypeEnum ; - owl:onProperty MIXS:0000795 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000230 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:WeekdayEnum ; - owl:onProperty MIXS:0000848 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000222 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:Double ; - owl:onProperty MIXS:0000760 ], + owl:onClass nmdc_sub_schema:WallFinishMatEnum ; + owl:onProperty MIXS:0000842 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:WindowVertPosEnum ; - owl:onProperty MIXS:0000857 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000008 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:DoorTypeMetalEnum ; - owl:onProperty MIXS:0000796 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000238 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000229 ], + owl:onClass nmdc_sub_schema:RoomLocEnum ; + owl:onProperty MIXS:0000823 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000167 ], + owl:onProperty MIXS:0000009 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000231 ], + owl:onProperty MIXS:0000242 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000221 ], + owl:onProperty MIXS:0000144 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000778 ], + owl:onClass nmdc_sub_schema:Integer ; + owl:onProperty MIXS:0000237 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:SurfMaterialEnum ; owl:onProperty MIXS:0000758 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000170 ], + owl:onClass nmdc_sub_schema:WindowMatEnum ; + owl:onProperty MIXS:0000853 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000775 ], + owl:onProperty MIXS:0000216 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000026 ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000756 ], + owl:onClass nmdc_sub_schema:FloorFinishMatEnum ; + owl:onProperty MIXS:0000804 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000832 ], + owl:onClass nmdc_sub_schema:FloorCondEnum ; + owl:onProperty MIXS:0000803 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000214 ], + owl:onProperty MIXS:0000225 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000243 ], + owl:onClass nmdc_sub_schema:IndoorSurfEnum ; + owl:onProperty MIXS:0000764 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000165 ], + owl:onClass nmdc_sub_schema:Integer ; + owl:onProperty MIXS:0000235 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:MechStrucEnum ; - owl:onProperty MIXS:0000815 ], + owl:onClass nmdc_sub_schema:IndoorSpaceEnum ; + owl:onProperty MIXS:0000763 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000855 ], + owl:onClass nmdc_sub_schema:Double ; + owl:onProperty MIXS:0000760 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass nmdc_sub_schema:TrainStatLocEnum ; + owl:onProperty MIXS:0000838 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000244 ], + owl:onProperty MIXS:0000819 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:DoorDirectEnum ; - owl:onProperty MIXS:0000789 ], + owl:onClass nmdc_sub_schema:HandidnessEnum ; + owl:onProperty MIXS:0000809 ], [ a owl:Restriction ; - owl:allValuesFrom nmdc_sub_schema:BuildOccupTypeEnum ; - owl:onProperty MIXS:0000761 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass nmdc_sub_schema:ShadingDeviceTypeEnum ; + owl:onProperty MIXS:0000835 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:RoomTypeEnum ; - owl:onProperty MIXS:0000825 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000165 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000009 ], + owl:onProperty MIXS:0000221 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:RoomConnectedEnum ; - owl:onProperty MIXS:0000826 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000844 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:DrawingsEnum ; - owl:onProperty MIXS:0000798 ], + owl:onClass nmdc_sub_schema:CeilFinishMatEnum ; + owl:onProperty MIXS:0000780 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:HandidnessEnum ; - owl:onProperty MIXS:0000809 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000834 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:WindowHorizPosEnum ; - owl:onProperty MIXS:0000851 ], + owl:onClass nmdc_sub_schema:OccupDocumentEnum ; + owl:onProperty MIXS:0000816 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000218 ], + owl:onClass nmdc_sub_schema:DoorTypeWoodEnum ; + owl:onProperty MIXS:0000797 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000121 ], + owl:onProperty MIXS:0000097 ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc_sub_schema:SubstructureTypeEnum ; + owl:onProperty MIXS:0000767 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000228 ], + owl:onProperty MIXS:0000756 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:WindowTypeEnum ; - owl:onProperty MIXS:0000856 ], + owl:onClass nmdc_sub_schema:SampFloorEnum ; + owl:onProperty MIXS:0000828 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000854 ], + owl:onProperty MIXS:0000026 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000230 ], + owl:onProperty nmdc_sub_schema:ecosystem ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000123 ], + owl:onClass nmdc_sub_schema:IntWallCondEnum ; + owl:onProperty MIXS:0000813 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000321 ], + owl:onProperty MIXS:0000778 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:DoorLocEnum ; - owl:onProperty MIXS:0000790 ], + owl:onClass nmdc_sub_schema:HeatDelivLocEnum ; + owl:onProperty MIXS:0000810 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass nmdc_sub_schema:CeilCondEnum ; + owl:onProperty MIXS:0000779 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000236 ], + owl:onProperty MIXS:0000140 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:WallFinishMatEnum ; - owl:onProperty MIXS:0000842 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty nmdc_sub_schema:specific_ecosystem ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass nmdc_sub_schema:WindowLocEnum ; + owl:onProperty MIXS:0000852 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000169 ], + owl:onProperty MIXS:0000197 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000844 ], + owl:onProperty MIXS:0000011 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000140 ], + owl:onProperty MIXS:0000219 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:VisMediaEnum ; - owl:onProperty MIXS:0000840 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000018 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000122 ], + owl:onProperty MIXS:0000832 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000232 ], + owl:onProperty MIXS:0000785 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass nmdc_sub_schema:ShadingDeviceCondEnum ; + owl:onProperty MIXS:0000831 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000834 ], + owl:onClass nmdc_sub_schema:FloorWaterMoldEnum ; + owl:onProperty MIXS:0000805 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000222 ], + owl:onProperty MIXS:0000800 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000234 ], + owl:onProperty MIXS:0000770 ], [ a owl:Restriction ; - owl:allValuesFrom nmdc_sub_schema:SurfAirContEnum ; - owl:onProperty MIXS:0000759 ], + owl:allValuesFrom nmdc_sub_schema:HeatCoolTypeEnum ; + owl:onProperty MIXS:0000766 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:CeilCondEnum ; - owl:onProperty MIXS:0000779 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000721 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:WallTextureEnum ; - owl:onProperty MIXS:0000846 ], + owl:onClass nmdc_sub_schema:DoorTypeMetalEnum ; + owl:onProperty MIXS:0000796 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:WallLocEnum ; - owl:onProperty MIXS:0000843 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000198 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000772 ], + owl:onProperty MIXS:0000233 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:RoomSampPosEnum ; - owl:onProperty MIXS:0000824 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000243 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:HeatDelivLocEnum ; - owl:onProperty MIXS:0000810 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty nmdc_sub_schema:ecosystem_subtype ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000246 ], + owl:onProperty MIXS:0000192 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:WaterFeatTypeEnum ; - owl:onProperty MIXS:0000847 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000246 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000197 ], + owl:onClass nmdc_sub_schema:DoorCondEnum ; + owl:onProperty MIXS:0000788 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:env_package ], + owl:onProperty MIXS:0000781 ], nmdc_sub_schema:DhInterface, nmdc_sub_schema:DhMultiviewCommonColumnsMixin, nmdc_sub_schema:SampIdNewTermsMixin ; @@ -4263,25 +4263,29 @@ nmdc_sub_schema:EmslInterface a owl:Class, rdfs:label "EmslInterface" ; dcterms:title "Emsl" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass nmdc_sub_schema:Integer ; + owl:onProperty ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000026 ], + owl:onProperty MIXS:0001107 ], [ a owl:Restriction ; owl:onClass nmdc_sub_schema:SampleTypeEnum ; owl:onProperty ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:OxyStatSampEnum ; - owl:onProperty MIXS:0000753 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:Integer ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:onClass nmdc_sub_schema:Float ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass nmdc_sub_schema:String ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], [ a owl:Class ; owl:intersectionOf ( [ a owl:Restriction ; owl:allValuesFrom nmdc_sub_schema:AnalysisTypeEnum ; @@ -4290,19 +4294,15 @@ nmdc_sub_schema:EmslInterface a owl:Class, owl:someValuesFrom nmdc_sub_schema:AnalysisTypeEnum ] ) ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:Integer ; - owl:onProperty ], - [ a owl:Restriction ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], + owl:onProperty MIXS:0000026 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001107 ], + owl:onClass nmdc_sub_schema:OxyStatSampEnum ; + owl:onProperty MIXS:0000753 ], [ a owl:Restriction ; - owl:onClass nmdc_sub_schema:Float ; - owl:onProperty ; + owl:onClass nmdc_sub_schema:String ; + owl:onProperty ; owl:qualifiedCardinality 1 ], nmdc_sub_schema:DhInterface, nmdc_sub_schema:DhMultiviewCommonColumnsMixin ; @@ -5927,27 +5927,27 @@ nmdc_sub_schema:HostAssociatedInterface a owl:Class, rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000013 ], + owl:onProperty MIXS:0000110 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001318 ], + owl:onProperty MIXS:0000113 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:env_package ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000871 ], + owl:onClass nmdc_sub_schema:BiolStatEnum ; + owl:onProperty MIXS:0000858 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000859 ], + owl:onProperty MIXS:0000888 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001298 ], + owl:onProperty MIXS:0000264 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; @@ -5955,31 +5955,27 @@ nmdc_sub_schema:HostAssociatedInterface a owl:Class, [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000874 ], + owl:onProperty MIXS:0000010 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; owl:onProperty MIXS:0000869 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:SampCaptStatusEnum ; - owl:onProperty MIXS:0000860 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem ], + owl:onProperty MIXS:0000321 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000256 ], + owl:onProperty MIXS:0001107 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000009 ], + owl:onProperty MIXS:0000861 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000026 ], + owl:onProperty MIXS:0001318 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; @@ -5987,221 +5983,225 @@ nmdc_sub_schema:HostAssociatedInterface a owl:Class, [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem_category ], + owl:onProperty MIXS:0000258 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000870 ], - [ a owl:Class ; - owl:intersectionOf ( [ a owl:Restriction ; - owl:allValuesFrom nmdc_sub_schema:AnalysisTypeEnum ; - owl:onProperty ] [ a owl:Restriction ; - owl:onProperty ; - owl:someValuesFrom nmdc_sub_schema:AnalysisTypeEnum ] ) ], + owl:onProperty MIXS:0000018 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000251 ], + owl:onClass nmdc_sub_schema:HostSexEnum ; + owl:onProperty MIXS:0000811 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000110 ], + owl:onProperty MIXS:0000011 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001107 ], + owl:onProperty MIXS:0000016 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:specific_ecosystem ], + owl:onProperty MIXS:0000257 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000872 ], + owl:onProperty nmdc_sub_schema:ecosystem_category ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000888 ], + owl:onProperty MIXS:0000014 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000103 ], + owl:onProperty MIXS:0000867 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000875 ], + owl:onProperty nmdc_sub_schema:ecosystem ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000752 ], + owl:onProperty MIXS:0001225 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000113 ], + owl:onProperty MIXS:0000094 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000264 ], + owl:onProperty MIXS:0000116 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem_subtype ], + owl:onProperty nmdc_sub_schema:env_package ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000247 ], + owl:onProperty MIXS:0000872 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000259 ], + owl:onProperty MIXS:0001298 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000016 ], + owl:onProperty MIXS:0000752 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000014 ], + owl:onProperty MIXS:0000013 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000755 ], + owl:onProperty MIXS:0000183 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000017 ], + owl:onProperty nmdc_sub_schema:ecosystem_type ], + [ a owl:Class ; + owl:intersectionOf ( [ a owl:Restriction ; + owl:allValuesFrom nmdc_sub_schema:AnalysisTypeEnum ; + owl:onProperty ] [ a owl:Restriction ; + owl:onProperty ; + owl:someValuesFrom nmdc_sub_schema:AnalysisTypeEnum ] ) ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onClass nmdc_sub_schema:SampDisStageEnum ; + owl:onProperty MIXS:0000249 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000250 ], + owl:onProperty MIXS:0000875 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000094 ], + owl:onProperty nmdc_sub_schema:specific_ecosystem ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:BiolStatEnum ; - owl:onProperty MIXS:0000858 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000247 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000002 ], + owl:onProperty MIXS:0000255 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000258 ], + owl:onProperty MIXS:0000874 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000183 ], + owl:onProperty MIXS:0000261 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000257 ], + owl:onProperty MIXS:0000859 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000260 ], + owl:onProperty MIXS:0000009 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem_type ], + owl:onProperty MIXS:0000263 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000008 ], + owl:onProperty MIXS:0000755 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000263 ], + owl:onProperty MIXS:0000002 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000010 ], + owl:onProperty MIXS:0000260 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000018 ], + owl:onClass nmdc_sub_schema:OxyStatSampEnum ; + owl:onProperty MIXS:0000753 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:SampDisStageEnum ; - owl:onProperty MIXS:0000249 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000259 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000751 ], + owl:onProperty MIXS:0000103 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000116 ], + owl:onProperty MIXS:0000871 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000255 ], + owl:onProperty MIXS:0000256 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001225 ], + owl:onProperty MIXS:0000751 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000252 ], + owl:onProperty MIXS:0000017 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000861 ], + owl:onProperty MIXS:0000365 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; owl:onProperty MIXS:0000274 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:HostSexEnum ; - owl:onProperty MIXS:0000811 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000026 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000866 ], + owl:onProperty MIXS:0000870 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000754 ], + owl:onProperty MIXS:0000866 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000867 ], + owl:onProperty MIXS:0000008 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:OxyStatSampEnum ; - owl:onProperty MIXS:0000753 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000012 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000321 ], + owl:onProperty MIXS:0000250 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000261 ], + owl:onProperty MIXS:0000251 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000012 ], + owl:onProperty MIXS:0000754 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000011 ], + owl:onProperty nmdc_sub_schema:ecosystem_subtype ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000365 ], + owl:onClass nmdc_sub_schema:SampCaptStatusEnum ; + owl:onProperty MIXS:0000860 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; owl:onProperty MIXS:0000093 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000252 ], nmdc_sub_schema:DhInterface, nmdc_sub_schema:DhMultiviewCommonColumnsMixin, nmdc_sub_schema:SampIdNewTermsMixin ; @@ -6318,50 +6318,38 @@ nmdc_sub_schema:HostAssociatedInterface a owl:Class, nmdc_sub_schema:JgiMgInterface a owl:Class, linkml:ClassDefinition ; rdfs:label "JgiMgInterface" ; - dcterms:title "JGI MG" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; + dcterms:title "JGI MG" ; + rdfs:subClassOf [ a owl:Restriction ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass nmdc_sub_schema:Float ; + owl:onProperty nmdc_sub_schema:dna_absorb1 ], [ a owl:Restriction ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty ; + owl:onClass nmdc_sub_schema:YesNoEnum ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:onClass nmdc_sub_schema:Float ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], + owl:onClass nmdc_sub_schema:OxyStatSampEnum ; + owl:onProperty MIXS:0000753 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000026 ], + owl:onProperty MIXS:0001107 ], [ a owl:Restriction ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass nmdc_sub_schema:DnaSampleFormatEnum ; - owl:onProperty ; + owl:onClass nmdc_sub_schema:String ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Class ; owl:intersectionOf ( [ a owl:Restriction ; @@ -6369,13 +6357,21 @@ nmdc_sub_schema:JgiMgInterface a owl:Class, owl:onProperty ] [ a owl:Restriction ; owl:onProperty ; owl:someValuesFrom nmdc_sub_schema:AnalysisTypeEnum ] ) ], + [ a owl:Restriction ; + owl:onClass nmdc_sub_schema:Float ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass nmdc_sub_schema:YesNoEnum ; - owl:onProperty ; + owl:onClass nmdc_sub_schema:String ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass nmdc_sub_schema:String ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass nmdc_sub_schema:String ; @@ -6386,25 +6382,29 @@ nmdc_sub_schema:JgiMgInterface a owl:Class, owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; + owl:onClass nmdc_sub_schema:DnaSampleFormatEnum ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:onClass nmdc_sub_schema:Float ; - owl:onProperty nmdc_sub_schema:dna_absorb1 ], + owl:onProperty ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass nmdc_sub_schema:String ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:Float ; owl:onProperty nmdc_sub_schema:dna_absorb2 ], - [ a owl:Restriction ; - owl:onClass nmdc_sub_schema:Float ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:OxyStatSampEnum ; - owl:onProperty MIXS:0000753 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001107 ], + owl:onProperty MIXS:0000026 ], nmdc_sub_schema:DhInterface, nmdc_sub_schema:DhMultiviewCommonColumnsMixin ; skos:definition "jgi_mg dh_interface" . @@ -6414,33 +6414,13 @@ nmdc_sub_schema:JgiMtInterface a owl:Class, rdfs:label "JgiMtInterface" ; dcterms:title "JGI MT" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass nmdc_sub_schema:JgiContTypeEnum ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000026 ], - [ a owl:Restriction ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass nmdc_sub_schema:String ; owl:onProperty ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass nmdc_sub_schema:YesNoEnum ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:Float ; - owl:onProperty nmdc_sub_schema:rna_absorb2 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0001107 ], [ a owl:Class ; owl:intersectionOf ( [ a owl:Restriction ; owl:allValuesFrom nmdc_sub_schema:AnalysisTypeEnum ; @@ -6448,57 +6428,77 @@ nmdc_sub_schema:JgiMtInterface a owl:Class, owl:onProperty ; owl:someValuesFrom nmdc_sub_schema:AnalysisTypeEnum ] ) ], [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], + owl:onProperty ], [ a owl:Restriction ; owl:onClass nmdc_sub_schema:String ; owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass nmdc_sub_schema:RnaSampleFormatEnum ; - owl:onProperty ; + owl:onClass nmdc_sub_schema:Float ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass nmdc_sub_schema:String ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass nmdc_sub_schema:String ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:Float ; owl:onProperty nmdc_sub_schema:rna_absorb1 ], [ a owl:Restriction ; - owl:onClass nmdc_sub_schema:Float ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000026 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:OxyStatSampEnum ; owl:onProperty MIXS:0000753 ], [ a owl:Restriction ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001107 ], + owl:onClass nmdc_sub_schema:YesNoEnum ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass nmdc_sub_schema:RnaSampleFormatEnum ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass nmdc_sub_schema:JgiContTypeEnum ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass nmdc_sub_schema:Float ; owl:onProperty ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass nmdc_sub_schema:Float ; + owl:onProperty nmdc_sub_schema:rna_absorb2 ], [ a owl:Restriction ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onProperty ; + owl:qualifiedCardinality 1 ], nmdc_sub_schema:DhInterface, nmdc_sub_schema:DhMultiviewCommonColumnsMixin ; skos:definition "jgi_mt dh_interface" . @@ -6634,207 +6634,207 @@ nmdc_sub_schema:PlantAssociatedInterface a owl:Class, rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000011 ], + owl:onProperty MIXS:0000256 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000012 ], + owl:onProperty nmdc_sub_schema:specific_ecosystem ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000250 ], + owl:onProperty MIXS:0000569 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000018 ], + owl:onProperty MIXS:0001061 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:SampDisStageEnum ; - owl:onProperty MIXS:0000249 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000264 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000567 ], + owl:onProperty MIXS:0000321 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000255 ], + owl:onProperty MIXS:0000559 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001043 ], + owl:onProperty MIXS:0000002 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onProperty MIXS:0000008 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000755 ], + owl:onProperty MIXS:0000553 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000248 ], + owl:onProperty MIXS:0001225 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000017 ], + owl:onProperty MIXS:0000591 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001060 ], + owl:onProperty MIXS:0000590 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000002 ], + owl:onProperty MIXS:0000581 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000590 ], + owl:onProperty MIXS:0000752 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001068 ], + owl:onProperty MIXS:0000013 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000365 ], + owl:onProperty MIXS:0001057 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001318 ], + owl:onProperty MIXS:0001069 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000578 ], + owl:onProperty MIXS:0000575 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000551 ], + owl:onProperty MIXS:0001052 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000010 ], + owl:onProperty MIXS:0000580 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000569 ], + owl:onProperty MIXS:0000093 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000874 ], + owl:onProperty MIXS:0001070 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001063 ], + owl:onProperty MIXS:0001038 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:OxyStatSampEnum ; - owl:onProperty MIXS:0000753 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000551 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000573 ], + owl:onProperty MIXS:0001060 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000009 ], + owl:onProperty MIXS:0001318 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000571 ], + owl:onProperty MIXS:0000113 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000026 ], + owl:onProperty nmdc_sub_schema:ecosystem_type ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:GrowthHabitEnum ; - owl:onProperty MIXS:0001044 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0001058 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem_type ], + owl:onProperty MIXS:0001063 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:SampCaptStatusEnum ; - owl:onProperty MIXS:0000860 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty nmdc_sub_schema:ecosystem_subtype ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000579 ], + owl:onProperty MIXS:0001056 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000558 ], + owl:onClass nmdc_sub_schema:BiolStatEnum ; + owl:onProperty MIXS:0000858 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001040 ], + owl:onProperty MIXS:0000183 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000008 ], + owl:onProperty MIXS:0000582 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem_subtype ], + owl:onProperty MIXS:0000257 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000116 ], + owl:onProperty MIXS:0000557 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000580 ], + owl:onProperty MIXS:0000011 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000591 ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000553 ], + owl:onClass nmdc_sub_schema:GrowthHabitEnum ; + owl:onProperty MIXS:0001044 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000581 ], + owl:onProperty MIXS:0000577 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:PlantSexEnum ; - owl:onProperty MIXS:0001059 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0001040 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000557 ], + owl:onProperty MIXS:0000573 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; owl:onProperty MIXS:0000014 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001070 ], + owl:onClass nmdc_sub_schema:SampCaptStatusEnum ; + owl:onProperty MIXS:0000860 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000555 ], + owl:onProperty MIXS:0000255 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000582 ], + owl:onProperty MIXS:0000570 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001057 ], + owl:onProperty MIXS:0000576 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000559 ], + owl:onProperty MIXS:0000751 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem ], + owl:onProperty MIXS:0000012 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; @@ -6842,173 +6842,173 @@ nmdc_sub_schema:PlantAssociatedInterface a owl:Class, [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000257 ], + owl:onProperty MIXS:0000578 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001061 ], + owl:onClass nmdc_sub_schema:SampDisStageEnum ; + owl:onProperty MIXS:0000249 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000247 ], + owl:onProperty MIXS:0000017 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000016 ], + owl:onProperty MIXS:0000568 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000859 ], + owl:onProperty MIXS:0000018 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000576 ], + owl:onProperty MIXS:0000755 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem_category ], + owl:onProperty MIXS:0000859 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000556 ], + owl:onClass nmdc_sub_schema:PlantSexEnum ; + owl:onProperty MIXS:0001059 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000113 ], + owl:onProperty nmdc_sub_schema:ecosystem_category ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000264 ], + owl:onProperty MIXS:0001298 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001038 ], + owl:onProperty MIXS:0000874 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000575 ], - [ a owl:Class ; - owl:intersectionOf ( [ a owl:Restriction ; - owl:allValuesFrom nmdc_sub_schema:AnalysisTypeEnum ; - owl:onProperty ] [ a owl:Restriction ; - owl:onProperty ; - owl:someValuesFrom nmdc_sub_schema:AnalysisTypeEnum ] ) ], + owl:onProperty MIXS:0000561 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000013 ], + owl:onProperty MIXS:0000103 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001107 ], + owl:onProperty MIXS:0000250 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001298 ], + owl:onProperty MIXS:0000251 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001062 ], + owl:onProperty MIXS:0000579 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000110 ], + owl:onProperty MIXS:0001043 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001225 ], + owl:onProperty MIXS:0000556 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000183 ], + owl:onProperty MIXS:0001062 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:env_package ], + owl:onProperty MIXS:0000026 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000751 ], + owl:onProperty MIXS:0000016 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000752 ], + owl:onProperty MIXS:0000001 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000754 ], + owl:onClass nmdc_sub_schema:OxyStatSampEnum ; + owl:onProperty MIXS:0000753 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000570 ], + owl:onProperty MIXS:0001041 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:BiolStatEnum ; - owl:onProperty MIXS:0000858 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000555 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000577 ], + owl:onProperty MIXS:0000365 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000103 ], + owl:onProperty MIXS:0000010 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000001 ], + owl:onProperty MIXS:0001107 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000093 ], + owl:onProperty MIXS:0000558 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001058 ], + owl:onProperty MIXS:0000560 ], + [ a owl:Class ; + owl:intersectionOf ( [ a owl:Restriction ; + owl:allValuesFrom nmdc_sub_schema:AnalysisTypeEnum ; + owl:onProperty ] [ a owl:Restriction ; + owl:onProperty ; + owl:someValuesFrom nmdc_sub_schema:AnalysisTypeEnum ] ) ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000560 ], + owl:onProperty MIXS:0000248 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000251 ], + owl:onProperty MIXS:0001068 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001041 ], + owl:onProperty MIXS:0000116 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000256 ], + owl:onProperty MIXS:0000009 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:specific_ecosystem ], + owl:onProperty nmdc_sub_schema:env_package ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001069 ], + owl:onProperty MIXS:0000571 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000568 ], + owl:onProperty MIXS:0000247 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000561 ], + owl:onProperty MIXS:0000110 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001052 ], + owl:onProperty nmdc_sub_schema:ecosystem ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001056 ], + owl:onProperty MIXS:0000754 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000321 ], + owl:onProperty MIXS:0000567 ], nmdc_sub_schema:DhInterface, nmdc_sub_schema:DhMultiviewCommonColumnsMixin, nmdc_sub_schema:SampIdNewTermsMixin ; @@ -7597,369 +7597,369 @@ nmdc_sub_schema:SedimentInterface a owl:Class, rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000014 ], + owl:onProperty MIXS:0000432 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000008 ], + owl:onProperty MIXS:0000490 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000436 ], + owl:onProperty MIXS:0000515 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem_type ], + owl:onProperty MIXS:0000434 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:specific_ecosystem ], + owl:onProperty MIXS:0000427 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000178 ], + owl:onProperty MIXS:0000206 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem ], + owl:onProperty MIXS:0000162 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:SedimentTypeEnum ; - owl:onProperty MIXS:0001078 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000173 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000430 ], + owl:onProperty MIXS:0000009 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000013 ], + owl:onProperty MIXS:0001106 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onProperty MIXS:0000205 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000525 ], + owl:onProperty MIXS:0000175 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000182 ], + owl:onProperty MIXS:0000429 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem_subtype ], + owl:onProperty MIXS:0000421 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001106 ], + owl:onProperty MIXS:0000012 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000634 ], + owl:onProperty MIXS:0000533 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000433 ], + owl:onProperty MIXS:0000113 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000009 ], + owl:onProperty MIXS:0000191 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000751 ], + owl:onClass nmdc_sub_schema:TidalStageEnum ; + owl:onProperty MIXS:0000750 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000435 ], + owl:onProperty MIXS:0000016 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000110 ], + owl:onProperty MIXS:0000176 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000017 ], + owl:onProperty MIXS:0000014 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000113 ], + owl:onProperty MIXS:0000180 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000026 ], + owl:onProperty MIXS:0000755 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000503 ], + owl:onProperty MIXS:0000116 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000018 ], + owl:onProperty MIXS:0000179 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000174 ], + owl:onProperty MIXS:0000516 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000010 ], + owl:onClass nmdc_sub_schema:OxyStatSampEnum ; + owl:onProperty MIXS:0000753 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000426 ], + owl:onProperty MIXS:0000428 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000412 ], + owl:onProperty MIXS:0001225 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000755 ], + owl:onProperty nmdc_sub_schema:specific_ecosystem ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000012 ], + owl:onProperty MIXS:0000017 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000428 ], + owl:onProperty MIXS:0000101 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000752 ], + owl:onProperty MIXS:0000426 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000505 ], + owl:onProperty MIXS:0000177 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000172 ], + owl:onProperty MIXS:0000424 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000191 ], + owl:onProperty MIXS:0000011 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000205 ], + owl:onProperty MIXS:0000503 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000204 ], + owl:onClass nmdc_sub_schema:Double ; + owl:onProperty MIXS:0001001 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000425 ], + owl:onProperty MIXS:0000321 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000515 ], - [ a owl:Class ; - owl:intersectionOf ( [ a owl:Restriction ; - owl:allValuesFrom nmdc_sub_schema:AnalysisTypeEnum ; - owl:onProperty ] [ a owl:Restriction ; - owl:onProperty ; - owl:someValuesFrom nmdc_sub_schema:AnalysisTypeEnum ] ) ], + owl:onProperty MIXS:0000502 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000001 ], + owl:onProperty MIXS:0000425 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000016 ], + owl:onProperty MIXS:0000181 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000119 ], + owl:onProperty MIXS:0000093 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000137 ], + owl:onProperty MIXS:0000431 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001225 ], + owl:onProperty MIXS:0000103 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000421 ], + owl:onProperty MIXS:0000178 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000173 ], + owl:onProperty MIXS:0000498 ], + [ a owl:Class ; + owl:intersectionOf ( [ a owl:Restriction ; + owl:allValuesFrom nmdc_sub_schema:AnalysisTypeEnum ; + owl:onProperty ] [ a owl:Restriction ; + owl:onProperty ; + owl:someValuesFrom nmdc_sub_schema:AnalysisTypeEnum ] ) ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000530 ], + owl:onProperty MIXS:0000013 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000431 ], + owl:onProperty MIXS:0000182 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000162 ], + owl:onProperty MIXS:0000185 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000516 ], + owl:onProperty MIXS:0000211 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000002 ], + owl:onProperty MIXS:0000010 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000432 ], + owl:onProperty MIXS:0000204 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000177 ], + owl:onProperty MIXS:0000508 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000103 ], + owl:onProperty MIXS:0000525 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000434 ], + owl:onProperty MIXS:0000026 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000101 ], + owl:onProperty MIXS:0000137 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000181 ], + owl:onProperty MIXS:0000119 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000490 ], + owl:onProperty MIXS:0000110 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000211 ], + owl:onProperty MIXS:0000172 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000504 ], + owl:onProperty MIXS:0000412 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000185 ], + owl:onProperty MIXS:0001107 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000176 ], + owl:onProperty MIXS:0000752 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000175 ], + owl:onProperty MIXS:0000018 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000754 ], + owl:onProperty MIXS:0000436 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000180 ], + owl:onProperty MIXS:0000183 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000498 ], + owl:onProperty MIXS:0000008 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:OxyStatSampEnum ; - owl:onProperty MIXS:0000753 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty nmdc_sub_schema:ecosystem_type ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000321 ], + owl:onProperty MIXS:0000174 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000423 ], + owl:onProperty MIXS:0000002 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000310 ], + owl:onProperty nmdc_sub_schema:ecosystem ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000502 ], + owl:onProperty MIXS:0000751 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001107 ], + owl:onProperty MIXS:0000184 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000206 ], + owl:onProperty MIXS:0000310 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:env_package ], + owl:onProperty MIXS:0000754 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:TidalStageEnum ; - owl:onProperty MIXS:0000750 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000179 ], + owl:onProperty nmdc_sub_schema:ecosystem_category ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:Double ; - owl:onProperty MIXS:0001001 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000430 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem_category ], + owl:onProperty MIXS:0000423 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000093 ], + owl:onProperty nmdc_sub_schema:ecosystem_subtype ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000533 ], + owl:onProperty MIXS:0000001 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000116 ], + owl:onProperty nmdc_sub_schema:env_package ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000429 ], + owl:onProperty MIXS:0000504 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000508 ], + owl:onProperty MIXS:0000433 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000184 ], + owl:onProperty MIXS:0000505 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000427 ], + owl:onProperty MIXS:0000435 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000183 ], + owl:onProperty MIXS:0000634 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000011 ], + owl:onProperty MIXS:0000530 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000424 ], + owl:onClass nmdc_sub_schema:SedimentTypeEnum ; + owl:onProperty MIXS:0001078 ], nmdc_sub_schema:DhInterface, nmdc_sub_schema:DhMultiviewCommonColumnsMixin, nmdc_sub_schema:SampIdNewTermsMixin ; @@ -8085,259 +8085,252 @@ nmdc_sub_schema:SoilInterface a owl:Class, linkml:ClassDefinition ; rdfs:label "SoilInterface" ; dcterms:title "Soil" ; - rdfs:subClassOf [ a owl:Class ; - owl:intersectionOf ( [ a owl:Restriction ; - owl:allValuesFrom nmdc_sub_schema:AnalysisTypeEnum ; - owl:onProperty ] [ a owl:Restriction ; - owl:onProperty ; - owl:someValuesFrom nmdc_sub_schema:AnalysisTypeEnum ] ) ], - [ a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000320 ], + owl:onProperty MIXS:0000642 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001107 ], + owl:onProperty MIXS:0000650 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000652 ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000643 ], + owl:onProperty MIXS:0000558 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000530 ], + owl:onProperty MIXS:0000321 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onClass nmdc_sub_schema:SoilHorizonEnum ; + owl:onProperty MIXS:0001082 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000310 ], + owl:onProperty MIXS:0000103 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001043 ], + owl:onProperty MIXS:0000016 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000331 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:CurLandUseEnum ; - owl:onProperty MIXS:0001080 ], + owl:onProperty nmdc_sub_schema:ecosystem ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:ProfilePositionEnum ; - owl:onProperty MIXS:0001084 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000591 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onProperty MIXS:0000093 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onProperty MIXS:0000328 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000323 ], + owl:onProperty MIXS:0000645 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:OxyStatSampEnum ; - owl:onProperty MIXS:0000753 ], + owl:onClass nmdc_sub_schema:FaoClassEnum ; + owl:onProperty MIXS:0001083 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000103 ], + owl:onProperty MIXS:0000316 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:zinc ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000339 ], + owl:onProperty MIXS:0000312 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onProperty MIXS:0000330 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000533 ], + owl:onProperty MIXS:0000110 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000012 ], + owl:onProperty MIXS:0000643 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000338 ], + owl:onProperty MIXS:0000341 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000558 ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000204 ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000591 ], + owl:onProperty nmdc_sub_schema:env_package ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000644 ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000328 ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000551 ], + owl:onProperty MIXS:0000018 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000735 ], + owl:onProperty nmdc_sub_schema:manganese ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem_category ], + owl:onProperty MIXS:0000332 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onProperty nmdc_sub_schema:zinc ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000642 ], + owl:onProperty MIXS:0000335 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000316 ], + owl:onProperty nmdc_sub_schema:lbceq ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001038 ], + owl:onProperty MIXS:0000310 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000322 ], + owl:onProperty MIXS:0000001 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001040 ], + owl:onProperty MIXS:0000646 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000525 ], + owl:onProperty MIXS:0000331 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000093 ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc_sub_schema:TillageEnum ; - owl:onProperty MIXS:0001081 ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000569 ], + owl:onProperty MIXS:0000183 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem_type ], + owl:onProperty MIXS:0000530 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:lbc_thirty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000337 ], + owl:onProperty MIXS:0001038 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onProperty MIXS:0000339 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000321 ], + owl:onClass nmdc_sub_schema:BioticRelationshipEnum ; + owl:onProperty MIXS:0000028 ], + [ a owl:Class ; + owl:intersectionOf ( [ a owl:Restriction ; + owl:allValuesFrom nmdc_sub_schema:AnalysisTypeEnum ; + owl:onProperty ] [ a owl:Restriction ; + owl:onProperty ; + owl:someValuesFrom nmdc_sub_schema:AnalysisTypeEnum ] ) ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001225 ], + owl:onProperty nmdc_sub_schema:ecosystem_type ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000001 ], + owl:onProperty MIXS:0000736 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000185 ], + owl:onProperty nmdc_sub_schema:nitrate_nitrogen ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000327 ], + owl:onProperty MIXS:0000315 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000334 ], + owl:onProperty MIXS:0000113 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000117 ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000318 ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000312 ], + owl:onProperty nmdc_sub_schema:lbc_thirty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:BioticRelationshipEnum ; - owl:onProperty MIXS:0000028 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000008 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onProperty MIXS:0000607 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000330 ], + owl:onProperty nmdc_sub_schema:ammonium_nitrogen ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000650 ], + owl:onProperty MIXS:0000639 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:lbceq ], + owl:onProperty MIXS:0000323 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001106 ], + owl:onProperty MIXS:0000324 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000505 ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000009 ], + owl:onProperty MIXS:0001043 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; @@ -8345,215 +8338,222 @@ nmdc_sub_schema:SoilInterface a owl:Class, [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem_subtype ], + owl:onProperty MIXS:0001086 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000343 ], + owl:onProperty MIXS:0000652 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000568 ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onProperty MIXS:0000314 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000335 ], + owl:onProperty MIXS:0000337 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:env_package ], + owl:onProperty MIXS:0000010 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onProperty MIXS:0000336 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000008 ], + owl:onProperty MIXS:0000322 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000646 ], + owl:onProperty MIXS:0000012 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onProperty MIXS:0000117 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000010 ], + owl:onProperty MIXS:0000334 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:nitrate_nitrogen ], + owl:onClass nmdc_sub_schema:Double ; + owl:onProperty MIXS:0001001 ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc_sub_schema:TillageEnum ; + owl:onProperty MIXS:0001081 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000110 ], + owl:onProperty MIXS:0000569 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass nmdc_sub_schema:CurLandUseEnum ; + owl:onProperty MIXS:0001080 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000332 ], + owl:onProperty MIXS:0000205 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000315 ], + owl:onProperty MIXS:0000002 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000647 ], + owl:onProperty MIXS:0000185 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000639 ], + owl:onProperty MIXS:0000533 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000736 ], + owl:onProperty MIXS:0000735 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onProperty MIXS:0000644 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001086 ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onClass nmdc_sub_schema:OxyStatSampEnum ; + owl:onProperty MIXS:0000753 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000205 ], + owl:onProperty MIXS:0000318 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000329 ], + owl:onProperty MIXS:0001107 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000014 ], + owl:onProperty MIXS:0000204 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000314 ], + owl:onProperty MIXS:0000319 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:SoilHorizonEnum ; - owl:onProperty MIXS:0001082 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000336 ], + owl:onProperty MIXS:0000327 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ammonium_nitrogen ], + owl:onProperty MIXS:0000320 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000645 ], + owl:onProperty MIXS:0000568 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onProperty MIXS:0000009 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000026 ], + owl:onClass nmdc_sub_schema:DrainageClassEnum ; + owl:onProperty MIXS:0001085 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000113 ], + owl:onProperty MIXS:0001225 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:specific_ecosystem ], + owl:onProperty MIXS:0000551 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:manganese ], + owl:onProperty MIXS:0000343 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000183 ], + owl:onProperty MIXS:0001106 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onProperty MIXS:0000014 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onProperty nmdc_sub_schema:nitrite_nitrogen ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000324 ], + owl:onProperty MIXS:0000525 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000013 ], + owl:onProperty MIXS:0000329 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:FaoClassEnum ; - owl:onProperty MIXS:0001083 ], + owl:onClass nmdc_sub_schema:ProfilePositionEnum ; + owl:onProperty MIXS:0001084 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000002 ], + owl:onProperty MIXS:0001040 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000016 ], + owl:onProperty MIXS:0000338 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:nitrite_nitrogen ], + owl:onProperty MIXS:0000647 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000319 ], + owl:onProperty nmdc_sub_schema:specific_ecosystem ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000011 ], + owl:onProperty nmdc_sub_schema:ecosystem_category ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000341 ], + owl:onProperty MIXS:0000026 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000607 ], + owl:onProperty MIXS:0000011 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:Double ; - owl:onProperty MIXS:0001001 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onProperty MIXS:0000013 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000018 ], + owl:onProperty nmdc_sub_schema:ecosystem_subtype ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000751 ], + owl:onProperty MIXS:0000505 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:DrainageClassEnum ; - owl:onProperty MIXS:0001085 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000751 ], nmdc_sub_schema:DhInterface, nmdc_sub_schema:DhMultiviewCommonColumnsMixin, nmdc_sub_schema:SampIdNewTermsMixin, @@ -8567,15 +8567,15 @@ nmdc_sub_schema:SoilMixsInspiredMixin a owl:Class, rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; @@ -8583,19 +8583,19 @@ nmdc_sub_schema:SoilMixsInspiredMixin a owl:Class, [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; @@ -8603,27 +8603,27 @@ nmdc_sub_schema:SoilMixsInspiredMixin a owl:Class, [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; @@ -9298,83 +9298,83 @@ nmdc_sub_schema:WastewaterSludgeInterface a owl:Class, rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001107 ], + owl:onProperty MIXS:0001225 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000018 ], + owl:onProperty nmdc_sub_schema:ecosystem_type ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000660 ], + owl:onProperty MIXS:0000661 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000421 ], + owl:onProperty MIXS:0000755 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000661 ], + owl:onProperty MIXS:0000026 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000349 ], + owl:onProperty MIXS:0000350 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000752 ], + owl:onProperty MIXS:0000656 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000754 ], + owl:onProperty MIXS:0000002 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001106 ], + owl:onProperty MIXS:0000321 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000657 ], + owl:onProperty MIXS:0000017 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000348 ], + owl:onProperty MIXS:0000011 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000689 ], + owl:onProperty MIXS:0000673 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:env_package ], + owl:onProperty MIXS:0001106 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000116 ], + owl:onClass nmdc_sub_schema:OxyStatSampEnum ; + owl:onProperty MIXS:0000753 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000113 ], + owl:onProperty nmdc_sub_schema:ecosystem_category ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem_category ], + owl:onProperty nmdc_sub_schema:env_package ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onProperty MIXS:0000352 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000669 ], + owl:onProperty nmdc_sub_schema:ecosystem_subtype ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000110 ], + owl:onProperty MIXS:0000348 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000505 ], + owl:onProperty MIXS:0000664 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; @@ -9382,145 +9382,141 @@ nmdc_sub_schema:WastewaterSludgeInterface a owl:Class, [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000665 ], + owl:onProperty MIXS:0000113 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000664 ], + owl:onProperty MIXS:0000505 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem_subtype ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:OxyStatSampEnum ; - owl:onProperty MIXS:0000753 ], + owl:onProperty MIXS:0000351 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000672 ], - [ a owl:Class ; - owl:intersectionOf ( [ a owl:Restriction ; - owl:allValuesFrom nmdc_sub_schema:AnalysisTypeEnum ; - owl:onProperty ] [ a owl:Restriction ; - owl:onProperty ; - owl:someValuesFrom nmdc_sub_schema:AnalysisTypeEnum ] ) ], + owl:onProperty MIXS:0000018 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000425 ], + owl:onProperty MIXS:0000012 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000751 ], + owl:onProperty MIXS:0000653 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:specific_ecosystem ], + owl:onProperty MIXS:0000116 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000009 ], + owl:onProperty MIXS:0000183 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:Double ; - owl:onProperty MIXS:0001001 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000102 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001225 ], + owl:onProperty MIXS:0000009 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000428 ], + owl:onProperty MIXS:0000752 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000321 ], + owl:onProperty MIXS:0000010 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000011 ], + owl:onProperty MIXS:0000425 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000351 ], + owl:onProperty MIXS:0000421 ], + [ a owl:Class ; + owl:intersectionOf ( [ a owl:Restriction ; + owl:allValuesFrom nmdc_sub_schema:AnalysisTypeEnum ; + owl:onProperty ] [ a owl:Restriction ; + owl:onProperty ; + owl:someValuesFrom nmdc_sub_schema:AnalysisTypeEnum ] ) ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000002 ], + owl:onProperty MIXS:0000353 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000656 ], + owl:onProperty MIXS:0000013 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; owl:onProperty MIXS:0000103 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000014 ], + owl:onClass nmdc_sub_schema:Double ; + owl:onProperty MIXS:0001001 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000353 ], + owl:onProperty MIXS:0000669 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000008 ], + owl:onProperty MIXS:0000754 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000102 ], + owl:onProperty MIXS:0000428 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000755 ], + owl:onProperty MIXS:0000665 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000150 ], + owl:onProperty MIXS:0000001 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000010 ], + owl:onProperty MIXS:0001107 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000012 ], + owl:onProperty MIXS:0000014 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem_type ], + owl:onProperty MIXS:0000662 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000183 ], + owl:onProperty MIXS:0000349 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000001 ], + owl:onProperty MIXS:0000657 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000662 ], + owl:onProperty MIXS:0000008 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000350 ], + owl:onProperty MIXS:0000751 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000215 ], + owl:onProperty MIXS:0000672 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000673 ], + owl:onProperty MIXS:0000150 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000026 ], + owl:onProperty nmdc_sub_schema:ecosystem ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; @@ -9528,23 +9524,27 @@ nmdc_sub_schema:WastewaterSludgeInterface a owl:Class, [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000017 ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000013 ], + owl:onProperty nmdc_sub_schema:specific_ecosystem ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem ], + owl:onProperty MIXS:0000660 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000352 ], + owl:onProperty MIXS:0000689 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000653 ], + owl:onProperty MIXS:0000215 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000110 ], nmdc_sub_schema:DhInterface, nmdc_sub_schema:DhMultiviewCommonColumnsMixin, nmdc_sub_schema:SampIdNewTermsMixin ; @@ -9577,109 +9577,95 @@ nmdc_sub_schema:WaterInterface a owl:Class, rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000423 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000137 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem_subtype ], + owl:onProperty MIXS:0000172 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001106 ], + owl:onProperty MIXS:0000174 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:env_package ], + owl:onProperty MIXS:0000728 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000009 ], + owl:onProperty MIXS:0000741 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000738 ], + owl:onProperty MIXS:0000119 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000181 ], + owl:onProperty MIXS:0000430 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000427 ], + owl:onProperty MIXS:0000008 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000001 ], + owl:onProperty MIXS:0000698 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem_category ], + owl:onProperty MIXS:0000179 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000755 ], + owl:onProperty MIXS:0000428 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000172 ], + owl:onProperty MIXS:0000106 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000298 ], - [ a owl:Class ; - owl:intersectionOf ( [ a owl:Restriction ; - owl:allValuesFrom nmdc_sub_schema:AnalysisTypeEnum ; - owl:onProperty ] [ a owl:Restriction ; - owl:onProperty ; - owl:someValuesFrom nmdc_sub_schema:AnalysisTypeEnum ] ) ], + owl:onProperty MIXS:0000433 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000505 ], + owl:onProperty MIXS:0000738 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000706 ], + owl:onProperty MIXS:0000505 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000176 ], + owl:onProperty MIXS:0000755 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000182 ], + owl:onProperty MIXS:0000204 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000435 ], + owl:onClass nmdc_sub_schema:Double ; + owl:onProperty MIXS:0001001 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000421 ], + owl:onProperty MIXS:0000424 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000516 ], + owl:onProperty MIXS:0000180 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000745 ], + owl:onProperty MIXS:0000014 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000179 ], + owl:onProperty MIXS:0000298 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000424 ], + owl:onProperty MIXS:0000013 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000429 ], + owl:onProperty MIXS:0000502 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; @@ -9687,127 +9673,127 @@ nmdc_sub_schema:WaterInterface a owl:Class, [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000016 ], + owl:onProperty MIXS:0000093 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000754 ], + owl:onProperty MIXS:0000183 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000692 ], + owl:onProperty MIXS:0000102 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000752 ], + owl:onProperty MIXS:0000137 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000432 ], + owl:onProperty MIXS:0000429 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000174 ], + owl:onProperty MIXS:0000751 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000436 ], + owl:onProperty MIXS:0000178 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000426 ], + owl:onProperty MIXS:0000498 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty ], + owl:onProperty MIXS:0001097 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000683 ], + owl:onProperty MIXS:0000016 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000116 ], + owl:onProperty MIXS:0000110 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001097 ], + owl:onProperty MIXS:0000426 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000704 ], + owl:onProperty MIXS:0001225 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000008 ], + owl:onProperty nmdc_sub_schema:env_package ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000425 ], + owl:onProperty MIXS:0000017 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000011 ], + owl:onProperty MIXS:0000703 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000162 ], + owl:onProperty nmdc_sub_schema:ecosystem ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000502 ], + owl:onProperty MIXS:0001107 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000204 ], + owl:onProperty MIXS:0000103 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000498 ], + owl:onProperty MIXS:0000634 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000093 ], + owl:onProperty MIXS:0000181 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000412 ], + owl:onProperty MIXS:0000736 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000508 ], + owl:onProperty MIXS:0000504 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001225 ], + owl:onProperty MIXS:0000203 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000751 ], + owl:onProperty nmdc_sub_schema:ecosystem_subtype ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000430 ], + owl:onProperty MIXS:0000421 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000203 ], + owl:onProperty MIXS:0000113 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000106 ], + owl:onProperty MIXS:0000692 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000703 ], + owl:onProperty MIXS:0000515 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000014 ], + owl:onProperty MIXS:0000706 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000735 ], + owl:onProperty MIXS:0000002 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; @@ -9815,71 +9801,75 @@ nmdc_sub_schema:WaterInterface a owl:Class, [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000018 ], + owl:onProperty MIXS:0000435 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000177 ], + owl:onProperty MIXS:0000436 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000175 ], + owl:onProperty MIXS:0000432 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000434 ], + owl:onProperty MIXS:0001106 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000321 ], + owl:onProperty MIXS:0000508 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000741 ], + owl:onProperty MIXS:0000412 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000310 ], + owl:onProperty MIXS:0000018 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000728 ], + owl:onProperty MIXS:0000173 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000428 ], + owl:onProperty MIXS:0000191 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000634 ], + owl:onProperty MIXS:0000184 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000205 ], + owl:onProperty MIXS:0000175 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass nmdc_sub_schema:TidalStageEnum ; + owl:onProperty MIXS:0000750 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000183 ], + owl:onProperty MIXS:0000683 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000102 ], + owl:onProperty nmdc_sub_schema:ecosystem_type ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000736 ], + owl:onProperty MIXS:0000010 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000490 ], + owl:onProperty MIXS:0000423 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000013 ], + owl:onProperty MIXS:0000011 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000180 ], + owl:onProperty MIXS:0000012 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; @@ -9887,111 +9877,117 @@ nmdc_sub_schema:WaterInterface a owl:Class, [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000119 ], + owl:onProperty MIXS:0000001 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem_type ], + owl:onProperty MIXS:0000176 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000012 ], + owl:onProperty MIXS:0000745 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000178 ], + owl:onClass nmdc_sub_schema:OxyStatSampEnum ; + owl:onProperty MIXS:0000753 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000515 ], + owl:onProperty MIXS:0000182 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0001107 ], + owl:onProperty MIXS:0000162 ], + [ a owl:Class ; + owl:intersectionOf ( [ a owl:Restriction ; + owl:allValuesFrom nmdc_sub_schema:AnalysisTypeEnum ; + owl:onProperty ] [ a owl:Restriction ; + owl:onProperty ; + owl:someValuesFrom nmdc_sub_schema:AnalysisTypeEnum ] ) ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000504 ], + owl:onProperty MIXS:0000735 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000113 ], + owl:onProperty MIXS:0000427 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:specific_ecosystem ], + owl:onProperty MIXS:0000434 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000002 ], + owl:onProperty MIXS:0000516 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000110 ], + owl:onProperty nmdc_sub_schema:ecosystem_category ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000191 ], + owl:onProperty MIXS:0000425 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000026 ], + owl:onProperty MIXS:0000116 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:Double ; - owl:onProperty MIXS:0001001 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000310 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000173 ], + owl:onProperty MIXS:0000026 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000017 ], + owl:onProperty MIXS:0000719 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000103 ], + owl:onProperty MIXS:0000684 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty nmdc_sub_schema:ecosystem ], + owl:onProperty MIXS:0000009 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000684 ], + owl:onProperty MIXS:0000754 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:TidalStageEnum ; - owl:onProperty MIXS:0000750 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty MIXS:0000752 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000433 ], + owl:onProperty MIXS:0000490 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass nmdc_sub_schema:OxyStatSampEnum ; - owl:onProperty MIXS:0000753 ], + owl:onClass nmdc_sub_schema:String ; + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000719 ], + owl:onProperty MIXS:0000177 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000184 ], + owl:onProperty nmdc_sub_schema:specific_ecosystem ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000010 ], + owl:onProperty MIXS:0000747 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000747 ], + owl:onProperty MIXS:0000205 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; - owl:onProperty MIXS:0000698 ], + owl:onProperty MIXS:0000704 ], nmdc_sub_schema:DhInterface, nmdc_sub_schema:DhMultiviewCommonColumnsMixin, nmdc_sub_schema:SampIdNewTermsMixin ; @@ -16569,8 +16565,8 @@ nmdc_sub_schema:BioticRelationshipEnum a owl:Class, linkml:EnumDefinition ; rdfs:label "BioticRelationshipEnum", "biotic_relationship_enum" ; - owl:unionOf ( ), - ( ) ; + owl:unionOf ( ), + ( ) ; linkml:permissible_values , , , @@ -16973,6 +16969,18 @@ MIXS:0000183 a owl:ObjectProperty, nmdc_sub_schema:occurrence "1" ; nmdc_sub_schema:preferred_unit "practical salinity unit, percentage" . +MIXS:0000321 a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "horizon_meth" ; + dcterms:title "soil horizon method" ; + rdfs:range nmdc_sub_schema:String ; + rdfs:subPropertyOf nmdc_sub_schema:core_field ; + skos:altLabel "soil horizon method" ; + skos:definition "Reference or method used in determining the horizon" ; + skos:exactMatch MIXS:0000321 ; + nmdc_sub_schema:expected_value "PMID,DOI or url" ; + nmdc_sub_schema:occurrence "1" . + MIXS:0000751 a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "chem_administration" ; @@ -17172,18 +17180,6 @@ MIXS:0000113 a owl:ObjectProperty, nmdc_sub_schema:expected_value "measurement value" ; nmdc_sub_schema:preferred_unit "degree Celsius" . -MIXS:0000321 a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "horizon_meth" ; - dcterms:title "soil horizon method" ; - rdfs:range nmdc_sub_schema:String ; - rdfs:subPropertyOf nmdc_sub_schema:core_field ; - skos:altLabel "soil horizon method" ; - skos:definition "Reference or method used in determining the horizon" ; - skos:exactMatch MIXS:0000321 ; - nmdc_sub_schema:expected_value "PMID,DOI or url" ; - nmdc_sub_schema:occurrence "1" . - nmdc_sub_schema:DnaSampleFormatEnum a owl:Class, linkml:EnumDefinition ; rdfs:label "DnaSampleFormatEnum", @@ -17303,13 +17299,7 @@ nmdc_sub_schema:DhMultiviewCommonColumnsMixin a owl:Class, linkml:ClassDefinition ; rdfs:label "DhMultiviewCommonColumnsMixin" ; dcterms:title "Dh Mutliview Common Columns" ; - rdfs:subClassOf [ a owl:Class ; - owl:intersectionOf ( [ a owl:Restriction ; - owl:allValuesFrom nmdc_sub_schema:AnalysisTypeEnum ; - owl:onProperty ] [ a owl:Restriction ; - owl:onProperty ; - owl:someValuesFrom nmdc_sub_schema:AnalysisTypeEnum ] ) ], - [ a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:String ; owl:onProperty MIXS:0000026 ], @@ -17321,6 +17311,12 @@ nmdc_sub_schema:DhMultiviewCommonColumnsMixin a owl:Class, owl:maxQualifiedCardinality 1 ; owl:onClass nmdc_sub_schema:OxyStatSampEnum ; owl:onProperty MIXS:0000753 ], + [ a owl:Class ; + owl:intersectionOf ( [ a owl:Restriction ; + owl:allValuesFrom nmdc_sub_schema:AnalysisTypeEnum ; + owl:onProperty ] [ a owl:Restriction ; + owl:onProperty ; + owl:someValuesFrom nmdc_sub_schema:AnalysisTypeEnum ] ) ], linkml:mixin ; skos:definition "Mixin with DhMutliviewCommon Columns" . diff --git a/project/sqlschema/nmdc_submission_schema.sql b/project/sqlschema/nmdc_submission_schema.sql index 6d213f83..58d2f10e 100644 --- a/project/sqlschema/nmdc_submission_schema.sql +++ b/project/sqlschema/nmdc_submission_schema.sql @@ -20,7 +20,6 @@ CREATE TABLE "AirInterface" ( env_package TEXT, experimental_factor TEXT, geo_loc_name TEXT, - horizon_meth TEXT, humidity TEXT, lat_lon TEXT, methane TEXT, @@ -48,10 +47,11 @@ CREATE TABLE "AirInterface" ( volatile_org_comp TEXT, wind_direction TEXT, wind_speed TEXT, + horizon_meth TEXT, analysis_type VARCHAR(22) NOT NULL, samp_name TEXT, source_mat_id TEXT, - PRIMARY KEY ("air_PM_concen", alt, barometric_press, carb_dioxide, carb_monoxide, chem_administration, collection_date, depth, ecosystem, ecosystem_category, ecosystem_subtype, ecosystem_type, elev, env_broad_scale, env_local_scale, env_medium, env_package, experimental_factor, geo_loc_name, horizon_meth, humidity, lat_lon, methane, misc_param, organism_count, oxy_stat_samp, oxygen, perturbation, pollutants, salinity, samp_collec_device, samp_collec_method, samp_mat_process, samp_size, samp_store_dur, samp_store_loc, samp_store_temp, sample_link, size_frac, solar_irradiance, specific_ecosystem, "temp", ventilation_rate, ventilation_type, volatile_org_comp, wind_direction, wind_speed, analysis_type, samp_name, source_mat_id) + PRIMARY KEY ("air_PM_concen", alt, barometric_press, carb_dioxide, carb_monoxide, chem_administration, collection_date, depth, ecosystem, ecosystem_category, ecosystem_subtype, ecosystem_type, elev, env_broad_scale, env_local_scale, env_medium, env_package, experimental_factor, geo_loc_name, humidity, lat_lon, methane, misc_param, organism_count, oxy_stat_samp, oxygen, perturbation, pollutants, salinity, samp_collec_device, samp_collec_method, samp_mat_process, samp_size, samp_store_dur, samp_store_loc, samp_store_temp, sample_link, size_frac, solar_irradiance, specific_ecosystem, "temp", ventilation_rate, ventilation_type, volatile_org_comp, wind_direction, wind_speed, horizon_meth, analysis_type, samp_name, source_mat_id) ); CREATE TABLE "BiofilmInterface" ( @@ -90,7 +90,6 @@ CREATE TABLE "BiofilmInterface" ( experimental_factor TEXT, geo_loc_name TEXT, glucosidase_act TEXT, - horizon_meth TEXT, lat_lon TEXT, magnesium TEXT, mean_frict_vel TEXT, @@ -138,10 +137,11 @@ CREATE TABLE "BiofilmInterface" ( tot_org_carb TEXT, turbidity TEXT, water_content TEXT, + horizon_meth TEXT, analysis_type VARCHAR(22) NOT NULL, samp_name TEXT, source_mat_id TEXT, - PRIMARY KEY (alkalinity, alkyl_diethers, alt, aminopept_act, ammonium, bacteria_carb_prod, biomass, bishomohopanol, bromide, calcium, carb_nitro_ratio, chem_administration, chloride, chlorophyll, collection_date, depth, diether_lipids, diss_carb_dioxide, diss_hydrogen, diss_inorg_carb, diss_org_carb, diss_org_nitro, diss_oxygen, ecosystem, ecosystem_category, ecosystem_subtype, ecosystem_type, elev, env_broad_scale, env_local_scale, env_medium, env_package, experimental_factor, geo_loc_name, glucosidase_act, horizon_meth, lat_lon, magnesium, mean_frict_vel, mean_peak_frict_vel, methane, misc_param, n_alkanes, nitrate, nitrite, nitro, org_carb, org_matter, org_nitro, organism_count, oxy_stat_samp, part_org_carb, perturbation, petroleum_hydrocarb, ph, ph_meth, phaeopigments, phosphate, phosplipid_fatt_acid, potassium, pressure, redox_potential, salinity, samp_collec_device, samp_collec_method, samp_mat_process, samp_size, samp_store_dur, samp_store_loc, samp_store_temp, sample_link, silicate, size_frac, sodium, specific_ecosystem, sulfate, sulfide, "temp", tot_carb, tot_nitro_content, tot_org_carb, turbidity, water_content, analysis_type, samp_name, source_mat_id) + PRIMARY KEY (alkalinity, alkyl_diethers, alt, aminopept_act, ammonium, bacteria_carb_prod, biomass, bishomohopanol, bromide, calcium, carb_nitro_ratio, chem_administration, chloride, chlorophyll, collection_date, depth, diether_lipids, diss_carb_dioxide, diss_hydrogen, diss_inorg_carb, diss_org_carb, diss_org_nitro, diss_oxygen, ecosystem, ecosystem_category, ecosystem_subtype, ecosystem_type, elev, env_broad_scale, env_local_scale, env_medium, env_package, experimental_factor, geo_loc_name, glucosidase_act, lat_lon, magnesium, mean_frict_vel, mean_peak_frict_vel, methane, misc_param, n_alkanes, nitrate, nitrite, nitro, org_carb, org_matter, org_nitro, organism_count, oxy_stat_samp, part_org_carb, perturbation, petroleum_hydrocarb, ph, ph_meth, phaeopigments, phosphate, phosplipid_fatt_acid, potassium, pressure, redox_potential, salinity, samp_collec_device, samp_collec_method, samp_mat_process, samp_size, samp_store_dur, samp_store_loc, samp_store_temp, sample_link, silicate, size_frac, sodium, specific_ecosystem, sulfate, sulfide, "temp", tot_carb, tot_nitro_content, tot_org_carb, turbidity, water_content, horizon_meth, analysis_type, samp_name, source_mat_id) ); CREATE TABLE "BuiltEnvInterface" ( @@ -229,7 +229,6 @@ CREATE TABLE "BuiltEnvInterface" ( heat_sys_deliv_meth TEXT, heat_system_id TEXT, height_carper_fiber TEXT, - horizon_meth TEXT, indoor_space VARCHAR(11), indoor_surf VARCHAR(11), inside_lux TEXT, @@ -325,11 +324,12 @@ CREATE TABLE "BuiltEnvInterface" ( window_type VARCHAR(23), window_vert_pos VARCHAR(6), window_water_mold TEXT, + horizon_meth TEXT, oxy_stat_samp VARCHAR(9), analysis_type VARCHAR(22) NOT NULL, samp_name TEXT, source_mat_id TEXT, - PRIMARY KEY (abs_air_humidity, address, adj_room, aero_struc, air_temp, alt, amount_light, arch_struc, avg_dew_point, avg_occup, avg_temp, bathroom_count, bedroom_count, build_docs, build_occup_type, building_setting, built_struc_age, built_struc_set, built_struc_type, carb_dioxide, ceil_area, ceil_cond, ceil_finish_mat, ceil_struc, ceil_texture, ceil_thermal_mass, ceil_type, ceil_water_mold, collection_date, cool_syst_id, date_last_rain, depth, dew_point, door_comp_type, door_cond, door_direct, door_loc, door_mat, door_move, door_size, door_type, door_type_metal, door_type_wood, door_water_mold, drawings, ecosystem, ecosystem_category, ecosystem_subtype, ecosystem_type, elev, elevator, env_broad_scale, env_local_scale, env_medium, env_package, escalator, exp_duct, exp_pipe, experimental_factor, ext_door, ext_wall_orient, ext_window_orient, filter_type, fireplace_type, floor_age, floor_area, floor_cond, floor_count, floor_finish_mat, floor_struc, floor_thermal_mass, floor_water_mold, freq_clean, freq_cook, furniture, gender_restroom, geo_loc_name, hall_count, handidness, heat_cool_type, heat_deliv_loc, heat_sys_deliv_meth, heat_system_id, height_carper_fiber, horizon_meth, indoor_space, indoor_surf, inside_lux, int_wall_cond, last_clean, lat_lon, light_type, max_occup, mech_struc, number_pets, number_plants, number_resident, occup_density_samp, occup_document, occup_samp, organism_count, pres_animal_insect, quad_pos, rel_air_humidity, rel_humidity_out, rel_samp_loc, room_air_exch_rate, room_architec_elem, room_condt, room_connected, room_count, room_dim, room_door_dist, room_door_share, room_hallway, room_loc, room_moist_dam_hist, room_net_area, room_occup, room_samp_pos, room_type, room_vol, room_wall_share, room_window_count, samp_floor, samp_room_id, samp_sort_meth, samp_time_out, samp_weather, sample_link, season, season_use, shad_dev_water_mold, shading_device_cond, shading_device_loc, shading_device_mat, shading_device_type, size_frac, space_typ_state, specific, specific_ecosystem, specific_humidity, substructure_type, surf_air_cont, surf_humidity, surf_material, surf_moisture, surf_moisture_ph, surf_temp, "temp", temp_out, train_line, train_stat_loc, train_stop_loc, typ_occup_density, ventilation_type, vis_media, wall_area, wall_const_type, wall_finish_mat, wall_height, wall_loc, wall_surf_treatment, wall_texture, wall_thermal_mass, wall_water_mold, water_feat_size, water_feat_type, weekday, window_cond, window_cover, window_horiz_pos, window_loc, window_mat, window_open_freq, window_size, window_status, window_type, window_vert_pos, window_water_mold, oxy_stat_samp, analysis_type, samp_name, source_mat_id) + PRIMARY KEY (abs_air_humidity, address, adj_room, aero_struc, air_temp, alt, amount_light, arch_struc, avg_dew_point, avg_occup, avg_temp, bathroom_count, bedroom_count, build_docs, build_occup_type, building_setting, built_struc_age, built_struc_set, built_struc_type, carb_dioxide, ceil_area, ceil_cond, ceil_finish_mat, ceil_struc, ceil_texture, ceil_thermal_mass, ceil_type, ceil_water_mold, collection_date, cool_syst_id, date_last_rain, depth, dew_point, door_comp_type, door_cond, door_direct, door_loc, door_mat, door_move, door_size, door_type, door_type_metal, door_type_wood, door_water_mold, drawings, ecosystem, ecosystem_category, ecosystem_subtype, ecosystem_type, elev, elevator, env_broad_scale, env_local_scale, env_medium, env_package, escalator, exp_duct, exp_pipe, experimental_factor, ext_door, ext_wall_orient, ext_window_orient, filter_type, fireplace_type, floor_age, floor_area, floor_cond, floor_count, floor_finish_mat, floor_struc, floor_thermal_mass, floor_water_mold, freq_clean, freq_cook, furniture, gender_restroom, geo_loc_name, hall_count, handidness, heat_cool_type, heat_deliv_loc, heat_sys_deliv_meth, heat_system_id, height_carper_fiber, indoor_space, indoor_surf, inside_lux, int_wall_cond, last_clean, lat_lon, light_type, max_occup, mech_struc, number_pets, number_plants, number_resident, occup_density_samp, occup_document, occup_samp, organism_count, pres_animal_insect, quad_pos, rel_air_humidity, rel_humidity_out, rel_samp_loc, room_air_exch_rate, room_architec_elem, room_condt, room_connected, room_count, room_dim, room_door_dist, room_door_share, room_hallway, room_loc, room_moist_dam_hist, room_net_area, room_occup, room_samp_pos, room_type, room_vol, room_wall_share, room_window_count, samp_floor, samp_room_id, samp_sort_meth, samp_time_out, samp_weather, sample_link, season, season_use, shad_dev_water_mold, shading_device_cond, shading_device_loc, shading_device_mat, shading_device_type, size_frac, space_typ_state, specific, specific_ecosystem, specific_humidity, substructure_type, surf_air_cont, surf_humidity, surf_material, surf_moisture, surf_moisture_ph, surf_temp, "temp", temp_out, train_line, train_stat_loc, train_stop_loc, typ_occup_density, ventilation_type, vis_media, wall_area, wall_const_type, wall_finish_mat, wall_height, wall_loc, wall_surf_treatment, wall_texture, wall_thermal_mass, wall_water_mold, water_feat_size, water_feat_type, weekday, window_cond, window_cover, window_horiz_pos, window_loc, window_mat, window_open_freq, window_size, window_status, window_type, window_vert_pos, window_water_mold, horizon_meth, oxy_stat_samp, analysis_type, samp_name, source_mat_id) ); CREATE TABLE "EmslInterface" ( @@ -388,7 +388,6 @@ CREATE TABLE "HcrCoresInterface" ( hcr_geol_age VARCHAR(13), hcr_pressure TEXT, hcr_temp TEXT, - horizon_meth TEXT, lat_lon TEXT, lithology VARCHAR(12), magnesium TEXT, @@ -449,10 +448,11 @@ CREATE TABLE "HcrCoresInterface" ( viscosity TEXT, win TEXT, xylene TEXT, + horizon_meth TEXT, analysis_type VARCHAR(22) NOT NULL, samp_name TEXT, source_mat_id TEXT, - PRIMARY KEY (additional_info, alkalinity, alkalinity_method, ammonium, api, aromatics_pc, asphaltenes_pc, basin, benzene, calcium, chem_administration, chloride, collection_date, density, depos_env, depth, diss_carb_dioxide, diss_inorg_carb, diss_inorg_phosp, diss_iron, diss_org_carb, diss_oxygen_fluid, ecosystem, ecosystem_category, ecosystem_subtype, ecosystem_type, elev, env_broad_scale, env_local_scale, env_medium, env_package, ethylbenzene, experimental_factor, field, geo_loc_name, hc_produced, hcr, hcr_fw_salinity, hcr_geol_age, hcr_pressure, hcr_temp, horizon_meth, lat_lon, lithology, magnesium, misc_param, nitrate, nitrite, org_count_qpcr_info, organism_count, owc_tvdss, oxy_stat_samp, permeability, ph, ph_meth, porosity, potassium, pour_point, pressure, reservoir, resins_pc, salinity, samp_collec_device, samp_collec_method, samp_mat_process, samp_md, samp_size, samp_store_dur, samp_store_loc, samp_store_temp, samp_subtype, samp_transport_cond, samp_tvdss, samp_type, samp_well_name, sample_link, saturates_pc, size_frac, sodium, specific_ecosystem, sr_dep_env, sr_geol_age, sr_kerog_type, sr_lithology, sulfate, sulfate_fw, sulfide, suspend_solids, tan, "temp", toluene, tot_iron, tot_nitro, tot_phosp, tot_sulfur, tvdss_of_hcr_press, tvdss_of_hcr_temp, vfa, vfa_fw, viscosity, win, xylene, analysis_type, samp_name, source_mat_id) + PRIMARY KEY (additional_info, alkalinity, alkalinity_method, ammonium, api, aromatics_pc, asphaltenes_pc, basin, benzene, calcium, chem_administration, chloride, collection_date, density, depos_env, depth, diss_carb_dioxide, diss_inorg_carb, diss_inorg_phosp, diss_iron, diss_org_carb, diss_oxygen_fluid, ecosystem, ecosystem_category, ecosystem_subtype, ecosystem_type, elev, env_broad_scale, env_local_scale, env_medium, env_package, ethylbenzene, experimental_factor, field, geo_loc_name, hc_produced, hcr, hcr_fw_salinity, hcr_geol_age, hcr_pressure, hcr_temp, lat_lon, lithology, magnesium, misc_param, nitrate, nitrite, org_count_qpcr_info, organism_count, owc_tvdss, oxy_stat_samp, permeability, ph, ph_meth, porosity, potassium, pour_point, pressure, reservoir, resins_pc, salinity, samp_collec_device, samp_collec_method, samp_mat_process, samp_md, samp_size, samp_store_dur, samp_store_loc, samp_store_temp, samp_subtype, samp_transport_cond, samp_tvdss, samp_type, samp_well_name, sample_link, saturates_pc, size_frac, sodium, specific_ecosystem, sr_dep_env, sr_geol_age, sr_kerog_type, sr_lithology, sulfate, sulfate_fw, sulfide, suspend_solids, tan, "temp", toluene, tot_iron, tot_nitro, tot_phosp, tot_sulfur, tvdss_of_hcr_press, tvdss_of_hcr_temp, vfa, vfa_fw, viscosity, win, xylene, horizon_meth, analysis_type, samp_name, source_mat_id) ); CREATE TABLE "HcrFluidsSwabsInterface" ( @@ -502,7 +502,6 @@ CREATE TABLE "HcrFluidsSwabsInterface" ( hcr_geol_age VARCHAR(13), hcr_pressure TEXT, hcr_temp TEXT, - horizon_meth TEXT, iw_bt_date_well TEXT, iwf TEXT, lat_lon TEXT, @@ -563,10 +562,11 @@ CREATE TABLE "HcrFluidsSwabsInterface" ( water_prod_rate TEXT, win TEXT, xylene TEXT, + horizon_meth TEXT, analysis_type VARCHAR(22) NOT NULL, samp_name TEXT, source_mat_id TEXT, - PRIMARY KEY (add_recov_method, additional_info, alkalinity, alkalinity_method, ammonium, api, aromatics_pc, asphaltenes_pc, basin, benzene, biocide, biocide_admin_method, calcium, chem_administration, chem_treat_method, chem_treatment, chloride, collection_date, density, depos_env, depth, diss_carb_dioxide, diss_inorg_carb, diss_inorg_phosp, diss_iron, diss_org_carb, diss_oxygen_fluid, ecosystem, ecosystem_category, ecosystem_subtype, ecosystem_type, elev, env_broad_scale, env_local_scale, env_medium, env_package, ethylbenzene, experimental_factor, field, geo_loc_name, hc_produced, hcr, hcr_fw_salinity, hcr_geol_age, hcr_pressure, hcr_temp, horizon_meth, iw_bt_date_well, iwf, lat_lon, lithology, magnesium, misc_param, nitrate, nitrite, org_count_qpcr_info, organism_count, oxy_stat_samp, ph, ph_meth, potassium, pour_point, pressure, prod_rate, prod_start_date, reservoir, resins_pc, salinity, samp_collec_device, samp_collec_method, samp_collect_point, samp_loc_corr_rate, samp_mat_process, samp_preserv, samp_size, samp_store_dur, samp_store_loc, samp_store_temp, samp_subtype, samp_transport_cond, samp_type, samp_well_name, sample_link, saturates_pc, size_frac, sodium, specific_ecosystem, sulfate, sulfate_fw, sulfide, suspend_solids, tan, "temp", toluene, tot_iron, tot_nitro, tot_phosp, tot_sulfur, tvdss_of_hcr_press, tvdss_of_hcr_temp, vfa, vfa_fw, viscosity, water_cut, water_prod_rate, win, xylene, analysis_type, samp_name, source_mat_id) + PRIMARY KEY (add_recov_method, additional_info, alkalinity, alkalinity_method, ammonium, api, aromatics_pc, asphaltenes_pc, basin, benzene, biocide, biocide_admin_method, calcium, chem_administration, chem_treat_method, chem_treatment, chloride, collection_date, density, depos_env, depth, diss_carb_dioxide, diss_inorg_carb, diss_inorg_phosp, diss_iron, diss_org_carb, diss_oxygen_fluid, ecosystem, ecosystem_category, ecosystem_subtype, ecosystem_type, elev, env_broad_scale, env_local_scale, env_medium, env_package, ethylbenzene, experimental_factor, field, geo_loc_name, hc_produced, hcr, hcr_fw_salinity, hcr_geol_age, hcr_pressure, hcr_temp, iw_bt_date_well, iwf, lat_lon, lithology, magnesium, misc_param, nitrate, nitrite, org_count_qpcr_info, organism_count, oxy_stat_samp, ph, ph_meth, potassium, pour_point, pressure, prod_rate, prod_start_date, reservoir, resins_pc, salinity, samp_collec_device, samp_collec_method, samp_collect_point, samp_loc_corr_rate, samp_mat_process, samp_preserv, samp_size, samp_store_dur, samp_store_loc, samp_store_temp, samp_subtype, samp_transport_cond, samp_type, samp_well_name, sample_link, saturates_pc, size_frac, sodium, specific_ecosystem, sulfate, sulfate_fw, sulfide, suspend_solids, tan, "temp", toluene, tot_iron, tot_nitro, tot_phosp, tot_sulfur, tvdss_of_hcr_press, tvdss_of_hcr_temp, vfa, vfa_fw, viscosity, water_cut, water_prod_rate, win, xylene, horizon_meth, analysis_type, samp_name, source_mat_id) ); CREATE TABLE "HostAssociatedInterface" ( @@ -591,7 +591,6 @@ CREATE TABLE "HostAssociatedInterface" ( genetic_mod TEXT, geo_loc_name TEXT, gravidity TEXT, - horizon_meth TEXT, host_age TEXT, host_body_habitat TEXT, host_body_product TEXT, @@ -636,10 +635,11 @@ CREATE TABLE "HostAssociatedInterface" ( size_frac TEXT, specific_ecosystem TEXT, "temp" TEXT, + horizon_meth TEXT, analysis_type VARCHAR(22) NOT NULL, samp_name TEXT, source_mat_id TEXT, - PRIMARY KEY (alt, ances_data, biol_stat, blood_press_diast, blood_press_syst, chem_administration, collection_date, depth, ecosystem, ecosystem_category, ecosystem_subtype, ecosystem_type, elev, env_broad_scale, env_local_scale, env_medium, env_package, experimental_factor, genetic_mod, geo_loc_name, gravidity, horizon_meth, host_age, host_body_habitat, host_body_product, host_body_site, host_body_temp, host_color, host_common_name, host_diet, host_dry_mass, host_family_relation, host_genotype, host_growth_cond, host_height, host_last_meal, host_length, host_life_stage, host_phenotype, host_sex, host_shape, host_subject_id, host_subspecf_genlin, host_substrate, host_symbiont, host_taxid, host_tot_mass, lat_lon, misc_param, organism_count, oxy_stat_samp, perturbation, salinity, samp_capt_status, samp_collec_device, samp_collec_method, samp_dis_stage, samp_mat_process, samp_size, samp_store_dur, samp_store_loc, samp_store_temp, sample_link, size_frac, specific_ecosystem, "temp", analysis_type, samp_name, source_mat_id) + PRIMARY KEY (alt, ances_data, biol_stat, blood_press_diast, blood_press_syst, chem_administration, collection_date, depth, ecosystem, ecosystem_category, ecosystem_subtype, ecosystem_type, elev, env_broad_scale, env_local_scale, env_medium, env_package, experimental_factor, genetic_mod, geo_loc_name, gravidity, host_age, host_body_habitat, host_body_product, host_body_site, host_body_temp, host_color, host_common_name, host_diet, host_dry_mass, host_family_relation, host_genotype, host_growth_cond, host_height, host_last_meal, host_length, host_life_stage, host_phenotype, host_sex, host_shape, host_subject_id, host_subspecf_genlin, host_substrate, host_symbiont, host_taxid, host_tot_mass, lat_lon, misc_param, organism_count, oxy_stat_samp, perturbation, salinity, samp_capt_status, samp_collec_device, samp_collec_method, samp_dis_stage, samp_mat_process, samp_size, samp_store_dur, samp_store_loc, samp_store_temp, sample_link, size_frac, specific_ecosystem, "temp", horizon_meth, analysis_type, samp_name, source_mat_id) ); CREATE TABLE "JgiMgInterface" ( @@ -722,7 +722,6 @@ CREATE TABLE "MiscEnvsInterface" ( env_package TEXT, experimental_factor TEXT, geo_loc_name TEXT, - horizon_meth TEXT, lat_lon TEXT, misc_param TEXT, nitrate TEXT, @@ -757,10 +756,11 @@ CREATE TABLE "MiscEnvsInterface" ( sulfide TEXT, "temp" TEXT, water_current TEXT, + horizon_meth TEXT, analysis_type VARCHAR(22) NOT NULL, samp_name TEXT, source_mat_id TEXT, - PRIMARY KEY (alkalinity, alt, ammonium, biomass, bromide, calcium, chem_administration, chloride, chlorophyll, collection_date, density, depth, diether_lipids, diss_carb_dioxide, diss_hydrogen, diss_inorg_carb, diss_org_nitro, diss_oxygen, ecosystem, ecosystem_category, ecosystem_subtype, ecosystem_type, elev, env_broad_scale, env_local_scale, env_medium, env_package, experimental_factor, geo_loc_name, horizon_meth, lat_lon, misc_param, nitrate, nitrite, nitro, org_carb, org_matter, org_nitro, organism_count, oxy_stat_samp, perturbation, ph, ph_meth, phosphate, phosplipid_fatt_acid, potassium, pressure, salinity, samp_collec_device, samp_collec_method, samp_mat_process, samp_size, samp_store_dur, samp_store_loc, samp_store_temp, sample_link, silicate, size_frac, sodium, specific_ecosystem, sulfate, sulfide, "temp", water_current, analysis_type, samp_name, source_mat_id) + PRIMARY KEY (alkalinity, alt, ammonium, biomass, bromide, calcium, chem_administration, chloride, chlorophyll, collection_date, density, depth, diether_lipids, diss_carb_dioxide, diss_hydrogen, diss_inorg_carb, diss_org_nitro, diss_oxygen, ecosystem, ecosystem_category, ecosystem_subtype, ecosystem_type, elev, env_broad_scale, env_local_scale, env_medium, env_package, experimental_factor, geo_loc_name, lat_lon, misc_param, nitrate, nitrite, nitro, org_carb, org_matter, org_nitro, organism_count, oxy_stat_samp, perturbation, ph, ph_meth, phosphate, phosplipid_fatt_acid, potassium, pressure, salinity, samp_collec_device, samp_collec_method, samp_mat_process, samp_size, samp_store_dur, samp_store_loc, samp_store_temp, sample_link, silicate, size_frac, sodium, specific_ecosystem, sulfate, sulfide, "temp", water_current, horizon_meth, analysis_type, samp_name, source_mat_id) ); CREATE TABLE "PlantAssociatedInterface" ( @@ -795,7 +795,6 @@ CREATE TABLE "PlantAssociatedInterface" ( growth_habit VARCHAR(10), growth_hormone_regm TEXT, herbicide_regm TEXT, - horizon_meth TEXT, host_age TEXT, host_common_name TEXT, host_dry_mass TEXT, @@ -855,10 +854,11 @@ CREATE TABLE "PlantAssociatedInterface" ( tiss_cult_growth_med TEXT, water_temp_regm TEXT, watering_regm TEXT, + horizon_meth TEXT, analysis_type VARCHAR(22) NOT NULL, samp_name TEXT, source_mat_id TEXT, - PRIMARY KEY (air_temp_regm, ances_data, antibiotic_regm, biol_stat, biotic_regm, chem_administration, chem_mutagen, climate_environment, collection_date, cult_root_med, depth, ecosystem, ecosystem_category, ecosystem_subtype, ecosystem_type, elev, env_broad_scale, env_local_scale, env_medium, env_package, experimental_factor, fertilizer_regm, fungicide_regm, gaseous_environment, genetic_mod, geo_loc_name, gravity, growth_facil, growth_habit, growth_hormone_regm, herbicide_regm, horizon_meth, host_age, host_common_name, host_dry_mass, host_genotype, host_height, host_length, host_life_stage, host_phenotype, host_subspecf_genlin, host_symbiont, host_taxid, host_tot_mass, host_wet_mass, humidity_regm, lat_lon, light_regm, mechanical_damage, mineral_nutr_regm, misc_param, non_min_nutr_regm, organism_count, oxy_stat_samp, perturbation, pesticide_regm, ph_regm, plant_growth_med, plant_product, plant_sex, plant_struc, radiation_regm, rainfall_regm, root_cond, root_med_carbon, root_med_macronutr, root_med_micronutr, root_med_ph, root_med_regl, root_med_solid, root_med_suppl, salinity, salt_regm, samp_capt_status, samp_collec_device, samp_collec_method, samp_dis_stage, samp_mat_process, samp_size, samp_store_dur, samp_store_loc, samp_store_temp, sample_link, season_environment, size_frac, specific_ecosystem, standing_water_regm, "temp", tiss_cult_growth_med, water_temp_regm, watering_regm, analysis_type, samp_name, source_mat_id) + PRIMARY KEY (air_temp_regm, ances_data, antibiotic_regm, biol_stat, biotic_regm, chem_administration, chem_mutagen, climate_environment, collection_date, cult_root_med, depth, ecosystem, ecosystem_category, ecosystem_subtype, ecosystem_type, elev, env_broad_scale, env_local_scale, env_medium, env_package, experimental_factor, fertilizer_regm, fungicide_regm, gaseous_environment, genetic_mod, geo_loc_name, gravity, growth_facil, growth_habit, growth_hormone_regm, herbicide_regm, host_age, host_common_name, host_dry_mass, host_genotype, host_height, host_length, host_life_stage, host_phenotype, host_subspecf_genlin, host_symbiont, host_taxid, host_tot_mass, host_wet_mass, humidity_regm, lat_lon, light_regm, mechanical_damage, mineral_nutr_regm, misc_param, non_min_nutr_regm, organism_count, oxy_stat_samp, perturbation, pesticide_regm, ph_regm, plant_growth_med, plant_product, plant_sex, plant_struc, radiation_regm, rainfall_regm, root_cond, root_med_carbon, root_med_macronutr, root_med_micronutr, root_med_ph, root_med_regl, root_med_solid, root_med_suppl, salinity, salt_regm, samp_capt_status, samp_collec_device, samp_collec_method, samp_dis_stage, samp_mat_process, samp_size, samp_store_dur, samp_store_loc, samp_store_temp, sample_link, season_environment, size_frac, specific_ecosystem, standing_water_regm, "temp", tiss_cult_growth_med, water_temp_regm, watering_regm, horizon_meth, analysis_type, samp_name, source_mat_id) ); CREATE TABLE "SampleData" ( @@ -913,7 +913,6 @@ CREATE TABLE "SedimentInterface" ( experimental_factor TEXT, geo_loc_name TEXT, glucosidase_act TEXT, - horizon_meth TEXT, lat_lon TEXT, magnesium TEXT, mean_frict_vel TEXT, @@ -966,10 +965,11 @@ CREATE TABLE "SedimentInterface" ( tot_org_carb TEXT, turbidity TEXT, water_content TEXT, + horizon_meth TEXT, analysis_type VARCHAR(22) NOT NULL, samp_name TEXT, source_mat_id TEXT, - PRIMARY KEY (alkalinity, alkyl_diethers, aminopept_act, ammonium, bacteria_carb_prod, biomass, bishomohopanol, bromide, calcium, carb_nitro_ratio, chem_administration, chloride, chlorophyll, collection_date, density, depth, diether_lipids, diss_carb_dioxide, diss_hydrogen, diss_inorg_carb, diss_org_carb, diss_org_nitro, diss_oxygen, ecosystem, ecosystem_category, ecosystem_subtype, ecosystem_type, elev, env_broad_scale, env_local_scale, env_medium, env_package, experimental_factor, geo_loc_name, glucosidase_act, horizon_meth, lat_lon, magnesium, mean_frict_vel, mean_peak_frict_vel, methane, misc_param, n_alkanes, nitrate, nitrite, nitro, org_carb, org_matter, org_nitro, organism_count, oxy_stat_samp, part_org_carb, particle_class, perturbation, petroleum_hydrocarb, ph, ph_meth, phaeopigments, phosphate, phosplipid_fatt_acid, porosity, potassium, pressure, redox_potential, salinity, samp_collec_device, samp_collec_method, samp_mat_process, samp_size, samp_store_dur, samp_store_loc, samp_store_temp, sample_link, sediment_type, silicate, size_frac, sodium, specific_ecosystem, sulfate, sulfide, "temp", tidal_stage, tot_carb, tot_depth_water_col, tot_nitro_content, tot_org_carb, turbidity, water_content, analysis_type, samp_name, source_mat_id) + PRIMARY KEY (alkalinity, alkyl_diethers, aminopept_act, ammonium, bacteria_carb_prod, biomass, bishomohopanol, bromide, calcium, carb_nitro_ratio, chem_administration, chloride, chlorophyll, collection_date, density, depth, diether_lipids, diss_carb_dioxide, diss_hydrogen, diss_inorg_carb, diss_org_carb, diss_org_nitro, diss_oxygen, ecosystem, ecosystem_category, ecosystem_subtype, ecosystem_type, elev, env_broad_scale, env_local_scale, env_medium, env_package, experimental_factor, geo_loc_name, glucosidase_act, lat_lon, magnesium, mean_frict_vel, mean_peak_frict_vel, methane, misc_param, n_alkanes, nitrate, nitrite, nitro, org_carb, org_matter, org_nitro, organism_count, oxy_stat_samp, part_org_carb, particle_class, perturbation, petroleum_hydrocarb, ph, ph_meth, phaeopigments, phosphate, phosplipid_fatt_acid, porosity, potassium, pressure, redox_potential, salinity, samp_collec_device, samp_collec_method, samp_mat_process, samp_size, samp_store_dur, samp_store_loc, samp_store_temp, sample_link, sediment_type, silicate, size_frac, sodium, specific_ecosystem, sulfate, sulfide, "temp", tidal_stage, tot_carb, tot_depth_water_col, tot_nitro_content, tot_org_carb, turbidity, water_content, horizon_meth, analysis_type, samp_name, source_mat_id) ); CREATE TABLE "SoilInterface" ( @@ -1114,7 +1114,6 @@ CREATE TABLE "WastewaterSludgeInterface" ( experimental_factor TEXT, gaseous_substances TEXT, geo_loc_name TEXT, - horizon_meth TEXT, indust_eff_percent TEXT, inorg_particles TEXT, lat_lon TEXT, @@ -1153,10 +1152,11 @@ CREATE TABLE "WastewaterSludgeInterface" ( tot_nitro TEXT, tot_phosphate TEXT, wastewater_type TEXT, + horizon_meth TEXT, analysis_type VARCHAR(22) NOT NULL, samp_name TEXT, source_mat_id TEXT, - PRIMARY KEY (alkalinity, biochem_oxygen_dem, chem_administration, chem_oxygen_dem, collection_date, depth, ecosystem, ecosystem_category, ecosystem_subtype, ecosystem_type, efficiency_percent, elev, emulsions, env_broad_scale, env_local_scale, env_medium, env_package, experimental_factor, gaseous_substances, geo_loc_name, horizon_meth, indust_eff_percent, inorg_particles, lat_lon, misc_param, nitrate, org_particles, organism_count, oxy_stat_samp, perturbation, ph, ph_meth, phosphate, pre_treatment, primary_treatment, reactor_type, salinity, samp_collec_device, samp_collec_method, samp_mat_process, samp_size, samp_store_dur, samp_store_loc, samp_store_temp, sample_link, secondary_treatment, sewage_type, size_frac, sludge_retent_time, sodium, soluble_inorg_mat, soluble_org_mat, specific_ecosystem, suspend_solids, "temp", tertiary_treatment, tot_nitro, tot_phosphate, wastewater_type, analysis_type, samp_name, source_mat_id) + PRIMARY KEY (alkalinity, biochem_oxygen_dem, chem_administration, chem_oxygen_dem, collection_date, depth, ecosystem, ecosystem_category, ecosystem_subtype, ecosystem_type, efficiency_percent, elev, emulsions, env_broad_scale, env_local_scale, env_medium, env_package, experimental_factor, gaseous_substances, geo_loc_name, indust_eff_percent, inorg_particles, lat_lon, misc_param, nitrate, org_particles, organism_count, oxy_stat_samp, perturbation, ph, ph_meth, phosphate, pre_treatment, primary_treatment, reactor_type, salinity, samp_collec_device, samp_collec_method, samp_mat_process, samp_size, samp_store_dur, samp_store_loc, samp_store_temp, sample_link, secondary_treatment, sewage_type, size_frac, sludge_retent_time, sodium, soluble_inorg_mat, soluble_org_mat, specific_ecosystem, suspend_solids, "temp", tertiary_treatment, tot_nitro, tot_phosphate, wastewater_type, horizon_meth, analysis_type, samp_name, source_mat_id) ); CREATE TABLE "WaterInterface" ( @@ -1204,7 +1204,6 @@ CREATE TABLE "WaterInterface" ( fluor TEXT, geo_loc_name TEXT, glucosidase_act TEXT, - horizon_meth TEXT, lat_lon TEXT, light_intensity TEXT, mean_frict_vel TEXT, @@ -1264,5 +1263,5 @@ CREATE TABLE "WaterInterface" ( analysis_type VARCHAR(22) NOT NULL, samp_name TEXT, source_mat_id TEXT, - PRIMARY KEY (alkalinity, alkalinity_method, alkyl_diethers, aminopept_act, ammonium, atmospheric_data, bac_prod, bac_resp, bacteria_carb_prod, biomass, bishomohopanol, bromide, calcium, carb_nitro_ratio, chem_administration, chloride, chlorophyll, collection_date, conduc, density, depth, diether_lipids, diss_carb_dioxide, diss_hydrogen, diss_inorg_carb, diss_inorg_nitro, diss_inorg_phosp, diss_org_carb, diss_org_nitro, diss_oxygen, down_par, ecosystem, ecosystem_category, ecosystem_subtype, ecosystem_type, elev, env_broad_scale, env_local_scale, env_medium, env_package, experimental_factor, fluor, geo_loc_name, glucosidase_act, horizon_meth, lat_lon, light_intensity, mean_frict_vel, mean_peak_frict_vel, misc_param, n_alkanes, nitrate, nitrite, nitro, org_carb, org_matter, org_nitro, organism_count, oxy_stat_samp, part_org_carb, part_org_nitro, perturbation, petroleum_hydrocarb, ph, ph_meth, phaeopigments, phosphate, phosplipid_fatt_acid, photon_flux, potassium, pressure, primary_prod, redox_potential, salinity, samp_collec_device, samp_collec_method, samp_mat_process, samp_size, samp_store_dur, samp_store_loc, samp_store_temp, sample_link, silicate, size_frac, size_frac_low, size_frac_up, sodium, soluble_react_phosp, specific_ecosystem, sulfate, sulfide, suspend_part_matter, "temp", tidal_stage, tot_depth_water_col, tot_diss_nitro, tot_inorg_nitro, tot_nitro, tot_part_carb, turbidity, water_current, analysis_type, samp_name, source_mat_id) + PRIMARY KEY (alkalinity, alkalinity_method, alkyl_diethers, aminopept_act, ammonium, atmospheric_data, bac_prod, bac_resp, bacteria_carb_prod, biomass, bishomohopanol, bromide, calcium, carb_nitro_ratio, chem_administration, chloride, chlorophyll, collection_date, conduc, density, depth, diether_lipids, diss_carb_dioxide, diss_hydrogen, diss_inorg_carb, diss_inorg_nitro, diss_inorg_phosp, diss_org_carb, diss_org_nitro, diss_oxygen, down_par, ecosystem, ecosystem_category, ecosystem_subtype, ecosystem_type, elev, env_broad_scale, env_local_scale, env_medium, env_package, experimental_factor, fluor, geo_loc_name, glucosidase_act, lat_lon, light_intensity, mean_frict_vel, mean_peak_frict_vel, misc_param, n_alkanes, nitrate, nitrite, nitro, org_carb, org_matter, org_nitro, organism_count, oxy_stat_samp, part_org_carb, part_org_nitro, perturbation, petroleum_hydrocarb, ph, ph_meth, phaeopigments, phosphate, phosplipid_fatt_acid, photon_flux, potassium, pressure, primary_prod, redox_potential, salinity, samp_collec_device, samp_collec_method, samp_mat_process, samp_size, samp_store_dur, samp_store_loc, samp_store_temp, sample_link, silicate, size_frac, size_frac_low, size_frac_up, sodium, soluble_react_phosp, specific_ecosystem, sulfate, sulfide, suspend_part_matter, "temp", tidal_stage, tot_depth_water_col, tot_diss_nitro, tot_inorg_nitro, tot_nitro, tot_part_carb, turbidity, water_current, analysis_type, samp_name, source_mat_id) ); diff --git a/src/data/valid/SampleData-water-data-exhaustive-max-generic.yaml b/src/data/valid/SampleData-water-data-exhaustive-max-generic.yaml index 45c8f6d7..8907d847 100644 --- a/src/data/valid/SampleData-water-data-exhaustive-max-generic.yaml +++ b/src/data/valid/SampleData-water-data-exhaustive-max-generic.yaml @@ -46,7 +46,6 @@ water_data: fluor: 100 units geo_loc_name: 'xyz: xyz, xyz' glucosidase_act: 100 units - horizon_meth: xyz lat_lon: 78 89 light_intensity: 100 units mean_frict_vel: 100 units diff --git a/src/data/valid/SampleData-water-data-exhaustive.yaml b/src/data/valid/SampleData-water-data-exhaustive.yaml index c23e6ceb..5f5aacd4 100644 --- a/src/data/valid/SampleData-water-data-exhaustive.yaml +++ b/src/data/valid/SampleData-water-data-exhaustive.yaml @@ -46,7 +46,6 @@ water_data: fluor: 2.5 volts geo_loc_name: 'USA: Maryland, Bethesda' glucosidase_act: 5 mol per liter per hour - horizon_meth: xyz lat_lon: 78 89 light_intensity: 0.3 lux mean_frict_vel: 0.5 meter per second diff --git a/src/nmdc_submission_schema/datamodel/nmdc_submission_schema.py b/src/nmdc_submission_schema/datamodel/nmdc_submission_schema.py index 5279fe35..e2517096 100644 --- a/src/nmdc_submission_schema/datamodel/nmdc_submission_schema.py +++ b/src/nmdc_submission_schema/datamodel/nmdc_submission_schema.py @@ -1,5 +1,5 @@ # Auto generated from nmdc_submission_schema.yaml by pythongen.py version: 0.0.1 -# Generation date: 2023-08-17T18:01:22 +# Generation date: 2023-09-26T16:55:45 # Schema: nmdc_submission_schema # # id: https://example.com/nmdc_submission_schema @@ -43,6 +43,7 @@ KEGG_ORTHOLOGY = CurieNamespace('KEGG_ORTHOLOGY', 'http://identifiers.org/kegg.orthology/') KEGG_REACTION = CurieNamespace('KEGG_REACTION', 'http://identifiers.org/kegg.reaction/') KEGG_PATHWAY = CurieNamespace('KEGG_PATHWAY', 'http://identifiers.org/kegg.pathway/') +MASSIVE = CurieNamespace('MASSIVE', 'http://example.com/') MIXS = CurieNamespace('MIXS', 'https://w3id.org/mixs/') MIXS_YAML = CurieNamespace('MIXS_yaml', 'https://raw.githubusercontent.com/microbiomedata/mixs/main/model/schema/') METACYC = CurieNamespace('MetaCyc', 'https://identifiers.org/metacyc.reaction/') @@ -55,6 +56,7 @@ UNIPROTKB = CurieNamespace('UniProtKB', 'https://identifiers.org/uniprot/') BIOLINK = CurieNamespace('biolink', 'https://w3id.org/biolink/vocab/') DCTERMS = CurieNamespace('dcterms', 'http://purl.org/dc/terms/') +DOI = CurieNamespace('doi', 'http://example.com/') EMSL = CurieNamespace('emsl', 'http://example.org/emsl_in_mongodb/') EMSL_PROJECT = CurieNamespace('emsl_project', 'https://bioregistry.io/emsl.project:') GENERIC = CurieNamespace('generic', 'https://example.com/generic/') @@ -483,7 +485,6 @@ class AirInterface(DhInterface): env_package: Optional[str] = None experimental_factor: Optional[str] = None geo_loc_name: Optional[str] = None - horizon_meth: Optional[str] = None humidity: Optional[str] = None lat_lon: Optional[str] = None methane: Optional[str] = None @@ -511,6 +512,7 @@ class AirInterface(DhInterface): volatile_org_comp: Optional[str] = None wind_direction: Optional[str] = None wind_speed: Optional[str] = None + horizon_meth: Optional[str] = None samp_name: Optional[str] = None source_mat_id: Optional[str] = None @@ -628,9 +630,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.geo_loc_name is not None and not isinstance(self.geo_loc_name, str): self.geo_loc_name = str(self.geo_loc_name) - if self.horizon_meth is not None and not isinstance(self.horizon_meth, str): - self.horizon_meth = str(self.horizon_meth) - if self.humidity is not None and not isinstance(self.humidity, str): self.humidity = str(self.humidity) @@ -745,9 +744,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.experimental_factor is not None and not isinstance(self.experimental_factor, str): self.experimental_factor = str(self.experimental_factor) - if self.horizon_meth is not None and not isinstance(self.horizon_meth, str): - self.horizon_meth = str(self.horizon_meth) - if self.humidity is not None and not isinstance(self.humidity, str): self.humidity = str(self.humidity) @@ -820,6 +816,9 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.wind_speed is not None and not isinstance(self.wind_speed, str): self.wind_speed = str(self.wind_speed) + if self.horizon_meth is not None and not isinstance(self.horizon_meth, str): + self.horizon_meth = str(self.horizon_meth) + if self.samp_name is not None and not isinstance(self.samp_name, str): self.samp_name = str(self.samp_name) @@ -877,7 +876,6 @@ class BiofilmInterface(DhInterface): experimental_factor: Optional[str] = None geo_loc_name: Optional[str] = None glucosidase_act: Optional[str] = None - horizon_meth: Optional[str] = None lat_lon: Optional[str] = None magnesium: Optional[str] = None mean_frict_vel: Optional[str] = None @@ -925,6 +923,7 @@ class BiofilmInterface(DhInterface): tot_org_carb: Optional[str] = None turbidity: Optional[str] = None water_content: Optional[str] = None + horizon_meth: Optional[str] = None samp_name: Optional[str] = None source_mat_id: Optional[str] = None @@ -1090,9 +1089,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.glucosidase_act is not None and not isinstance(self.glucosidase_act, str): self.glucosidase_act = str(self.glucosidase_act) - if self.horizon_meth is not None and not isinstance(self.horizon_meth, str): - self.horizon_meth = str(self.horizon_meth) - if self.lat_lon is not None and not isinstance(self.lat_lon, str): self.lat_lon = str(self.lat_lon) @@ -1315,9 +1311,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.glucosidase_act is not None and not isinstance(self.glucosidase_act, str): self.glucosidase_act = str(self.glucosidase_act) - if self.horizon_meth is not None and not isinstance(self.horizon_meth, str): - self.horizon_meth = str(self.horizon_meth) - if self.magnesium is not None and not isinstance(self.magnesium, str): self.magnesium = str(self.magnesium) @@ -1450,6 +1443,9 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.water_content is not None and not isinstance(self.water_content, str): self.water_content = str(self.water_content) + if self.horizon_meth is not None and not isinstance(self.horizon_meth, str): + self.horizon_meth = str(self.horizon_meth) + if self.samp_name is not None and not isinstance(self.samp_name, str): self.samp_name = str(self.samp_name) @@ -1556,7 +1552,6 @@ class BuiltEnvInterface(DhInterface): heat_sys_deliv_meth: Optional[str] = None heat_system_id: Optional[str] = None height_carper_fiber: Optional[str] = None - horizon_meth: Optional[str] = None indoor_space: Optional[Union[str, "IndoorSpaceEnum"]] = None indoor_surf: Optional[Union[str, "IndoorSurfEnum"]] = None inside_lux: Optional[str] = None @@ -1652,6 +1647,7 @@ class BuiltEnvInterface(DhInterface): window_type: Optional[Union[str, "WindowTypeEnum"]] = None window_vert_pos: Optional[Union[str, "WindowVertPosEnum"]] = None window_water_mold: Optional[str] = None + horizon_meth: Optional[str] = None oxy_stat_samp: Optional[Union[str, "OxyStatSampEnum"]] = None samp_name: Optional[str] = None source_mat_id: Optional[str] = None @@ -1963,9 +1959,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.height_carper_fiber is not None and not isinstance(self.height_carper_fiber, str): self.height_carper_fiber = str(self.height_carper_fiber) - if self.horizon_meth is not None and not isinstance(self.horizon_meth, str): - self.horizon_meth = str(self.horizon_meth) - if self.indoor_space is not None and not isinstance(self.indoor_space, IndoorSpaceEnum): self.indoor_space = IndoorSpaceEnum(self.indoor_space) @@ -2485,9 +2478,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.height_carper_fiber is not None and not isinstance(self.height_carper_fiber, str): self.height_carper_fiber = str(self.height_carper_fiber) - if self.horizon_meth is not None and not isinstance(self.horizon_meth, str): - self.horizon_meth = str(self.horizon_meth) - if self.indoor_space is not None and not isinstance(self.indoor_space, IndoorSpaceEnum): self.indoor_space = IndoorSpaceEnum(self.indoor_space) @@ -2770,6 +2760,9 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.window_water_mold is not None and not isinstance(self.window_water_mold, str): self.window_water_mold = str(self.window_water_mold) + if self.horizon_meth is not None and not isinstance(self.horizon_meth, str): + self.horizon_meth = str(self.horizon_meth) + if self.oxy_stat_samp is not None and not isinstance(self.oxy_stat_samp, OxyStatSampEnum): self.oxy_stat_samp = OxyStatSampEnum(self.oxy_stat_samp) @@ -2922,7 +2915,6 @@ class HcrCoresInterface(DhInterface): hcr_geol_age: Optional[Union[str, "HcrGeolAgeEnum"]] = None hcr_pressure: Optional[str] = None hcr_temp: Optional[str] = None - horizon_meth: Optional[str] = None lat_lon: Optional[str] = None lithology: Optional[Union[str, "LithologyEnum"]] = None magnesium: Optional[str] = None @@ -2983,6 +2975,7 @@ class HcrCoresInterface(DhInterface): viscosity: Optional[str] = None win: Optional[str] = None xylene: Optional[str] = None + horizon_meth: Optional[str] = None samp_name: Optional[str] = None source_mat_id: Optional[str] = None @@ -3166,9 +3159,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.hcr_temp is not None and not isinstance(self.hcr_temp, str): self.hcr_temp = str(self.hcr_temp) - if self.horizon_meth is not None and not isinstance(self.horizon_meth, str): - self.horizon_meth = str(self.horizon_meth) - if self.lat_lon is not None and not isinstance(self.lat_lon, str): self.lat_lon = str(self.lat_lon) @@ -3448,9 +3438,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.hcr_temp is not None and not isinstance(self.hcr_temp, str): self.hcr_temp = str(self.hcr_temp) - if self.horizon_meth is not None and not isinstance(self.horizon_meth, str): - self.horizon_meth = str(self.horizon_meth) - if self.lithology is not None and not isinstance(self.lithology, LithologyEnum): self.lithology = LithologyEnum(self.lithology) @@ -3622,6 +3609,9 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.xylene is not None and not isinstance(self.xylene, str): self.xylene = str(self.xylene) + if self.horizon_meth is not None and not isinstance(self.horizon_meth, str): + self.horizon_meth = str(self.horizon_meth) + if self.samp_name is not None and not isinstance(self.samp_name, str): self.samp_name = str(self.samp_name) @@ -3690,7 +3680,6 @@ class HcrFluidsSwabsInterface(DhInterface): hcr_geol_age: Optional[Union[str, "HcrGeolAgeEnum"]] = None hcr_pressure: Optional[str] = None hcr_temp: Optional[str] = None - horizon_meth: Optional[str] = None iw_bt_date_well: Optional[str] = None iwf: Optional[str] = None lat_lon: Optional[str] = None @@ -3751,6 +3740,7 @@ class HcrFluidsSwabsInterface(DhInterface): water_prod_rate: Optional[str] = None win: Optional[str] = None xylene: Optional[str] = None + horizon_meth: Optional[str] = None samp_name: Optional[str] = None source_mat_id: Optional[str] = None @@ -3949,9 +3939,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.hcr_temp is not None and not isinstance(self.hcr_temp, str): self.hcr_temp = str(self.hcr_temp) - if self.horizon_meth is not None and not isinstance(self.horizon_meth, str): - self.horizon_meth = str(self.horizon_meth) - if self.iw_bt_date_well is not None and not isinstance(self.iw_bt_date_well, str): self.iw_bt_date_well = str(self.iw_bt_date_well) @@ -4246,9 +4233,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.hcr_temp is not None and not isinstance(self.hcr_temp, str): self.hcr_temp = str(self.hcr_temp) - if self.horizon_meth is not None and not isinstance(self.horizon_meth, str): - self.horizon_meth = str(self.horizon_meth) - if self.iw_bt_date_well is not None and not isinstance(self.iw_bt_date_well, str): self.iw_bt_date_well = str(self.iw_bt_date_well) @@ -4420,6 +4404,9 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.xylene is not None and not isinstance(self.xylene, str): self.xylene = str(self.xylene) + if self.horizon_meth is not None and not isinstance(self.horizon_meth, str): + self.horizon_meth = str(self.horizon_meth) + if self.samp_name is not None and not isinstance(self.samp_name, str): self.samp_name = str(self.samp_name) @@ -4463,7 +4450,6 @@ class HostAssociatedInterface(DhInterface): genetic_mod: Optional[str] = None geo_loc_name: Optional[str] = None gravidity: Optional[str] = None - horizon_meth: Optional[str] = None host_age: Optional[str] = None host_body_habitat: Optional[str] = None host_body_product: Optional[str] = None @@ -4508,6 +4494,7 @@ class HostAssociatedInterface(DhInterface): size_frac: Optional[str] = None specific_ecosystem: Optional[str] = None temp: Optional[str] = None + horizon_meth: Optional[str] = None samp_name: Optional[str] = None source_mat_id: Optional[str] = None @@ -4631,9 +4618,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.gravidity is not None and not isinstance(self.gravidity, str): self.gravidity = str(self.gravidity) - if self.horizon_meth is not None and not isinstance(self.horizon_meth, str): - self.horizon_meth = str(self.horizon_meth) - if self.host_age is not None and not isinstance(self.host_age, str): self.host_age = str(self.host_age) @@ -4805,9 +4789,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.gravidity is not None and not isinstance(self.gravidity, str): self.gravidity = str(self.gravidity) - if self.horizon_meth is not None and not isinstance(self.horizon_meth, str): - self.horizon_meth = str(self.horizon_meth) - if self.host_age is not None and not isinstance(self.host_age, str): self.host_age = str(self.host_age) @@ -4931,6 +4912,9 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.temp is not None and not isinstance(self.temp, str): self.temp = str(self.temp) + if self.horizon_meth is not None and not isinstance(self.horizon_meth, str): + self.horizon_meth = str(self.horizon_meth) + if self.samp_name is not None and not isinstance(self.samp_name, str): self.samp_name = str(self.samp_name) @@ -5360,7 +5344,6 @@ class MiscEnvsInterface(DhInterface): env_package: Optional[str] = None experimental_factor: Optional[str] = None geo_loc_name: Optional[str] = None - horizon_meth: Optional[str] = None lat_lon: Optional[str] = None misc_param: Optional[str] = None nitrate: Optional[str] = None @@ -5395,6 +5378,7 @@ class MiscEnvsInterface(DhInterface): sulfide: Optional[str] = None temp: Optional[str] = None water_current: Optional[str] = None + horizon_meth: Optional[str] = None samp_name: Optional[str] = None source_mat_id: Optional[str] = None @@ -5542,9 +5526,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.geo_loc_name is not None and not isinstance(self.geo_loc_name, str): self.geo_loc_name = str(self.geo_loc_name) - if self.horizon_meth is not None and not isinstance(self.horizon_meth, str): - self.horizon_meth = str(self.horizon_meth) - if self.lat_lon is not None and not isinstance(self.lat_lon, str): self.lat_lon = str(self.lat_lon) @@ -5710,9 +5691,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.experimental_factor is not None and not isinstance(self.experimental_factor, str): self.experimental_factor = str(self.experimental_factor) - if self.horizon_meth is not None and not isinstance(self.horizon_meth, str): - self.horizon_meth = str(self.horizon_meth) - if self.misc_param is not None and not isinstance(self.misc_param, str): self.misc_param = str(self.misc_param) @@ -5806,6 +5784,9 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.water_current is not None and not isinstance(self.water_current, str): self.water_current = str(self.water_current) + if self.horizon_meth is not None and not isinstance(self.horizon_meth, str): + self.horizon_meth = str(self.horizon_meth) + if self.samp_name is not None and not isinstance(self.samp_name, str): self.samp_name = str(self.samp_name) @@ -5859,7 +5840,6 @@ class PlantAssociatedInterface(DhInterface): growth_habit: Optional[Union[str, "GrowthHabitEnum"]] = None growth_hormone_regm: Optional[str] = None herbicide_regm: Optional[str] = None - horizon_meth: Optional[str] = None host_age: Optional[str] = None host_common_name: Optional[str] = None host_dry_mass: Optional[str] = None @@ -5919,6 +5899,7 @@ class PlantAssociatedInterface(DhInterface): tiss_cult_growth_med: Optional[str] = None water_temp_regm: Optional[str] = None watering_regm: Optional[str] = None + horizon_meth: Optional[str] = None samp_name: Optional[str] = None source_mat_id: Optional[str] = None @@ -6077,9 +6058,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.herbicide_regm is not None and not isinstance(self.herbicide_regm, str): self.herbicide_regm = str(self.herbicide_regm) - if self.horizon_meth is not None and not isinstance(self.horizon_meth, str): - self.horizon_meth = str(self.horizon_meth) - if self.host_age is not None and not isinstance(self.host_age, str): self.host_age = str(self.host_age) @@ -6323,9 +6301,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.herbicide_regm is not None and not isinstance(self.herbicide_regm, str): self.herbicide_regm = str(self.herbicide_regm) - if self.horizon_meth is not None and not isinstance(self.horizon_meth, str): - self.horizon_meth = str(self.horizon_meth) - if self.host_age is not None and not isinstance(self.host_age, str): self.host_age = str(self.host_age) @@ -6494,6 +6469,9 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.watering_regm is not None and not isinstance(self.watering_regm, str): self.watering_regm = str(self.watering_regm) + if self.horizon_meth is not None and not isinstance(self.horizon_meth, str): + self.horizon_meth = str(self.horizon_meth) + if self.samp_name is not None and not isinstance(self.samp_name, str): self.samp_name = str(self.samp_name) @@ -6551,7 +6529,6 @@ class SedimentInterface(DhInterface): experimental_factor: Optional[str] = None geo_loc_name: Optional[str] = None glucosidase_act: Optional[str] = None - horizon_meth: Optional[str] = None lat_lon: Optional[str] = None magnesium: Optional[str] = None mean_frict_vel: Optional[str] = None @@ -6604,6 +6581,7 @@ class SedimentInterface(DhInterface): tot_org_carb: Optional[str] = None turbidity: Optional[str] = None water_content: Optional[str] = None + horizon_meth: Optional[str] = None samp_name: Optional[str] = None source_mat_id: Optional[str] = None @@ -6769,9 +6747,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.glucosidase_act is not None and not isinstance(self.glucosidase_act, str): self.glucosidase_act = str(self.glucosidase_act) - if self.horizon_meth is not None and not isinstance(self.horizon_meth, str): - self.horizon_meth = str(self.horizon_meth) - if self.lat_lon is not None and not isinstance(self.lat_lon, str): self.lat_lon = str(self.lat_lon) @@ -7009,9 +6984,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.glucosidase_act is not None and not isinstance(self.glucosidase_act, str): self.glucosidase_act = str(self.glucosidase_act) - if self.horizon_meth is not None and not isinstance(self.horizon_meth, str): - self.horizon_meth = str(self.horizon_meth) - if self.magnesium is not None and not isinstance(self.magnesium, str): self.magnesium = str(self.magnesium) @@ -7159,6 +7131,9 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.water_content is not None and not isinstance(self.water_content, str): self.water_content = str(self.water_content) + if self.horizon_meth is not None and not isinstance(self.horizon_meth, str): + self.horizon_meth = str(self.horizon_meth) + if self.samp_name is not None and not isinstance(self.samp_name, str): self.samp_name = str(self.samp_name) @@ -8015,7 +7990,6 @@ class WastewaterSludgeInterface(DhInterface): experimental_factor: Optional[str] = None gaseous_substances: Optional[str] = None geo_loc_name: Optional[str] = None - horizon_meth: Optional[str] = None indust_eff_percent: Optional[str] = None inorg_particles: Optional[str] = None lat_lon: Optional[str] = None @@ -8054,6 +8028,7 @@ class WastewaterSludgeInterface(DhInterface): tot_nitro: Optional[str] = None tot_phosphate: Optional[str] = None wastewater_type: Optional[str] = None + horizon_meth: Optional[str] = None samp_name: Optional[str] = None source_mat_id: Optional[str] = None @@ -8174,9 +8149,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.geo_loc_name is not None and not isinstance(self.geo_loc_name, str): self.geo_loc_name = str(self.geo_loc_name) - if self.horizon_meth is not None and not isinstance(self.horizon_meth, str): - self.horizon_meth = str(self.horizon_meth) - if self.indust_eff_percent is not None and not isinstance(self.indust_eff_percent, str): self.indust_eff_percent = str(self.indust_eff_percent) @@ -8327,9 +8299,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.gaseous_substances is not None and not isinstance(self.gaseous_substances, str): self.gaseous_substances = str(self.gaseous_substances) - if self.horizon_meth is not None and not isinstance(self.horizon_meth, str): - self.horizon_meth = str(self.horizon_meth) - if self.indust_eff_percent is not None and not isinstance(self.indust_eff_percent, str): self.indust_eff_percent = str(self.indust_eff_percent) @@ -8435,6 +8404,9 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.wastewater_type is not None and not isinstance(self.wastewater_type, str): self.wastewater_type = str(self.wastewater_type) + if self.horizon_meth is not None and not isinstance(self.horizon_meth, str): + self.horizon_meth = str(self.horizon_meth) + if self.samp_name is not None and not isinstance(self.samp_name, str): self.samp_name = str(self.samp_name) @@ -8501,7 +8473,6 @@ class WaterInterface(DhInterface): fluor: Optional[str] = None geo_loc_name: Optional[str] = None glucosidase_act: Optional[str] = None - horizon_meth: Optional[str] = None lat_lon: Optional[str] = None light_intensity: Optional[str] = None mean_frict_vel: Optional[str] = None @@ -8735,9 +8706,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.glucosidase_act is not None and not isinstance(self.glucosidase_act, str): self.glucosidase_act = str(self.glucosidase_act) - if self.horizon_meth is not None and not isinstance(self.horizon_meth, str): - self.horizon_meth = str(self.horizon_meth) - if self.lat_lon is not None and not isinstance(self.lat_lon, str): self.lat_lon = str(self.lat_lon) @@ -9017,9 +8985,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.glucosidase_act is not None and not isinstance(self.glucosidase_act, str): self.glucosidase_act = str(self.glucosidase_act) - if self.horizon_meth is not None and not isinstance(self.horizon_meth, str): - self.horizon_meth = str(self.horizon_meth) - if self.lat_lon is not None and not isinstance(self.lat_lon, str): self.lat_lon = str(self.lat_lon) @@ -10867,160 +10832,188 @@ class OxyStatSampEnum(EnumDefinitionImpl): description="placeholder enum descr, DO NOT SORT", ) -class HeatCoolTypeEnum(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="HeatCoolTypeEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "radiant system", - PermissibleValue(text="radiant system")) - setattr(cls, "heat pump", - PermissibleValue(text="heat pump")) - setattr(cls, "forced air system", - PermissibleValue(text="forced air system")) - setattr(cls, "steam forced heat", - PermissibleValue(text="steam forced heat")) - setattr(cls, "wood stove", - PermissibleValue(text="wood stove")) - -class WeekdayEnum(EnumDefinitionImpl): +class MechStrucEnum(EnumDefinitionImpl): - Monday = PermissibleValue(text="Monday") - Tuesday = PermissibleValue(text="Tuesday") - Wednesday = PermissibleValue(text="Wednesday") - Thursday = PermissibleValue(text="Thursday") - Friday = PermissibleValue(text="Friday") - Saturday = PermissibleValue(text="Saturday") - Sunday = PermissibleValue(text="Sunday") + subway = PermissibleValue(text="subway") + coach = PermissibleValue(text="coach") + carriage = PermissibleValue(text="carriage") + elevator = PermissibleValue(text="elevator") + escalator = PermissibleValue(text="escalator") + boat = PermissibleValue(text="boat") + train = PermissibleValue(text="train") + car = PermissibleValue(text="car") + bus = PermissibleValue(text="bus") _defn = EnumDefinition( - name="WeekdayEnum", + name="MechStrucEnum", ) -class WindowLocEnum(EnumDefinitionImpl): +class WindowVertPosEnum(EnumDefinitionImpl): - north = PermissibleValue(text="north") - south = PermissibleValue(text="south") - east = PermissibleValue(text="east") - west = PermissibleValue(text="west") + bottom = PermissibleValue(text="bottom") + middle = PermissibleValue(text="middle") + top = PermissibleValue(text="top") + low = PermissibleValue(text="low") + high = PermissibleValue(text="high") _defn = EnumDefinition( - name="WindowLocEnum", + name="WindowVertPosEnum", ) -class VisMediaEnum(EnumDefinitionImpl): +class WaterFeatTypeEnum(EnumDefinitionImpl): - photos = PermissibleValue(text="photos") - videos = PermissibleValue(text="videos") - interiors = PermissibleValue(text="interiors") - equipment = PermissibleValue(text="equipment") + fountain = PermissibleValue(text="fountain") + pool = PermissibleValue(text="pool") + stream = PermissibleValue(text="stream") + waterfall = PermissibleValue(text="waterfall") _defn = EnumDefinition( - name="VisMediaEnum", + name="WaterFeatTypeEnum", ) @classmethod def _addvals(cls): - setattr(cls, "commonly of the building", - PermissibleValue(text="commonly of the building")) - setattr(cls, "site context (adjacent buildings, vegetation, terrain, streets)", - PermissibleValue(text="site context (adjacent buildings, vegetation, terrain, streets)")) - setattr(cls, "3D scans", - PermissibleValue(text="3D scans")) + setattr(cls, "standing feature", + PermissibleValue(text="standing feature")) -class RelSampLocEnum(EnumDefinitionImpl): +class DoorDirectEnum(EnumDefinitionImpl): + + inward = PermissibleValue(text="inward") + outward = PermissibleValue(text="outward") + sideways = PermissibleValue(text="sideways") _defn = EnumDefinition( - name="RelSampLocEnum", + name="DoorDirectEnum", ) - @classmethod - def _addvals(cls): - setattr(cls, "edge of car", - PermissibleValue(text="edge of car")) - setattr(cls, "center of car", - PermissibleValue(text="center of car")) - setattr(cls, "under a seat", - PermissibleValue(text="under a seat")) - -class DoorMatEnum(EnumDefinitionImpl): +class BuildDocsEnum(EnumDefinitionImpl): - aluminum = PermissibleValue(text="aluminum") - fiberboard = PermissibleValue(text="fiberboard") - fiberglass = PermissibleValue(text="fiberglass") - metal = PermissibleValue(text="metal") - vinyl = PermissibleValue(text="vinyl") - wood = PermissibleValue(text="wood") + schedule = PermissibleValue(text="schedule") + sections = PermissibleValue(text="sections") + submittals = PermissibleValue(text="submittals") + windows = PermissibleValue(text="windows") _defn = EnumDefinition( - name="DoorMatEnum", + name="BuildDocsEnum", ) @classmethod def _addvals(cls): - setattr(cls, "cellular PVC", - PermissibleValue(text="cellular PVC")) - setattr(cls, "engineered plastic", - PermissibleValue(text="engineered plastic")) - setattr(cls, "thermoplastic alloy", - PermissibleValue(text="thermoplastic alloy")) - setattr(cls, "wood/plastic composite", - PermissibleValue(text="wood/plastic composite")) + setattr(cls, "building information model", + PermissibleValue(text="building information model")) + setattr(cls, "commissioning report", + PermissibleValue(text="commissioning report")) + setattr(cls, "complaint logs", + PermissibleValue(text="complaint logs")) + setattr(cls, "contract administration", + PermissibleValue(text="contract administration")) + setattr(cls, "cost estimate", + PermissibleValue(text="cost estimate")) + setattr(cls, "janitorial schedules or logs", + PermissibleValue(text="janitorial schedules or logs")) + setattr(cls, "maintenance plans", + PermissibleValue(text="maintenance plans")) + setattr(cls, "shop drawings", + PermissibleValue(text="shop drawings")) + setattr(cls, "ventilation system", + PermissibleValue(text="ventilation system")) -class CeilCondEnum(EnumDefinitionImpl): +class DoorLocEnum(EnumDefinitionImpl): - new = PermissibleValue(text="new") - damaged = PermissibleValue(text="damaged") - rupture = PermissibleValue(text="rupture") + north = PermissibleValue(text="north") + south = PermissibleValue(text="south") + east = PermissibleValue(text="east") + west = PermissibleValue(text="west") _defn = EnumDefinition( - name="CeilCondEnum", + name="DoorLocEnum", ) - @classmethod - def _addvals(cls): - setattr(cls, "visible wear", - PermissibleValue(text="visible wear")) - setattr(cls, "needs repair", - PermissibleValue(text="needs repair")) +class ExtWindowOrientEnum(EnumDefinitionImpl): -class OccupDocumentEnum(EnumDefinitionImpl): + north = PermissibleValue(text="north") + south = PermissibleValue(text="south") + east = PermissibleValue(text="east") + west = PermissibleValue(text="west") + northeast = PermissibleValue(text="northeast") + southeast = PermissibleValue(text="southeast") + southwest = PermissibleValue(text="southwest") + northwest = PermissibleValue(text="northwest") - estimate = PermissibleValue(text="estimate") - videos = PermissibleValue(text="videos") + _defn = EnumDefinition( + name="ExtWindowOrientEnum", + ) + +class RoomTypeEnum(EnumDefinitionImpl): + + attic = PermissibleValue(text="attic") + bathroom = PermissibleValue(text="bathroom") + closet = PermissibleValue(text="closet") + elevator = PermissibleValue(text="elevator") + hallway = PermissibleValue(text="hallway") + kitchen = PermissibleValue(text="kitchen") + stairwell = PermissibleValue(text="stairwell") + lobby = PermissibleValue(text="lobby") + vestibule = PermissibleValue(text="vestibule") + laboratory_wet = PermissibleValue(text="laboratory_wet") + laboratory_dry = PermissibleValue(text="laboratory_dry") + gymnasium = PermissibleValue(text="gymnasium") + natatorium = PermissibleValue(text="natatorium") + auditorium = PermissibleValue(text="auditorium") + lockers = PermissibleValue(text="lockers") + cafe = PermissibleValue(text="cafe") + warehouse = PermissibleValue(text="warehouse") _defn = EnumDefinition( - name="OccupDocumentEnum", + name="RoomTypeEnum", ) @classmethod def _addvals(cls): - setattr(cls, "automated count", - PermissibleValue(text="automated count")) - setattr(cls, "manual count", - PermissibleValue(text="manual count")) + setattr(cls, "conference room", + PermissibleValue(text="conference room")) + setattr(cls, "examining room", + PermissibleValue(text="examining room")) + setattr(cls, "mail room", + PermissibleValue(text="mail room")) + setattr(cls, "private office", + PermissibleValue(text="private office")) + setattr(cls, "open office", + PermissibleValue(text="open office")) + setattr(cls, ",restroom", + PermissibleValue(text=",restroom")) + setattr(cls, "mechanical or electrical room", + PermissibleValue(text="mechanical or electrical room")) + setattr(cls, "data center", + PermissibleValue(text="data center")) -class TrainStatLocEnum(EnumDefinitionImpl): +class BuildOccupTypeEnum(EnumDefinitionImpl): - riverside = PermissibleValue(text="riverside") + office = PermissibleValue(text="office") + market = PermissibleValue(text="market") + restaurant = PermissibleValue(text="restaurant") + residence = PermissibleValue(text="residence") + school = PermissibleValue(text="school") + residential = PermissibleValue(text="residential") + commercial = PermissibleValue(text="commercial") + airport = PermissibleValue(text="airport") _defn = EnumDefinition( - name="TrainStatLocEnum", + name="BuildOccupTypeEnum", ) @classmethod def _addvals(cls): - setattr(cls, "south station above ground", - PermissibleValue(text="south station above ground")) - setattr(cls, "south station underground", - PermissibleValue(text="south station underground")) - setattr(cls, "south station amtrak", - PermissibleValue(text="south station amtrak")) - setattr(cls, "forest hills", - PermissibleValue(text="forest hills")) + setattr(cls, "low rise", + PermissibleValue(text="low rise")) + setattr(cls, "high rise", + PermissibleValue(text="high rise")) + setattr(cls, "wood framed", + PermissibleValue(text="wood framed")) + setattr(cls, "health care", + PermissibleValue(text="health care")) + setattr(cls, "sports complex", + PermissibleValue(text="sports complex")) class SurfMaterialEnum(EnumDefinitionImpl): @@ -11050,200 +11043,286 @@ def _addvals(cls): setattr(cls, "stainless steel", PermissibleValue(text="stainless steel")) -class SurfAirContEnum(EnumDefinitionImpl): - - dust = PermissibleValue(text="dust") - radon = PermissibleValue(text="radon") - nutrients = PermissibleValue(text="nutrients") - biocides = PermissibleValue(text="biocides") +class WindowTypeEnum(EnumDefinitionImpl): _defn = EnumDefinition( - name="SurfAirContEnum", + name="WindowTypeEnum", ) @classmethod def _addvals(cls): - setattr(cls, "organic matter", - PermissibleValue(text="organic matter")) - setattr(cls, "particulate matter", - PermissibleValue(text="particulate matter")) - setattr(cls, "volatile organic compounds", - PermissibleValue(text="volatile organic compounds")) - setattr(cls, "biological contaminants", - PermissibleValue(text="biological contaminants")) + setattr(cls, "single-hung sash window", + PermissibleValue(text="single-hung sash window")) + setattr(cls, "horizontal sash window", + PermissibleValue(text="horizontal sash window")) + setattr(cls, "fixed window", + PermissibleValue(text="fixed window")) -class DoorTypeWoodEnum(EnumDefinitionImpl): +class IndoorSpaceEnum(EnumDefinitionImpl): - battened = PermissibleValue(text="battened") - flush = PermissibleValue(text="flush") - louvered = PermissibleValue(text="louvered") + bedroom = PermissibleValue(text="bedroom") + office = PermissibleValue(text="office") + bathroom = PermissibleValue(text="bathroom") + foyer = PermissibleValue(text="foyer") + kitchen = PermissibleValue(text="kitchen") + hallway = PermissibleValue(text="hallway") + elevator = PermissibleValue(text="elevator") _defn = EnumDefinition( - name="DoorTypeWoodEnum", + name="IndoorSpaceEnum", ) @classmethod def _addvals(cls): - setattr(cls, "bettened and ledged", - PermissibleValue(text="bettened and ledged")) - setattr(cls, "ledged and braced", - PermissibleValue(text="ledged and braced")) - setattr(cls, "ledged and framed", - PermissibleValue(text="ledged and framed")) - setattr(cls, "ledged, braced and frame", - PermissibleValue(text="ledged, braced and frame")) - setattr(cls, "framed and paneled", - PermissibleValue(text="framed and paneled")) - setattr(cls, "glashed or sash", - PermissibleValue(text="glashed or sash")) - setattr(cls, "wire gauged", - PermissibleValue(text="wire gauged")) + setattr(cls, "locker room", + PermissibleValue(text="locker room")) -class WaterFeatTypeEnum(EnumDefinitionImpl): +class FloorWaterMoldEnum(EnumDefinitionImpl): - fountain = PermissibleValue(text="fountain") - pool = PermissibleValue(text="pool") - stream = PermissibleValue(text="stream") - waterfall = PermissibleValue(text="waterfall") + condensation = PermissibleValue(text="condensation") _defn = EnumDefinition( - name="WaterFeatTypeEnum", + name="FloorWaterMoldEnum", ) @classmethod def _addvals(cls): - setattr(cls, "standing feature", - PermissibleValue(text="standing feature")) + setattr(cls, "mold odor", + PermissibleValue(text="mold odor")) + setattr(cls, "wet floor", + PermissibleValue(text="wet floor")) + setattr(cls, "water stains", + PermissibleValue(text="water stains")) + setattr(cls, "wall discoloration", + PermissibleValue(text="wall discoloration")) + setattr(cls, "floor discoloration", + PermissibleValue(text="floor discoloration")) + setattr(cls, "ceiling discoloration", + PermissibleValue(text="ceiling discoloration")) + setattr(cls, "peeling paint or wallpaper", + PermissibleValue(text="peeling paint or wallpaper")) + setattr(cls, "bulging walls", + PermissibleValue(text="bulging walls")) -class HeatDelivLocEnum(EnumDefinitionImpl): +class ExtWallOrientEnum(EnumDefinitionImpl): north = PermissibleValue(text="north") south = PermissibleValue(text="south") east = PermissibleValue(text="east") west = PermissibleValue(text="west") + northeast = PermissibleValue(text="northeast") + southeast = PermissibleValue(text="southeast") + southwest = PermissibleValue(text="southwest") + northwest = PermissibleValue(text="northwest") _defn = EnumDefinition( - name="HeatDelivLocEnum", + name="ExtWallOrientEnum", ) -class RoomConnectedEnum(EnumDefinitionImpl): +class RoomCondtEnum(EnumDefinitionImpl): - attic = PermissibleValue(text="attic") - bathroom = PermissibleValue(text="bathroom") - closet = PermissibleValue(text="closet") - elevator = PermissibleValue(text="elevator") - hallway = PermissibleValue(text="hallway") - kitchen = PermissibleValue(text="kitchen") - office = PermissibleValue(text="office") - stairwell = PermissibleValue(text="stairwell") + new = PermissibleValue(text="new") + damaged = PermissibleValue(text="damaged") + rupture = PermissibleValue(text="rupture") _defn = EnumDefinition( - name="RoomConnectedEnum", + name="RoomCondtEnum", ) @classmethod def _addvals(cls): - setattr(cls, "conference room", - PermissibleValue(text="conference room")) - setattr(cls, "examining room", - PermissibleValue(text="examining room")) - setattr(cls, "mail room", - PermissibleValue(text="mail room")) + setattr(cls, "visible wear", + PermissibleValue(text="visible wear")) + setattr(cls, "needs repair", + PermissibleValue(text="needs repair")) + setattr(cls, "visible signs of mold/mildew", + PermissibleValue(text="visible signs of mold/mildew")) -class RoomSampPosEnum(EnumDefinitionImpl): +class DoorCompTypeEnum(EnumDefinitionImpl): - center = PermissibleValue(text="center") + revolving = PermissibleValue(text="revolving") + sliding = PermissibleValue(text="sliding") + telescopic = PermissibleValue(text="telescopic") _defn = EnumDefinition( - name="RoomSampPosEnum", + name="DoorCompTypeEnum", ) @classmethod def _addvals(cls): - setattr(cls, "north corner", - PermissibleValue(text="north corner")) - setattr(cls, "south corner", - PermissibleValue(text="south corner")) - setattr(cls, "west corner", - PermissibleValue(text="west corner")) - setattr(cls, "east corner", - PermissibleValue(text="east corner")) - setattr(cls, "northeast corner", - PermissibleValue(text="northeast corner")) - setattr(cls, "northwest corner", - PermissibleValue(text="northwest corner")) - setattr(cls, "southeast corner", - PermissibleValue(text="southeast corner")) - setattr(cls, "southwest corner", - PermissibleValue(text="southwest corner")) + setattr(cls, "metal covered", + PermissibleValue(text="metal covered")) -class HandidnessEnum(EnumDefinitionImpl): +class CeilTypeEnum(EnumDefinitionImpl): - ambidexterity = PermissibleValue(text="ambidexterity") + cathedral = PermissibleValue(text="cathedral") + dropped = PermissibleValue(text="dropped") + concave = PermissibleValue(text="concave") + coffered = PermissibleValue(text="coffered") + cove = PermissibleValue(text="cove") + stretched = PermissibleValue(text="stretched") _defn = EnumDefinition( - name="HandidnessEnum", + name="CeilTypeEnum", ) @classmethod def _addvals(cls): - setattr(cls, "left handedness", - PermissibleValue(text="left handedness")) - setattr(cls, "mixed-handedness", - PermissibleValue(text="mixed-handedness")) - setattr(cls, "right handedness", - PermissibleValue(text="right handedness")) + setattr(cls, "barrel-shaped", + PermissibleValue(text="barrel-shaped")) -class DrawingsEnum(EnumDefinitionImpl): +class CeilFinishMatEnum(EnumDefinitionImpl): - operation = PermissibleValue(text="operation") - construction = PermissibleValue(text="construction") - bid = PermissibleValue(text="bid") - design = PermissibleValue(text="design") - diagram = PermissibleValue(text="diagram") - sketch = PermissibleValue(text="sketch") + drywall = PermissibleValue(text="drywall") + tiles = PermissibleValue(text="tiles") + PVC = PermissibleValue(text="PVC") + plasterboard = PermissibleValue(text="plasterboard") + metal = PermissibleValue(text="metal") + fiberglass = PermissibleValue(text="fiberglass") + stucco = PermissibleValue(text="stucco") + wood = PermissibleValue(text="wood") _defn = EnumDefinition( - name="DrawingsEnum", + name="CeilFinishMatEnum", ) @classmethod def _addvals(cls): - setattr(cls, "as built", - PermissibleValue(text="as built")) - setattr(cls, "building navigation map", - PermissibleValue(text="building navigation map")) + setattr(cls, "mineral fibre", + PermissibleValue(text="mineral fibre")) + setattr(cls, "mineral wool/calcium silicate", + PermissibleValue(text="mineral wool/calcium silicate")) -class RoomLocEnum(EnumDefinitionImpl): +class FurnitureEnum(EnumDefinitionImpl): + + cabinet = PermissibleValue(text="cabinet") + chair = PermissibleValue(text="chair") + desks = PermissibleValue(text="desks") _defn = EnumDefinition( - name="RoomLocEnum", + name="FurnitureEnum", + ) + +class ArchStrucEnum(EnumDefinitionImpl): + + building = PermissibleValue(text="building") + shed = PermissibleValue(text="shed") + home = PermissibleValue(text="home") + + _defn = EnumDefinition( + name="ArchStrucEnum", + ) + +class WallFinishMatEnum(EnumDefinitionImpl): + + plaster = PermissibleValue(text="plaster") + tile = PermissibleValue(text="tile") + terrazzo = PermissibleValue(text="terrazzo") + wood = PermissibleValue(text="wood") + metal = PermissibleValue(text="metal") + masonry = PermissibleValue(text="masonry") + + _defn = EnumDefinition( + name="WallFinishMatEnum", ) @classmethod def _addvals(cls): - setattr(cls, "corner room", - PermissibleValue(text="corner room")) - setattr(cls, "interior room", - PermissibleValue(text="interior room")) - setattr(cls, "exterior wall", - PermissibleValue(text="exterior wall")) + setattr(cls, "gypsum plaster", + PermissibleValue(text="gypsum plaster")) + setattr(cls, "veneer plaster", + PermissibleValue(text="veneer plaster")) + setattr(cls, "gypsum board", + PermissibleValue(text="gypsum board")) + setattr(cls, "stone facing", + PermissibleValue(text="stone facing")) + setattr(cls, "acoustical treatment", + PermissibleValue(text="acoustical treatment")) -class ExtWallOrientEnum(EnumDefinitionImpl): +class DoorMatEnum(EnumDefinitionImpl): - north = PermissibleValue(text="north") - south = PermissibleValue(text="south") - east = PermissibleValue(text="east") - west = PermissibleValue(text="west") - northeast = PermissibleValue(text="northeast") - southeast = PermissibleValue(text="southeast") - southwest = PermissibleValue(text="southwest") - northwest = PermissibleValue(text="northwest") + aluminum = PermissibleValue(text="aluminum") + fiberboard = PermissibleValue(text="fiberboard") + fiberglass = PermissibleValue(text="fiberglass") + metal = PermissibleValue(text="metal") + vinyl = PermissibleValue(text="vinyl") + wood = PermissibleValue(text="wood") _defn = EnumDefinition( - name="ExtWallOrientEnum", + name="DoorMatEnum", + ) + + @classmethod + def _addvals(cls): + setattr(cls, "cellular PVC", + PermissibleValue(text="cellular PVC")) + setattr(cls, "engineered plastic", + PermissibleValue(text="engineered plastic")) + setattr(cls, "thermoplastic alloy", + PermissibleValue(text="thermoplastic alloy")) + setattr(cls, "wood/plastic composite", + PermissibleValue(text="wood/plastic composite")) + +class TrainStopLocEnum(EnumDefinitionImpl): + + end = PermissibleValue(text="end") + mid = PermissibleValue(text="mid") + downtown = PermissibleValue(text="downtown") + + _defn = EnumDefinition( + name="TrainStopLocEnum", + ) + +class OccupDocumentEnum(EnumDefinitionImpl): + + estimate = PermissibleValue(text="estimate") + videos = PermissibleValue(text="videos") + + _defn = EnumDefinition( + name="OccupDocumentEnum", + ) + + @classmethod + def _addvals(cls): + setattr(cls, "automated count", + PermissibleValue(text="automated count")) + setattr(cls, "manual count", + PermissibleValue(text="manual count")) + +class FloorFinishMatEnum(EnumDefinitionImpl): + + tile = PermissibleValue(text="tile") + carpet = PermissibleValue(text="carpet") + rug = PermissibleValue(text="rug") + lineoleum = PermissibleValue(text="lineoleum") + stone = PermissibleValue(text="stone") + bamboo = PermissibleValue(text="bamboo") + cork = PermissibleValue(text="cork") + terrazo = PermissibleValue(text="terrazo") + concrete = PermissibleValue(text="concrete") + none = PermissibleValue(text="none") + sealed = PermissibleValue(text="sealed") + paint = PermissibleValue(text="paint") + + _defn = EnumDefinition( + name="FloorFinishMatEnum", ) + @classmethod + def _addvals(cls): + setattr(cls, "wood strip or parquet", + PermissibleValue(text="wood strip or parquet")) + setattr(cls, "laminate wood", + PermissibleValue(text="laminate wood")) + setattr(cls, "vinyl composition tile", + PermissibleValue(text="vinyl composition tile")) + setattr(cls, "sheet vinyl", + PermissibleValue(text="sheet vinyl")) + setattr(cls, "clear finish", + PermissibleValue(text="clear finish")) + setattr(cls, "none or unfinished", + PermissibleValue(text="none or unfinished")) + class SampWeatherEnum(EnumDefinitionImpl): cloudy = PermissibleValue(text="cloudy") @@ -11286,14 +11365,25 @@ def _addvals(cls): setattr(cls, "wood-framed", PermissibleValue(text="wood-framed")) -class DoorTypeEnum(EnumDefinitionImpl): +class BuildingSettingEnum(EnumDefinitionImpl): - composite = PermissibleValue(text="composite") - metal = PermissibleValue(text="metal") - wooden = PermissibleValue(text="wooden") + urban = PermissibleValue(text="urban") + suburban = PermissibleValue(text="suburban") + exurban = PermissibleValue(text="exurban") + rural = PermissibleValue(text="rural") _defn = EnumDefinition( - name="DoorTypeEnum", + name="BuildingSettingEnum", + ) + +class WindowHorizPosEnum(EnumDefinitionImpl): + + left = PermissibleValue(text="left") + middle = PermissibleValue(text="middle") + right = PermissibleValue(text="right") + + _defn = EnumDefinition( + name="WindowHorizPosEnum", ) class WindowCondEnum(EnumDefinitionImpl): @@ -11313,117 +11403,164 @@ def _addvals(cls): setattr(cls, "visible wear", PermissibleValue(text="visible wear")) -class SpecificEnum(EnumDefinitionImpl): +class SeasonUseEnum(EnumDefinitionImpl): - operation = PermissibleValue(text="operation") - construction = PermissibleValue(text="construction") - bid = PermissibleValue(text="bid") - design = PermissibleValue(text="design") - photos = PermissibleValue(text="photos") + Spring = PermissibleValue(text="Spring") + Summer = PermissibleValue(text="Summer") + Fall = PermissibleValue(text="Fall") + Winter = PermissibleValue(text="Winter") _defn = EnumDefinition( - name="SpecificEnum", + name="SeasonUseEnum", ) - @classmethod - def _addvals(cls): - setattr(cls, "as built", - PermissibleValue(text="as built")) +class ShadingDeviceCondEnum(EnumDefinitionImpl): -class WallConstTypeEnum(EnumDefinitionImpl): + damaged = PermissibleValue(text="damaged") + new = PermissibleValue(text="new") + rupture = PermissibleValue(text="rupture") _defn = EnumDefinition( - name="WallConstTypeEnum", + name="ShadingDeviceCondEnum", ) @classmethod def _addvals(cls): - setattr(cls, "frame construction", - PermissibleValue(text="frame construction")) - setattr(cls, "joisted masonry", - PermissibleValue(text="joisted masonry")) - setattr(cls, "light noncombustible", - PermissibleValue(text="light noncombustible")) - setattr(cls, "masonry noncombustible", - PermissibleValue(text="masonry noncombustible")) - setattr(cls, "modified fire resistive", - PermissibleValue(text="modified fire resistive")) - setattr(cls, "fire resistive", - PermissibleValue(text="fire resistive")) + setattr(cls, "needs repair", + PermissibleValue(text="needs repair")) + setattr(cls, "visible wear", + PermissibleValue(text="visible wear")) -class WindowTypeEnum(EnumDefinitionImpl): +class SurfAirContEnum(EnumDefinitionImpl): + + dust = PermissibleValue(text="dust") + radon = PermissibleValue(text="radon") + nutrients = PermissibleValue(text="nutrients") + biocides = PermissibleValue(text="biocides") _defn = EnumDefinition( - name="WindowTypeEnum", + name="SurfAirContEnum", ) @classmethod def _addvals(cls): - setattr(cls, "single-hung sash window", - PermissibleValue(text="single-hung sash window")) - setattr(cls, "horizontal sash window", - PermissibleValue(text="horizontal sash window")) - setattr(cls, "fixed window", - PermissibleValue(text="fixed window")) + setattr(cls, "organic matter", + PermissibleValue(text="organic matter")) + setattr(cls, "particulate matter", + PermissibleValue(text="particulate matter")) + setattr(cls, "volatile organic compounds", + PermissibleValue(text="volatile organic compounds")) + setattr(cls, "biological contaminants", + PermissibleValue(text="biological contaminants")) -class TrainLineEnum(EnumDefinitionImpl): +class LightTypeEnum(EnumDefinitionImpl): - red = PermissibleValue(text="red") - green = PermissibleValue(text="green") - orange = PermissibleValue(text="orange") + none = PermissibleValue(text="none") _defn = EnumDefinition( - name="TrainLineEnum", + name="LightTypeEnum", ) -class WallLocEnum(EnumDefinitionImpl): - - north = PermissibleValue(text="north") - south = PermissibleValue(text="south") - east = PermissibleValue(text="east") - west = PermissibleValue(text="west") + @classmethod + def _addvals(cls): + setattr(cls, "natural light", + PermissibleValue(text="natural light")) + setattr(cls, "electric light", + PermissibleValue(text="electric light")) + setattr(cls, "desk lamp", + PermissibleValue(text="desk lamp")) + setattr(cls, "flourescent lights", + PermissibleValue(text="flourescent lights")) + +class CeilTextureEnum(EnumDefinitionImpl): + + knockdown = PermissibleValue(text="knockdown") + popcorn = PermissibleValue(text="popcorn") + smooth = PermissibleValue(text="smooth") + swirl = PermissibleValue(text="swirl") _defn = EnumDefinition( - name="WallLocEnum", + name="CeilTextureEnum", ) -class DoorCondEnum(EnumDefinitionImpl): + @classmethod + def _addvals(cls): + setattr(cls, "crows feet", + PermissibleValue(text="crows feet")) + setattr(cls, "crows-foot stomp", + PermissibleValue(text="crows-foot stomp")) + setattr(cls, "double skip", + PermissibleValue(text="double skip")) + setattr(cls, "hawk and trowel", + PermissibleValue(text="hawk and trowel")) + setattr(cls, "orange peel", + PermissibleValue(text="orange peel")) + setattr(cls, "rosebud stomp", + PermissibleValue(text="rosebud stomp")) + setattr(cls, "Santa-Fe texture", + PermissibleValue(text="Santa-Fe texture")) + setattr(cls, "skip trowel", + PermissibleValue(text="skip trowel")) + setattr(cls, "stomp knockdown", + PermissibleValue(text="stomp knockdown")) + +class CeilCondEnum(EnumDefinitionImpl): - damaged = PermissibleValue(text="damaged") new = PermissibleValue(text="new") + damaged = PermissibleValue(text="damaged") rupture = PermissibleValue(text="rupture") _defn = EnumDefinition( - name="DoorCondEnum", + name="CeilCondEnum", ) @classmethod def _addvals(cls): - setattr(cls, "needs repair", - PermissibleValue(text="needs repair")) setattr(cls, "visible wear", PermissibleValue(text="visible wear")) + setattr(cls, "needs repair", + PermissibleValue(text="needs repair")) -class LightTypeEnum(EnumDefinitionImpl): +class RoomSampPosEnum(EnumDefinitionImpl): - none = PermissibleValue(text="none") + center = PermissibleValue(text="center") _defn = EnumDefinition( - name="LightTypeEnum", + name="RoomSampPosEnum", ) @classmethod def _addvals(cls): - setattr(cls, "natural light", - PermissibleValue(text="natural light")) - setattr(cls, "electric light", - PermissibleValue(text="electric light")) - setattr(cls, "desk lamp", - PermissibleValue(text="desk lamp")) - setattr(cls, "flourescent lights", - PermissibleValue(text="flourescent lights")) + setattr(cls, "north corner", + PermissibleValue(text="north corner")) + setattr(cls, "south corner", + PermissibleValue(text="south corner")) + setattr(cls, "west corner", + PermissibleValue(text="west corner")) + setattr(cls, "east corner", + PermissibleValue(text="east corner")) + setattr(cls, "northeast corner", + PermissibleValue(text="northeast corner")) + setattr(cls, "northwest corner", + PermissibleValue(text="northwest corner")) + setattr(cls, "southeast corner", + PermissibleValue(text="southeast corner")) + setattr(cls, "southwest corner", + PermissibleValue(text="southwest corner")) -class RoomTypeEnum(EnumDefinitionImpl): +class WindowMatEnum(EnumDefinitionImpl): + + clad = PermissibleValue(text="clad") + fiberglass = PermissibleValue(text="fiberglass") + metal = PermissibleValue(text="metal") + vinyl = PermissibleValue(text="vinyl") + wood = PermissibleValue(text="wood") + + _defn = EnumDefinition( + name="WindowMatEnum", + ) + +class RoomConnectedEnum(EnumDefinitionImpl): attic = PermissibleValue(text="attic") bathroom = PermissibleValue(text="bathroom") @@ -11431,20 +11568,11 @@ class RoomTypeEnum(EnumDefinitionImpl): elevator = PermissibleValue(text="elevator") hallway = PermissibleValue(text="hallway") kitchen = PermissibleValue(text="kitchen") + office = PermissibleValue(text="office") stairwell = PermissibleValue(text="stairwell") - lobby = PermissibleValue(text="lobby") - vestibule = PermissibleValue(text="vestibule") - laboratory_wet = PermissibleValue(text="laboratory_wet") - laboratory_dry = PermissibleValue(text="laboratory_dry") - gymnasium = PermissibleValue(text="gymnasium") - natatorium = PermissibleValue(text="natatorium") - auditorium = PermissibleValue(text="auditorium") - lockers = PermissibleValue(text="lockers") - cafe = PermissibleValue(text="cafe") - warehouse = PermissibleValue(text="warehouse") _defn = EnumDefinition( - name="RoomTypeEnum", + name="RoomConnectedEnum", ) @classmethod @@ -11455,83 +11583,53 @@ def _addvals(cls): PermissibleValue(text="examining room")) setattr(cls, "mail room", PermissibleValue(text="mail room")) - setattr(cls, "private office", - PermissibleValue(text="private office")) - setattr(cls, "open office", - PermissibleValue(text="open office")) - setattr(cls, ",restroom", - PermissibleValue(text=",restroom")) - setattr(cls, "mechanical or electrical room", - PermissibleValue(text="mechanical or electrical room")) - setattr(cls, "data center", - PermissibleValue(text="data center")) - -class WindowCoverEnum(EnumDefinitionImpl): - - blinds = PermissibleValue(text="blinds") - curtains = PermissibleValue(text="curtains") - none = PermissibleValue(text="none") - - _defn = EnumDefinition( - name="WindowCoverEnum", - ) -class DoorMoveEnum(EnumDefinitionImpl): +class SpecificEnum(EnumDefinitionImpl): - collapsible = PermissibleValue(text="collapsible") - folding = PermissibleValue(text="folding") - revolving = PermissibleValue(text="revolving") - sliding = PermissibleValue(text="sliding") - swinging = PermissibleValue(text="swinging") + operation = PermissibleValue(text="operation") + construction = PermissibleValue(text="construction") + bid = PermissibleValue(text="bid") + design = PermissibleValue(text="design") + photos = PermissibleValue(text="photos") _defn = EnumDefinition( - name="DoorMoveEnum", + name="SpecificEnum", ) @classmethod def _addvals(cls): - setattr(cls, "rolling shutter", - PermissibleValue(text="rolling shutter")) + setattr(cls, "as built", + PermissibleValue(text="as built")) -class DoorDirectEnum(EnumDefinitionImpl): +class WallSurfTreatmentEnum(EnumDefinitionImpl): - inward = PermissibleValue(text="inward") - outward = PermissibleValue(text="outward") - sideways = PermissibleValue(text="sideways") + painted = PermissibleValue(text="painted") + paneling = PermissibleValue(text="paneling") + stucco = PermissibleValue(text="stucco") + fabric = PermissibleValue(text="fabric") _defn = EnumDefinition( - name="DoorDirectEnum", + name="WallSurfTreatmentEnum", ) -class WindowMatEnum(EnumDefinitionImpl): - - clad = PermissibleValue(text="clad") - fiberglass = PermissibleValue(text="fiberglass") - metal = PermissibleValue(text="metal") - vinyl = PermissibleValue(text="vinyl") - wood = PermissibleValue(text="wood") - - _defn = EnumDefinition( - name="WindowMatEnum", - ) + @classmethod + def _addvals(cls): + setattr(cls, "wall paper", + PermissibleValue(text="wall paper")) + setattr(cls, "no treatment", + PermissibleValue(text="no treatment")) -class ShadingDeviceCondEnum(EnumDefinitionImpl): +class WindowLocEnum(EnumDefinitionImpl): - damaged = PermissibleValue(text="damaged") - new = PermissibleValue(text="new") - rupture = PermissibleValue(text="rupture") + north = PermissibleValue(text="north") + south = PermissibleValue(text="south") + east = PermissibleValue(text="east") + west = PermissibleValue(text="west") _defn = EnumDefinition( - name="ShadingDeviceCondEnum", + name="WindowLocEnum", ) - @classmethod - def _addvals(cls): - setattr(cls, "needs repair", - PermissibleValue(text="needs repair")) - setattr(cls, "visible wear", - PermissibleValue(text="visible wear")) - class ShadingDeviceTypeEnum(EnumDefinitionImpl): tree = PermissibleValue(text="tree") @@ -11581,361 +11679,276 @@ def _addvals(cls): setattr(cls, "needs repair", PermissibleValue(text="needs repair")) -class DoorTypeMetalEnum(EnumDefinitionImpl): +class DoorTypeEnum(EnumDefinitionImpl): - collapsible = PermissibleValue(text="collapsible") - hollow = PermissibleValue(text="hollow") + composite = PermissibleValue(text="composite") + metal = PermissibleValue(text="metal") + wooden = PermissibleValue(text="wooden") _defn = EnumDefinition( - name="DoorTypeMetalEnum", + name="DoorTypeEnum", + ) + +class DoorTypeWoodEnum(EnumDefinitionImpl): + + battened = PermissibleValue(text="battened") + flush = PermissibleValue(text="flush") + louvered = PermissibleValue(text="louvered") + + _defn = EnumDefinition( + name="DoorTypeWoodEnum", ) @classmethod def _addvals(cls): - setattr(cls, "corrugated steel", - PermissibleValue(text="corrugated steel")) - setattr(cls, "rolling shutters", - PermissibleValue(text="rolling shutters")) - setattr(cls, "steel plate", - PermissibleValue(text="steel plate")) + setattr(cls, "bettened and ledged", + PermissibleValue(text="bettened and ledged")) + setattr(cls, "ledged and braced", + PermissibleValue(text="ledged and braced")) + setattr(cls, "ledged and framed", + PermissibleValue(text="ledged and framed")) + setattr(cls, "ledged, braced and frame", + PermissibleValue(text="ledged, braced and frame")) + setattr(cls, "framed and paneled", + PermissibleValue(text="framed and paneled")) + setattr(cls, "glashed or sash", + PermissibleValue(text="glashed or sash")) + setattr(cls, "wire gauged", + PermissibleValue(text="wire gauged")) -class WallTextureEnum(EnumDefinitionImpl): +class DrawingsEnum(EnumDefinitionImpl): - knockdown = PermissibleValue(text="knockdown") - popcorn = PermissibleValue(text="popcorn") - smooth = PermissibleValue(text="smooth") - swirl = PermissibleValue(text="swirl") + operation = PermissibleValue(text="operation") + construction = PermissibleValue(text="construction") + bid = PermissibleValue(text="bid") + design = PermissibleValue(text="design") + diagram = PermissibleValue(text="diagram") + sketch = PermissibleValue(text="sketch") _defn = EnumDefinition( - name="WallTextureEnum", + name="DrawingsEnum", ) @classmethod def _addvals(cls): - setattr(cls, "crows feet", - PermissibleValue(text="crows feet")) - setattr(cls, "crows-foot stomp", - PermissibleValue(text="crows-foot stomp")) - setattr(cls, "", - PermissibleValue(text="")) - setattr(cls, "double skip", - PermissibleValue(text="double skip")) - setattr(cls, "hawk and trowel", - PermissibleValue(text="hawk and trowel")) - setattr(cls, "orange peel", - PermissibleValue(text="orange peel")) - setattr(cls, "rosebud stomp", - PermissibleValue(text="rosebud stomp")) - setattr(cls, "Santa-Fe texture", - PermissibleValue(text="Santa-Fe texture")) - setattr(cls, "skip trowel", - PermissibleValue(text="skip trowel")) - setattr(cls, "stomp knockdown", - PermissibleValue(text="stomp knockdown")) - -class BuildDocsEnum(EnumDefinitionImpl): - - schedule = PermissibleValue(text="schedule") - sections = PermissibleValue(text="sections") - submittals = PermissibleValue(text="submittals") - windows = PermissibleValue(text="windows") - - _defn = EnumDefinition( - name="BuildDocsEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "building information model", - PermissibleValue(text="building information model")) - setattr(cls, "commissioning report", - PermissibleValue(text="commissioning report")) - setattr(cls, "complaint logs", - PermissibleValue(text="complaint logs")) - setattr(cls, "contract administration", - PermissibleValue(text="contract administration")) - setattr(cls, "cost estimate", - PermissibleValue(text="cost estimate")) - setattr(cls, "janitorial schedules or logs", - PermissibleValue(text="janitorial schedules or logs")) - setattr(cls, "maintenance plans", - PermissibleValue(text="maintenance plans")) - setattr(cls, "shop drawings", - PermissibleValue(text="shop drawings")) - setattr(cls, "ventilation system", - PermissibleValue(text="ventilation system")) + setattr(cls, "as built", + PermissibleValue(text="as built")) + setattr(cls, "building navigation map", + PermissibleValue(text="building navigation map")) -class BuildingSettingEnum(EnumDefinitionImpl): +class WindowCoverEnum(EnumDefinitionImpl): - urban = PermissibleValue(text="urban") - suburban = PermissibleValue(text="suburban") - exurban = PermissibleValue(text="exurban") - rural = PermissibleValue(text="rural") + blinds = PermissibleValue(text="blinds") + curtains = PermissibleValue(text="curtains") + none = PermissibleValue(text="none") _defn = EnumDefinition( - name="BuildingSettingEnum", + name="WindowCoverEnum", ) -class WallFinishMatEnum(EnumDefinitionImpl): +class DoorCondEnum(EnumDefinitionImpl): - plaster = PermissibleValue(text="plaster") - tile = PermissibleValue(text="tile") - terrazzo = PermissibleValue(text="terrazzo") - wood = PermissibleValue(text="wood") - metal = PermissibleValue(text="metal") - masonry = PermissibleValue(text="masonry") + damaged = PermissibleValue(text="damaged") + new = PermissibleValue(text="new") + rupture = PermissibleValue(text="rupture") _defn = EnumDefinition( - name="WallFinishMatEnum", + name="DoorCondEnum", ) @classmethod def _addvals(cls): - setattr(cls, "gypsum plaster", - PermissibleValue(text="gypsum plaster")) - setattr(cls, "veneer plaster", - PermissibleValue(text="veneer plaster")) - setattr(cls, "gypsum board", - PermissibleValue(text="gypsum board")) - setattr(cls, "stone facing", - PermissibleValue(text="stone facing")) - setattr(cls, "acoustical treatment", - PermissibleValue(text="acoustical treatment")) + setattr(cls, "needs repair", + PermissibleValue(text="needs repair")) + setattr(cls, "visible wear", + PermissibleValue(text="visible wear")) -class BuildOccupTypeEnum(EnumDefinitionImpl): +class FilterTypeEnum(EnumDefinitionImpl): - office = PermissibleValue(text="office") - market = PermissibleValue(text="market") - restaurant = PermissibleValue(text="restaurant") - residence = PermissibleValue(text="residence") - school = PermissibleValue(text="school") - residential = PermissibleValue(text="residential") - commercial = PermissibleValue(text="commercial") - airport = PermissibleValue(text="airport") + HEPA = PermissibleValue(text="HEPA") + electrostatic = PermissibleValue(text="electrostatic") _defn = EnumDefinition( - name="BuildOccupTypeEnum", + name="FilterTypeEnum", ) @classmethod def _addvals(cls): - setattr(cls, "low rise", - PermissibleValue(text="low rise")) - setattr(cls, "high rise", - PermissibleValue(text="high rise")) - setattr(cls, "wood framed", - PermissibleValue(text="wood framed")) - setattr(cls, "health care", - PermissibleValue(text="health care")) - setattr(cls, "sports complex", - PermissibleValue(text="sports complex")) + setattr(cls, "particulate air filter", + PermissibleValue(text="particulate air filter")) + setattr(cls, "chemical air filter", + PermissibleValue(text="chemical air filter")) + setattr(cls, "low-MERV pleated media", + PermissibleValue(text="low-MERV pleated media")) + setattr(cls, "gas-phase or ultraviolet air treatments", + PermissibleValue(text="gas-phase or ultraviolet air treatments")) -class CeilTextureEnum(EnumDefinitionImpl): +class FloorCondEnum(EnumDefinitionImpl): - knockdown = PermissibleValue(text="knockdown") - popcorn = PermissibleValue(text="popcorn") - smooth = PermissibleValue(text="smooth") - swirl = PermissibleValue(text="swirl") + new = PermissibleValue(text="new") + damaged = PermissibleValue(text="damaged") + rupture = PermissibleValue(text="rupture") _defn = EnumDefinition( - name="CeilTextureEnum", + name="FloorCondEnum", ) @classmethod def _addvals(cls): - setattr(cls, "crows feet", - PermissibleValue(text="crows feet")) - setattr(cls, "crows-foot stomp", - PermissibleValue(text="crows-foot stomp")) - setattr(cls, "double skip", - PermissibleValue(text="double skip")) - setattr(cls, "hawk and trowel", - PermissibleValue(text="hawk and trowel")) - setattr(cls, "orange peel", - PermissibleValue(text="orange peel")) - setattr(cls, "rosebud stomp", - PermissibleValue(text="rosebud stomp")) - setattr(cls, "Santa-Fe texture", - PermissibleValue(text="Santa-Fe texture")) - setattr(cls, "skip trowel", - PermissibleValue(text="skip trowel")) - setattr(cls, "stomp knockdown", - PermissibleValue(text="stomp knockdown")) + setattr(cls, "visible wear", + PermissibleValue(text="visible wear")) + setattr(cls, "needs repair", + PermissibleValue(text="needs repair")) -class FloorWaterMoldEnum(EnumDefinitionImpl): +class DoorTypeMetalEnum(EnumDefinitionImpl): - condensation = PermissibleValue(text="condensation") + collapsible = PermissibleValue(text="collapsible") + hollow = PermissibleValue(text="hollow") _defn = EnumDefinition( - name="FloorWaterMoldEnum", + name="DoorTypeMetalEnum", ) @classmethod def _addvals(cls): - setattr(cls, "mold odor", - PermissibleValue(text="mold odor")) - setattr(cls, "wet floor", - PermissibleValue(text="wet floor")) - setattr(cls, "water stains", - PermissibleValue(text="water stains")) - setattr(cls, "wall discoloration", - PermissibleValue(text="wall discoloration")) - setattr(cls, "floor discoloration", - PermissibleValue(text="floor discoloration")) - setattr(cls, "ceiling discoloration", - PermissibleValue(text="ceiling discoloration")) - setattr(cls, "peeling paint or wallpaper", - PermissibleValue(text="peeling paint or wallpaper")) - setattr(cls, "bulging walls", - PermissibleValue(text="bulging walls")) + setattr(cls, "corrugated steel", + PermissibleValue(text="corrugated steel")) + setattr(cls, "rolling shutters", + PermissibleValue(text="rolling shutters")) + setattr(cls, "steel plate", + PermissibleValue(text="steel plate")) -class CeilTypeEnum(EnumDefinitionImpl): +class GenderRestroomEnum(EnumDefinitionImpl): - cathedral = PermissibleValue(text="cathedral") - dropped = PermissibleValue(text="dropped") - concave = PermissibleValue(text="concave") - coffered = PermissibleValue(text="coffered") - cove = PermissibleValue(text="cove") - stretched = PermissibleValue(text="stretched") + female = PermissibleValue(text="female") + male = PermissibleValue(text="male") + unisex = PermissibleValue(text="unisex") _defn = EnumDefinition( - name="CeilTypeEnum", + name="GenderRestroomEnum", ) @classmethod def _addvals(cls): - setattr(cls, "barrel-shaped", - PermissibleValue(text="barrel-shaped")) + setattr(cls, "all gender", + PermissibleValue(text="all gender")) + setattr(cls, "gender neurtral", + PermissibleValue(text="gender neurtral")) + setattr(cls, "male and female", + PermissibleValue(text="male and female")) -class DoorLocEnum(EnumDefinitionImpl): +class WeekdayEnum(EnumDefinitionImpl): - north = PermissibleValue(text="north") - south = PermissibleValue(text="south") - east = PermissibleValue(text="east") - west = PermissibleValue(text="west") + Monday = PermissibleValue(text="Monday") + Tuesday = PermissibleValue(text="Tuesday") + Wednesday = PermissibleValue(text="Wednesday") + Thursday = PermissibleValue(text="Thursday") + Friday = PermissibleValue(text="Friday") + Saturday = PermissibleValue(text="Saturday") + Sunday = PermissibleValue(text="Sunday") _defn = EnumDefinition( - name="DoorLocEnum", + name="WeekdayEnum", ) -class DoorCompTypeEnum(EnumDefinitionImpl): +class SubstructureTypeEnum(EnumDefinitionImpl): - revolving = PermissibleValue(text="revolving") - sliding = PermissibleValue(text="sliding") - telescopic = PermissibleValue(text="telescopic") + crawlspace = PermissibleValue(text="crawlspace") + basement = PermissibleValue(text="basement") _defn = EnumDefinition( - name="DoorCompTypeEnum", + name="SubstructureTypeEnum", ) @classmethod def _addvals(cls): - setattr(cls, "metal covered", - PermissibleValue(text="metal covered")) - -class MechStrucEnum(EnumDefinitionImpl): - - subway = PermissibleValue(text="subway") - coach = PermissibleValue(text="coach") - carriage = PermissibleValue(text="carriage") - elevator = PermissibleValue(text="elevator") - escalator = PermissibleValue(text="escalator") - boat = PermissibleValue(text="boat") - train = PermissibleValue(text="train") - car = PermissibleValue(text="car") - bus = PermissibleValue(text="bus") - - _defn = EnumDefinition( - name="MechStrucEnum", - ) - -class WallSurfTreatmentEnum(EnumDefinitionImpl): + setattr(cls, "slab on grade", + PermissibleValue(text="slab on grade")) - painted = PermissibleValue(text="painted") - paneling = PermissibleValue(text="paneling") - stucco = PermissibleValue(text="stucco") - fabric = PermissibleValue(text="fabric") +class RelSampLocEnum(EnumDefinitionImpl): _defn = EnumDefinition( - name="WallSurfTreatmentEnum", + name="RelSampLocEnum", ) @classmethod def _addvals(cls): - setattr(cls, "wall paper", - PermissibleValue(text="wall paper")) - setattr(cls, "no treatment", - PermissibleValue(text="no treatment")) - -class RoomCondtEnum(EnumDefinitionImpl): + setattr(cls, "edge of car", + PermissibleValue(text="edge of car")) + setattr(cls, "center of car", + PermissibleValue(text="center of car")) + setattr(cls, "under a seat", + PermissibleValue(text="under a seat")) - new = PermissibleValue(text="new") - damaged = PermissibleValue(text="damaged") - rupture = PermissibleValue(text="rupture") +class QuadPosEnum(EnumDefinitionImpl): _defn = EnumDefinition( - name="RoomCondtEnum", + name="QuadPosEnum", ) @classmethod def _addvals(cls): - setattr(cls, "visible wear", - PermissibleValue(text="visible wear")) - setattr(cls, "needs repair", - PermissibleValue(text="needs repair")) - setattr(cls, "visible signs of mold/mildew", - PermissibleValue(text="visible signs of mold/mildew")) - -class ExtWindowOrientEnum(EnumDefinitionImpl): - - north = PermissibleValue(text="north") - south = PermissibleValue(text="south") - east = PermissibleValue(text="east") - west = PermissibleValue(text="west") - northeast = PermissibleValue(text="northeast") - southeast = PermissibleValue(text="southeast") - southwest = PermissibleValue(text="southwest") - northwest = PermissibleValue(text="northwest") - - _defn = EnumDefinition( - name="ExtWindowOrientEnum", - ) + setattr(cls, "North side", + PermissibleValue(text="North side")) + setattr(cls, "West side", + PermissibleValue(text="West side")) + setattr(cls, "South side", + PermissibleValue(text="South side")) + setattr(cls, "East side", + PermissibleValue(text="East side")) -class IndoorSpaceEnum(EnumDefinitionImpl): +class WallTextureEnum(EnumDefinitionImpl): - bedroom = PermissibleValue(text="bedroom") - office = PermissibleValue(text="office") - bathroom = PermissibleValue(text="bathroom") - foyer = PermissibleValue(text="foyer") - kitchen = PermissibleValue(text="kitchen") - hallway = PermissibleValue(text="hallway") - elevator = PermissibleValue(text="elevator") + knockdown = PermissibleValue(text="knockdown") + popcorn = PermissibleValue(text="popcorn") + smooth = PermissibleValue(text="smooth") + swirl = PermissibleValue(text="swirl") _defn = EnumDefinition( - name="IndoorSpaceEnum", + name="WallTextureEnum", ) @classmethod def _addvals(cls): - setattr(cls, "locker room", - PermissibleValue(text="locker room")) - -class FloorCondEnum(EnumDefinitionImpl): + setattr(cls, "crows feet", + PermissibleValue(text="crows feet")) + setattr(cls, "crows-foot stomp", + PermissibleValue(text="crows-foot stomp")) + setattr(cls, "", + PermissibleValue(text="")) + setattr(cls, "double skip", + PermissibleValue(text="double skip")) + setattr(cls, "hawk and trowel", + PermissibleValue(text="hawk and trowel")) + setattr(cls, "orange peel", + PermissibleValue(text="orange peel")) + setattr(cls, "rosebud stomp", + PermissibleValue(text="rosebud stomp")) + setattr(cls, "Santa-Fe texture", + PermissibleValue(text="Santa-Fe texture")) + setattr(cls, "skip trowel", + PermissibleValue(text="skip trowel")) + setattr(cls, "stomp knockdown", + PermissibleValue(text="stomp knockdown")) - new = PermissibleValue(text="new") - damaged = PermissibleValue(text="damaged") - rupture = PermissibleValue(text="rupture") +class HeatCoolTypeEnum(EnumDefinitionImpl): _defn = EnumDefinition( - name="FloorCondEnum", + name="HeatCoolTypeEnum", ) @classmethod def _addvals(cls): - setattr(cls, "visible wear", - PermissibleValue(text="visible wear")) - setattr(cls, "needs repair", - PermissibleValue(text="needs repair")) + setattr(cls, "radiant system", + PermissibleValue(text="radiant system")) + setattr(cls, "heat pump", + PermissibleValue(text="heat pump")) + setattr(cls, "forced air system", + PermissibleValue(text="forced air system")) + setattr(cls, "steam forced heat", + PermissibleValue(text="steam forced heat")) + setattr(cls, "wood stove", + PermissibleValue(text="wood stove")) class SampFloorEnum(EnumDefinitionImpl): @@ -11953,122 +11966,118 @@ def _addvals(cls): setattr(cls, "2nd floor", PermissibleValue(text="2nd floor")) -class FilterTypeEnum(EnumDefinitionImpl): +class WallLocEnum(EnumDefinitionImpl): - HEPA = PermissibleValue(text="HEPA") - electrostatic = PermissibleValue(text="electrostatic") + north = PermissibleValue(text="north") + south = PermissibleValue(text="south") + east = PermissibleValue(text="east") + west = PermissibleValue(text="west") _defn = EnumDefinition( - name="FilterTypeEnum", + name="WallLocEnum", ) - @classmethod - def _addvals(cls): - setattr(cls, "particulate air filter", - PermissibleValue(text="particulate air filter")) - setattr(cls, "chemical air filter", - PermissibleValue(text="chemical air filter")) - setattr(cls, "low-MERV pleated media", - PermissibleValue(text="low-MERV pleated media")) - setattr(cls, "gas-phase or ultraviolet air treatments", - PermissibleValue(text="gas-phase or ultraviolet air treatments")) - -class TrainStopLocEnum(EnumDefinitionImpl): +class DoorMoveEnum(EnumDefinitionImpl): - end = PermissibleValue(text="end") - mid = PermissibleValue(text="mid") - downtown = PermissibleValue(text="downtown") + collapsible = PermissibleValue(text="collapsible") + folding = PermissibleValue(text="folding") + revolving = PermissibleValue(text="revolving") + sliding = PermissibleValue(text="sliding") + swinging = PermissibleValue(text="swinging") _defn = EnumDefinition( - name="TrainStopLocEnum", + name="DoorMoveEnum", ) -class FloorFinishMatEnum(EnumDefinitionImpl): + @classmethod + def _addvals(cls): + setattr(cls, "rolling shutter", + PermissibleValue(text="rolling shutter")) - tile = PermissibleValue(text="tile") - carpet = PermissibleValue(text="carpet") - rug = PermissibleValue(text="rug") - lineoleum = PermissibleValue(text="lineoleum") - stone = PermissibleValue(text="stone") - bamboo = PermissibleValue(text="bamboo") - cork = PermissibleValue(text="cork") - terrazo = PermissibleValue(text="terrazo") - concrete = PermissibleValue(text="concrete") - none = PermissibleValue(text="none") - sealed = PermissibleValue(text="sealed") - paint = PermissibleValue(text="paint") +class WallConstTypeEnum(EnumDefinitionImpl): _defn = EnumDefinition( - name="FloorFinishMatEnum", + name="WallConstTypeEnum", ) @classmethod def _addvals(cls): - setattr(cls, "wood strip or parquet", - PermissibleValue(text="wood strip or parquet")) - setattr(cls, "laminate wood", - PermissibleValue(text="laminate wood")) - setattr(cls, "vinyl composition tile", - PermissibleValue(text="vinyl composition tile")) - setattr(cls, "sheet vinyl", - PermissibleValue(text="sheet vinyl")) - setattr(cls, "clear finish", - PermissibleValue(text="clear finish")) - setattr(cls, "none or unfinished", - PermissibleValue(text="none or unfinished")) + setattr(cls, "frame construction", + PermissibleValue(text="frame construction")) + setattr(cls, "joisted masonry", + PermissibleValue(text="joisted masonry")) + setattr(cls, "light noncombustible", + PermissibleValue(text="light noncombustible")) + setattr(cls, "masonry noncombustible", + PermissibleValue(text="masonry noncombustible")) + setattr(cls, "modified fire resistive", + PermissibleValue(text="modified fire resistive")) + setattr(cls, "fire resistive", + PermissibleValue(text="fire resistive")) -class SeasonUseEnum(EnumDefinitionImpl): +class HandidnessEnum(EnumDefinitionImpl): - Spring = PermissibleValue(text="Spring") - Summer = PermissibleValue(text="Summer") - Fall = PermissibleValue(text="Fall") - Winter = PermissibleValue(text="Winter") + ambidexterity = PermissibleValue(text="ambidexterity") _defn = EnumDefinition( - name="SeasonUseEnum", + name="HandidnessEnum", ) -class FurnitureEnum(EnumDefinitionImpl): + @classmethod + def _addvals(cls): + setattr(cls, "left handedness", + PermissibleValue(text="left handedness")) + setattr(cls, "mixed-handedness", + PermissibleValue(text="mixed-handedness")) + setattr(cls, "right handedness", + PermissibleValue(text="right handedness")) - cabinet = PermissibleValue(text="cabinet") - chair = PermissibleValue(text="chair") - desks = PermissibleValue(text="desks") +class VisMediaEnum(EnumDefinitionImpl): + + photos = PermissibleValue(text="photos") + videos = PermissibleValue(text="videos") + interiors = PermissibleValue(text="interiors") + equipment = PermissibleValue(text="equipment") _defn = EnumDefinition( - name="FurnitureEnum", + name="VisMediaEnum", ) -class QuadPosEnum(EnumDefinitionImpl): + @classmethod + def _addvals(cls): + setattr(cls, "commonly of the building", + PermissibleValue(text="commonly of the building")) + setattr(cls, "site context (adjacent buildings, vegetation, terrain, streets)", + PermissibleValue(text="site context (adjacent buildings, vegetation, terrain, streets)")) + setattr(cls, "3D scans", + PermissibleValue(text="3D scans")) + +class RoomLocEnum(EnumDefinitionImpl): _defn = EnumDefinition( - name="QuadPosEnum", + name="RoomLocEnum", ) @classmethod def _addvals(cls): - setattr(cls, "North side", - PermissibleValue(text="North side")) - setattr(cls, "West side", - PermissibleValue(text="West side")) - setattr(cls, "South side", - PermissibleValue(text="South side")) - setattr(cls, "East side", - PermissibleValue(text="East side")) + setattr(cls, "corner room", + PermissibleValue(text="corner room")) + setattr(cls, "interior room", + PermissibleValue(text="interior room")) + setattr(cls, "exterior wall", + PermissibleValue(text="exterior wall")) -class SubstructureTypeEnum(EnumDefinitionImpl): +class HeatDelivLocEnum(EnumDefinitionImpl): - crawlspace = PermissibleValue(text="crawlspace") - basement = PermissibleValue(text="basement") + north = PermissibleValue(text="north") + south = PermissibleValue(text="south") + east = PermissibleValue(text="east") + west = PermissibleValue(text="west") _defn = EnumDefinition( - name="SubstructureTypeEnum", + name="HeatDelivLocEnum", ) - @classmethod - def _addvals(cls): - setattr(cls, "slab on grade", - PermissibleValue(text="slab on grade")) - class IndoorSurfEnum(EnumDefinitionImpl): cabinet = PermissibleValue(text="cabinet") @@ -12089,96 +12098,77 @@ def _addvals(cls): setattr(cls, "vent cover", PermissibleValue(text="vent cover")) -class CeilFinishMatEnum(EnumDefinitionImpl): +class TrainLineEnum(EnumDefinitionImpl): - drywall = PermissibleValue(text="drywall") - tiles = PermissibleValue(text="tiles") - PVC = PermissibleValue(text="PVC") - plasterboard = PermissibleValue(text="plasterboard") - metal = PermissibleValue(text="metal") - fiberglass = PermissibleValue(text="fiberglass") - stucco = PermissibleValue(text="stucco") - wood = PermissibleValue(text="wood") + red = PermissibleValue(text="red") + green = PermissibleValue(text="green") + orange = PermissibleValue(text="orange") _defn = EnumDefinition( - name="CeilFinishMatEnum", + name="TrainLineEnum", ) - @classmethod - def _addvals(cls): - setattr(cls, "mineral fibre", - PermissibleValue(text="mineral fibre")) - setattr(cls, "mineral wool/calcium silicate", - PermissibleValue(text="mineral wool/calcium silicate")) - -class GenderRestroomEnum(EnumDefinitionImpl): +class TrainStatLocEnum(EnumDefinitionImpl): - female = PermissibleValue(text="female") - male = PermissibleValue(text="male") - unisex = PermissibleValue(text="unisex") + riverside = PermissibleValue(text="riverside") _defn = EnumDefinition( - name="GenderRestroomEnum", + name="TrainStatLocEnum", ) @classmethod def _addvals(cls): - setattr(cls, "all gender", - PermissibleValue(text="all gender")) - setattr(cls, "gender neurtral", - PermissibleValue(text="gender neurtral")) - setattr(cls, "male and female", - PermissibleValue(text="male and female")) - -class WindowHorizPosEnum(EnumDefinitionImpl): - - left = PermissibleValue(text="left") - middle = PermissibleValue(text="middle") - right = PermissibleValue(text="right") - - _defn = EnumDefinition( - name="WindowHorizPosEnum", - ) + setattr(cls, "south station above ground", + PermissibleValue(text="south station above ground")) + setattr(cls, "south station underground", + PermissibleValue(text="south station underground")) + setattr(cls, "south station amtrak", + PermissibleValue(text="south station amtrak")) + setattr(cls, "forest hills", + PermissibleValue(text="forest hills")) -class WindowVertPosEnum(EnumDefinitionImpl): +class HcrEnum(EnumDefinitionImpl): - bottom = PermissibleValue(text="bottom") - middle = PermissibleValue(text="middle") - top = PermissibleValue(text="top") - low = PermissibleValue(text="low") - high = PermissibleValue(text="high") + Coalbed = PermissibleValue(text="Coalbed") + Shale = PermissibleValue(text="Shale") + other = PermissibleValue(text="other") _defn = EnumDefinition( - name="WindowVertPosEnum", + name="HcrEnum", ) -class ArchStrucEnum(EnumDefinitionImpl): - - building = PermissibleValue(text="building") - shed = PermissibleValue(text="shed") - home = PermissibleValue(text="home") - - _defn = EnumDefinition( - name="ArchStrucEnum", - ) + @classmethod + def _addvals(cls): + setattr(cls, "Oil Reservoir", + PermissibleValue(text="Oil Reservoir")) + setattr(cls, "Gas Reservoir", + PermissibleValue(text="Gas Reservoir")) + setattr(cls, "Oil Sand", + PermissibleValue(text="Oil Sand")) + setattr(cls, "Tight Oil Reservoir", + PermissibleValue(text="Tight Oil Reservoir")) + setattr(cls, "Tight Gas Reservoir", + PermissibleValue(text="Tight Gas Reservoir")) -class HcProducedEnum(EnumDefinitionImpl): +class SampCollectPointEnum(EnumDefinitionImpl): - Oil = PermissibleValue(text="Oil") - Gas = PermissibleValue(text="Gas") - Bitumen = PermissibleValue(text="Bitumen") + well = PermissibleValue(text="well") + wellhead = PermissibleValue(text="wellhead") + separator = PermissibleValue(text="separator") other = PermissibleValue(text="other") _defn = EnumDefinition( - name="HcProducedEnum", + name="SampCollectPointEnum", ) @classmethod def _addvals(cls): - setattr(cls, "Gas-Condensate", - PermissibleValue(text="Gas-Condensate")) - setattr(cls, "Coalbed Methane", - PermissibleValue(text="Coalbed Methane")) + setattr(cls, "test well", + PermissibleValue(text="test well")) + setattr(cls, "drilling rig", + PermissibleValue(text="drilling rig")) + setattr(cls, "storage tank", + PermissibleValue(text="storage tank")) class HcrGeolAgeEnum(EnumDefinitionImpl): @@ -12205,25 +12195,71 @@ class HcrGeolAgeEnum(EnumDefinitionImpl): name="HcrGeolAgeEnum", ) -class SampCollectPointEnum(EnumDefinitionImpl): +class OxyStatSampEnum(EnumDefinitionImpl): - well = PermissibleValue(text="well") - wellhead = PermissibleValue(text="wellhead") - separator = PermissibleValue(text="separator") + aerobic = PermissibleValue(text="aerobic") + anaerobic = PermissibleValue(text="anaerobic") other = PermissibleValue(text="other") _defn = EnumDefinition( - name="SampCollectPointEnum", + name="OxyStatSampEnum", + ) + +class LithologyEnum(EnumDefinitionImpl): + + Basement = PermissibleValue(text="Basement") + Chalk = PermissibleValue(text="Chalk") + Chert = PermissibleValue(text="Chert") + Coal = PermissibleValue(text="Coal") + Conglomerate = PermissibleValue(text="Conglomerate") + Diatomite = PermissibleValue(text="Diatomite") + Dolomite = PermissibleValue(text="Dolomite") + Limestone = PermissibleValue(text="Limestone") + Sandstone = PermissibleValue(text="Sandstone") + Shale = PermissibleValue(text="Shale") + Siltstone = PermissibleValue(text="Siltstone") + Volcanic = PermissibleValue(text="Volcanic") + other = PermissibleValue(text="other") + + _defn = EnumDefinition( + name="LithologyEnum", + ) + +class HcProducedEnum(EnumDefinitionImpl): + + Oil = PermissibleValue(text="Oil") + Gas = PermissibleValue(text="Gas") + Bitumen = PermissibleValue(text="Bitumen") + other = PermissibleValue(text="other") + + _defn = EnumDefinition( + name="HcProducedEnum", ) @classmethod def _addvals(cls): - setattr(cls, "test well", - PermissibleValue(text="test well")) - setattr(cls, "drilling rig", - PermissibleValue(text="drilling rig")) - setattr(cls, "storage tank", - PermissibleValue(text="storage tank")) + setattr(cls, "Gas-Condensate", + PermissibleValue(text="Gas-Condensate")) + setattr(cls, "Coalbed Methane", + PermissibleValue(text="Coalbed Methane")) + +class SampSubtypeEnum(EnumDefinitionImpl): + + biofilm = PermissibleValue(text="biofilm") + other = PermissibleValue(text="other") + + _defn = EnumDefinition( + name="SampSubtypeEnum", + ) + + @classmethod + def _addvals(cls): + setattr(cls, "oil phase", + PermissibleValue(text="oil phase")) + setattr(cls, "water phase", + PermissibleValue(text="water phase")) + setattr(cls, "not applicable", + PermissibleValue(text="not applicable")) class DeposEnvEnum(EnumDefinitionImpl): @@ -12252,89 +12288,49 @@ def _addvals(cls): setattr(cls, "Transitional - Beach", PermissibleValue(text="Transitional - Beach")) setattr(cls, "Transitional - Lake", - PermissibleValue(text="Transitional - Lake")) - setattr(cls, "Marine - Shallow", - PermissibleValue(text="Marine - Shallow")) - setattr(cls, "Marine - Deep", - PermissibleValue(text="Marine - Deep")) - setattr(cls, "Marine - Reef", - PermissibleValue(text="Marine - Reef")) - setattr(cls, "Other - Evaporite", - PermissibleValue(text="Other - Evaporite")) - setattr(cls, "Other - Glacial", - PermissibleValue(text="Other - Glacial")) - setattr(cls, "Other - Volcanic", - PermissibleValue(text="Other - Volcanic")) - -class OxyStatSampEnum(EnumDefinitionImpl): - - aerobic = PermissibleValue(text="aerobic") - anaerobic = PermissibleValue(text="anaerobic") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="OxyStatSampEnum", - ) - -class HcrEnum(EnumDefinitionImpl): - - Coalbed = PermissibleValue(text="Coalbed") - Shale = PermissibleValue(text="Shale") - other = PermissibleValue(text="other") - - _defn = EnumDefinition( - name="HcrEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "Oil Reservoir", - PermissibleValue(text="Oil Reservoir")) - setattr(cls, "Gas Reservoir", - PermissibleValue(text="Gas Reservoir")) - setattr(cls, "Oil Sand", - PermissibleValue(text="Oil Sand")) - setattr(cls, "Tight Oil Reservoir", - PermissibleValue(text="Tight Oil Reservoir")) - setattr(cls, "Tight Gas Reservoir", - PermissibleValue(text="Tight Gas Reservoir")) + PermissibleValue(text="Transitional - Lake")) + setattr(cls, "Marine - Shallow", + PermissibleValue(text="Marine - Shallow")) + setattr(cls, "Marine - Deep", + PermissibleValue(text="Marine - Deep")) + setattr(cls, "Marine - Reef", + PermissibleValue(text="Marine - Reef")) + setattr(cls, "Other - Evaporite", + PermissibleValue(text="Other - Evaporite")) + setattr(cls, "Other - Glacial", + PermissibleValue(text="Other - Glacial")) + setattr(cls, "Other - Volcanic", + PermissibleValue(text="Other - Volcanic")) -class SampSubtypeEnum(EnumDefinitionImpl): +class SrKerogTypeEnum(EnumDefinitionImpl): - biofilm = PermissibleValue(text="biofilm") other = PermissibleValue(text="other") _defn = EnumDefinition( - name="SampSubtypeEnum", + name="SrKerogTypeEnum", ) @classmethod def _addvals(cls): - setattr(cls, "oil phase", - PermissibleValue(text="oil phase")) - setattr(cls, "water phase", - PermissibleValue(text="water phase")) - setattr(cls, "not applicable", - PermissibleValue(text="not applicable")) + setattr(cls, "Type I", + PermissibleValue(text="Type I")) + setattr(cls, "Type II", + PermissibleValue(text="Type II")) + setattr(cls, "Type III", + PermissibleValue(text="Type III")) + setattr(cls, "Type IV", + PermissibleValue(text="Type IV")) -class LithologyEnum(EnumDefinitionImpl): +class SrLithologyEnum(EnumDefinitionImpl): - Basement = PermissibleValue(text="Basement") - Chalk = PermissibleValue(text="Chalk") - Chert = PermissibleValue(text="Chert") + Clastic = PermissibleValue(text="Clastic") + Carbonate = PermissibleValue(text="Carbonate") Coal = PermissibleValue(text="Coal") - Conglomerate = PermissibleValue(text="Conglomerate") - Diatomite = PermissibleValue(text="Diatomite") - Dolomite = PermissibleValue(text="Dolomite") - Limestone = PermissibleValue(text="Limestone") - Sandstone = PermissibleValue(text="Sandstone") - Shale = PermissibleValue(text="Shale") - Siltstone = PermissibleValue(text="Siltstone") - Volcanic = PermissibleValue(text="Volcanic") + Biosilicieous = PermissibleValue(text="Biosilicieous") other = PermissibleValue(text="other") _defn = EnumDefinition( - name="LithologyEnum", + name="SrLithologyEnum", ) class SrGeolAgeEnum(EnumDefinitionImpl): @@ -12374,35 +12370,49 @@ class SrDepEnvEnum(EnumDefinitionImpl): name="SrDepEnvEnum", ) -class SrKerogTypeEnum(EnumDefinitionImpl): +class ProfilePositionEnum(EnumDefinitionImpl): - other = PermissibleValue(text="other") + summit = PermissibleValue(text="summit") + shoulder = PermissibleValue(text="shoulder") + backslope = PermissibleValue(text="backslope") + footslope = PermissibleValue(text="footslope") + toeslope = PermissibleValue(text="toeslope") _defn = EnumDefinition( - name="SrKerogTypeEnum", + name="ProfilePositionEnum", ) - @classmethod - def _addvals(cls): - setattr(cls, "Type I", - PermissibleValue(text="Type I")) - setattr(cls, "Type II", - PermissibleValue(text="Type II")) - setattr(cls, "Type III", - PermissibleValue(text="Type III")) - setattr(cls, "Type IV", - PermissibleValue(text="Type IV")) - -class SrLithologyEnum(EnumDefinitionImpl): +class FaoClassEnum(EnumDefinitionImpl): - Clastic = PermissibleValue(text="Clastic") - Carbonate = PermissibleValue(text="Carbonate") - Coal = PermissibleValue(text="Coal") - Biosilicieous = PermissibleValue(text="Biosilicieous") - other = PermissibleValue(text="other") + Acrisols = PermissibleValue(text="Acrisols") + Andosols = PermissibleValue(text="Andosols") + Arenosols = PermissibleValue(text="Arenosols") + Cambisols = PermissibleValue(text="Cambisols") + Chernozems = PermissibleValue(text="Chernozems") + Ferralsols = PermissibleValue(text="Ferralsols") + Fluvisols = PermissibleValue(text="Fluvisols") + Gleysols = PermissibleValue(text="Gleysols") + Greyzems = PermissibleValue(text="Greyzems") + Gypsisols = PermissibleValue(text="Gypsisols") + Histosols = PermissibleValue(text="Histosols") + Kastanozems = PermissibleValue(text="Kastanozems") + Lithosols = PermissibleValue(text="Lithosols") + Luvisols = PermissibleValue(text="Luvisols") + Nitosols = PermissibleValue(text="Nitosols") + Phaeozems = PermissibleValue(text="Phaeozems") + Planosols = PermissibleValue(text="Planosols") + Podzols = PermissibleValue(text="Podzols") + Podzoluvisols = PermissibleValue(text="Podzoluvisols") + Rankers = PermissibleValue(text="Rankers") + Regosols = PermissibleValue(text="Regosols") + Rendzinas = PermissibleValue(text="Rendzinas") + Solonchaks = PermissibleValue(text="Solonchaks") + Solonetz = PermissibleValue(text="Solonetz") + Vertisols = PermissibleValue(text="Vertisols") + Yermosols = PermissibleValue(text="Yermosols") _defn = EnumDefinition( - name="SrLithologyEnum", + name="FaoClassEnum", ) class BioticRelationshipEnum(EnumDefinitionImpl): @@ -12420,88 +12430,6 @@ def _addvals(cls): setattr(cls, "free living", PermissibleValue(text="free living")) -class DrainageClassEnum(EnumDefinitionImpl): - - poorly = PermissibleValue(text="poorly") - well = PermissibleValue(text="well") - - _defn = EnumDefinition( - name="DrainageClassEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "very poorly", - PermissibleValue(text="very poorly")) - setattr(cls, "somewhat poorly", - PermissibleValue(text="somewhat poorly")) - setattr(cls, "moderately well", - PermissibleValue(text="moderately well")) - setattr(cls, "excessively drained", - PermissibleValue(text="excessively drained")) - -class CurLandUseEnum(EnumDefinitionImpl): - - badlands = PermissibleValue(text="badlands") - cities = PermissibleValue(text="cities") - conifers = PermissibleValue(text="conifers") - farmstead = PermissibleValue(text="farmstead") - gravel = PermissibleValue(text="gravel") - hardwoods = PermissibleValue(text="hardwoods") - hayland = PermissibleValue(text="hayland") - marshlands = PermissibleValue(text="marshlands") - meadows = PermissibleValue(text="meadows") - mudflats = PermissibleValue(text="mudflats") - pastureland = PermissibleValue(text="pastureland") - rainforest = PermissibleValue(text="rainforest") - rangeland = PermissibleValue(text="rangeland") - rock = PermissibleValue(text="rock") - sand = PermissibleValue(text="sand") - swamp = PermissibleValue(text="swamp") - tropical = PermissibleValue(text="tropical") - tundra = PermissibleValue(text="tundra") - - _defn = EnumDefinition( - name="CurLandUseEnum", - ) - - @classmethod - def _addvals(cls): - setattr(cls, "crop trees", - PermissibleValue(text="crop trees")) - setattr(cls, "horticultural plants", - PermissibleValue(text="horticultural plants")) - setattr(cls, "industrial areas", - PermissibleValue(text="industrial areas")) - setattr(cls, "intermixed hardwood and conifers", - PermissibleValue(text="intermixed hardwood and conifers")) - setattr(cls, "mines/quarries", - PermissibleValue(text="mines/quarries")) - setattr(cls, "oil waste areas", - PermissibleValue(text="oil waste areas")) - setattr(cls, "permanent snow or ice", - PermissibleValue(text="permanent snow or ice")) - setattr(cls, "roads/railroads", - PermissibleValue(text="roads/railroads")) - setattr(cls, "row crops", - PermissibleValue(text="row crops")) - setattr(cls, "saline seeps", - PermissibleValue(text="saline seeps")) - setattr(cls, "salt flats", - PermissibleValue(text="salt flats")) - setattr(cls, "shrub crops", - PermissibleValue(text="shrub crops")) - setattr(cls, "shrub land", - PermissibleValue(text="shrub land")) - setattr(cls, "small grains", - PermissibleValue(text="small grains")) - setattr(cls, "successional shrub land", - PermissibleValue(text="successional shrub land")) - setattr(cls, "vegetable crops", - PermissibleValue(text="vegetable crops")) - setattr(cls, "vine crops", - PermissibleValue(text="vine crops")) - class SoilHorizonEnum(EnumDefinitionImpl): Permafrost = PermissibleValue(text="Permafrost") @@ -12527,18 +12455,26 @@ def _addvals(cls): setattr(cls, "M horizon", PermissibleValue(text="M horizon")) -class ProfilePositionEnum(EnumDefinitionImpl): +class DrainageClassEnum(EnumDefinitionImpl): - summit = PermissibleValue(text="summit") - shoulder = PermissibleValue(text="shoulder") - backslope = PermissibleValue(text="backslope") - footslope = PermissibleValue(text="footslope") - toeslope = PermissibleValue(text="toeslope") + poorly = PermissibleValue(text="poorly") + well = PermissibleValue(text="well") _defn = EnumDefinition( - name="ProfilePositionEnum", + name="DrainageClassEnum", ) + @classmethod + def _addvals(cls): + setattr(cls, "very poorly", + PermissibleValue(text="very poorly")) + setattr(cls, "somewhat poorly", + PermissibleValue(text="somewhat poorly")) + setattr(cls, "moderately well", + PermissibleValue(text="moderately well")) + setattr(cls, "excessively drained", + PermissibleValue(text="excessively drained")) + class TillageEnum(EnumDefinitionImpl): drill = PermissibleValue(text="drill") @@ -12550,70 +12486,80 @@ class TillageEnum(EnumDefinitionImpl): name="TillageEnum", ) - @classmethod - def _addvals(cls): - setattr(cls, "cutting disc", - PermissibleValue(text="cutting disc")) - setattr(cls, "ridge till", - PermissibleValue(text="ridge till")) - setattr(cls, "strip tillage", - PermissibleValue(text="strip tillage")) - setattr(cls, "zonal tillage", - PermissibleValue(text="zonal tillage")) - setattr(cls, "disc plough", - PermissibleValue(text="disc plough")) - -class FaoClassEnum(EnumDefinitionImpl): - - Acrisols = PermissibleValue(text="Acrisols") - Andosols = PermissibleValue(text="Andosols") - Arenosols = PermissibleValue(text="Arenosols") - Cambisols = PermissibleValue(text="Cambisols") - Chernozems = PermissibleValue(text="Chernozems") - Ferralsols = PermissibleValue(text="Ferralsols") - Fluvisols = PermissibleValue(text="Fluvisols") - Gleysols = PermissibleValue(text="Gleysols") - Greyzems = PermissibleValue(text="Greyzems") - Gypsisols = PermissibleValue(text="Gypsisols") - Histosols = PermissibleValue(text="Histosols") - Kastanozems = PermissibleValue(text="Kastanozems") - Lithosols = PermissibleValue(text="Lithosols") - Luvisols = PermissibleValue(text="Luvisols") - Nitosols = PermissibleValue(text="Nitosols") - Phaeozems = PermissibleValue(text="Phaeozems") - Planosols = PermissibleValue(text="Planosols") - Podzols = PermissibleValue(text="Podzols") - Podzoluvisols = PermissibleValue(text="Podzoluvisols") - Rankers = PermissibleValue(text="Rankers") - Regosols = PermissibleValue(text="Regosols") - Rendzinas = PermissibleValue(text="Rendzinas") - Solonchaks = PermissibleValue(text="Solonchaks") - Solonetz = PermissibleValue(text="Solonetz") - Vertisols = PermissibleValue(text="Vertisols") - Yermosols = PermissibleValue(text="Yermosols") - - _defn = EnumDefinition( - name="FaoClassEnum", - ) - -class SampCaptStatusEnum(EnumDefinitionImpl): + @classmethod + def _addvals(cls): + setattr(cls, "cutting disc", + PermissibleValue(text="cutting disc")) + setattr(cls, "ridge till", + PermissibleValue(text="ridge till")) + setattr(cls, "strip tillage", + PermissibleValue(text="strip tillage")) + setattr(cls, "zonal tillage", + PermissibleValue(text="zonal tillage")) + setattr(cls, "disc plough", + PermissibleValue(text="disc plough")) - other = PermissibleValue(text="other") +class CurLandUseEnum(EnumDefinitionImpl): + + badlands = PermissibleValue(text="badlands") + cities = PermissibleValue(text="cities") + conifers = PermissibleValue(text="conifers") + farmstead = PermissibleValue(text="farmstead") + gravel = PermissibleValue(text="gravel") + hardwoods = PermissibleValue(text="hardwoods") + hayland = PermissibleValue(text="hayland") + marshlands = PermissibleValue(text="marshlands") + meadows = PermissibleValue(text="meadows") + mudflats = PermissibleValue(text="mudflats") + pastureland = PermissibleValue(text="pastureland") + rainforest = PermissibleValue(text="rainforest") + rangeland = PermissibleValue(text="rangeland") + rock = PermissibleValue(text="rock") + sand = PermissibleValue(text="sand") + swamp = PermissibleValue(text="swamp") + tropical = PermissibleValue(text="tropical") + tundra = PermissibleValue(text="tundra") _defn = EnumDefinition( - name="SampCaptStatusEnum", + name="CurLandUseEnum", ) @classmethod def _addvals(cls): - setattr(cls, "active surveillance in response to an outbreak", - PermissibleValue(text="active surveillance in response to an outbreak")) - setattr(cls, "active surveillance not initiated by an outbreak", - PermissibleValue(text="active surveillance not initiated by an outbreak")) - setattr(cls, "farm sample", - PermissibleValue(text="farm sample")) - setattr(cls, "market sample", - PermissibleValue(text="market sample")) + setattr(cls, "crop trees", + PermissibleValue(text="crop trees")) + setattr(cls, "horticultural plants", + PermissibleValue(text="horticultural plants")) + setattr(cls, "industrial areas", + PermissibleValue(text="industrial areas")) + setattr(cls, "intermixed hardwood and conifers", + PermissibleValue(text="intermixed hardwood and conifers")) + setattr(cls, "mines/quarries", + PermissibleValue(text="mines/quarries")) + setattr(cls, "oil waste areas", + PermissibleValue(text="oil waste areas")) + setattr(cls, "permanent snow or ice", + PermissibleValue(text="permanent snow or ice")) + setattr(cls, "roads/railroads", + PermissibleValue(text="roads/railroads")) + setattr(cls, "row crops", + PermissibleValue(text="row crops")) + setattr(cls, "saline seeps", + PermissibleValue(text="saline seeps")) + setattr(cls, "salt flats", + PermissibleValue(text="salt flats")) + setattr(cls, "shrub crops", + PermissibleValue(text="shrub crops")) + setattr(cls, "shrub land", + PermissibleValue(text="shrub land")) + setattr(cls, "small grains", + PermissibleValue(text="small grains")) + setattr(cls, "successional shrub land", + PermissibleValue(text="successional shrub land")) + setattr(cls, "vegetable crops", + PermissibleValue(text="vegetable crops")) + setattr(cls, "vine crops", + PermissibleValue(text="vine crops")) class PlantSexEnum(EnumDefinitionImpl): @@ -12651,20 +12597,27 @@ class PlantSexEnum(EnumDefinitionImpl): name="PlantSexEnum", ) -class GrowthHabitEnum(EnumDefinitionImpl): +class BiolStatEnum(EnumDefinitionImpl): - erect = PermissibleValue(text="erect") - spreading = PermissibleValue(text="spreading") - prostrate = PermissibleValue(text="prostrate") + wild = PermissibleValue(text="wild") + natural = PermissibleValue(text="natural") + hybrid = PermissibleValue(text="hybrid") + mutant = PermissibleValue(text="mutant") _defn = EnumDefinition( - name="GrowthHabitEnum", + name="BiolStatEnum", ) @classmethod def _addvals(cls): - setattr(cls, "semi-erect", - PermissibleValue(text="semi-erect")) + setattr(cls, "semi-natural", + PermissibleValue(text="semi-natural")) + setattr(cls, "inbred line", + PermissibleValue(text="inbred line")) + setattr(cls, "breeder's line", + PermissibleValue(text="breeder's line")) + setattr(cls, "clonal selection", + PermissibleValue(text="clonal selection")) class SampDisStageEnum(EnumDefinitionImpl): @@ -12683,44 +12636,39 @@ def _addvals(cls): setattr(cls, "growth and reproduction", PermissibleValue(text="growth and reproduction")) -class BiolStatEnum(EnumDefinitionImpl): +class SampCaptStatusEnum(EnumDefinitionImpl): - wild = PermissibleValue(text="wild") - natural = PermissibleValue(text="natural") - hybrid = PermissibleValue(text="hybrid") - mutant = PermissibleValue(text="mutant") + other = PermissibleValue(text="other") _defn = EnumDefinition( - name="BiolStatEnum", + name="SampCaptStatusEnum", ) @classmethod def _addvals(cls): - setattr(cls, "semi-natural", - PermissibleValue(text="semi-natural")) - setattr(cls, "inbred line", - PermissibleValue(text="inbred line")) - setattr(cls, "breeder's line", - PermissibleValue(text="breeder's line")) - setattr(cls, "clonal selection", - PermissibleValue(text="clonal selection")) + setattr(cls, "active surveillance in response to an outbreak", + PermissibleValue(text="active surveillance in response to an outbreak")) + setattr(cls, "active surveillance not initiated by an outbreak", + PermissibleValue(text="active surveillance not initiated by an outbreak")) + setattr(cls, "farm sample", + PermissibleValue(text="farm sample")) + setattr(cls, "market sample", + PermissibleValue(text="market sample")) -class TidalStageEnum(EnumDefinitionImpl): +class GrowthHabitEnum(EnumDefinitionImpl): + + erect = PermissibleValue(text="erect") + spreading = PermissibleValue(text="spreading") + prostrate = PermissibleValue(text="prostrate") _defn = EnumDefinition( - name="TidalStageEnum", + name="GrowthHabitEnum", ) @classmethod def _addvals(cls): - setattr(cls, "low tide", - PermissibleValue(text="low tide")) - setattr(cls, "ebb tide", - PermissibleValue(text="ebb tide")) - setattr(cls, "flood tide", - PermissibleValue(text="flood tide")) - setattr(cls, "high tide", - PermissibleValue(text="high tide")) + setattr(cls, "semi-erect", + PermissibleValue(text="semi-erect")) class SedimentTypeEnum(EnumDefinitionImpl): @@ -12733,6 +12681,23 @@ class SedimentTypeEnum(EnumDefinitionImpl): name="SedimentTypeEnum", ) +class TidalStageEnum(EnumDefinitionImpl): + + _defn = EnumDefinition( + name="TidalStageEnum", + ) + + @classmethod + def _addvals(cls): + setattr(cls, "low tide", + PermissibleValue(text="low tide")) + setattr(cls, "ebb tide", + PermissibleValue(text="ebb tide")) + setattr(cls, "flood tide", + PermissibleValue(text="flood tide")) + setattr(cls, "high tide", + PermissibleValue(text="high tide")) + class HostSexEnum(EnumDefinitionImpl): female = PermissibleValue(text="female") @@ -14546,40 +14511,40 @@ class slots: slots.zinc = Slot(uri=NMDC_SUB_SCHEMA.zinc, name="zinc", curie=NMDC_SUB_SCHEMA.curie('zinc'), model_uri=NMDC_SUB_SCHEMA.zinc, domain=None, range=Optional[str]) -slots.core_field = Slot(uri=NMDC_SUB_SCHEMA.core_field, name="core field", curie=NMDC_SUB_SCHEMA.curie('core_field'), - model_uri=NMDC_SUB_SCHEMA.core_field, domain=None, range=Optional[str]) - -slots.id = Slot(uri=NMDC_SUB_SCHEMA.id, name="id", curie=NMDC_SUB_SCHEMA.curie('id'), - model_uri=NMDC_SUB_SCHEMA.id, domain=None, range=URIRef, +slots.alternative_identifiers = Slot(uri=NMDC_SUB_SCHEMA.alternative_identifiers, name="alternative_identifiers", curie=NMDC_SUB_SCHEMA.curie('alternative_identifiers'), + model_uri=NMDC_SUB_SCHEMA.alternative_identifiers, domain=None, range=Optional[Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]], pattern=re.compile(r'^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$')) -slots.language = Slot(uri=NMDC_SUB_SCHEMA.language, name="language", curie=NMDC_SUB_SCHEMA.curie('language'), - model_uri=NMDC_SUB_SCHEMA.language, domain=None, range=Optional[str]) +slots.investigation_field = Slot(uri=NMDC_SUB_SCHEMA.investigation_field, name="investigation field", curie=NMDC_SUB_SCHEMA.curie('investigation_field'), + model_uri=NMDC_SUB_SCHEMA.investigation_field, domain=None, range=Optional[str]) slots.description = Slot(uri=DCTERMS.description, name="description", curie=DCTERMS.curie('description'), model_uri=NMDC_SUB_SCHEMA.description, domain=None, range=Optional[str]) +slots.core_field = Slot(uri=NMDC_SUB_SCHEMA.core_field, name="core field", curie=NMDC_SUB_SCHEMA.curie('core_field'), + model_uri=NMDC_SUB_SCHEMA.core_field, domain=None, range=Optional[str]) + slots.nucleic_acid_sequence_source_field = Slot(uri=NMDC_SUB_SCHEMA.nucleic_acid_sequence_source_field, name="nucleic acid sequence source field", curie=NMDC_SUB_SCHEMA.curie('nucleic_acid_sequence_source_field'), model_uri=NMDC_SUB_SCHEMA.nucleic_acid_sequence_source_field, domain=None, range=Optional[str]) -slots.environment_field = Slot(uri=NMDC_SUB_SCHEMA.environment_field, name="environment field", curie=NMDC_SUB_SCHEMA.curie('environment_field'), - model_uri=NMDC_SUB_SCHEMA.environment_field, domain=None, range=Optional[str]) +slots.id = Slot(uri=NMDC_SUB_SCHEMA.id, name="id", curie=NMDC_SUB_SCHEMA.curie('id'), + model_uri=NMDC_SUB_SCHEMA.id, domain=None, range=URIRef, + pattern=re.compile(r'^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$')) -slots.gold_path_field = Slot(uri=NMDC_SUB_SCHEMA.gold_path_field, name="gold_path_field", curie=NMDC_SUB_SCHEMA.curie('gold_path_field'), - model_uri=NMDC_SUB_SCHEMA.gold_path_field, domain=None, range=Optional[str]) +slots.language = Slot(uri=NMDC_SUB_SCHEMA.language, name="language", curie=NMDC_SUB_SCHEMA.curie('language'), + model_uri=NMDC_SUB_SCHEMA.language, domain=None, range=Optional[str]) -slots.alternative_identifiers = Slot(uri=NMDC_SUB_SCHEMA.alternative_identifiers, name="alternative_identifiers", curie=NMDC_SUB_SCHEMA.curie('alternative_identifiers'), - model_uri=NMDC_SUB_SCHEMA.alternative_identifiers, domain=None, range=Optional[Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]], - pattern=re.compile(r'^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$')) +slots.attribute = Slot(uri=NMDC_SUB_SCHEMA.attribute, name="attribute", curie=NMDC_SUB_SCHEMA.curie('attribute'), + model_uri=NMDC_SUB_SCHEMA.attribute, domain=None, range=Optional[str]) slots.name = Slot(uri=NMDC_SUB_SCHEMA.name, name="name", curie=NMDC_SUB_SCHEMA.curie('name'), model_uri=NMDC_SUB_SCHEMA.name, domain=None, range=Optional[str]) -slots.investigation_field = Slot(uri=NMDC_SUB_SCHEMA.investigation_field, name="investigation field", curie=NMDC_SUB_SCHEMA.curie('investigation_field'), - model_uri=NMDC_SUB_SCHEMA.investigation_field, domain=None, range=Optional[str]) +slots.gold_path_field = Slot(uri=NMDC_SUB_SCHEMA.gold_path_field, name="gold_path_field", curie=NMDC_SUB_SCHEMA.curie('gold_path_field'), + model_uri=NMDC_SUB_SCHEMA.gold_path_field, domain=None, range=Optional[str]) -slots.attribute = Slot(uri=NMDC_SUB_SCHEMA.attribute, name="attribute", curie=NMDC_SUB_SCHEMA.curie('attribute'), - model_uri=NMDC_SUB_SCHEMA.attribute, domain=None, range=Optional[str]) +slots.environment_field = Slot(uri=NMDC_SUB_SCHEMA.environment_field, name="environment field", curie=NMDC_SUB_SCHEMA.curie('environment_field'), + model_uri=NMDC_SUB_SCHEMA.environment_field, domain=None, range=Optional[str]) slots.biomaterial_purity = Slot(uri=NMDC_SUB_SCHEMA.biomaterial_purity, name="biomaterial_purity", curie=NMDC_SUB_SCHEMA.curie('biomaterial_purity'), model_uri=NMDC_SUB_SCHEMA.biomaterial_purity, domain=None, range=Optional[str]) @@ -14653,9 +14618,6 @@ class slots: model_uri=NMDC_SUB_SCHEMA.AirInterface_geo_loc_name, domain=AirInterface, range=str, pattern=re.compile(r'^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$')) -slots.AirInterface_horizon_meth = Slot(uri=MIXS['0000321'], name="AirInterface_horizon_meth", curie=MIXS.curie('0000321'), - model_uri=NMDC_SUB_SCHEMA.AirInterface_horizon_meth, domain=AirInterface, range=Optional[str]) - slots.AirInterface_humidity = Slot(uri=MIXS['0000100'], name="AirInterface_humidity", curie=MIXS.curie('0000100'), model_uri=NMDC_SUB_SCHEMA.AirInterface_humidity, domain=AirInterface, range=Optional[str], pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+ +\S.*$')) @@ -14753,6 +14715,9 @@ class slots: model_uri=NMDC_SUB_SCHEMA.AirInterface_wind_speed, domain=AirInterface, range=Optional[str], pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+ +\S.*$')) +slots.AirInterface_horizon_meth = Slot(uri=MIXS['0000321'], name="AirInterface_horizon_meth", curie=MIXS.curie('0000321'), + model_uri=NMDC_SUB_SCHEMA.AirInterface_horizon_meth, domain=AirInterface, range=Optional[str]) + slots.BiofilmInterface_alkalinity = Slot(uri=MIXS['0000421'], name="BiofilmInterface_alkalinity", curie=MIXS.curie('0000421'), model_uri=NMDC_SUB_SCHEMA.BiofilmInterface_alkalinity, domain=BiofilmInterface, range=Optional[str], pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+ +\S.*$')) @@ -14886,9 +14851,6 @@ class slots: model_uri=NMDC_SUB_SCHEMA.BiofilmInterface_glucosidase_act, domain=BiofilmInterface, range=Optional[str], pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+ +\S.*$')) -slots.BiofilmInterface_horizon_meth = Slot(uri=MIXS['0000321'], name="BiofilmInterface_horizon_meth", curie=MIXS.curie('0000321'), - model_uri=NMDC_SUB_SCHEMA.BiofilmInterface_horizon_meth, domain=BiofilmInterface, range=Optional[str]) - slots.BiofilmInterface_lat_lon = Slot(uri=MIXS['0000009'], name="BiofilmInterface_lat_lon", curie=MIXS.curie('0000009'), model_uri=NMDC_SUB_SCHEMA.BiofilmInterface_lat_lon, domain=BiofilmInterface, range=str, pattern=re.compile(r'^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$')) @@ -15066,6 +15028,9 @@ class slots: model_uri=NMDC_SUB_SCHEMA.BiofilmInterface_water_content, domain=BiofilmInterface, range=Optional[str], pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?%? \S.+$')) +slots.BiofilmInterface_horizon_meth = Slot(uri=MIXS['0000321'], name="BiofilmInterface_horizon_meth", curie=MIXS.curie('0000321'), + model_uri=NMDC_SUB_SCHEMA.BiofilmInterface_horizon_meth, domain=BiofilmInterface, range=Optional[str]) + slots.BuiltEnvInterface_abs_air_humidity = Slot(uri=MIXS['0000122'], name="BuiltEnvInterface_abs_air_humidity", curie=MIXS.curie('0000122'), model_uri=NMDC_SUB_SCHEMA.BuiltEnvInterface_abs_air_humidity, domain=BuiltEnvInterface, range=Optional[str], pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+ +\S.*$')) @@ -15344,9 +15309,6 @@ class slots: model_uri=NMDC_SUB_SCHEMA.BuiltEnvInterface_height_carper_fiber, domain=BuiltEnvInterface, range=Optional[str], pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+ +\S.*$')) -slots.BuiltEnvInterface_horizon_meth = Slot(uri=MIXS['0000321'], name="BuiltEnvInterface_horizon_meth", curie=MIXS.curie('0000321'), - model_uri=NMDC_SUB_SCHEMA.BuiltEnvInterface_horizon_meth, domain=BuiltEnvInterface, range=Optional[str]) - slots.BuiltEnvInterface_indoor_space = Slot(uri=MIXS['0000763'], name="BuiltEnvInterface_indoor_space", curie=MIXS.curie('0000763'), model_uri=NMDC_SUB_SCHEMA.BuiltEnvInterface_indoor_space, domain=BuiltEnvInterface, range=Optional[Union[str, "IndoorSpaceEnum"]]) @@ -15658,6 +15620,9 @@ class slots: slots.BuiltEnvInterface_window_water_mold = Slot(uri=MIXS['0000854'], name="BuiltEnvInterface_window_water_mold", curie=MIXS.curie('0000854'), model_uri=NMDC_SUB_SCHEMA.BuiltEnvInterface_window_water_mold, domain=BuiltEnvInterface, range=Optional[str]) +slots.BuiltEnvInterface_horizon_meth = Slot(uri=MIXS['0000321'], name="BuiltEnvInterface_horizon_meth", curie=MIXS.curie('0000321'), + model_uri=NMDC_SUB_SCHEMA.BuiltEnvInterface_horizon_meth, domain=BuiltEnvInterface, range=Optional[str]) + slots.BuiltEnvInterface_oxy_stat_samp = Slot(uri=MIXS['0000753'], name="BuiltEnvInterface_oxy_stat_samp", curie=MIXS.curie('0000753'), model_uri=NMDC_SUB_SCHEMA.BuiltEnvInterface_oxy_stat_samp, domain=BuiltEnvInterface, range=Optional[Union[str, "OxyStatSampEnum"]]) @@ -15830,9 +15795,6 @@ class slots: slots.HcrCoresInterface_hcr_temp = Slot(uri=MIXS['0000393'], name="HcrCoresInterface_hcr_temp", curie=MIXS.curie('0000393'), model_uri=NMDC_SUB_SCHEMA.HcrCoresInterface_hcr_temp, domain=HcrCoresInterface, range=Optional[str]) -slots.HcrCoresInterface_horizon_meth = Slot(uri=MIXS['0000321'], name="HcrCoresInterface_horizon_meth", curie=MIXS.curie('0000321'), - model_uri=NMDC_SUB_SCHEMA.HcrCoresInterface_horizon_meth, domain=HcrCoresInterface, range=Optional[str]) - slots.HcrCoresInterface_lat_lon = Slot(uri=MIXS['0000009'], name="HcrCoresInterface_lat_lon", curie=MIXS.curie('0000009'), model_uri=NMDC_SUB_SCHEMA.HcrCoresInterface_lat_lon, domain=HcrCoresInterface, range=str, pattern=re.compile(r'^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$')) @@ -16048,6 +16010,9 @@ class slots: model_uri=NMDC_SUB_SCHEMA.HcrCoresInterface_xylene, domain=HcrCoresInterface, range=Optional[str], pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+ +\S.*$')) +slots.HcrCoresInterface_horizon_meth = Slot(uri=MIXS['0000321'], name="HcrCoresInterface_horizon_meth", curie=MIXS.curie('0000321'), + model_uri=NMDC_SUB_SCHEMA.HcrCoresInterface_horizon_meth, domain=HcrCoresInterface, range=Optional[str]) + slots.HcrFluidsSwabsInterface_add_recov_method = Slot(uri=MIXS['0001009'], name="HcrFluidsSwabsInterface_add_recov_method", curie=MIXS.curie('0001009'), model_uri=NMDC_SUB_SCHEMA.HcrFluidsSwabsInterface_add_recov_method, domain=HcrFluidsSwabsInterface, range=Optional[str]) @@ -16210,9 +16175,6 @@ class slots: slots.HcrFluidsSwabsInterface_hcr_temp = Slot(uri=MIXS['0000393'], name="HcrFluidsSwabsInterface_hcr_temp", curie=MIXS.curie('0000393'), model_uri=NMDC_SUB_SCHEMA.HcrFluidsSwabsInterface_hcr_temp, domain=HcrFluidsSwabsInterface, range=Optional[str]) -slots.HcrFluidsSwabsInterface_horizon_meth = Slot(uri=MIXS['0000321'], name="HcrFluidsSwabsInterface_horizon_meth", curie=MIXS.curie('0000321'), - model_uri=NMDC_SUB_SCHEMA.HcrFluidsSwabsInterface_horizon_meth, domain=HcrFluidsSwabsInterface, range=Optional[str]) - slots.HcrFluidsSwabsInterface_iw_bt_date_well = Slot(uri=MIXS['0001010'], name="HcrFluidsSwabsInterface_iw_bt_date_well", curie=MIXS.curie('0001010'), model_uri=NMDC_SUB_SCHEMA.HcrFluidsSwabsInterface_iw_bt_date_well, domain=HcrFluidsSwabsInterface, range=Optional[str]) @@ -16431,6 +16393,9 @@ class slots: model_uri=NMDC_SUB_SCHEMA.HcrFluidsSwabsInterface_xylene, domain=HcrFluidsSwabsInterface, range=Optional[str], pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+ +\S.*$')) +slots.HcrFluidsSwabsInterface_horizon_meth = Slot(uri=MIXS['0000321'], name="HcrFluidsSwabsInterface_horizon_meth", curie=MIXS.curie('0000321'), + model_uri=NMDC_SUB_SCHEMA.HcrFluidsSwabsInterface_horizon_meth, domain=HcrFluidsSwabsInterface, range=Optional[str]) + slots.HostAssociatedInterface_alt = Slot(uri=MIXS['0000094'], name="HostAssociatedInterface_alt", curie=MIXS.curie('0000094'), model_uri=NMDC_SUB_SCHEMA.HostAssociatedInterface_alt, domain=HostAssociatedInterface, range=Optional[str], pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+ +\S.*$')) @@ -16504,9 +16469,6 @@ class slots: slots.HostAssociatedInterface_gravidity = Slot(uri=MIXS['0000875'], name="HostAssociatedInterface_gravidity", curie=MIXS.curie('0000875'), model_uri=NMDC_SUB_SCHEMA.HostAssociatedInterface_gravidity, domain=HostAssociatedInterface, range=Optional[str]) -slots.HostAssociatedInterface_horizon_meth = Slot(uri=MIXS['0000321'], name="HostAssociatedInterface_horizon_meth", curie=MIXS.curie('0000321'), - model_uri=NMDC_SUB_SCHEMA.HostAssociatedInterface_horizon_meth, domain=HostAssociatedInterface, range=Optional[str]) - slots.HostAssociatedInterface_host_age = Slot(uri=MIXS['0000255'], name="HostAssociatedInterface_host_age", curie=MIXS.curie('0000255'), model_uri=NMDC_SUB_SCHEMA.HostAssociatedInterface_host_age, domain=HostAssociatedInterface, range=Optional[str], pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+ +\S.*$')) @@ -16656,6 +16618,9 @@ class slots: model_uri=NMDC_SUB_SCHEMA.HostAssociatedInterface_temp, domain=HostAssociatedInterface, range=Optional[str], pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+ +\S.*$')) +slots.HostAssociatedInterface_horizon_meth = Slot(uri=MIXS['0000321'], name="HostAssociatedInterface_horizon_meth", curie=MIXS.curie('0000321'), + model_uri=NMDC_SUB_SCHEMA.HostAssociatedInterface_horizon_meth, domain=HostAssociatedInterface, range=Optional[str]) + slots.JgiMgInterface_dna_absorb1 = Slot(uri=NMDC['nmdc/dna_absorb1'], name="JgiMgInterface_dna_absorb1", curie=NMDC.curie('nmdc/dna_absorb1'), model_uri=NMDC_SUB_SCHEMA.JgiMgInterface_dna_absorb1, domain=JgiMgInterface, range=Optional[float]) @@ -16877,9 +16842,6 @@ class slots: model_uri=NMDC_SUB_SCHEMA.MiscEnvsInterface_geo_loc_name, domain=MiscEnvsInterface, range=str, pattern=re.compile(r'^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$')) -slots.MiscEnvsInterface_horizon_meth = Slot(uri=MIXS['0000321'], name="MiscEnvsInterface_horizon_meth", curie=MIXS.curie('0000321'), - model_uri=NMDC_SUB_SCHEMA.MiscEnvsInterface_horizon_meth, domain=MiscEnvsInterface, range=Optional[str]) - slots.MiscEnvsInterface_lat_lon = Slot(uri=MIXS['0000009'], name="MiscEnvsInterface_lat_lon", curie=MIXS.curie('0000009'), model_uri=NMDC_SUB_SCHEMA.MiscEnvsInterface_lat_lon, domain=MiscEnvsInterface, range=str, pattern=re.compile(r'^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$')) @@ -17005,6 +16967,9 @@ class slots: model_uri=NMDC_SUB_SCHEMA.MiscEnvsInterface_water_current, domain=MiscEnvsInterface, range=Optional[str], pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+ +\S.*$')) +slots.MiscEnvsInterface_horizon_meth = Slot(uri=MIXS['0000321'], name="MiscEnvsInterface_horizon_meth", curie=MIXS.curie('0000321'), + model_uri=NMDC_SUB_SCHEMA.MiscEnvsInterface_horizon_meth, domain=MiscEnvsInterface, range=Optional[str]) + slots.PlantAssociatedInterface_air_temp_regm = Slot(uri=MIXS['0000551'], name="PlantAssociatedInterface_air_temp_regm", curie=MIXS.curie('0000551'), model_uri=NMDC_SUB_SCHEMA.PlantAssociatedInterface_air_temp_regm, domain=PlantAssociatedInterface, range=Optional[str]) @@ -17105,9 +17070,6 @@ class slots: slots.PlantAssociatedInterface_herbicide_regm = Slot(uri=MIXS['0000561'], name="PlantAssociatedInterface_herbicide_regm", curie=MIXS.curie('0000561'), model_uri=NMDC_SUB_SCHEMA.PlantAssociatedInterface_herbicide_regm, domain=PlantAssociatedInterface, range=Optional[str]) -slots.PlantAssociatedInterface_horizon_meth = Slot(uri=MIXS['0000321'], name="PlantAssociatedInterface_horizon_meth", curie=MIXS.curie('0000321'), - model_uri=NMDC_SUB_SCHEMA.PlantAssociatedInterface_horizon_meth, domain=PlantAssociatedInterface, range=Optional[str]) - slots.PlantAssociatedInterface_host_age = Slot(uri=MIXS['0000255'], name="PlantAssociatedInterface_host_age", curie=MIXS.curie('0000255'), model_uri=NMDC_SUB_SCHEMA.PlantAssociatedInterface_host_age, domain=PlantAssociatedInterface, range=Optional[str], pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+ +\S.*$')) @@ -17308,6 +17270,9 @@ class slots: slots.PlantAssociatedInterface_watering_regm = Slot(uri=MIXS['0000591'], name="PlantAssociatedInterface_watering_regm", curie=MIXS.curie('0000591'), model_uri=NMDC_SUB_SCHEMA.PlantAssociatedInterface_watering_regm, domain=PlantAssociatedInterface, range=Optional[str]) +slots.PlantAssociatedInterface_horizon_meth = Slot(uri=MIXS['0000321'], name="PlantAssociatedInterface_horizon_meth", curie=MIXS.curie('0000321'), + model_uri=NMDC_SUB_SCHEMA.PlantAssociatedInterface_horizon_meth, domain=PlantAssociatedInterface, range=Optional[str]) + slots.SedimentInterface_alkalinity = Slot(uri=MIXS['0000421'], name="SedimentInterface_alkalinity", curie=MIXS.curie('0000421'), model_uri=NMDC_SUB_SCHEMA.SedimentInterface_alkalinity, domain=SedimentInterface, range=Optional[str], pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+ +\S.*$')) @@ -17441,9 +17406,6 @@ class slots: model_uri=NMDC_SUB_SCHEMA.SedimentInterface_glucosidase_act, domain=SedimentInterface, range=Optional[str], pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+ +\S.*$')) -slots.SedimentInterface_horizon_meth = Slot(uri=MIXS['0000321'], name="SedimentInterface_horizon_meth", curie=MIXS.curie('0000321'), - model_uri=NMDC_SUB_SCHEMA.SedimentInterface_horizon_meth, domain=SedimentInterface, range=Optional[str]) - slots.SedimentInterface_lat_lon = Slot(uri=MIXS['0000009'], name="SedimentInterface_lat_lon", curie=MIXS.curie('0000009'), model_uri=NMDC_SUB_SCHEMA.SedimentInterface_lat_lon, domain=SedimentInterface, range=str, pattern=re.compile(r'^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$')) @@ -17638,6 +17600,9 @@ class slots: model_uri=NMDC_SUB_SCHEMA.SedimentInterface_water_content, domain=SedimentInterface, range=Optional[str], pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?%? \S.+$')) +slots.SedimentInterface_horizon_meth = Slot(uri=MIXS['0000321'], name="SedimentInterface_horizon_meth", curie=MIXS.curie('0000321'), + model_uri=NMDC_SUB_SCHEMA.SedimentInterface_horizon_meth, domain=SedimentInterface, range=Optional[str]) + slots.SoilInterface_agrochem_addition = Slot(uri=MIXS['0000639'], name="SoilInterface_agrochem_addition", curie=MIXS.curie('0000639'), model_uri=NMDC_SUB_SCHEMA.SoilInterface_agrochem_addition, domain=SoilInterface, range=Optional[str], pattern=re.compile(r'.*')) @@ -18110,9 +18075,6 @@ class slots: model_uri=NMDC_SUB_SCHEMA.WastewaterSludgeInterface_geo_loc_name, domain=WastewaterSludgeInterface, range=str, pattern=re.compile(r'^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$')) -slots.WastewaterSludgeInterface_horizon_meth = Slot(uri=MIXS['0000321'], name="WastewaterSludgeInterface_horizon_meth", curie=MIXS.curie('0000321'), - model_uri=NMDC_SUB_SCHEMA.WastewaterSludgeInterface_horizon_meth, domain=WastewaterSludgeInterface, range=Optional[str]) - slots.WastewaterSludgeInterface_indust_eff_percent = Slot(uri=MIXS['0000662'], name="WastewaterSludgeInterface_indust_eff_percent", curie=MIXS.curie('0000662'), model_uri=NMDC_SUB_SCHEMA.WastewaterSludgeInterface_indust_eff_percent, domain=WastewaterSludgeInterface, range=Optional[str], pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+ +\S.*$')) @@ -18247,6 +18209,9 @@ class slots: slots.WastewaterSludgeInterface_wastewater_type = Slot(uri=MIXS['0000353'], name="WastewaterSludgeInterface_wastewater_type", curie=MIXS.curie('0000353'), model_uri=NMDC_SUB_SCHEMA.WastewaterSludgeInterface_wastewater_type, domain=WastewaterSludgeInterface, range=Optional[str]) +slots.WastewaterSludgeInterface_horizon_meth = Slot(uri=MIXS['0000321'], name="WastewaterSludgeInterface_horizon_meth", curie=MIXS.curie('0000321'), + model_uri=NMDC_SUB_SCHEMA.WastewaterSludgeInterface_horizon_meth, domain=WastewaterSludgeInterface, range=Optional[str]) + slots.WaterInterface_alkalinity = Slot(uri=MIXS['0000421'], name="WaterInterface_alkalinity", curie=MIXS.curie('0000421'), model_uri=NMDC_SUB_SCHEMA.WaterInterface_alkalinity, domain=WaterInterface, range=Optional[str], pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+ +\S.*$')) @@ -18414,9 +18379,6 @@ class slots: model_uri=NMDC_SUB_SCHEMA.WaterInterface_glucosidase_act, domain=WaterInterface, range=Optional[str], pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+ +\S.*$')) -slots.WaterInterface_horizon_meth = Slot(uri=MIXS['0000321'], name="WaterInterface_horizon_meth", curie=MIXS.curie('0000321'), - model_uri=NMDC_SUB_SCHEMA.WaterInterface_horizon_meth, domain=WaterInterface, range=Optional[str]) - slots.WaterInterface_lat_lon = Slot(uri=MIXS['0000009'], name="WaterInterface_lat_lon", curie=MIXS.curie('0000009'), model_uri=NMDC_SUB_SCHEMA.WaterInterface_lat_lon, domain=WaterInterface, range=Optional[str], pattern=re.compile(r'^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$')) diff --git a/src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml b/src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml index fc4410f5..c84a46a6 100644 --- a/src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml +++ b/src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml @@ -24,21 +24,36 @@ prefixes: schema: prefix_prefix: schema prefix_reference: http://schema.org/ + Contaminant: + prefix_prefix: Contaminant + prefix_reference: http://example.org/contaminant/ EFO: prefix_prefix: EFO prefix_reference: http://www.ebi.ac.uk/efo/ ISA: prefix_prefix: ISA prefix_reference: http://example.com/isa/ + KEGG.ORTHOLOGY: + prefix_prefix: KEGG.ORTHOLOGY + prefix_reference: http://identifiers.org/kegg.orthology/ + MASSIVE: + prefix_prefix: MASSIVE + prefix_reference: http://example.com/ MetaNetX: prefix_prefix: MetaNetX prefix_reference: http://example.com/metanetx/ RetroRules: prefix_prefix: RetroRules prefix_reference: http://example.com/retrorules/ + doi: + prefix_prefix: doi + prefix_reference: http://example.com/ emsl.project: prefix_prefix: emsl.project prefix_reference: 'https://bioregistry.io/emsl.project:' + emsl: + prefix_prefix: emsl + prefix_reference: http://example.org/emsl_in_mongodb/ generic: prefix_prefix: generic prefix_reference: https://example.com/generic/ @@ -69,9 +84,6 @@ prefixes: nmdc: prefix_prefix: nmdc prefix_reference: https://w3id.org/nmdc/ - skos: - prefix_prefix: skos - prefix_reference: http://www.w3.org/2004/02/skos/core# prov: prefix_prefix: prov prefix_reference: http://www.w3.org/ns/prov# @@ -81,12 +93,9 @@ prefixes: rdfs: prefix_prefix: rdfs prefix_reference: http://www.w3.org/2000/01/rdf-schema# - emsl: - prefix_prefix: emsl - prefix_reference: http://example.org/emsl_in_mongodb/ - Contaminant: - prefix_prefix: Contaminant - prefix_reference: http://example.org/contaminant/ + skos: + prefix_prefix: skos + prefix_reference: http://www.w3.org/2004/02/skos/core# KEGG.COMPOUND: prefix_prefix: KEGG.COMPOUND prefix_reference: http://identifiers.org/kegg.compound/ @@ -132,9 +141,6 @@ prefixes: GO: prefix_prefix: GO prefix_reference: http://purl.obolibrary.org/obo/GO_ - KEGG.ORTHOLOGY: - prefix_prefix: KEGG.ORTHOLOGY - prefix_reference: http://identifiers.org/kegg.orthology/ KEGG.REACTION: prefix_prefix: KEGG.REACTION prefix_reference: http://identifiers.org/kegg.reaction/ @@ -1560,40 +1566,98 @@ enums: other: text: other description: placeholder PV descr, DO NOT SORT - heat_cool_type_enum: - name: heat_cool_type_enum + mech_struc_enum: + name: mech_struc_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: - radiant system: - text: radiant system - heat pump: - text: heat pump - forced air system: - text: forced air system - steam forced heat: - text: steam forced heat - wood stove: - text: wood stove - weekday_enum: - name: weekday_enum + subway: + text: subway + coach: + text: coach + carriage: + text: carriage + elevator: + text: elevator + escalator: + text: escalator + boat: + text: boat + train: + text: train + car: + text: car + bus: + text: bus + window_vert_pos_enum: + name: window_vert_pos_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: - Monday: - text: Monday - Tuesday: - text: Tuesday - Wednesday: - text: Wednesday - Thursday: - text: Thursday - Friday: - text: Friday - Saturday: - text: Saturday - Sunday: - text: Sunday - window_loc_enum: - name: window_loc_enum + bottom: + text: bottom + middle: + text: middle + top: + text: top + low: + text: low + high: + text: high + water_feat_type_enum: + name: water_feat_type_enum + from_schema: https://example.com/nmdc_submission_schema + permissible_values: + fountain: + text: fountain + pool: + text: pool + standing feature: + text: standing feature + stream: + text: stream + waterfall: + text: waterfall + door_direct_enum: + name: door_direct_enum + from_schema: https://example.com/nmdc_submission_schema + permissible_values: + inward: + text: inward + outward: + text: outward + sideways: + text: sideways + build_docs_enum: + name: build_docs_enum + from_schema: https://example.com/nmdc_submission_schema + permissible_values: + building information model: + text: building information model + commissioning report: + text: commissioning report + complaint logs: + text: complaint logs + contract administration: + text: contract administration + cost estimate: + text: cost estimate + janitorial schedules or logs: + text: janitorial schedules or logs + maintenance plans: + text: maintenance plans + schedule: + text: schedule + sections: + text: sections + shop drawings: + text: shop drawings + submittals: + text: submittals + ventilation system: + text: ventilation system + windows: + text: windows + door_loc_enum: + name: door_loc_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: north: @@ -1604,98 +1668,110 @@ enums: text: east west: text: west - vis_media_enum: - name: vis_media_enum - from_schema: https://example.com/nmdc_submission_schema - permissible_values: - photos: - text: photos - videos: - text: videos - commonly of the building: - text: commonly of the building - site context (adjacent buildings, vegetation, terrain, streets): - text: site context (adjacent buildings, vegetation, terrain, streets) - interiors: - text: interiors - equipment: - text: equipment - 3D scans: - text: 3D scans - rel_samp_loc_enum: - name: rel_samp_loc_enum - from_schema: https://example.com/nmdc_submission_schema - permissible_values: - edge of car: - text: edge of car - center of car: - text: center of car - under a seat: - text: under a seat - door_mat_enum: - name: door_mat_enum - from_schema: https://example.com/nmdc_submission_schema - permissible_values: - aluminum: - text: aluminum - cellular PVC: - text: cellular PVC - engineered plastic: - text: engineered plastic - fiberboard: - text: fiberboard - fiberglass: - text: fiberglass - metal: - text: metal - thermoplastic alloy: - text: thermoplastic alloy - vinyl: - text: vinyl - wood: - text: wood - wood/plastic composite: - text: wood/plastic composite - ceil_cond_enum: - name: ceil_cond_enum + ext_window_orient_enum: + name: ext_window_orient_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: - new: - text: new - visible wear: - text: visible wear - needs repair: - text: needs repair - damaged: - text: damaged - rupture: - text: rupture - occup_document_enum: - name: occup_document_enum + north: + text: north + south: + text: south + east: + text: east + west: + text: west + northeast: + text: northeast + southeast: + text: southeast + southwest: + text: southwest + northwest: + text: northwest + room_type_enum: + name: room_type_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: - automated count: - text: automated count - estimate: - text: estimate - manual count: - text: manual count - videos: - text: videos - train_stat_loc_enum: - name: train_stat_loc_enum + attic: + text: attic + bathroom: + text: bathroom + closet: + text: closet + conference room: + text: conference room + elevator: + text: elevator + examining room: + text: examining room + hallway: + text: hallway + kitchen: + text: kitchen + mail room: + text: mail room + private office: + text: private office + open office: + text: open office + stairwell: + text: stairwell + ',restroom': + text: ',restroom' + lobby: + text: lobby + vestibule: + text: vestibule + mechanical or electrical room: + text: mechanical or electrical room + data center: + text: data center + laboratory_wet: + text: laboratory_wet + laboratory_dry: + text: laboratory_dry + gymnasium: + text: gymnasium + natatorium: + text: natatorium + auditorium: + text: auditorium + lockers: + text: lockers + cafe: + text: cafe + warehouse: + text: warehouse + build_occup_type_enum: + name: build_occup_type_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: - south station above ground: - text: south station above ground - south station underground: - text: south station underground - south station amtrak: - text: south station amtrak - forest hills: - text: forest hills - riverside: - text: riverside + office: + text: office + market: + text: market + restaurant: + text: restaurant + residence: + text: residence + school: + text: school + residential: + text: residential + commercial: + text: commercial + low rise: + text: low rise + high rise: + text: high rise + wood framed: + text: wood framed + health care: + text: health care + airport: + text: airport + sports complex: + text: sports complex surf_material_enum: name: surf_material_enum from_schema: https://example.com/nmdc_submission_schema @@ -1730,166 +1806,58 @@ enums: text: vinyl wood: text: wood - surf_air_cont_enum: - name: surf_air_cont_enum - from_schema: https://example.com/nmdc_submission_schema - permissible_values: - dust: - text: dust - organic matter: - text: organic matter - particulate matter: - text: particulate matter - volatile organic compounds: - text: volatile organic compounds - biological contaminants: - text: biological contaminants - radon: - text: radon - nutrients: - text: nutrients - biocides: - text: biocides - door_type_wood_enum: - name: door_type_wood_enum - from_schema: https://example.com/nmdc_submission_schema - permissible_values: - bettened and ledged: - text: bettened and ledged - battened: - text: battened - ledged and braced: - text: ledged and braced - ledged and framed: - text: ledged and framed - ledged, braced and frame: - text: ledged, braced and frame - framed and paneled: - text: framed and paneled - glashed or sash: - text: glashed or sash - flush: - text: flush - louvered: - text: louvered - wire gauged: - text: wire gauged - water_feat_type_enum: - name: water_feat_type_enum - from_schema: https://example.com/nmdc_submission_schema - permissible_values: - fountain: - text: fountain - pool: - text: pool - standing feature: - text: standing feature - stream: - text: stream - waterfall: - text: waterfall - heat_deliv_loc_enum: - name: heat_deliv_loc_enum + window_type_enum: + name: window_type_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: - north: - text: north - south: - text: south - east: - text: east - west: - text: west - room_connected_enum: - name: room_connected_enum + single-hung sash window: + text: single-hung sash window + horizontal sash window: + text: horizontal sash window + fixed window: + text: fixed window + indoor_space_enum: + name: indoor_space_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: - attic: - text: attic + bedroom: + text: bedroom + office: + text: office bathroom: text: bathroom - closet: - text: closet - conference room: - text: conference room - elevator: - text: elevator - examining room: - text: examining room - hallway: - text: hallway + foyer: + text: foyer kitchen: text: kitchen - mail room: - text: mail room - office: - text: office - stairwell: - text: stairwell - room_samp_pos_enum: - name: room_samp_pos_enum - from_schema: https://example.com/nmdc_submission_schema - permissible_values: - north corner: - text: north corner - south corner: - text: south corner - west corner: - text: west corner - east corner: - text: east corner - northeast corner: - text: northeast corner - northwest corner: - text: northwest corner - southeast corner: - text: southeast corner - southwest corner: - text: southwest corner - center: - text: center - handidness_enum: - name: handidness_enum - from_schema: https://example.com/nmdc_submission_schema - permissible_values: - ambidexterity: - text: ambidexterity - left handedness: - text: left handedness - mixed-handedness: - text: mixed-handedness - right handedness: - text: right handedness - drawings_enum: - name: drawings_enum - from_schema: https://example.com/nmdc_submission_schema - permissible_values: - operation: - text: operation - as built: - text: as built - construction: - text: construction - bid: - text: bid - design: - text: design - building navigation map: - text: building navigation map - diagram: - text: diagram - sketch: - text: sketch - room_loc_enum: - name: room_loc_enum + locker room: + text: locker room + hallway: + text: hallway + elevator: + text: elevator + floor_water_mold_enum: + name: floor_water_mold_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: - corner room: - text: corner room - interior room: - text: interior room - exterior wall: - text: exterior wall + mold odor: + text: mold odor + wet floor: + text: wet floor + water stains: + text: water stains + wall discoloration: + text: wall discoloration + floor discoloration: + text: floor discoloration + ceiling discoloration: + text: ceiling discoloration + peeling paint or wallpaper: + text: peeling paint or wallpaper + bulging walls: + text: bulging walls + condensation: + text: condensation ext_wall_orient_enum: name: ext_wall_orient_enum from_schema: https://example.com/nmdc_submission_schema @@ -1910,6 +1878,208 @@ enums: text: southwest northwest: text: northwest + room_condt_enum: + name: room_condt_enum + from_schema: https://example.com/nmdc_submission_schema + permissible_values: + new: + text: new + visible wear: + text: visible wear + needs repair: + text: needs repair + damaged: + text: damaged + rupture: + text: rupture + visible signs of mold/mildew: + text: visible signs of mold/mildew + door_comp_type_enum: + name: door_comp_type_enum + from_schema: https://example.com/nmdc_submission_schema + permissible_values: + metal covered: + text: metal covered + revolving: + text: revolving + sliding: + text: sliding + telescopic: + text: telescopic + ceil_type_enum: + name: ceil_type_enum + from_schema: https://example.com/nmdc_submission_schema + permissible_values: + cathedral: + text: cathedral + dropped: + text: dropped + concave: + text: concave + barrel-shaped: + text: barrel-shaped + coffered: + text: coffered + cove: + text: cove + stretched: + text: stretched + ceil_finish_mat_enum: + name: ceil_finish_mat_enum + from_schema: https://example.com/nmdc_submission_schema + permissible_values: + drywall: + text: drywall + mineral fibre: + text: mineral fibre + tiles: + text: tiles + PVC: + text: PVC + plasterboard: + text: plasterboard + metal: + text: metal + fiberglass: + text: fiberglass + stucco: + text: stucco + mineral wool/calcium silicate: + text: mineral wool/calcium silicate + wood: + text: wood + furniture_enum: + name: furniture_enum + from_schema: https://example.com/nmdc_submission_schema + permissible_values: + cabinet: + text: cabinet + chair: + text: chair + desks: + text: desks + arch_struc_enum: + name: arch_struc_enum + from_schema: https://example.com/nmdc_submission_schema + permissible_values: + building: + text: building + shed: + text: shed + home: + text: home + wall_finish_mat_enum: + name: wall_finish_mat_enum + from_schema: https://example.com/nmdc_submission_schema + permissible_values: + plaster: + text: plaster + gypsum plaster: + text: gypsum plaster + veneer plaster: + text: veneer plaster + gypsum board: + text: gypsum board + tile: + text: tile + terrazzo: + text: terrazzo + stone facing: + text: stone facing + acoustical treatment: + text: acoustical treatment + wood: + text: wood + metal: + text: metal + masonry: + text: masonry + door_mat_enum: + name: door_mat_enum + from_schema: https://example.com/nmdc_submission_schema + permissible_values: + aluminum: + text: aluminum + cellular PVC: + text: cellular PVC + engineered plastic: + text: engineered plastic + fiberboard: + text: fiberboard + fiberglass: + text: fiberglass + metal: + text: metal + thermoplastic alloy: + text: thermoplastic alloy + vinyl: + text: vinyl + wood: + text: wood + wood/plastic composite: + text: wood/plastic composite + train_stop_loc_enum: + name: train_stop_loc_enum + from_schema: https://example.com/nmdc_submission_schema + permissible_values: + end: + text: end + mid: + text: mid + downtown: + text: downtown + occup_document_enum: + name: occup_document_enum + from_schema: https://example.com/nmdc_submission_schema + permissible_values: + automated count: + text: automated count + estimate: + text: estimate + manual count: + text: manual count + videos: + text: videos + floor_finish_mat_enum: + name: floor_finish_mat_enum + from_schema: https://example.com/nmdc_submission_schema + permissible_values: + tile: + text: tile + wood strip or parquet: + text: wood strip or parquet + carpet: + text: carpet + rug: + text: rug + laminate wood: + text: laminate wood + lineoleum: + text: lineoleum + vinyl composition tile: + text: vinyl composition tile + sheet vinyl: + text: sheet vinyl + stone: + text: stone + bamboo: + text: bamboo + cork: + text: cork + terrazo: + text: terrazo + concrete: + text: concrete + none: + text: none + sealed: + text: sealed + clear finish: + text: clear finish + paint: + text: paint + none or unfinished: + text: none or unfinished samp_weather_enum: name: samp_weather_enum from_schema: https://example.com/nmdc_submission_schema @@ -1950,16 +2120,28 @@ enums: text: wood-framed concrete: text: concrete - door_type_enum: - name: door_type_enum + building_setting_enum: + name: building_setting_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: - composite: - text: composite - metal: - text: metal - wooden: - text: wooden + urban: + text: urban + suburban: + text: suburban + exurban: + text: exurban + rural: + text: rural + window_horiz_pos_enum: + name: window_horiz_pos_enum + from_schema: https://example.com/nmdc_submission_schema + permissible_values: + left: + text: left + middle: + text: middle + right: + text: right window_cond_enum: name: window_cond_enum from_schema: https://example.com/nmdc_submission_schema @@ -1974,72 +2156,20 @@ enums: text: rupture visible wear: text: visible wear - specific_enum: - name: specific_enum - from_schema: https://example.com/nmdc_submission_schema - permissible_values: - operation: - text: operation - as built: - text: as built - construction: - text: construction - bid: - text: bid - design: - text: design - photos: - text: photos - wall_const_type_enum: - name: wall_const_type_enum - from_schema: https://example.com/nmdc_submission_schema - permissible_values: - frame construction: - text: frame construction - joisted masonry: - text: joisted masonry - light noncombustible: - text: light noncombustible - masonry noncombustible: - text: masonry noncombustible - modified fire resistive: - text: modified fire resistive - fire resistive: - text: fire resistive - window_type_enum: - name: window_type_enum - from_schema: https://example.com/nmdc_submission_schema - permissible_values: - single-hung sash window: - text: single-hung sash window - horizontal sash window: - text: horizontal sash window - fixed window: - text: fixed window - train_line_enum: - name: train_line_enum - from_schema: https://example.com/nmdc_submission_schema - permissible_values: - red: - text: red - green: - text: green - orange: - text: orange - wall_loc_enum: - name: wall_loc_enum + season_use_enum: + name: season_use_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: - north: - text: north - south: - text: south - east: - text: east - west: - text: west - door_cond_enum: - name: door_cond_enum + Spring: + text: Spring + Summer: + text: Summer + Fall: + text: Fall + Winter: + text: Winter + shading_device_cond_enum: + name: shading_device_cond_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: damaged: @@ -2052,22 +2182,122 @@ enums: text: rupture visible wear: text: visible wear - light_type_enum: - name: light_type_enum + surf_air_cont_enum: + name: surf_air_cont_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: - natural light: - text: natural light - electric light: - text: electric light - desk lamp: - text: desk lamp - flourescent lights: - text: flourescent lights - none: - text: none - room_type_enum: - name: room_type_enum + dust: + text: dust + organic matter: + text: organic matter + particulate matter: + text: particulate matter + volatile organic compounds: + text: volatile organic compounds + biological contaminants: + text: biological contaminants + radon: + text: radon + nutrients: + text: nutrients + biocides: + text: biocides + light_type_enum: + name: light_type_enum + from_schema: https://example.com/nmdc_submission_schema + permissible_values: + natural light: + text: natural light + electric light: + text: electric light + desk lamp: + text: desk lamp + flourescent lights: + text: flourescent lights + none: + text: none + ceil_texture_enum: + name: ceil_texture_enum + from_schema: https://example.com/nmdc_submission_schema + permissible_values: + crows feet: + text: crows feet + crows-foot stomp: + text: crows-foot stomp + double skip: + text: double skip + hawk and trowel: + text: hawk and trowel + knockdown: + text: knockdown + popcorn: + text: popcorn + orange peel: + text: orange peel + rosebud stomp: + text: rosebud stomp + Santa-Fe texture: + text: Santa-Fe texture + skip trowel: + text: skip trowel + smooth: + text: smooth + stomp knockdown: + text: stomp knockdown + swirl: + text: swirl + ceil_cond_enum: + name: ceil_cond_enum + from_schema: https://example.com/nmdc_submission_schema + permissible_values: + new: + text: new + visible wear: + text: visible wear + needs repair: + text: needs repair + damaged: + text: damaged + rupture: + text: rupture + room_samp_pos_enum: + name: room_samp_pos_enum + from_schema: https://example.com/nmdc_submission_schema + permissible_values: + north corner: + text: north corner + south corner: + text: south corner + west corner: + text: west corner + east corner: + text: east corner + northeast corner: + text: northeast corner + northwest corner: + text: northwest corner + southeast corner: + text: southeast corner + southwest corner: + text: southwest corner + center: + text: center + window_mat_enum: + name: window_mat_enum + from_schema: https://example.com/nmdc_submission_schema + permissible_values: + clad: + text: clad + fiberglass: + text: fiberglass + metal: + text: metal + vinyl: + text: vinyl + wood: + text: wood + room_connected_enum: + name: room_connected_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: attic: @@ -2088,102 +2318,54 @@ enums: text: kitchen mail room: text: mail room - private office: - text: private office - open office: - text: open office + office: + text: office stairwell: text: stairwell - ',restroom': - text: ',restroom' - lobby: - text: lobby - vestibule: - text: vestibule - mechanical or electrical room: - text: mechanical or electrical room - data center: - text: data center - laboratory_wet: - text: laboratory_wet - laboratory_dry: - text: laboratory_dry - gymnasium: - text: gymnasium - natatorium: - text: natatorium - auditorium: - text: auditorium - lockers: - text: lockers - cafe: - text: cafe - warehouse: - text: warehouse - window_cover_enum: - name: window_cover_enum - from_schema: https://example.com/nmdc_submission_schema - permissible_values: - blinds: - text: blinds - curtains: - text: curtains - none: - text: none - door_move_enum: - name: door_move_enum - from_schema: https://example.com/nmdc_submission_schema - permissible_values: - collapsible: - text: collapsible - folding: - text: folding - revolving: - text: revolving - rolling shutter: - text: rolling shutter - sliding: - text: sliding - swinging: - text: swinging - door_direct_enum: - name: door_direct_enum + specific_enum: + name: specific_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: - inward: - text: inward - outward: - text: outward - sideways: - text: sideways - window_mat_enum: - name: window_mat_enum + operation: + text: operation + as built: + text: as built + construction: + text: construction + bid: + text: bid + design: + text: design + photos: + text: photos + wall_surf_treatment_enum: + name: wall_surf_treatment_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: - clad: - text: clad - fiberglass: - text: fiberglass - metal: - text: metal - vinyl: - text: vinyl - wood: - text: wood - shading_device_cond_enum: - name: shading_device_cond_enum + painted: + text: painted + wall paper: + text: wall paper + no treatment: + text: no treatment + paneling: + text: paneling + stucco: + text: stucco + fabric: + text: fabric + window_loc_enum: + name: window_loc_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: - damaged: - text: damaged - needs repair: - text: needs repair - new: - text: new - rupture: - text: rupture - visible wear: - text: visible wear + north: + text: north + south: + text: south + east: + text: east + west: + text: west shading_device_type_enum: name: shading_device_type_enum from_schema: https://example.com/nmdc_submission_schema @@ -2226,6 +2408,114 @@ enums: text: damaged rupture: text: rupture + door_type_enum: + name: door_type_enum + from_schema: https://example.com/nmdc_submission_schema + permissible_values: + composite: + text: composite + metal: + text: metal + wooden: + text: wooden + door_type_wood_enum: + name: door_type_wood_enum + from_schema: https://example.com/nmdc_submission_schema + permissible_values: + bettened and ledged: + text: bettened and ledged + battened: + text: battened + ledged and braced: + text: ledged and braced + ledged and framed: + text: ledged and framed + ledged, braced and frame: + text: ledged, braced and frame + framed and paneled: + text: framed and paneled + glashed or sash: + text: glashed or sash + flush: + text: flush + louvered: + text: louvered + wire gauged: + text: wire gauged + drawings_enum: + name: drawings_enum + from_schema: https://example.com/nmdc_submission_schema + permissible_values: + operation: + text: operation + as built: + text: as built + construction: + text: construction + bid: + text: bid + design: + text: design + building navigation map: + text: building navigation map + diagram: + text: diagram + sketch: + text: sketch + window_cover_enum: + name: window_cover_enum + from_schema: https://example.com/nmdc_submission_schema + permissible_values: + blinds: + text: blinds + curtains: + text: curtains + none: + text: none + door_cond_enum: + name: door_cond_enum + from_schema: https://example.com/nmdc_submission_schema + permissible_values: + damaged: + text: damaged + needs repair: + text: needs repair + new: + text: new + rupture: + text: rupture + visible wear: + text: visible wear + filter_type_enum: + name: filter_type_enum + from_schema: https://example.com/nmdc_submission_schema + permissible_values: + particulate air filter: + text: particulate air filter + chemical air filter: + text: chemical air filter + low-MERV pleated media: + text: low-MERV pleated media + HEPA: + text: HEPA + electrostatic: + text: electrostatic + gas-phase or ultraviolet air treatments: + text: gas-phase or ultraviolet air treatments + floor_cond_enum: + name: floor_cond_enum + from_schema: https://example.com/nmdc_submission_schema + permissible_values: + new: + text: new + visible wear: + text: visible wear + needs repair: + text: needs repair + damaged: + text: damaged + rupture: + text: rupture door_type_metal_enum: name: door_type_metal_enum from_schema: https://example.com/nmdc_submission_schema @@ -2240,144 +2530,82 @@ enums: text: rolling shutters steel plate: text: steel plate - wall_texture_enum: - name: wall_texture_enum + gender_restroom_enum: + name: gender_restroom_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: - crows feet: - text: crows feet - crows-foot stomp: - text: crows-foot stomp - '': - text: '' - double skip: - text: double skip - hawk and trowel: - text: hawk and trowel - knockdown: - text: knockdown - popcorn: - text: popcorn - orange peel: - text: orange peel - rosebud stomp: - text: rosebud stomp - Santa-Fe texture: - text: Santa-Fe texture - skip trowel: - text: skip trowel - smooth: - text: smooth - stomp knockdown: - text: stomp knockdown - swirl: - text: swirl - build_docs_enum: - name: build_docs_enum + all gender: + text: all gender + female: + text: female + gender neurtral: + text: gender neurtral + male: + text: male + male and female: + text: male and female + unisex: + text: unisex + weekday_enum: + name: weekday_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: - building information model: - text: building information model - commissioning report: - text: commissioning report - complaint logs: - text: complaint logs - contract administration: - text: contract administration - cost estimate: - text: cost estimate - janitorial schedules or logs: - text: janitorial schedules or logs - maintenance plans: - text: maintenance plans - schedule: - text: schedule - sections: - text: sections - shop drawings: - text: shop drawings - submittals: - text: submittals - ventilation system: - text: ventilation system - windows: - text: windows - building_setting_enum: - name: building_setting_enum + Monday: + text: Monday + Tuesday: + text: Tuesday + Wednesday: + text: Wednesday + Thursday: + text: Thursday + Friday: + text: Friday + Saturday: + text: Saturday + Sunday: + text: Sunday + substructure_type_enum: + name: substructure_type_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: - urban: - text: urban - suburban: - text: suburban - exurban: - text: exurban - rural: - text: rural - wall_finish_mat_enum: - name: wall_finish_mat_enum + crawlspace: + text: crawlspace + slab on grade: + text: slab on grade + basement: + text: basement + rel_samp_loc_enum: + name: rel_samp_loc_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: - plaster: - text: plaster - gypsum plaster: - text: gypsum plaster - veneer plaster: - text: veneer plaster - gypsum board: - text: gypsum board - tile: - text: tile - terrazzo: - text: terrazzo - stone facing: - text: stone facing - acoustical treatment: - text: acoustical treatment - wood: - text: wood - metal: - text: metal - masonry: - text: masonry - build_occup_type_enum: - name: build_occup_type_enum + edge of car: + text: edge of car + center of car: + text: center of car + under a seat: + text: under a seat + quad_pos_enum: + name: quad_pos_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: - office: - text: office - market: - text: market - restaurant: - text: restaurant - residence: - text: residence - school: - text: school - residential: - text: residential - commercial: - text: commercial - low rise: - text: low rise - high rise: - text: high rise - wood framed: - text: wood framed - health care: - text: health care - airport: - text: airport - sports complex: - text: sports complex - ceil_texture_enum: - name: ceil_texture_enum + North side: + text: North side + West side: + text: West side + South side: + text: South side + East side: + text: East side + wall_texture_enum: + name: wall_texture_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: crows feet: text: crows feet crows-foot stomp: text: crows-foot stomp + '': + text: '' double skip: text: double skip hawk and trowel: @@ -2400,48 +2628,34 @@ enums: text: stomp knockdown swirl: text: swirl - floor_water_mold_enum: - name: floor_water_mold_enum + heat_cool_type_enum: + name: heat_cool_type_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: - mold odor: - text: mold odor - wet floor: - text: wet floor - water stains: - text: water stains - wall discoloration: - text: wall discoloration - floor discoloration: - text: floor discoloration - ceiling discoloration: - text: ceiling discoloration - peeling paint or wallpaper: - text: peeling paint or wallpaper - bulging walls: - text: bulging walls - condensation: - text: condensation - ceil_type_enum: - name: ceil_type_enum + radiant system: + text: radiant system + heat pump: + text: heat pump + forced air system: + text: forced air system + steam forced heat: + text: steam forced heat + wood stove: + text: wood stove + samp_floor_enum: + name: samp_floor_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: - cathedral: - text: cathedral - dropped: - text: dropped - concave: - text: concave - barrel-shaped: - text: barrel-shaped - coffered: - text: coffered - cove: - text: cove - stretched: - text: stretched - door_loc_enum: - name: door_loc_enum + 1st floor: + text: 1st floor + 2nd floor: + text: 2nd floor + basement: + text: basement + lobby: + text: lobby + wall_loc_enum: + name: wall_loc_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: north: @@ -2452,248 +2666,90 @@ enums: text: east west: text: west - door_comp_type_enum: - name: door_comp_type_enum + door_move_enum: + name: door_move_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: - metal covered: - text: metal covered + collapsible: + text: collapsible + folding: + text: folding revolving: text: revolving + rolling shutter: + text: rolling shutter sliding: text: sliding - telescopic: - text: telescopic - mech_struc_enum: - name: mech_struc_enum - from_schema: https://example.com/nmdc_submission_schema - permissible_values: - subway: - text: subway - coach: - text: coach - carriage: - text: carriage - elevator: - text: elevator - escalator: - text: escalator - boat: - text: boat - train: - text: train - car: - text: car - bus: - text: bus - wall_surf_treatment_enum: - name: wall_surf_treatment_enum - from_schema: https://example.com/nmdc_submission_schema - permissible_values: - painted: - text: painted - wall paper: - text: wall paper - no treatment: - text: no treatment - paneling: - text: paneling - stucco: - text: stucco - fabric: - text: fabric - room_condt_enum: - name: room_condt_enum - from_schema: https://example.com/nmdc_submission_schema - permissible_values: - new: - text: new - visible wear: - text: visible wear - needs repair: - text: needs repair - damaged: - text: damaged - rupture: - text: rupture - visible signs of mold/mildew: - text: visible signs of mold/mildew - ext_window_orient_enum: - name: ext_window_orient_enum - from_schema: https://example.com/nmdc_submission_schema - permissible_values: - north: - text: north - south: - text: south - east: - text: east - west: - text: west - northeast: - text: northeast - southeast: - text: southeast - southwest: - text: southwest - northwest: - text: northwest - indoor_space_enum: - name: indoor_space_enum - from_schema: https://example.com/nmdc_submission_schema - permissible_values: - bedroom: - text: bedroom - office: - text: office - bathroom: - text: bathroom - foyer: - text: foyer - kitchen: - text: kitchen - locker room: - text: locker room - hallway: - text: hallway - elevator: - text: elevator - floor_cond_enum: - name: floor_cond_enum - from_schema: https://example.com/nmdc_submission_schema - permissible_values: - new: - text: new - visible wear: - text: visible wear - needs repair: - text: needs repair - damaged: - text: damaged - rupture: - text: rupture - samp_floor_enum: - name: samp_floor_enum - from_schema: https://example.com/nmdc_submission_schema - permissible_values: - 1st floor: - text: 1st floor - 2nd floor: - text: 2nd floor - basement: - text: basement - lobby: - text: lobby - filter_type_enum: - name: filter_type_enum - from_schema: https://example.com/nmdc_submission_schema - permissible_values: - particulate air filter: - text: particulate air filter - chemical air filter: - text: chemical air filter - low-MERV pleated media: - text: low-MERV pleated media - HEPA: - text: HEPA - electrostatic: - text: electrostatic - gas-phase or ultraviolet air treatments: - text: gas-phase or ultraviolet air treatments - train_stop_loc_enum: - name: train_stop_loc_enum - from_schema: https://example.com/nmdc_submission_schema - permissible_values: - end: - text: end - mid: - text: mid - downtown: - text: downtown - floor_finish_mat_enum: - name: floor_finish_mat_enum + swinging: + text: swinging + wall_const_type_enum: + name: wall_const_type_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: - tile: - text: tile - wood strip or parquet: - text: wood strip or parquet - carpet: - text: carpet - rug: - text: rug - laminate wood: - text: laminate wood - lineoleum: - text: lineoleum - vinyl composition tile: - text: vinyl composition tile - sheet vinyl: - text: sheet vinyl - stone: - text: stone - bamboo: - text: bamboo - cork: - text: cork - terrazo: - text: terrazo - concrete: - text: concrete - none: - text: none - sealed: - text: sealed - clear finish: - text: clear finish - paint: - text: paint - none or unfinished: - text: none or unfinished - season_use_enum: - name: season_use_enum + frame construction: + text: frame construction + joisted masonry: + text: joisted masonry + light noncombustible: + text: light noncombustible + masonry noncombustible: + text: masonry noncombustible + modified fire resistive: + text: modified fire resistive + fire resistive: + text: fire resistive + handidness_enum: + name: handidness_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: - Spring: - text: Spring - Summer: - text: Summer - Fall: - text: Fall - Winter: - text: Winter - furniture_enum: - name: furniture_enum + ambidexterity: + text: ambidexterity + left handedness: + text: left handedness + mixed-handedness: + text: mixed-handedness + right handedness: + text: right handedness + vis_media_enum: + name: vis_media_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: - cabinet: - text: cabinet - chair: - text: chair - desks: - text: desks - quad_pos_enum: - name: quad_pos_enum + photos: + text: photos + videos: + text: videos + commonly of the building: + text: commonly of the building + site context (adjacent buildings, vegetation, terrain, streets): + text: site context (adjacent buildings, vegetation, terrain, streets) + interiors: + text: interiors + equipment: + text: equipment + 3D scans: + text: 3D scans + room_loc_enum: + name: room_loc_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: - North side: - text: North side - West side: - text: West side - South side: - text: South side - East side: - text: East side - substructure_type_enum: - name: substructure_type_enum + corner room: + text: corner room + interior room: + text: interior room + exterior wall: + text: exterior wall + heat_deliv_loc_enum: + name: heat_deliv_loc_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: - crawlspace: - text: crawlspace - slab on grade: - text: slab on grade - basement: - text: basement + north: + text: north + south: + text: south + east: + text: east + west: + text: west indoor_surf_enum: name: indoor_surf_enum from_schema: https://example.com/nmdc_submission_schema @@ -2714,94 +2770,66 @@ enums: text: window wall: text: wall - ceil_finish_mat_enum: - name: ceil_finish_mat_enum - from_schema: https://example.com/nmdc_submission_schema - permissible_values: - drywall: - text: drywall - mineral fibre: - text: mineral fibre - tiles: - text: tiles - PVC: - text: PVC - plasterboard: - text: plasterboard - metal: - text: metal - fiberglass: - text: fiberglass - stucco: - text: stucco - mineral wool/calcium silicate: - text: mineral wool/calcium silicate - wood: - text: wood - gender_restroom_enum: - name: gender_restroom_enum - from_schema: https://example.com/nmdc_submission_schema - permissible_values: - all gender: - text: all gender - female: - text: female - gender neurtral: - text: gender neurtral - male: - text: male - male and female: - text: male and female - unisex: - text: unisex - window_horiz_pos_enum: - name: window_horiz_pos_enum + train_line_enum: + name: train_line_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: - left: - text: left - middle: - text: middle - right: - text: right - window_vert_pos_enum: - name: window_vert_pos_enum + red: + text: red + green: + text: green + orange: + text: orange + train_stat_loc_enum: + name: train_stat_loc_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: - bottom: - text: bottom - middle: - text: middle - top: - text: top - low: - text: low - high: - text: high - arch_struc_enum: - name: arch_struc_enum + south station above ground: + text: south station above ground + south station underground: + text: south station underground + south station amtrak: + text: south station amtrak + forest hills: + text: forest hills + riverside: + text: riverside + hcr_enum: + name: hcr_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: - building: - text: building - shed: - text: shed - home: - text: home - hc_produced_enum: - name: hc_produced_enum + Oil Reservoir: + text: Oil Reservoir + Gas Reservoir: + text: Gas Reservoir + Oil Sand: + text: Oil Sand + Coalbed: + text: Coalbed + Shale: + text: Shale + Tight Oil Reservoir: + text: Tight Oil Reservoir + Tight Gas Reservoir: + text: Tight Gas Reservoir + other: + text: other + samp_collect_point_enum: + name: samp_collect_point_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: - Oil: - text: Oil - Gas-Condensate: - text: Gas-Condensate - Gas: - text: Gas - Bitumen: - text: Bitumen - Coalbed Methane: - text: Coalbed Methane + well: + text: well + test well: + text: test well + drilling rig: + text: drilling rig + wellhead: + text: wellhead + separator: + text: separator + storage tank: + text: storage tank other: text: other hcr_geol_age_enum: @@ -2844,22 +2872,74 @@ enums: text: Triassic other: text: other - samp_collect_point_enum: - name: samp_collect_point_enum + oxy_stat_samp_enum: + name: oxy_stat_samp_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: - well: - text: well - test well: - text: test well - drilling rig: - text: drilling rig - wellhead: - text: wellhead - separator: - text: separator - storage tank: - text: storage tank + aerobic: + text: aerobic + anaerobic: + text: anaerobic + other: + text: other + lithology_enum: + name: lithology_enum + from_schema: https://example.com/nmdc_submission_schema + permissible_values: + Basement: + text: Basement + Chalk: + text: Chalk + Chert: + text: Chert + Coal: + text: Coal + Conglomerate: + text: Conglomerate + Diatomite: + text: Diatomite + Dolomite: + text: Dolomite + Limestone: + text: Limestone + Sandstone: + text: Sandstone + Shale: + text: Shale + Siltstone: + text: Siltstone + Volcanic: + text: Volcanic + other: + text: other + hc_produced_enum: + name: hc_produced_enum + from_schema: https://example.com/nmdc_submission_schema + permissible_values: + Oil: + text: Oil + Gas-Condensate: + text: Gas-Condensate + Gas: + text: Gas + Bitumen: + text: Bitumen + Coalbed Methane: + text: Coalbed Methane + other: + text: other + samp_subtype_enum: + name: samp_subtype_enum + from_schema: https://example.com/nmdc_submission_schema + permissible_values: + oil phase: + text: oil phase + water phase: + text: water phase + biofilm: + text: biofilm + not applicable: + text: not applicable other: text: other depos_env_enum: @@ -2898,78 +2978,32 @@ enums: text: Other - Volcanic other: text: other - oxy_stat_samp_enum: - name: oxy_stat_samp_enum - from_schema: https://example.com/nmdc_submission_schema - permissible_values: - aerobic: - text: aerobic - anaerobic: - text: anaerobic - other: - text: other - hcr_enum: - name: hcr_enum - from_schema: https://example.com/nmdc_submission_schema - permissible_values: - Oil Reservoir: - text: Oil Reservoir - Gas Reservoir: - text: Gas Reservoir - Oil Sand: - text: Oil Sand - Coalbed: - text: Coalbed - Shale: - text: Shale - Tight Oil Reservoir: - text: Tight Oil Reservoir - Tight Gas Reservoir: - text: Tight Gas Reservoir - other: - text: other - samp_subtype_enum: - name: samp_subtype_enum + sr_kerog_type_enum: + name: sr_kerog_type_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: - oil phase: - text: oil phase - water phase: - text: water phase - biofilm: - text: biofilm - not applicable: - text: not applicable + Type I: + text: Type I + Type II: + text: Type II + Type III: + text: Type III + Type IV: + text: Type IV other: text: other - lithology_enum: - name: lithology_enum + sr_lithology_enum: + name: sr_lithology_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: - Basement: - text: Basement - Chalk: - text: Chalk - Chert: - text: Chert + Clastic: + text: Clastic + Carbonate: + text: Carbonate Coal: text: Coal - Conglomerate: - text: Conglomerate - Diatomite: - text: Diatomite - Dolomite: - text: Dolomite - Limestone: - text: Limestone - Sandstone: - text: Sandstone - Shale: - text: Shale - Siltstone: - text: Siltstone - Volcanic: - text: Volcanic + Biosilicieous: + text: Biosilicieous other: text: other sr_geol_age_enum: @@ -3026,34 +3060,76 @@ enums: text: Marine other: text: other - sr_kerog_type_enum: - name: sr_kerog_type_enum + profile_position_enum: + name: profile_position_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: - Type I: - text: Type I - Type II: - text: Type II - Type III: - text: Type III - Type IV: - text: Type IV - other: - text: other - sr_lithology_enum: - name: sr_lithology_enum + summit: + text: summit + shoulder: + text: shoulder + backslope: + text: backslope + footslope: + text: footslope + toeslope: + text: toeslope + fao_class_enum: + name: fao_class_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: - Clastic: - text: Clastic - Carbonate: - text: Carbonate - Coal: - text: Coal - Biosilicieous: - text: Biosilicieous - other: - text: other + Acrisols: + text: Acrisols + Andosols: + text: Andosols + Arenosols: + text: Arenosols + Cambisols: + text: Cambisols + Chernozems: + text: Chernozems + Ferralsols: + text: Ferralsols + Fluvisols: + text: Fluvisols + Gleysols: + text: Gleysols + Greyzems: + text: Greyzems + Gypsisols: + text: Gypsisols + Histosols: + text: Histosols + Kastanozems: + text: Kastanozems + Lithosols: + text: Lithosols + Luvisols: + text: Luvisols + Nitosols: + text: Nitosols + Phaeozems: + text: Phaeozems + Planosols: + text: Planosols + Podzols: + text: Podzols + Podzoluvisols: + text: Podzoluvisols + Rankers: + text: Rankers + Regosols: + text: Regosols + Rendzinas: + text: Rendzinas + Solonchaks: + text: Solonchaks + Solonetz: + text: Solonetz + Vertisols: + text: Vertisols + Yermosols: + text: Yermosols biotic_relationship_enum: name: biotic_relationship_enum from_schema: https://example.com/nmdc_submission_schema @@ -3066,6 +3142,26 @@ enums: text: commensal symbiont: text: symbiont + soil_horizon_enum: + name: soil_horizon_enum + from_schema: https://example.com/nmdc_submission_schema + permissible_values: + O horizon: + text: O horizon + A horizon: + text: A horizon + E horizon: + text: E horizon + B horizon: + text: B horizon + C horizon: + text: C horizon + R layer: + text: R layer + Permafrost: + text: Permafrost + M horizon: + text: M horizon drainage_class_enum: name: drainage_class_enum from_schema: https://example.com/nmdc_submission_schema @@ -3082,6 +3178,28 @@ enums: text: well excessively drained: text: excessively drained + tillage_enum: + name: tillage_enum + from_schema: https://example.com/nmdc_submission_schema + permissible_values: + drill: + text: drill + cutting disc: + text: cutting disc + ridge till: + text: ridge till + strip tillage: + text: strip tillage + zonal tillage: + text: zonal tillage + chisel: + text: chisel + tined: + text: tined + mouldboard: + text: mouldboard + disc plough: + text: disc plough cur_land_use_enum: name: cur_land_use_enum from_schema: https://example.com/nmdc_submission_schema @@ -3274,132 +3392,6 @@ enums: value: vine crops (grapes) examples: - value: grapes - soil_horizon_enum: - name: soil_horizon_enum - from_schema: https://example.com/nmdc_submission_schema - permissible_values: - O horizon: - text: O horizon - A horizon: - text: A horizon - E horizon: - text: E horizon - B horizon: - text: B horizon - C horizon: - text: C horizon - R layer: - text: R layer - Permafrost: - text: Permafrost - M horizon: - text: M horizon - profile_position_enum: - name: profile_position_enum - from_schema: https://example.com/nmdc_submission_schema - permissible_values: - summit: - text: summit - shoulder: - text: shoulder - backslope: - text: backslope - footslope: - text: footslope - toeslope: - text: toeslope - tillage_enum: - name: tillage_enum - from_schema: https://example.com/nmdc_submission_schema - permissible_values: - drill: - text: drill - cutting disc: - text: cutting disc - ridge till: - text: ridge till - strip tillage: - text: strip tillage - zonal tillage: - text: zonal tillage - chisel: - text: chisel - tined: - text: tined - mouldboard: - text: mouldboard - disc plough: - text: disc plough - fao_class_enum: - name: fao_class_enum - from_schema: https://example.com/nmdc_submission_schema - permissible_values: - Acrisols: - text: Acrisols - Andosols: - text: Andosols - Arenosols: - text: Arenosols - Cambisols: - text: Cambisols - Chernozems: - text: Chernozems - Ferralsols: - text: Ferralsols - Fluvisols: - text: Fluvisols - Gleysols: - text: Gleysols - Greyzems: - text: Greyzems - Gypsisols: - text: Gypsisols - Histosols: - text: Histosols - Kastanozems: - text: Kastanozems - Lithosols: - text: Lithosols - Luvisols: - text: Luvisols - Nitosols: - text: Nitosols - Phaeozems: - text: Phaeozems - Planosols: - text: Planosols - Podzols: - text: Podzols - Podzoluvisols: - text: Podzoluvisols - Rankers: - text: Rankers - Regosols: - text: Regosols - Rendzinas: - text: Rendzinas - Solonchaks: - text: Solonchaks - Solonetz: - text: Solonetz - Vertisols: - text: Vertisols - Yermosols: - text: Yermosols - samp_capt_status_enum: - name: samp_capt_status_enum - from_schema: https://example.com/nmdc_submission_schema - permissible_values: - active surveillance in response to an outbreak: - text: active surveillance in response to an outbreak - active surveillance not initiated by an outbreak: - text: active surveillance not initiated by an outbreak - farm sample: - text: farm sample - market sample: - text: market sample - other: - text: other plant_sex_enum: name: plant_sex_enum from_schema: https://example.com/nmdc_submission_schema @@ -3462,34 +3454,6 @@ enums: text: Trioecious Unisexual: text: Unisexual - growth_habit_enum: - name: growth_habit_enum - from_schema: https://example.com/nmdc_submission_schema - permissible_values: - erect: - text: erect - semi-erect: - text: semi-erect - spreading: - text: spreading - prostrate: - text: prostrate - samp_dis_stage_enum: - name: samp_dis_stage_enum - from_schema: https://example.com/nmdc_submission_schema - permissible_values: - dissemination: - text: dissemination - growth and reproduction: - text: growth and reproduction - infection: - text: infection - inoculation: - text: inoculation - penetration: - text: penetration - other: - text: other biol_stat_enum: name: biol_stat_enum from_schema: https://example.com/nmdc_submission_schema @@ -3510,18 +3474,48 @@ enums: text: clonal selection mutant: text: mutant - tidal_stage_enum: - name: tidal_stage_enum + samp_dis_stage_enum: + name: samp_dis_stage_enum from_schema: https://example.com/nmdc_submission_schema permissible_values: - low tide: - text: low tide - ebb tide: - text: ebb tide - flood tide: - text: flood tide - high tide: - text: high tide + dissemination: + text: dissemination + growth and reproduction: + text: growth and reproduction + infection: + text: infection + inoculation: + text: inoculation + penetration: + text: penetration + other: + text: other + samp_capt_status_enum: + name: samp_capt_status_enum + from_schema: https://example.com/nmdc_submission_schema + permissible_values: + active surveillance in response to an outbreak: + text: active surveillance in response to an outbreak + active surveillance not initiated by an outbreak: + text: active surveillance not initiated by an outbreak + farm sample: + text: farm sample + market sample: + text: market sample + other: + text: other + growth_habit_enum: + name: growth_habit_enum + from_schema: https://example.com/nmdc_submission_schema + permissible_values: + erect: + text: erect + semi-erect: + text: semi-erect + spreading: + text: spreading + prostrate: + text: prostrate sediment_type_enum: name: sediment_type_enum from_schema: https://example.com/nmdc_submission_schema @@ -3534,6 +3528,18 @@ enums: text: hydrogenous lithogenous: text: lithogenous + tidal_stage_enum: + name: tidal_stage_enum + from_schema: https://example.com/nmdc_submission_schema + permissible_values: + low tide: + text: low tide + ebb tide: + text: ebb tide + flood tide: + text: flood tide + high tide: + text: high tide host_sex_enum: name: host_sex_enum from_schema: https://example.com/nmdc_submission_schema @@ -15120,11 +15126,34 @@ slots: is_a: attribute range: string multivalued: false + alternative_identifiers: + name: alternative_identifiers + description: A list of alternative identifiers for the entity. + from_schema: https://example.com/nmdc_submission_schema + multivalued: true + range: uriorcurie + pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$ + investigation field: + name: investigation field + description: field describing aspect of the investigation/study to which the sample belongs + from_schema: https://example.com/nmdc_submission_schema + abstract: true + description: + name: description + description: a human-readable description of a thing + from_schema: https://example.com/nmdc_submission_schema + slot_uri: dcterms:description + range: string + multivalued: false core field: name: core field description: basic fields from_schema: https://example.com/nmdc_submission_schema abstract: true + nucleic acid sequence source field: + name: nucleic acid sequence source field + from_schema: https://example.com/nmdc_submission_schema + abstract: true id: name: id description: A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI @@ -15146,22 +15175,23 @@ slots: description: Should use ISO 639-1 code e.g. "en", "fr" from_schema: https://example.com/nmdc_submission_schema range: language code - description: - name: description - description: a human-readable description of a thing - from_schema: https://example.com/nmdc_submission_schema - slot_uri: dcterms:description - range: string - multivalued: false - nucleic acid sequence source field: - name: nucleic acid sequence source field + attribute: + name: attribute + description: 'A attribute of a biosample. Examples: depth, habitat, material. For NMDC, attributes SHOULD be mapped to terms within a MIxS template' from_schema: https://example.com/nmdc_submission_schema + aliases: + - field + - property + - template field + - key + - characteristic abstract: true - environment field: - name: environment field - description: field describing environmental aspect of a sample + name: + name: name + description: A human readable label for an entity from_schema: https://example.com/nmdc_submission_schema - abstract: true + range: string + multivalued: false gold_path_field: name: gold_path_field description: This is a grouping for any of the gold path fields @@ -15170,35 +15200,11 @@ slots: abstract: true range: string multivalued: false - alternative_identifiers: - name: alternative_identifiers - description: A list of alternative identifiers for the entity. - from_schema: https://example.com/nmdc_submission_schema - multivalued: true - range: uriorcurie - pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$ - name: - name: name - description: A human readable label for an entity - from_schema: https://example.com/nmdc_submission_schema - range: string - multivalued: false - investigation field: - name: investigation field - description: field describing aspect of the investigation/study to which the sample belongs + environment field: + name: environment field + description: field describing environmental aspect of a sample from_schema: https://example.com/nmdc_submission_schema abstract: true - attribute: - name: attribute - description: 'A attribute of a biosample. Examples: depth, habitat, material. For NMDC, attributes SHOULD be mapped to terms within a MIxS template' - from_schema: https://example.com/nmdc_submission_schema - aliases: - - field - - property - - template field - - key - - characteristic - abstract: true biomaterial_purity: name: biomaterial_purity from_schema: https://example.com/nmdc_submission_schema @@ -15234,7 +15240,6 @@ classes: - env_package - experimental_factor - geo_loc_name - - horizon_meth - humidity - lat_lon - methane @@ -15730,32 +15735,6 @@ classes: range: string required: true pattern: '^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$' - horizon_meth: - name: horizon_meth - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' - description: Reference or method used in determining the horizon - title: horizon method - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - soil horizon method - rank: 19 - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000321 - multivalued: false - owner: Biosample - domain_of: - - Biosample - slot_group: mixs_section - range: string humidity: name: humidity annotations: @@ -16465,6 +16444,9 @@ classes: slot_group: mixs_core_section range: string pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ + horizon_meth: + name: horizon_meth + title: horizon method BiofilmInterface: name: BiofilmInterface description: biofilm dh_interface @@ -16510,7 +16492,6 @@ classes: - experimental_factor - geo_loc_name - glucosidase_act - - horizon_meth - lat_lon - magnesium - mean_frict_vel @@ -17488,32 +17469,6 @@ classes: slot_group: mixs_core_section range: string pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ - horizon_meth: - name: horizon_meth - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' - description: Reference or method used in determining the horizon - title: horizon method - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - soil horizon method - rank: 19 - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000321 - multivalued: false - owner: Biosample - domain_of: - - Biosample - slot_group: mixs_section - range: string lat_lon: name: lat_lon description: This is currently a required field but it's not clear if this should be required for human hosts @@ -18785,6 +18740,9 @@ classes: slot_group: mixs_section range: string pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?%? \S.+$ + horizon_meth: + name: horizon_meth + title: horizon method BuiltEnvInterface: name: BuiltEnvInterface description: built_env dh_interface @@ -18879,7 +18837,6 @@ classes: - heat_sys_deliv_meth - heat_system_id - height_carper_fiber - - horizon_meth - indoor_space - indoor_surf - inside_lux @@ -21124,32 +21081,6 @@ classes: slot_group: mixs_core_section range: string pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ - horizon_meth: - name: horizon_meth - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' - description: Reference or method used in determining the horizon - title: horizon method - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - soil horizon method - rank: 19 - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000321 - multivalued: false - owner: Biosample - domain_of: - - Biosample - slot_group: mixs_section - range: string indoor_space: name: indoor_space annotations: @@ -23613,6 +23544,9 @@ classes: - Biosample slot_group: mixs_core_section range: string + horizon_meth: + name: horizon_meth + title: horizon method oxy_stat_samp: name: oxy_stat_samp range: OxyStatSampEnum @@ -23795,7 +23729,6 @@ classes: - hcr_geol_age - hcr_pressure - hcr_temp - - horizon_meth - lat_lon - lithology - magnesium @@ -24940,32 +24873,6 @@ classes: - Biosample slot_group: mixs_core_section range: string - horizon_meth: - name: horizon_meth - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' - description: Reference or method used in determining the horizon - title: horizon method - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - soil horizon method - rank: 19 - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000321 - multivalued: false - owner: Biosample - domain_of: - - Biosample - slot_group: mixs_section - range: string lat_lon: name: lat_lon description: This is currently a required field but it's not clear if this should be required for human hosts @@ -26600,6 +26507,9 @@ classes: slot_group: mixs_core_section range: string pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ + horizon_meth: + name: horizon_meth + title: horizon method HcrFluidsSwabsInterface: name: HcrFluidsSwabsInterface description: hcr_fluids_swabs dh_interface @@ -26655,7 +26565,6 @@ classes: - hcr_geol_age - hcr_pressure - hcr_temp - - horizon_meth - iw_bt_date_well - iwf - lat_lon @@ -27935,32 +27844,6 @@ classes: - Biosample slot_group: mixs_core_section range: string - horizon_meth: - name: horizon_meth - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' - description: Reference or method used in determining the horizon - title: horizon method - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - soil horizon method - rank: 19 - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000321 - multivalued: false - owner: Biosample - domain_of: - - Biosample - slot_group: mixs_section - range: string iw_bt_date_well: name: iw_bt_date_well annotations: @@ -29600,6 +29483,9 @@ classes: slot_group: mixs_core_section range: string pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ + horizon_meth: + name: horizon_meth + title: horizon method HostAssociatedInterface: name: HostAssociatedInterface description: host_associated dh_interface @@ -29631,7 +29517,6 @@ classes: - genetic_mod - geo_loc_name - gravidity - - horizon_meth - host_age - host_body_habitat - host_body_product @@ -30188,32 +30073,6 @@ classes: - Biosample slot_group: mixs_core_section range: string - horizon_meth: - name: horizon_meth - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' - description: Reference or method used in determining the horizon - title: horizon method - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - soil horizon method - rank: 19 - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000321 - multivalued: false - owner: Biosample - domain_of: - - Biosample - slot_group: mixs_section - range: string host_age: name: host_age annotations: @@ -31356,6 +31215,9 @@ classes: slot_group: mixs_section range: string pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ + horizon_meth: + name: horizon_meth + title: horizon method JgiMgInterface: name: JgiMgInterface description: jgi_mg dh_interface @@ -32152,7 +32014,6 @@ classes: - env_package - experimental_factor - geo_loc_name - - horizon_meth - lat_lon - misc_param - nitrate @@ -32946,32 +32807,6 @@ classes: range: string required: true pattern: '^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$' - horizon_meth: - name: horizon_meth - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' - description: Reference or method used in determining the horizon - title: horizon method - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - soil horizon method - rank: 19 - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000321 - multivalued: false - owner: Biosample - domain_of: - - Biosample - slot_group: mixs_section - range: string lat_lon: name: lat_lon description: This is currently a required field but it's not clear if this should be required for human hosts @@ -33882,6 +33717,9 @@ classes: slot_group: mixs_core_section range: string pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ + horizon_meth: + name: horizon_meth + title: horizon method PlantAssociatedInterface: name: PlantAssociatedInterface description: plant_associated dh_interface @@ -33923,7 +33761,6 @@ classes: - growth_habit - growth_hormone_regm - herbicide_regm - - horizon_meth - host_age - host_common_name - host_dry_mass @@ -34772,32 +34609,6 @@ classes: - Biosample slot_group: mixs_core_section range: string - horizon_meth: - name: horizon_meth - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' - description: Reference or method used in determining the horizon - title: horizon method - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - soil horizon method - rank: 19 - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000321 - multivalued: false - owner: Biosample - domain_of: - - Biosample - slot_group: mixs_section - range: string host_age: name: host_age annotations: @@ -36371,6 +36182,9 @@ classes: slot_group: mixs_modified_section range: string recommended: true + horizon_meth: + name: horizon_meth + title: horizon method SedimentInterface: name: SedimentInterface description: sediment dh_interface @@ -36416,7 +36230,6 @@ classes: - experimental_factor - geo_loc_name - glucosidase_act - - horizon_meth - lat_lon - magnesium - mean_frict_vel @@ -37404,32 +37217,6 @@ classes: slot_group: mixs_core_section range: string pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ - horizon_meth: - name: horizon_meth - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' - description: Reference or method used in determining the horizon - title: horizon method - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - soil horizon method - rank: 19 - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000321 - multivalued: false - owner: Biosample - domain_of: - - Biosample - slot_group: mixs_section - range: string lat_lon: name: lat_lon description: This is currently a required field but it's not clear if this should be required for human hosts @@ -38839,6 +38626,9 @@ classes: slot_group: mixs_section range: string pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?%? \S.+$ + horizon_meth: + name: horizon_meth + title: horizon method SoilInterface: name: SoilInterface description: soil dh_interface @@ -41838,7 +41628,6 @@ classes: - experimental_factor - gaseous_substances - geo_loc_name - - horizon_meth - indust_eff_percent - inorg_particles - lat_lon @@ -42380,32 +42169,6 @@ classes: range: string required: true pattern: '^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$' - horizon_meth: - name: horizon_meth - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' - description: Reference or method used in determining the horizon - title: horizon method - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - soil horizon method - rank: 19 - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000321 - multivalued: false - owner: Biosample - domain_of: - - Biosample - slot_group: mixs_section - range: string indust_eff_percent: name: indust_eff_percent annotations: @@ -43415,6 +43178,9 @@ classes: - Biosample slot_group: mixs_core_section range: string + horizon_meth: + name: horizon_meth + title: horizon method WaterInterface: name: WaterInterface description: water dh_interface @@ -44690,32 +44456,6 @@ classes: slot_group: mixs_core_section range: string pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ - horizon_meth: - name: horizon_meth - annotations: - expected_value: - tag: expected_value - value: PMID,DOI or url - occurrence: - tag: occurrence - value: '1' - description: Reference or method used in determining the horizon - title: soil horizon method - examples: - - value: '' - from_schema: https://w3id.org/nmdc/nmdc - aliases: - - soil horizon method - rank: 19 - is_a: core field - string_serialization: '{PMID}|{DOI}|{URL}' - slot_uri: MIXS:0000321 - multivalued: false - owner: Biosample - domain_of: - - Biosample - slot_group: mixs_section - range: string lat_lon: name: lat_lon description: This is currently a required field but it's not clear if this should be required for human hosts