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nmdc.yaml
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id: https://w3id.org/nmdc/nmdc
name: NMDC
title: NMDC Schema
notes:
- "MetaCyc expansion assumes we're talking about metacyc reactions and not genes, compounds etc."
- "informal ## section delimiters should be replaced with subsets ?"
- "commented out insdc_biosample_identifiers insdc_secondary_sample_identifiers... need better understanding of id patterns (at least)"
- "commented out several MIxS terms assigned to Biosample because the definitions of those terms were commented out in mixs.yaml dues to shared slot uris"
description: >-
Schema for National Microbiome Data Collaborative (NMDC).
This schema is organized into multiple modules, such as:
* a set of core types for representing data values
* a subset of the mixs schema
* an annotation schema
* the NMDC schema itself, into which the other modules are imported
license: https://creativecommons.org/publicdomain/zero/1.0/
version: v7.7.6
imports:
- annotation
- core
- external_identifiers
- linkml:types
- mixs
- portal/emsl
- portal/jgi_metagenomics
- portal/jgi_metatranscriptomics
- portal/mixs_inspired
- portal/sample_id
- sample_prep
- workflow_execution_activity
prefixes:
EFO: http://www.ebi.ac.uk/efo/
ISA: http://example.com/isa/
MetaNetX: http://example.com/metanetx/
RetroRules: http://example.com/retrorules/
emsl.project: "https://bioregistry.io/emsl.project:"
generic: https://example.com/generic/
gnps.task: "https://bioregistry.io/gnps.task:"
gtpo: http://example.com/gtpo/
igsn: https://app.geosamples.org/sample/igsn/
jgi.proposal: "https://bioregistry.io/jgi.proposal:"
jgi: http://example.com/jgi/
linkml: https://w3id.org/linkml/
mgnify.proj: "https://identifiers.org/mgnify.proj:"
neon.identifier: http://example.org/neon/identifier/
neon.schema: http://example.org/neon/schema/
nmdc: https://w3id.org/nmdc/
skos: http://www.w3.org/2004/02/skos/core#
prov: http://www.w3.org/ns/prov#
rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
rdfs: http://www.w3.org/2000/01/rdf-schema#
xsd: http://www.w3.org/2001/XMLSchema#
# present in MongoDB
emsl: http://example.org/emsl_in_mongodb/
Contaminant: http://example.org/contaminant/
default_prefix: nmdc
default_range: string
default_curi_maps:
- obo_context
- idot_context
emit_prefixes:
- rdf
- rdfs
- skos
- xsd
settings:
id_nmdc_prefix: "^(nmdc)"
id_shoulder: "([0-9][a-z]{0,6}[0-9])"
id_blade: "([A-Za-z0-9]{1,})"
id_version: "(\\.[A-Za-z0-9]{1,})*"
id_locus: "(_[A-Za-z0-9_\\.-]+)?$"
subsets:
sample subset:
description:
Subset consisting of entities linked to the processing of samples. Currently,
this subset consists of study, omics process, and biosample.
data object subset:
description:
Subset consisting of the data objects that either inputs or outputs
of processes or workflows.
classes:
Database:
tree_root: true
aliases:
- NMDC metadata object
description:
An abstract holder for any set of metadata and data. It does not
need to correspond to an actual managed database top level holder class. When
translated to JSON-Schema this is the 'root' object. It should contain pointers
to other objects of interest
slots:
- library_preparation_set
- processed_sample_set
- extraction_set
- activity_set
- biosample_set
- data_object_set
- dissolving_activity_set
- functional_annotation_set
- genome_feature_set
- mags_activity_set
- material_sample_set
- material_sampling_activity_set
- metabolomics_analysis_activity_set
- metagenome_annotation_activity_set
- metagenome_assembly_set
- metagenome_sequencing_activity_set
- metaproteomics_analysis_activity_set
- metatranscriptome_activity_set
- nom_analysis_activity_set
- omics_processing_set
- reaction_activity_set
- read_qc_analysis_activity_set
- read_based_taxonomy_analysis_activity_set
- study_set
- field_research_site_set
- collecting_biosamples_from_site_set
- date_created
- etl_software_version
- metatranscriptome_activity_set
- pooling_set
- extraction_set
slot_usage:
date_created:
description: TODO
etl_software_version:
description: TODO
metatranscriptome_activity_set:
description: TODO
Pooling:
is_a: PlannedProcess # from core.yaml
slots:
slot_usage:
has_input:
minimum_cardinality: 2
has_output:
minimum_cardinality: 1
maximum_cardinality: 1
id:
required: true
structured_pattern:
syntax: "{id_nmdc_prefix}:poolp-{id_shoulder}-{id_blade}{id_version}{id_locus}"
interpolated: true
Extraction:
is_a: PlannedProcess # from core.yaml
slots:
- extraction_method
- extraction_target
- processing_institution
- protocol_link
- quality_control_report
- sample_mass
slot_usage:
has_input:
required: true
has_output:
required: true
id:
required: true
structured_pattern:
syntax: "{id_nmdc_prefix}:extrp-{id_shoulder}-{id_blade}{id_version}{id_locus}"
interpolated: true
Protocol:
slots:
- url
- name
QualityControlReport:
slots:
- status
- name
LibraryPreparation:
aliases:
- LibraryConstruction
is_a: PlannedProcess # from core.yaml
slots:
- library_preparation_kit
- library_type
- pcr_cycles
- processing_institution
close_mappings:
- OBI:0000711
comments:
- OBI:0000711 specifies a DNA input (but not ONLY a DNA input)
slot_usage:
has_input:
required: true
has_output:
required: true
id:
required: true
structured_pattern:
syntax: "{id_nmdc_prefix}:libprp-{id_shoulder}-{id_blade}{id_version}{id_locus}"
interpolated: true
FieldResearchSite:
aliases:
- research plot
description: A site, outside of a laboratory, from which biosamples may be collected.
is_a: Site
title: Field Research Site
comments:
- Provides grouping of biosamples at level that's more specific than belonging
to the same study
- be very clear that this could be part of a larger site
- In Bioscales, one might say that rhizosphere soil and bulk soil from around
the same plant were obtained at the same site. In this case, the site would
correspond to one tree.
- "might correspond to GOLD's identifier on a page like https://gold.jgi.doe.gov/biosample?id=Gb0305833"
slots:
- cur_vegetation
- elev
- geo_loc_name
- habitat # gold term... enumerated values?
- lat_lon
- local_class
- neon_deims_sdr_link # short-term addition for neon
- neon_eco_type # short-term addition for neon
- neon_soil_type # short-term addition for neon
- part_of
- soil_type
slot_usage:
id:
required: true
structured_pattern:
syntax: "{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}{id_version}{id_locus}"
interpolated: true
CollectingBiosamplesFromSite:
is_a: PlannedProcess
title: Collecting Biosamples From Site
comments:
- "this illustrates implementing a Biosample relation with a process class"
slot_usage:
has_input:
range: Site
# range: NamedThing
required: true
has_output:
range: Biosample
required: true
id:
required: true
structured_pattern:
syntax: "{id_nmdc_prefix}:clsite-{id_shoulder}-{id_blade}{id_version}{id_locus}"
interpolated: true
DataObject:
is_a: NamedThing
in_subset:
- data object subset
description:
"An object that primarily consists of symbols that represent information. Files,
records, and omics data are examples of data objects."
notes:
- removed previous id_prefixes value of GOLD, since we are now using pattern-based id validation
slots:
- file_size_bytes
- md5_checksum
- data_object_type
- compression_type
- was_generated_by
- url
- type
slot_usage:
name:
required: true
description:
required: true
id:
required: true
structured_pattern:
syntax: "{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}{id_version}{id_locus}"
interpolated: true
comments:
- removed id_prefixes value of GOLD, since we are now using pattern-based id validation
Biosample:
rules:
- title: dna_well_requires_plate
description: DNA samples shipped to JGI for metagenomic analysis in tubes can't have any value for their plate position.
preconditions:
slot_conditions:
dna_cont_well:
pattern: ".+"
postconditions:
slot_conditions:
dna_cont_type:
equals_string: plate
- title: dna_plate_requires_well
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
preconditions:
slot_conditions:
dna_cont_type:
equals_string: plate
postconditions:
slot_conditions:
dna_cont_well:
pattern: ^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$
- title: rna_well_requires_plate
description: RNA samples shipped to JGI for metagenomic analysis in tubes can't have any value for their plate position.
preconditions:
slot_conditions:
rna_cont_well:
pattern: ".+"
postconditions:
slot_conditions:
rna_cont_type:
equals_string: plate
- title: rna_plate_requires_well
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
preconditions:
slot_conditions:
rna_cont_type:
equals_string: plate
postconditions:
slot_conditions:
rna_cont_well:
pattern: ^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$
unique_keys:
samp_name_unique_key:
notes:
- "id is already required to be unique because it is the identifier in Biosample's parent class, NamedThing. Remember, notes like this could be exposed to end users. CJM suggested YAML # comment"
unique_key_slots:
- samp_name
is_a: MaterialEntity
in_subset:
- sample subset
aliases:
- sample
- material sample
- specimen
- biospecimen
description: >-
Biological source material which can be characterized by an experiment.
todos:
- could add GOLD and EBI's biosample definitions to the alt_descriptions?
notes:
- removed previous id_prefixes value of GOLD, since we are now using pattern-based id validation
alt_descriptions:
embl.ena:
A sample contains information about the sequenced source material.
Samples are associated with checklists, which define the fields used to annotate
the samples. Samples are always associated with a taxon.
slots:
- neon_biosample_identifiers
- host_taxid
- embargoed
- collected_from
- type
- img_identifiers
- samp_name
- biosample_categories
- type
- part_of
## Identifiers
- id
- alternative_identifiers
## external IDs, alternate IDs
- gold_biosample_identifiers
- insdc_biosample_identifiers
# - insdc_secondary_sample_identifiers
- emsl_biosample_identifiers
- igsn_biosample_identifiers
## MIXS slots
# - horizon
# - horizon_meth
# - microbial_biomass
# - microbial_biomass_meth
# - previous_land_use
# - previous_land_use_meth
# - samp_collect_device
# - texture
# - texture_meth
- abs_air_humidity
- add_recov_method
- additional_info
- address
- adj_room
- aero_struc
- agrochem_addition
- air_PM_concen
- air_temp
- air_temp_regm
- al_sat
- al_sat_meth
- alkalinity
- alkalinity_method
- alkyl_diethers
- alt
- aminopept_act
- ammonium
- ammonium_nitrogen
- amount_light
- ances_data
- annual_precpt
- annual_temp
- antibiotic_regm
- api
- arch_struc
- aromatics_pc
- asphaltenes_pc
- atmospheric_data
- avg_dew_point
- avg_occup
- avg_temp
- bac_prod
- bac_resp
- bacteria_carb_prod
- barometric_press
- basin
- bathroom_count
- bedroom_count
- benzene
- biochem_oxygen_dem
- biocide
- biocide_admin_method
- biol_stat
- biomass
- biotic_regm
- biotic_relationship
- bishomohopanol
- blood_press_diast
- blood_press_syst
- bromide
- build_docs
- build_occup_type
- building_setting
- built_struc_age
- built_struc_set
- built_struc_type
- calcium
- carb_dioxide
- carb_monoxide
- carb_nitro_ratio
- ceil_area
- ceil_cond
- ceil_finish_mat
- ceil_struc
- ceil_texture
- ceil_thermal_mass
- ceil_type
- ceil_water_mold
- chem_administration
- chem_mutagen
- chem_oxygen_dem
- chem_treat_method
- chem_treatment
- chimera_check
- chloride
- chlorophyll
- climate_environment
- collection_date
- conduc
- cool_syst_id
- core field
- crop_rotation
- cult_root_med
- cur_land_use
- cur_vegetation
- cur_vegetation_meth
- date_last_rain
- density
- depos_env
- depth
- dew_point
- diether_lipids
- diss_carb_dioxide
- diss_hydrogen
- diss_inorg_carb
- diss_inorg_nitro
- diss_inorg_phosp
- diss_iron
- diss_org_carb
- diss_org_nitro
- diss_oxygen
- diss_oxygen_fluid
- dna_cont_well
- 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
- down_par
- drainage_class
- drawings
- ecosystem
- ecosystem_category
- ecosystem_subtype
- ecosystem_type
- efficiency_percent
- elev
- elevator
- emulsions
- env_broad_scale
- env_local_scale
- env_medium
- env_package
- environment field
- escalator
- ethylbenzene
- exp_duct
- exp_pipe
- experimental_factor
- ext_door
- ext_wall_orient
- ext_window_orient
- extreme_event
- fao_class
- fertilizer_regm
- field
- filter_type
- fire
- fireplace_type
- flooding
- floor_age
- floor_area
- floor_cond
- floor_count
- floor_finish_mat
- floor_struc
- floor_thermal_mass
- floor_water_mold
- fluor
- freq_clean
- freq_cook
- fungicide_regm
- furniture
- gaseous_environment
- gaseous_substances
- gender_restroom
- genetic_mod
- geo_loc_name
- glucosidase_act
- gravidity
- gravity
- growth_facil
- growth_habit
- growth_hormone_regm
- hall_count
- handidness
- has numeric value
- has raw value
- has unit
- hc_produced
- hcr
- hcr_fw_salinity
- hcr_geol_age
- hcr_pressure
- hcr_temp
- heat_cool_type
- heat_deliv_loc
- heat_sys_deliv_meth
- heat_system_id
- heavy_metals
- heavy_metals_meth
- height_carper_fiber
- herbicide_regm
- 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
- host_wet_mass
- humidity
- humidity_regm
- indoor_space
- indoor_surf
- indust_eff_percent
- inorg_particles
- inside_lux
- int_wall_cond
- investigation field
- iw_bt_date_well
- iwf
- last_clean
- lat_lon
- lbc_thirty
- lbceq
- light_intensity
- light_regm
- light_type
- link_addit_analys
- link_class_info
- link_climate_info
- lithology
- local_class
- local_class_meth
- magnesium
- manganese
- max_occup
- mean_frict_vel
- mean_peak_frict_vel
- mech_struc
- mechanical_damage
- methane
- micro_biomass_meth
- microbial_biomass
- mineral_nutr_regm
- misc_param
- n_alkanes
- nitrate
- nitrate_nitrogen
- nitrite
- nitrite_nitrogen
- nitro
- non_min_nutr_regm
- nucl_acid_amp
- nucl_acid_ext
- nucleic acid sequence source field
- number_pets
- number_plants
- number_resident
- occup_density_samp
- occup_document
- occup_samp
- org_carb
- org_count_qpcr_info
- org_matter
- org_nitro
- org_particles
- organism_count
- owc_tvdss
- oxy_stat_samp
- oxygen
- part_org_carb
- part_org_nitro
- particle_class
- pcr_cond
- pcr_primers
- permeability
- perturbation
- pesticide_regm
- petroleum_hydrocarb
- ph
- ph_meth
- ph_regm
- phaeopigments
- phosphate
- phosplipid_fatt_acid
- photon_flux
- plant_growth_med
- plant_product
- plant_sex
- plant_struc
- pollutants
- pool_dna_extracts
- porosity
- potassium
- pour_point
- pre_treatment
- pres_animal_insect
- pressure
- prev_land_use_meth
- previous_land_use
- primary_prod
- primary_treatment
- prod_rate
- prod_start_date
- profile_position
- quad_pos
- radiation_regm
- rainfall_regm
- reactor_type
- redox_potential
- rel_air_humidity
- rel_humidity_out
- rel_samp_loc
- reservoir
- resins_pc
- 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
- root_cond
- root_med_carbon
- root_med_macronutr
- root_med_micronutr
- root_med_ph
- root_med_regl
- root_med_solid
- root_med_suppl
- salinity
- salinity_meth
- salt_regm
- samp_capt_status
- samp_collec_device
- samp_collec_method
- samp_collect_point
- samp_dis_stage
- samp_floor
- samp_loc_corr_rate
- samp_mat_process
- samp_md
- samp_name
- samp_preserv
- samp_room_id
- samp_size
- samp_sort_meth
- samp_store_dur
- samp_store_loc
- samp_store_temp
- samp_subtype
- samp_taxon_id
- samp_time_out
- samp_transport_cond
- samp_tvdss
- samp_type
- samp_vol_we_dna_ext
- samp_weather
- samp_well_name
- saturates_pc
- season
- season_environment
- season_precpt
- season_temp
- season_use
- secondary_treatment
- sediment_type
- seq_meth
- seq_quality_check
- sequencing field
- sewage_type
- shad_dev_water_mold
- shading_device_cond
- shading_device_loc
- shading_device_mat
- shading_device_type
- sieving
- silicate
- size_frac
- size_frac_low
- size_frac_up
- slope_aspect
- slope_gradient
- sludge_retent_time
- sodium
- soil_horizon
- soil_text_measure
- soil_texture_meth
- soil_type
- soil_type_meth
- solar_irradiance
- soluble_inorg_mat
- soluble_org_mat
- soluble_react_phosp
- source_mat_id
- space_typ_state
- specific
- specific_ecosystem
- specific_humidity
- sr_dep_env
- sr_geol_age
- sr_kerog_type
- sr_lithology
- standing_water_regm
- store_cond
- substructure_type
- sulfate
- sulfate_fw
- sulfide
- surf_air_cont
- surf_humidity
- surf_material
- surf_moisture
- surf_moisture_ph
- surf_temp
- suspend_part_matter
- suspend_solids
- tan
- target_gene
- target_subfragment
- temp
- temp_out
- tertiary_treatment
- tidal_stage
- tillage
- tiss_cult_growth_med
- toluene
- tot_carb
- tot_depth_water_col
- tot_diss_nitro
- tot_inorg_nitro
- tot_iron
- tot_nitro
- tot_nitro_cont_meth
- tot_nitro_content
- tot_org_c_meth
- tot_org_carb
- tot_part_carb
- tot_phosp
- tot_phosphate
- tot_sulfur
- train_line
- train_stat_loc
- train_stop_loc
- turbidity
- tvdss_of_hcr_press
- tvdss_of_hcr_temp
- typ_occup_density
- ventilation_rate
- ventilation_type
- vfa
- vfa_fw
- vis_media
- viscosity
- volatile_org_comp
- wall_area
- wall_const_type
- wall_finish_mat
- wall_height
- wall_loc
- wall_surf_treatment
- wall_texture
- wall_thermal_mass
- wall_water_mold
- wastewater_type
- water_cont_soil_meth
- water_content
- water_current
- water_cut
- water_feat_size
- water_feat_type
- water_prod_rate
- water_temp_regm
- watering_regm
- weekday
- win
- wind_direction
- wind_speed
- 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
- xylene
- zinc
## GOLD path fields
- ecosystem
- ecosystem_category
- ecosystem_type
- ecosystem_subtype
- specific_ecosystem
## GOLD specific fields
- add_date
- community
- habitat
- host_name
- location
- mod_date
- ncbi_taxonomy_name
- proport_woa_temperature
- salinity_category
- sample_collection_site
- soluble_iron_micromol
- subsurface_depth
## MIxS terms initially used in
## sample metadata submission portal (aka DataHarmonizer)
- air_temp_regm
- biotic_regm
- biotic_relationship
- climate_environment
- experimental_factor
- gaseous_environment
- growth_facil
- humidity_regm
- light_regm
# - micro_biomass_meth
- phosphate
- samp_collec_method
- samp_size
# - soil_text_measure
# - soil_texture_meth
- source_mat_id
- watering_regm
## sample metadata submission portal (aka DataHarmonizer) terms (EMSL, JGI, etc.)
## JGI fields
- dna_absorb1
- dna_absorb2
- dna_collect_site
- dna_concentration
- dna_cont_type
- dna_cont_well
- dna_container_id
- dna_dnase
- dna_isolate_meth
- dna_organisms
- dna_project_contact
- dna_samp_id
- dna_sample_format
- dna_sample_name
- dna_seq_project
- dna_seq_project_pi
- dna_seq_project_name
- dna_volume
- proposal_dna
- dnase_rna
- proposal_rna
- rna_absorb1
- rna_absorb2
- rna_collect_site
- rna_concentration
- rna_cont_type
- rna_cont_well
- rna_container_id
- rna_isolate_meth
- rna_organisms
- rna_project_contact
- rna_samp_id
- rna_sample_format
- rna_sample_name
- rna_seq_project
- rna_seq_project_pi
- rna_seq_project_name
- rna_volume