From dbc168c478cd8197d289678f24bd3e39ac409510 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Wed, 6 Nov 2024 09:19:30 -0800 Subject: [PATCH 1/9] stash progress --- .../scripts/generate_env_triad_enums.py | 59 +++++++++++++++++++ tests/inputs/env_local_input_example.tsv | 4 ++ tests/test_env_triad.py | 35 +++++++++++ 3 files changed, 98 insertions(+) create mode 100644 src/nmdc_submission_schema/scripts/generate_env_triad_enums.py create mode 100644 tests/inputs/env_local_input_example.tsv create mode 100644 tests/test_env_triad.py diff --git a/src/nmdc_submission_schema/scripts/generate_env_triad_enums.py b/src/nmdc_submission_schema/scripts/generate_env_triad_enums.py new file mode 100644 index 00000000..55288dba --- /dev/null +++ b/src/nmdc_submission_schema/scripts/generate_env_triad_enums.py @@ -0,0 +1,59 @@ +import json +from collections import defaultdict +from enum import Enum +from pathlib import Path +from typing import Dict, Set, Iterable, Optional + +import click +from linkml_runtime import SchemaView +from linkml_runtime.dumpers import yaml_dumper +from linkml_runtime.linkml_model import EnumDefinition, PermissibleValue, SchemaDefinition +from linkml_runtime.loaders import yaml_loader +import csv + + +def parse_tsv_to_dict(file_path): + """ + Parse a TSV file into a dictionary. + Assumes the first column is the key, and the rest are values. + + :param file_path: Path to the TSV file. + :return: Dictionary with the first column as keys and rows as values. + """ + data_dict = {} + + with open(file_path, mode='r', newline='', encoding='utf-8') as file: + reader = csv.reader(file, delimiter='\t') + for row in reader: + if row: + # Use the first column as the key and the rest as values + key = row[0] + values = row[1:] if len(row) > 1 else [] + data_dict[key] = values + + return data_dict + + +def inject_env_local_scale_terms (env_local_path: Path, input_schema_path: SchemaDefinition) -> SchemaDefinition: + """Inject gold pathway terms into the schema.""" + data = parse_tsv_to_dict(env_local_path) + print(data) + schemaview = SchemaView(input_schema_path) + + for term in data: + pvs = [PermissibleValue(text=term_id) for term in data] + schemaview.add_enum(EnumDefinition( + name='EnvironmentalTriadLocalEnum', + permissible_values=pvs + )) + + return schemaview.schema + +@click.command() +@click.option('--env-local-file', '-g', type=click.Path(exists=True)) +@click.option('--schema-input-file', '-i', type=click.File('r'), default="-") +@click.option('--schema-output-file', '-o', type=click.File('w'), default="-") +def main(env_local_file, input_file, output_file): + schema = yaml_loader.loads(input_file.read(), SchemaDefinition) + output = inject_env_local_scale_terms(Path(env_local_file), schema) + print(yaml_dumper.dumps(output), file=output_file) diff --git a/tests/inputs/env_local_input_example.tsv b/tests/inputs/env_local_input_example.tsv new file mode 100644 index 00000000..1c36a292 --- /dev/null +++ b/tests/inputs/env_local_input_example.tsv @@ -0,0 +1,4 @@ +term_id term_name +ENVO:00000077 agricultural soil +ENVO:00000170 dune soil +ENVO:00000111 forest soil diff --git a/tests/test_env_triad.py b/tests/test_env_triad.py new file mode 100644 index 00000000..819dfdef --- /dev/null +++ b/tests/test_env_triad.py @@ -0,0 +1,35 @@ +import pytest +from pathlib import Path +from click.testing import CliRunner +from src.nmdc_submission_schema.scripts.generate_env_triad_enums import main +from linkml_runtime.loaders import yaml_loader + +def test_inject_env_local_scale_terms_cli(): + runner = CliRunner() + + # Run the CLI command with the --env-local-file, --schema-input-file, and --schema-output-file options + result = runner.invoke( + main, + [ + "--env-local-file", str("/Users/SMoxon/Documents/src/submission-schema/tests/input/env_local_input_examlpe.tsv"), + "--schema-input-file", str("/Users/SMoxon/Documents/src/submission-schema/src/nmdc_submission_schema/schema/nmdc_submission_schema_base.yaml"), + "--schema-output-file", str("/Users/SMoxon/Documents/src/submission-schema/src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml") + ] + ) + + output_file = tmp_path / "output_schema.yaml" + + # Check that the command completed successfully + assert result.exit_code == 0, f"CLI command failed with error: {result.output}" + + output_schema = yaml_loader.load(output_file, SchemaDefinition) + + # Verify the enum was added to the schema + assert 'EnvironmentalTriadLocalEnum' in output_schema.enums + enum_def = output_schema.enums['EnvironmentalTriadLocalEnum'] + + # Check permissible values + expected_terms = ["TERM1", "TERM2", "TERM3"] + actual_terms = [pv.text for pv in enum_def.permissible_values] + + assert set(expected_terms) == set(actual_terms), "Permissible values do not match expected terms" From 816e16684ad629c443264b2e8fa9efb25dc85f0e Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Wed, 6 Nov 2024 12:06:18 -0800 Subject: [PATCH 2/9] add all three existing TSVs to the loading --- ...t_google_sheets_soil_env_medium_scale.tsv} | 0 poetry.lock | 2 +- pyproject.toml | 1 + .../schema/nmdc_submission_schema.yaml | 21607 +++++++++------- .../scripts/generate_env_triad_enums.py | 109 +- tests/test_env_triad.py | 2 + 6 files changed, 12515 insertions(+), 9206 deletions(-) rename notebooks/{post_google_sheets_soil_env_medium.tsv => post_google_sheets_soil_env_medium_scale.tsv} (100%) diff --git a/notebooks/post_google_sheets_soil_env_medium.tsv b/notebooks/post_google_sheets_soil_env_medium_scale.tsv similarity index 100% rename from notebooks/post_google_sheets_soil_env_medium.tsv rename to notebooks/post_google_sheets_soil_env_medium_scale.tsv diff --git a/poetry.lock b/poetry.lock index 3b78fc5e..98e3ea21 100644 --- a/poetry.lock +++ b/poetry.lock @@ -5964,4 +5964,4 @@ docs = [] [metadata] lock-version = "2.0" python-versions = "^3.9" -content-hash = "50f4e49d19751ca9a10414298890fd01e422b86c54c7e6c00e1dc33861ae8b5e" +content-hash = "dd041016cd4cc58ca23273b05fef79a60be0cfa29ef7d89e947b2ac9831ac140" diff --git a/pyproject.toml b/pyproject.toml index e12928d4..535cb997 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -22,6 +22,7 @@ python = "^3.9" linkml-runtime = "^1.6.2" textdistance = "^4.6.3" jupyter-datatables = "^0.3.9" +click = "^8.1.7" [tool.poetry.group.dev.dependencies] exhaustion-check = "^0.1.3" diff --git a/src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml b/src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml index a6385e12..e9b6ba71 100644 --- a/src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml +++ b/src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml @@ -1,5 +1,6 @@ name: nmdc_submission_schema -description: Schema for creating Data Harmonizer interfaces for biosamples based on MIxS and other standards +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: @@ -291,14 +292,18 @@ subsets: 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. + description: Subset consisting of the data objects that either inputs or outputs + of processes or workflows. from_schema: https://example.com/nmdc_submission_schema data_portal_subset: name: data_portal_subset - description: Subset consisting of entities that Kitware/nmdc-server use to populate the data portal. + description: Subset consisting of entities that Kitware/nmdc-server use to populate + the data portal. comments: - - Schema authors are responsible for alerting and supporting Kitware and nmdc-server authors about changes they will have to make if entities labeled with data_portal_subset are modified. - - Assignment of the data_portal_subset is incomplete in the schema. + - Schema authors are responsible for alerting and supporting Kitware and nmdc-server + authors about changes they will have to make if entities labeled with data_portal_subset + are modified. + - Assignment of the data_portal_subset is incomplete in the schema. from_schema: https://example.com/nmdc_submission_schema environment: name: environment @@ -314,7 +319,8 @@ subsets: from_schema: https://example.com/nmdc_submission_schema 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. + 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 sequencing: name: sequencing @@ -328,11 +334,11 @@ types: name: unit description: a string representation of a unit notes: - - why isn't this picked up from the nmdc.yaml import? + - why isn't this picked up from the nmdc.yaml import? from_schema: https://example.com/nmdc_submission_schema mappings: - - qud:Unit - - UO:0000000 + - qud:Unit + - UO:0000000 base: str uri: xsd:string decimal degree: @@ -351,27 +357,31 @@ types: name: float description: A real number that conforms to the xsd:float specification notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "float". + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "float". from_schema: https://example.com/nmdc_submission_schema exact_mappings: - - schema:Float + - schema:Float base: float uri: xsd:float string: name: string description: A character string notes: - - In RDF serializations, a slot with range of string is treated as a literal or type xsd:string. If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "string". + - In RDF serializations, a slot with range of string is treated as a literal or + type xsd:string. If you are authoring schemas in LinkML YAML, the type is + referenced with the lower case "string". from_schema: https://example.com/nmdc_submission_schema exact_mappings: - - schema:Text + - schema:Text base: str uri: xsd:string uriorcurie: name: uriorcurie description: a URI or a CURIE notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "uriorcurie". + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "uriorcurie". from_schema: https://example.com/nmdc_submission_schema base: URIorCURIE uri: xsd:anyURI @@ -380,52 +390,59 @@ types: name: integer description: An integer notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "integer". + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "integer". from_schema: https://example.com/nmdc_submission_schema exact_mappings: - - schema:Integer + - schema:Integer base: int uri: xsd:integer double: name: double description: A real number that conforms to the xsd:double specification notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "double". + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "double". from_schema: https://example.com/nmdc_submission_schema close_mappings: - - schema:Float + - schema:Float base: float uri: xsd:double decimal: name: decimal - description: A real number with arbitrary precision that conforms to the xsd:decimal specification + description: A real number with arbitrary precision that conforms to the xsd:decimal + specification notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "decimal". + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "decimal". from_schema: https://example.com/nmdc_submission_schema broad_mappings: - - schema:Number + - schema:Number base: Decimal uri: xsd:decimal boolean: name: boolean description: A binary (true or false) value notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "boolean". + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "boolean". from_schema: https://example.com/nmdc_submission_schema exact_mappings: - - schema:Boolean + - schema:Boolean base: Bool uri: xsd:boolean repr: bool time: name: time - description: A time object represents a (local) time of day, independent of any particular day + 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 - - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "time". + - URI is dateTime because OWL reasoners do not work with straight date or time + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "time". from_schema: https://example.com/nmdc_submission_schema exact_mappings: - - schema:Time + - schema:Time base: XSDTime uri: xsd:time repr: str @@ -433,11 +450,12 @@ types: 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 - - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "date". + - URI is dateTime because OWL reasoners don't work with straight date or time + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "date". from_schema: https://example.com/nmdc_submission_schema exact_mappings: - - schema:Date + - schema:Date base: XSDDate uri: xsd:date repr: str @@ -445,10 +463,11 @@ types: name: datetime description: The combination of a date and time notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "datetime". + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "datetime". from_schema: https://example.com/nmdc_submission_schema exact_mappings: - - schema:DateTime + - schema:DateTime base: XSDDateTime uri: xsd:dateTime repr: str @@ -456,7 +475,8 @@ types: name: date_or_datetime description: Either a date or a datetime notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "date_or_datetime". + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "date_or_datetime". from_schema: https://example.com/nmdc_submission_schema base: str uri: linkml:DateOrDatetime @@ -466,10 +486,11 @@ types: conforms_to: https://www.w3.org/TR/curie/ description: a compact URI notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "curie". + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "curie". comments: - - in RDF serializations this MUST be expanded to a URI - - in non-RDF serializations MAY be serialized as the compact representation + - 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 @@ -479,12 +500,15 @@ types: conforms_to: https://www.ietf.org/rfc/rfc3987.txt description: a complete URI notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "uri". + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "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 + - 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 + - schema:URL base: URI uri: xsd:anyURI repr: str @@ -492,7 +516,8 @@ types: name: ncname description: Prefix part of CURIE notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "ncname". + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "ncname". from_schema: https://example.com/nmdc_submission_schema base: NCName uri: xsd:string @@ -501,9 +526,10 @@ types: name: objectidentifier description: A URI or CURIE that represents an object in the model. notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "objectidentifier". + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "objectidentifier". comments: - - Used for inheritance and type checking + - Used for inheritance and type checking from_schema: https://example.com/nmdc_submission_schema base: ElementIdentifier uri: shex:iri @@ -512,7 +538,8 @@ types: name: nodeidentifier description: A URI, CURIE or BNODE that represents a node in a model. notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "nodeidentifier". + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "nodeidentifier". from_schema: https://example.com/nmdc_submission_schema base: NodeIdentifier uri: shex:nonLiteral @@ -520,9 +547,12 @@ types: jsonpointer: name: jsonpointer conforms_to: https://datatracker.ietf.org/doc/html/rfc6901 - description: A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. + description: A string encoding a JSON Pointer. The value of the string MUST conform + to JSON Point syntax and SHOULD dereference to a valid object within the current + instance document when encoded in tree form. notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "jsonpointer". + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "jsonpointer". from_schema: https://example.com/nmdc_submission_schema base: str uri: xsd:string @@ -530,9 +560,12 @@ types: jsonpath: name: jsonpath conforms_to: https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html - description: A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. + description: A string encoding a JSON Path. The value of the string MUST conform + to JSON Point syntax and SHOULD dereference to zero or more valid objects within + the current instance document when encoded in tree form. notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "jsonpath". + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "jsonpath". from_schema: https://example.com/nmdc_submission_schema base: str uri: xsd:string @@ -540,9 +573,12 @@ types: sparqlpath: name: sparqlpath conforms_to: https://www.w3.org/TR/sparql11-query/#propertypaths - description: A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. + description: A string encoding a SPARQL Property Path. The value of the string + MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects + within the current instance document when encoded as RDF. notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "sparqlpath". + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "sparqlpath". from_schema: https://example.com/nmdc_submission_schema base: str uri: xsd:string @@ -559,13 +595,13 @@ enums: tag: sntc_name value: samp_biotic_relationship notes: - - 'biotic_relationship_enum: free living' - - parasitism - - commensalism - - symbiotic - - mutualism + - 'biotic_relationship_enum: free living' + - parasitism + - commensalism + - symbiotic + - mutualism see_also: - - https://genomicsstandardsconsortium.github.io/mixs/biotic_relationship_enum/ + - https://genomicsstandardsconsortium.github.io/mixs/biotic_relationship_enum/ free living: text: free living mutualism: @@ -613,7 +649,8 @@ enums: soil: text: soil notes: - - I don't think this is a MIxS term anymore, so it make sense to define it here + - I don't think this is a MIxS term anymore, so it make sense to define it + here GrowthFacilEnum: name: GrowthFacilEnum from_schema: https://example.com/nmdc_submission_schema @@ -625,9 +662,9 @@ enums: tag: sntc_name value: growth_facility notes: - - string range according to MIxS + - string range according to MIxS see_also: - - https://genomicsstandardsconsortium.github.io/mixs/growth_facil/ + - https://genomicsstandardsconsortium.github.io/mixs/growth_facil/ field: text: field field_incubation: @@ -655,7 +692,7 @@ enums: tag: sntc_name value: oxygen_relationship see_also: - - https://genomicsstandardsconsortium.github.io/mixs/rel_to_oxygen_enum/ + - https://genomicsstandardsconsortium.github.io/mixs/rel_to_oxygen_enum/ anaerobe: text: anaerobe facultative: @@ -717,7 +754,8 @@ enums: 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). + - 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 lyophilized: @@ -733,118 +771,6 @@ enums: text: 'no' 'yes': text: 'yes' - EnvBroadScaleSoilEnum: - name: EnvBroadScaleSoilEnum - from_schema: https://example.com/nmdc_submission_schema - permissible_values: - arid biome [ENVO:01001838]: - text: arid biome [ENVO:01001838] - subalpine biome [ENVO:01001837]: - text: subalpine biome [ENVO:01001837] - montane biome [ENVO:01001836]: - text: montane biome [ENVO:01001836] - __montane savanna biome [ENVO:01000223]: - text: __montane savanna biome [ENVO:01000223] - __montane shrubland biome [ENVO:01000216]: - text: __montane shrubland biome [ENVO:01000216] - alpine biome [ENVO:01001835]: - text: alpine biome [ENVO:01001835] - __alpine tundra biome [ENVO:01001505]: - text: __alpine tundra biome [ENVO:01001505] - subpolar biome [ENVO:01001834]: - text: subpolar biome [ENVO:01001834] - subtropical biome [ENVO:01001832]: - text: subtropical biome [ENVO:01001832] - __mediterranean biome [ENVO:01001833]: - text: __mediterranean biome [ENVO:01001833] - ____mediterranean savanna biome [ENVO:01000229]: - text: ____mediterranean savanna biome [ENVO:01000229] - ____mediterranean shrubland biome [ENVO:01000217]: - text: ____mediterranean shrubland biome [ENVO:01000217] - ____mediterranean woodland biome [ENVO:01000208]: - text: ____mediterranean woodland biome [ENVO:01000208] - __subtropical woodland biome [ENVO:01000222]: - text: __subtropical woodland biome [ENVO:01000222] - __subtropical shrubland biome [ENVO:01000213]: - text: __subtropical shrubland biome [ENVO:01000213] - __subtropical savanna biome [ENVO:01000187]: - text: __subtropical savanna biome [ENVO:01000187] - temperate biome [ENVO:01001831]: - text: temperate biome [ENVO:01001831] - __temperate woodland biome [ENVO:01000221]: - text: __temperate woodland biome [ENVO:01000221] - __temperate shrubland biome [ENVO:01000215]: - text: __temperate shrubland biome [ENVO:01000215] - __temperate savanna biome [ENVO:01000189]: - text: __temperate savanna biome [ENVO:01000189] - tropical biome [ENVO:01001830]: - text: tropical biome [ENVO:01001830] - __tropical woodland biome [ENVO:01000220]: - text: __tropical woodland biome [ENVO:01000220] - __tropical shrubland biome [ENVO:01000214]: - text: __tropical shrubland biome [ENVO:01000214] - __tropical savanna biome [ENVO:01000188]: - text: __tropical savanna biome [ENVO:01000188] - polar biome [ENVO:01000339]: - text: polar biome [ENVO:01000339] - terrestrial biome [ENVO:00000446]: - text: terrestrial biome [ENVO:00000446] - __anthropogenic terrestrial biome [ENVO:01000219]: - text: __anthropogenic terrestrial biome [ENVO:01000219] - ____dense settlement biome [ENVO:01000248]: - text: ____dense settlement biome [ENVO:01000248] - ______urban biome [ENVO:01000249]: - text: ______urban biome [ENVO:01000249] - ____rangeland biome [ENVO:01000247]: - text: ____rangeland biome [ENVO:01000247] - ____village biome [ENVO:01000246]: - text: ____village biome [ENVO:01000246] - __mangrove biome [ENVO:01000181]: - text: __mangrove biome [ENVO:01000181] - __tundra biome [ENVO:01000180]: - text: __tundra biome [ENVO:01000180] - ____alpine tundra biome [ENVO:01001505]: - text: ____alpine tundra biome [ENVO:01001505] - __shrubland biome [ENVO:01000176]: - text: __shrubland biome [ENVO:01000176] - ____tidal mangrove shrubland [ENVO:01001369]: - text: ____tidal mangrove shrubland [ENVO:01001369] - ____xeric shrubland biome [ENVO:01000218]: - text: ____xeric shrubland biome [ENVO:01000218] - ____montane shrubland biome [ENVO:01000216]: - text: ____montane shrubland biome [ENVO:01000216] - ____temperate shrubland biome [ENVO:01000215]: - text: ____temperate shrubland biome [ENVO:01000215] - ____tropical shrubland biome [ENVO:01000214]: - text: ____tropical shrubland biome [ENVO:01000214] - ____subtropical shrubland biome [ENVO:01000213]: - text: ____subtropical shrubland biome [ENVO:01000213] - ______mediterranean shrubland biome [ENVO:01000217]: - text: ______mediterranean shrubland biome [ENVO:01000217] - __woodland biome [ENVO:01000175]: - text: __woodland biome [ENVO:01000175] - ____subtropical woodland biome [ENVO:01000222]: - text: ____subtropical woodland biome [ENVO:01000222] - ______mediterranean woodland biome [ENVO:01000208]: - text: ______mediterranean woodland biome [ENVO:01000208] - ____temperate woodland biome [ENVO:01000221]: - text: ____temperate woodland biome [ENVO:01000221] - ____tropical woodland biome [ENVO:01000220]: - text: ____tropical woodland biome [ENVO:01000220] - ____savanna biome [ENVO:01000178]: - text: ____savanna biome [ENVO:01000178] - ______montane savanna biome [ENVO:01000223]: - text: ______montane savanna biome [ENVO:01000223] - ______flooded savanna biome [ENVO:01000190]: - text: ______flooded savanna biome [ENVO:01000190] - ______temperate savanna biome [ENVO:01000189]: - text: ______temperate savanna biome [ENVO:01000189] - ______tropical savanna biome [ENVO:01000188]: - text: ______tropical savanna biome [ENVO:01000188] - ______subtropical savanna biome [ENVO:01000187]: - text: ______subtropical savanna biome [ENVO:01000187] - ________mediterranean savanna biome [ENVO:01000229]: - text: ________mediterranean savanna biome [ENVO:01000229] EnvMediumSoilEnum: name: EnvMediumSoilEnum from_schema: https://example.com/nmdc_submission_schema @@ -1053,194 +979,6 @@ enums: text: anthrosol [ENVO:00002230] arenosol [ENVO:00002229]: text: arenosol [ENVO:00002229] - EnvLocalScaleSoilEnum: - name: EnvLocalScaleSoilEnum - from_schema: https://example.com/nmdc_submission_schema - permissible_values: - astronomical body part [ENVO:01000813]: - text: astronomical body part [ENVO:01000813] - __coast [ENVO:01000687]: - text: __coast [ENVO:01000687] - __solid astronomical body part [ENVO:00000191]: - text: __solid astronomical body part [ENVO:00000191] - ______landform [ENVO:01001886]: - text: ______landform [ENVO:01001886] - ______channel [ENVO:03000117]: - text: ______channel [ENVO:03000117] - ________tunnel [ENVO:00000068]: - text: ________tunnel [ENVO:00000068] - ______surface landform [ENVO:01001884]: - text: ______surface landform [ENVO:01001884] - ________desert [ENVO:01001357]: - text: ________desert [ENVO:01001357] - ________outcrop [ENVO:01000302]: - text: ________outcrop [ENVO:01000302] - ________boulder field [ENVO:00000537]: - text: ________boulder field [ENVO:00000537] - ________landfill [ENVO:00000533]: - text: ________landfill [ENVO:00000533] - ________hummock [ENVO:00000516]: - text: ________hummock [ENVO:00000516] - ________terrace [ENVO:00000508]: - text: ________terrace [ENVO:00000508] - ________peninsula [ENVO:00000305]: - text: ________peninsula [ENVO:00000305] - ________shore [ENVO:00000304]: - text: ________shore [ENVO:00000304] - __________lake shore [ENVO:00000382]: - text: __________lake shore [ENVO:00000382] - ________dry lake [ENVO:00000277]: - text: ________dry lake [ENVO:00000277] - ________karst [ENVO:00000175]: - text: ________karst [ENVO:00000175] - ________isthmus [ENVO:00000174]: - text: ________isthmus [ENVO:00000174] - ________badland [ENVO:00000127]: - text: ________badland [ENVO:00000127] - ________volcanic feature [ENVO:00000094]: - text: ________volcanic feature [ENVO:00000094] - __________volcanic cone [ENVO:00000398]: - text: __________volcanic cone [ENVO:00000398] - ____________tuff cone [ENVO:01000664]: - text: ____________tuff cone [ENVO:01000664] - ________beach [ENVO:00000091]: - text: ________beach [ENVO:00000091] - ________plain [ENVO:00000086]: - text: ________plain [ENVO:00000086] - ________cave [ENVO:00000067]: - text: ________cave [ENVO:00000067] - ________spring [ENVO:00000027]: - text: ________spring [ENVO:00000027] - ______slope [ENVO:00002000]: - text: ______slope [ENVO:00002000] - ________talus slope [ENVO:01000334]: - text: ________talus slope [ENVO:01000334] - ________hillside [ENVO:01000333]: - text: ________hillside [ENVO:01000333] - ________levee [ENVO:00000178]: - text: ________levee [ENVO:00000178] - ________bank [ENVO:00000141]: - text: ________bank [ENVO:00000141] - ________cliff [ENVO:00000087]: - text: ________cliff [ENVO:00000087] - ______peak [ENVO:00000480]: - text: ______peak [ENVO:00000480] - ______depressed landform [ENVO:00000309]: - text: ______depressed landform [ENVO:00000309] - ________geographic basin [ENVO:03000015]: - text: ________geographic basin [ENVO:03000015] - __________valley [ENVO:00000100]: - text: __________valley [ENVO:00000100] - ____________canyon [ENVO:00000169]: - text: ____________canyon [ENVO:00000169] - ____________dry valley [ENVO:00000128]: - text: ____________dry valley [ENVO:00000128] - ____________glacial valley [ENVO:00000248]: - text: ____________glacial valley [ENVO:00000248] - ________pit [ENVO:01001871]: - text: ________pit [ENVO:01001871] - ________trench [ENVO:01000649]: - text: ________trench [ENVO:01000649] - ________swale [ENVO:00000543]: - text: ________swale [ENVO:00000543] - ________crater [ENVO:00000514]: - text: ________crater [ENVO:00000514] - __________impact crater [ENVO:01001071]: - text: __________impact crater [ENVO:01001071] - __________volcanic crater [ENVO:00000246]: - text: __________volcanic crater [ENVO:00000246] - __________caldera [ENVO:00000096]: - text: __________caldera [ENVO:00000096] - ________channel of a watercourse [ENVO:00000395]: - text: ________channel of a watercourse [ENVO:00000395] - __________strait [ENVO:00000394]: - text: __________strait [ENVO:00000394] - __________dry stream [ENVO:00000278]: - text: __________dry stream [ENVO:00000278] - ____________dry river [ENVO:01000995]: - text: ____________dry river [ENVO:01000995] - __________artificial channel [ENVO:00000121]: - text: __________artificial channel [ENVO:00000121] - ____________plumbing drain [ENVO:01000924]: - text: ____________plumbing drain [ENVO:01000924] - ____________ditch [ENVO:00000037]: - text: ____________ditch [ENVO:00000037] - ________sinkhole [ENVO:00000195]: - text: ________sinkhole [ENVO:00000195] - ______elevated landform [ENVO:00000176]: - text: ______elevated landform [ENVO:00000176] - ________flattened elevation [ENVO:01001491]: - text: ________flattened elevation [ENVO:01001491] - __________butte [ENVO:00000287]: - text: __________butte [ENVO:00000287] - __________plateau [ENVO:00000182]: - text: __________plateau [ENVO:00000182] - __________mesa [ENVO:00000179]: - text: __________mesa [ENVO:00000179] - ________pinnacle [ENVO:00000481]: - text: ________pinnacle [ENVO:00000481] - ________mount [ENVO:00000477]: - text: ________mount [ENVO:00000477] - __________hill [ENVO:00000083]: - text: __________hill [ENVO:00000083] - ____________dune [ENVO:00000170]: - text: ____________dune [ENVO:00000170] - __________mountain [ENVO:00000081]: - text: __________mountain [ENVO:00000081] - ________ridge [ENVO:00000283]: - text: ________ridge [ENVO:00000283] - ____part of a landmass [ENVO:01001781]: - text: ____part of a landmass [ENVO:01001781] - ______peninsula [ENVO:00000305]: - text: ______peninsula [ENVO:00000305] - ____geological fracture [ENVO:01000667]: - text: ____geological fracture [ENVO:01000667] - ______vein [ENVO:01000670]: - text: ______vein [ENVO:01000670] - ______geological fault [ENVO:01000668]: - text: ______geological fault [ENVO:01000668] - ________active geological fault [ENVO:01000669]: - text: ________active geological fault [ENVO:01000669] - ______volcano [ENVO:00000247]: - text: ______volcano [ENVO:00000247] - __field [ENVO:01000352]: - text: __field [ENVO:01000352] - ____lava field [ENVO:01000437]: - text: ____lava field [ENVO:01000437] - ____gravel field [ENVO:00000548]: - text: ____gravel field [ENVO:00000548] - ____woodland clearing [ENVO:00000444]: - text: ____woodland clearing [ENVO:00000444] - ____agricultural field [ENVO:00000114]: - text: ____agricultural field [ENVO:00000114] - ____snow field [ENVO:00000146]: - text: ____snow field [ENVO:00000146] - __geographic feature [ENVO:00000000]: - text: __geographic feature [ENVO:00000000] - ____hydrographic feature [ENVO:00000012]: - text: ____hydrographic feature [ENVO:00000012] - ______reef [ENVO:01001899]: - text: ______reef [ENVO:01001899] - ______inlet [ENVO:00000475]: - text: ______inlet [ENVO:00000475] - ______bar [ENVO:00000167]: - text: ______bar [ENVO:00000167] - ________tombolo [ENVO:00000420]: - text: ________tombolo [ENVO:00000420] - ____anthropogenic geographic feature [ENVO:00000002]: - text: ____anthropogenic geographic feature [ENVO:00000002] - ______yard [ENVO:03600053]: - text: ______yard [ENVO:03600053] - ________residential backyard [ENVO:03600033]: - text: ________residential backyard [ENVO:03600033] - ______market [ENVO:01000987]: - text: ______market [ENVO:01000987] - ______park [ENVO:00000562]: - text: ______park [ENVO:00000562] - ______well [ENVO:00000026]: - text: ______well [ENVO:00000026] - ______garden [ENVO:00000011]: - text: ______garden [ENVO:00000011] OxyStatSampEnum: name: OxyStatSampEnum from_schema: https://example.com/nmdc_submission_schema @@ -2339,8 +2077,8 @@ enums: text: crows feet crows-foot stomp: text: crows-foot stomp - '': - text: '' + ? '' + : text: '' double skip: text: double skip hawk and trowel: @@ -2772,10 +2510,10 @@ enums: tag: originally value: conifers (e.g. pine,spruce,fir,cypress) examples: - - value: cypress - - value: fir - - value: pine - - value: spruce + - value: cypress + - value: fir + - value: pine + - value: spruce crop trees: text: crop trees annotations: @@ -2783,10 +2521,10 @@ enums: tag: originally value: crop trees (nuts,fruit,christmas trees,nursery trees) examples: - - value: christmas trees - - value: fruit - - value: nursery trees - - value: nuts + - value: christmas trees + - value: fruit + - value: nursery trees + - value: nuts farmstead: text: farmstead gravel: @@ -2798,10 +2536,10 @@ enums: tag: originally value: hardwoods (e.g. oak,hickory,elm,aspen) examples: - - value: aspen - - value: elm - - value: hickory - - value: oak + - value: aspen + - value: elm + - value: hickory + - value: oak hayland: text: hayland horticultural plants: @@ -2811,7 +2549,7 @@ enums: tag: originally value: horticultural plants (e.g. tulips) examples: - - value: tulips + - value: tulips industrial areas: text: industrial areas intermixed hardwood and conifers: @@ -2823,9 +2561,9 @@ enums: tag: originally value: marshlands (grass,sedges,rushes) examples: - - value: grass - - value: rushes - - value: sedgees + - value: grass + - value: rushes + - value: sedgees meadows: text: meadows annotations: @@ -2833,11 +2571,11 @@ enums: tag: originally value: meadows (grasses,alfalfa,fescue,bromegrass,timothy) examples: - - value: alfalfa - - value: bromegrass - - value: fescue - - value: grasses - - value: timothy + - value: alfalfa + - value: bromegrass + - value: fescue + - value: grasses + - value: timothy mines/quarries: text: mines/quarries mudflats: @@ -2851,7 +2589,7 @@ enums: tag: originally value: pastureland (grasslands used for livestock grazing) comments: - - grasslands used for livestock grazing + - grasslands used for livestock grazing permanent snow or ice: text: permanent snow or ice rainforest: @@ -2859,9 +2597,10 @@ enums: annotations: originally: tag: originally - value: rainforest (evergreen forest receiving greater than 406 cm annual rainfall) + value: rainforest (evergreen forest receiving greater than 406 cm annual + rainfall) comments: - - evergreen forest receiving greater than 406 cm annual rainfall + - evergreen forest receiving greater than 406 cm annual rainfall rangeland: text: rangeland roads/railroads: @@ -2883,9 +2622,9 @@ enums: tag: originally value: shrub crops (blueberries,nursery ornamentals,filberts) examples: - - value: blueberries - - value: filberts - - value: nursery ornamentals + - value: blueberries + - value: filberts + - value: nursery ornamentals shrub land: text: shrub land annotations: @@ -2893,11 +2632,11 @@ enums: 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 + - value: creosote bush + - value: eucalyptus + - value: mesquite + - value: sage-brush + - value: shrub oak small grains: text: small grains successional shrub land: @@ -2905,22 +2644,24 @@ enums: 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 + 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) + value: swamp (permanent or semi-permanent water body dominated by woody + plants) comments: - - permanent or semi-permanent water body dominated by woody plants + - permanent or semi-permanent water body dominated by woody plants tropical: text: tropical annotations: @@ -2928,8 +2669,8 @@ enums: tag: originally value: tropical (e.g. mangrove,palms) examples: - - value: mangrove - - value: palms + - value: mangrove + - value: palms tundra: text: tundra annotations: @@ -2937,8 +2678,8 @@ enums: tag: originally value: tundra (mosses,lichens) examples: - - value: lichens - - value: mosses + - value: lichens + - value: mosses vegetable crops: text: vegetable crops vine crops: @@ -2948,7 +2689,7 @@ enums: tag: originally value: vine crops (grapes) examples: - - value: grapes + - value: grapes drainage_class_enum: name: drainage_class_enum from_schema: https://example.com/nmdc_submission_schema @@ -7055,6 +6796,563 @@ enums: text: Uranium contaminated Wetland zone: text: Wetland zone + EnvLocalScaleSoilEnum: + name: EnvLocalScaleSoilEnum + permissible_values: + abandoned watercourse [ENVO:00000524]: + text: abandoned watercourse [ENVO:00000524] + active permafrost layer [ENVO:04000009]: + text: active permafrost layer [ENVO:04000009] + agricultural ecosystem [ENVO:00000077]: + text: agricultural ecosystem [ENVO:00000077] + agricultural field [ENVO:00000114]: + text: agricultural field [ENVO:00000114] + alas [ENVO:00000438]: + text: alas [ENVO:00000438] + apron [ENVO:00000530]: + text: apron [ENVO:00000530] + arable land [ENVO:01001177]: + text: arable land [ENVO:01001177] + arete [ENVO:00000429]: + text: arete [ENVO:00000429] + badland [ENVO:00000127]: + text: badland [ENVO:00000127] + beach [ENVO:00000091]: + text: beach [ENVO:00000091] + beach ridge [ENVO:00000529]: + text: beach ridge [ENVO:00000529] + biochar [ENVO:2000007]: + text: biochar [ENVO:2000007] + blowout [ENVO:00000313]: + text: blowout [ENVO:00000313] + booth [ENVO:03501309]: + text: booth [ENVO:03501309] + borehole [ENVO:00002226]: + text: borehole [ENVO:00002226] + boundary wall [ENVO:01000466]: + text: boundary wall [ENVO:01000466] + bridge [ENVO:00000075]: + text: bridge [ENVO:00000075] + burrow [ENVO:01000429]: + text: burrow [ENVO:01000429] + butte [ENVO:00000287]: + text: butte [ENVO:00000287] + calanque [ENVO:00000567]: + text: calanque [ENVO:00000567] + caldera [ENVO:00000096]: + text: caldera [ENVO:00000096] + campground [ENVO:01000935]: + text: campground [ENVO:01000935] + canyon [ENVO:00000169]: + text: canyon [ENVO:00000169] + causeway [ENVO:00000158]: + text: causeway [ENVO:00000158] + cave [ENVO:00000067]: + text: cave [ENVO:00000067] + channel [ENVO:03000117]: + text: channel [ENVO:03000117] + cirque [ENVO:00000155]: + text: cirque [ENVO:00000155] + cliff [ENVO:00000087]: + text: cliff [ENVO:00000087] + continental divide [ENVO:00000293]: + text: continental divide [ENVO:00000293] + crater [ENVO:00000514]: + text: crater [ENVO:00000514] + crevasse [ENVO:00000320]: + text: crevasse [ENVO:00000320] + crevice [ENVO:01000294]: + text: crevice [ENVO:01000294] + cryosphere [ENVO:03000143]: + text: cryosphere [ENVO:03000143] + dam [ENVO:00000074]: + text: dam [ENVO:00000074] + dell [ENVO:00000439]: + text: dell [ENVO:00000439] + desert [ENVO:01001357]: + text: desert [ENVO:01001357] + drainage basin [ENVO:00000291]: + text: drainage basin [ENVO:00000291] + drawbridge [ENVO:03501245]: + text: drawbridge [ENVO:03501245] + driveway [ENVO:01001280]: + text: driveway [ENVO:01001280] + drumlin [ENVO:00000276]: + text: drumlin [ENVO:00000276] + dry lake [ENVO:00000277]: + text: dry lake [ENVO:00000277] + dune [ENVO:00000170]: + text: dune [ENVO:00000170] + escarpment [ENVO:00000280]: + text: escarpment [ENVO:00000280] + esker [ENVO:00000282]: + text: esker [ENVO:00000282] + fairground [ENVO:01000985]: + text: fairground [ENVO:01000985] + farm [ENVO:00000078]: + text: farm [ENVO:00000078] + fen [ENVO:00000232]: + text: fen [ENVO:00000232] + fence [ENVO:01000468]: + text: fence [ENVO:01000468] + firebreak [ENVO:03000132]: + text: firebreak [ENVO:03000132] + fjord [ENVO:00000039]: + text: fjord [ENVO:00000039] + flood plain [ENVO:00000255]: + text: flood plain [ENVO:00000255] + floodway [ENVO:00000256]: + text: floodway [ENVO:00000256] + fomite [ENVO:00010358]: + text: fomite [ENVO:00010358] + ford [ENVO:00000411]: + text: ford [ENVO:00000411] + forest ecosystem [ENVO:01001243]: + text: forest ecosystem [ENVO:01001243] + forested area [ENVO:00000111]: + text: forested area [ENVO:00000111] + frost heave [ENVO:01001568]: + text: frost heave [ENVO:01001568] + frost-formed hummock [ENVO:01001538]: + text: frost-formed hummock [ENVO:01001538] + frozen land [ENVO:01001524]: + text: frozen land [ENVO:01001524] + fumarole [ENVO:00000216]: + text: fumarole [ENVO:00000216] + garden [ENVO:00000011]: + text: garden [ENVO:00000011] + gas well [ENVO:01001870]: + text: gas well [ENVO:01001870] + glacier [ENVO:00000133]: + text: glacier [ENVO:00000133] + graben [ENVO:00000290]: + text: graben [ENVO:00000290] + grassland area [ENVO:00000106]: + text: grassland area [ENVO:00000106] + greenhouse [ENVO:03600087]: + text: greenhouse [ENVO:03600087] + harbour [ENVO:00000463]: + text: harbour [ENVO:00000463] + hedge [ENVO:00000046]: + text: hedge [ENVO:00000046] + hill [ENVO:00000083]: + text: hill [ENVO:00000083] + hillock [ENVO:03501238]: + text: hillock [ENVO:03501238] + hillside [ENVO:01000333]: + text: hillside [ENVO:01000333] + horst [ENVO:00000289]: + text: horst [ENVO:00000289] + hummock [ENVO:00000516]: + text: hummock [ENVO:00000516] + ice wedge [ENVO:03600068]: + text: ice wedge [ENVO:03600068] + isthmus [ENVO:00000174]: + text: isthmus [ENVO:00000174] + landfill [ENVO:00000533]: + text: landfill [ENVO:00000533] + landslide [ENVO:00000520]: + text: landslide [ENVO:00000520] + lock [ENVO:00000357]: + text: lock [ENVO:00000357] + marsh [ENVO:00000035]: + text: marsh [ENVO:00000035] + massif [ENVO:00000381]: + text: massif [ENVO:00000381] + meadow ecosystem [ENVO:00000108]: + text: meadow ecosystem [ENVO:00000108] + mesa [ENVO:00000179]: + text: mesa [ENVO:00000179] + mine [ENVO:00000076]: + text: mine [ENVO:00000076] + mine drainage [ENVO:00001996]: + text: mine drainage [ENVO:00001996] + monadnock [ENVO:00000432]: + text: monadnock [ENVO:00000432] + moraine [ENVO:00000177]: + text: moraine [ENVO:00000177] + mound [ENVO:00000180]: + text: mound [ENVO:00000180] + mountain [ENVO:00000081]: + text: mountain [ENVO:00000081] + oil spill [ENVO:00002061]: + text: oil spill [ENVO:00002061] + orchard [ENVO:00000115]: + text: orchard [ENVO:00000115] + outcrop [ENVO:01000302]: + text: outcrop [ENVO:01000302] + overpass [ENVO:03501248]: + text: overpass [ENVO:03501248] + park [ENVO:00000562]: + text: park [ENVO:00000562] + pasture [ENVO:00000266]: + text: pasture [ENVO:00000266] + peatland [ENVO:00000044]: + text: peatland [ENVO:00000044] + permafrost [ENVO:00000134]: + text: permafrost [ENVO:00000134] + pier [ENVO:00000563]: + text: pier [ENVO:00000563] + pinnacle [ENVO:00000481]: + text: pinnacle [ENVO:00000481] + pit [ENVO:01001871]: + text: pit [ENVO:01001871] + plain [ENVO:00000086]: + text: plain [ENVO:00000086] + plateau [ENVO:00000182]: + text: plateau [ENVO:00000182] + playground [ENVO:03500001]: + text: playground [ENVO:03500001] + polje [ENVO:00000325]: + text: polje [ENVO:00000325] + pond [ENVO:00000033]: + text: pond [ENVO:00000033] + prairie [ENVO:00000260]: + text: prairie [ENVO:00000260] + quarry [ENVO:00000284]: + text: quarry [ENVO:00000284] + ranch [ENVO:01001207]: + text: ranch [ENVO:01001207] + ravine [ENVO:01000446]: + text: ravine [ENVO:01000446] + refinery [ENVO:02000141]: + text: refinery [ENVO:02000141] + residential backyard [ENVO:03600033]: + text: residential backyard [ENVO:03600033] + rhizosphere [ENVO:00005801]: + text: rhizosphere [ENVO:00005801] + ridge [ENVO:00000283]: + text: ridge [ENVO:00000283] + river [ENVO:00000022]: + text: river [ENVO:00000022] + riverfront [ENVO:03501239]: + text: riverfront [ENVO:03501239] + road [ENVO:00000064]: + text: road [ENVO:00000064] + roadside [ENVO:01000447]: + text: roadside [ENVO:01000447] + rockfall [ENVO:00000521]: + text: rockfall [ENVO:00000521] + savanna [ENVO:00000261]: + text: savanna [ENVO:00000261] + shore [ENVO:00000304]: + text: shore [ENVO:00000304] + sidewalk [ENVO:01001279]: + text: sidewalk [ENVO:01001279] + sinkhole [ENVO:00000195]: + text: sinkhole [ENVO:00000195] + slope [ENVO:00002000]: + text: slope [ENVO:00002000] + soil cryoturbate [ENVO:01001665]: + text: soil cryoturbate [ENVO:01001665] + spring [ENVO:00000027]: + text: spring [ENVO:00000027] + stack [ENVO:00000419]: + text: stack [ENVO:00000419] + steppe [ENVO:00000262]: + text: steppe [ENVO:00000262] + stream [ENVO:00000023]: + text: stream [ENVO:00000023] + swale [ENVO:00000543]: + text: swale [ENVO:00000543] + terrace [ENVO:00000508]: + text: terrace [ENVO:00000508] + terracette [ENVO:00000441]: + text: terracette [ENVO:00000441] + thermokarst [ENVO:03000085]: + text: thermokarst [ENVO:03000085] + trench [ENVO:01000649]: + text: trench [ENVO:01000649] + tunnel [ENVO:00000068]: + text: tunnel [ENVO:00000068] + valley [ENVO:00000100]: + text: valley [ENVO:00000100] + vein [ENVO:01000670]: + text: vein [ENVO:01000670] + volcano [ENVO:00000247]: + text: volcano [ENVO:00000247] + wadi [ENVO:00000031]: + text: wadi [ENVO:00000031] + watershed [ENVO:00000292]: + text: watershed [ENVO:00000292] + wave-cut platform [ENVO:00000421]: + text: wave-cut platform [ENVO:00000421] + weir [ENVO:00000535]: + text: weir [ENVO:00000535] + well [ENVO:00000026]: + text: well [ENVO:00000026] + wetland ecosystem [ENVO:01001209]: + text: wetland ecosystem [ENVO:01001209] + woodland area [ENVO:00000109]: + text: woodland area [ENVO:00000109] + woodland clearing [ENVO:00000444]: + text: woodland clearing [ENVO:00000444] + EnvMediumScaleSoilEnum: + name: EnvMediumScaleSoilEnum + permissible_values: + acidic soil [ENVO:01001185]: + text: acidic soil [ENVO:01001185] + acrisol [ENVO:00002234]: + text: acrisol [ENVO:00002234] + albeluvisol [ENVO:00002233]: + text: albeluvisol [ENVO:00002233] + alisol [ENVO:00002231]: + text: alisol [ENVO:00002231] + allotment garden soil [ENVO:00005744]: + text: allotment garden soil [ENVO:00005744] + alluvial paddy field soil [ENVO:00005759]: + text: alluvial paddy field soil [ENVO:00005759] + alluvial soil [ENVO:00002871]: + text: alluvial soil [ENVO:00002871] + alluvial swamp soil [ENVO:00005758]: + text: alluvial swamp soil [ENVO:00005758] + alpine soil [ENVO:00005741]: + text: alpine soil [ENVO:00005741] + andosol [ENVO:00002232]: + text: andosol [ENVO:00002232] + anthrosol [ENVO:00002230]: + text: anthrosol [ENVO:00002230] + arable soil [ENVO:00005742]: + text: arable soil [ENVO:00005742] + arenosol [ENVO:00002229]: + text: arenosol [ENVO:00002229] + bare soil [ENVO:01001616]: + text: bare soil [ENVO:01001616] + beech forest soil [ENVO:00005770]: + text: beech forest soil [ENVO:00005770] + bluegrass field soil [ENVO:00005789]: + text: bluegrass field soil [ENVO:00005789] + bulk soil [ENVO:00005802]: + text: bulk soil [ENVO:00005802] + burned soil [ENVO:00005760]: + text: burned soil [ENVO:00005760] + calcisol [ENVO:00002239]: + text: calcisol [ENVO:00002239] + cambisol [ENVO:00002235]: + text: cambisol [ENVO:00002235] + chernozem [ENVO:00002237]: + text: chernozem [ENVO:00002237] + clay soil [ENVO:00002262]: + text: clay soil [ENVO:00002262] + compacted soil [ENVO:06105205]: + text: compacted soil [ENVO:06105205] + compost soil [ENVO:00005747]: + text: compost soil [ENVO:00005747] + cryosol [ENVO:00002236]: + text: cryosol [ENVO:00002236] + dry soil [ENVO:00005748]: + text: dry soil [ENVO:00005748] + durisol [ENVO:00002238]: + text: durisol [ENVO:00002238] + eucalyptus forest soil [ENVO:00005787]: + text: eucalyptus forest soil [ENVO:00005787] + ferralsol [ENVO:00002246]: + text: ferralsol [ENVO:00002246] + fertilized soil [ENVO:00005754]: + text: fertilized soil [ENVO:00005754] + fluvisol [ENVO:00002273]: + text: fluvisol [ENVO:00002273] + friable-frozen soil [ENVO:01001528]: + text: friable-frozen soil [ENVO:01001528] + frost-susceptible soil [ENVO:01001638]: + text: frost-susceptible soil [ENVO:01001638] + frozen compost soil [ENVO:00005765]: + text: frozen compost soil [ENVO:00005765] + gleysol [ENVO:00002244]: + text: gleysol [ENVO:00002244] + gypsisol [ENVO:00002245]: + text: gypsisol [ENVO:00002245] + hard-frozen soil [ENVO:01001525]: + text: hard-frozen soil [ENVO:01001525] + heat stressed soil [ENVO:00005781]: + text: heat stressed soil [ENVO:00005781] + histosol [ENVO:00002243]: + text: histosol [ENVO:00002243] + jungle soil [ENVO:00005751]: + text: jungle soil [ENVO:00005751] + kastanozem [ENVO:00002240]: + text: kastanozem [ENVO:00002240] + lawn soil [ENVO:00005756]: + text: lawn soil [ENVO:00005756] + leafy wood soil [ENVO:00005783]: + text: leafy wood soil [ENVO:00005783] + leptosol [ENVO:00002241]: + text: leptosol [ENVO:00002241] + limed soil [ENVO:00005766]: + text: limed soil [ENVO:00005766] + lixisol [ENVO:00002242]: + text: lixisol [ENVO:00002242] + loam [ENVO:00002258]: + text: loam [ENVO:00002258] + luvisol [ENVO:00002248]: + text: luvisol [ENVO:00002248] + manured soil [ENVO:00005767]: + text: manured soil [ENVO:00005767] + mountain forest soil [ENVO:00005769]: + text: mountain forest soil [ENVO:00005769] + muddy soil [ENVO:00005771]: + text: muddy soil [ENVO:00005771] + nitisol [ENVO:00002247]: + text: nitisol [ENVO:00002247] + orchid soil [ENVO:00005768]: + text: orchid soil [ENVO:00005768] + ornithogenic soil [ENVO:00005782]: + text: ornithogenic soil [ENVO:00005782] + paddy field soil [ENVO:00005740]: + text: paddy field soil [ENVO:00005740] + pathogen-suppressive soil [ENVO:03600036]: + text: pathogen-suppressive soil [ENVO:03600036] + phaeozem [ENVO:00002249]: + text: phaeozem [ENVO:00002249] + planosol [ENVO:00002251]: + text: planosol [ENVO:00002251] + plastic-frozen soil [ENVO:01001527]: + text: plastic-frozen soil [ENVO:01001527] + plinthosol [ENVO:00002250]: + text: plinthosol [ENVO:00002250] + podzol [ENVO:00002257]: + text: podzol [ENVO:00002257] + red soil [ENVO:00005790]: + text: red soil [ENVO:00005790] + regosol [ENVO:00002256]: + text: regosol [ENVO:00002256] + rubber plantation soil [ENVO:00005788]: + text: rubber plantation soil [ENVO:00005788] + sawah soil [ENVO:00005752]: + text: sawah soil [ENVO:00005752] + soil [ENVO:00001998]: + text: soil [ENVO:00001998] + solonchak [ENVO:00002252]: + text: solonchak [ENVO:00002252] + solonetz [ENVO:00002255]: + text: solonetz [ENVO:00002255] + spruce forest soil [ENVO:00005784]: + text: spruce forest soil [ENVO:00005784] + stagnosol [ENVO:00002274]: + text: stagnosol [ENVO:00002274] + surface soil [ENVO:02000059]: + text: surface soil [ENVO:02000059] + technosol [ENVO:00002275]: + text: technosol [ENVO:00002275] + tropical soil [ENVO:00005778]: + text: tropical soil [ENVO:00005778] + ultisol [ENVO:01001397]: + text: ultisol [ENVO:01001397] + umbrisol [ENVO:00002253]: + text: umbrisol [ENVO:00002253] + upland soil [ENVO:00005786]: + text: upland soil [ENVO:00005786] + vegetable garden soil [ENVO:00005779]: + text: vegetable garden soil [ENVO:00005779] + vertisol [ENVO:00002254]: + text: vertisol [ENVO:00002254] + EnvBroadScaleSoilEnum: + name: EnvBroadScaleSoilEnum + permissible_values: + alpine tundra biome [ENVO:01001505]: + text: alpine tundra biome [ENVO:01001505] + anthropogenic terrestrial biome [ENVO:01000219]: + text: anthropogenic terrestrial biome [ENVO:01000219] + broadleaf forest biome [ENVO:01000197]: + text: broadleaf forest biome [ENVO:01000197] + coniferous forest biome [ENVO:01000196]: + text: coniferous forest biome [ENVO:01000196] + cropland biome [ENVO:01000245]: + text: cropland biome [ENVO:01000245] + flooded grassland biome [ENVO:01000195]: + text: flooded grassland biome [ENVO:01000195] + flooded savanna biome [ENVO:01000190]: + text: flooded savanna biome [ENVO:01000190] + forest biome [ENVO:01000174]: + text: forest biome [ENVO:01000174] + grassland biome [ENVO:01000177]: + text: grassland biome [ENVO:01000177] + mangrove biome [ENVO:01000181]: + text: mangrove biome [ENVO:01000181] + mediterranean forest biome [ENVO:01000199]: + text: mediterranean forest biome [ENVO:01000199] + mediterranean grassland biome [ENVO:01000224]: + text: mediterranean grassland biome [ENVO:01000224] + mediterranean savanna biome [ENVO:01000229]: + text: mediterranean savanna biome [ENVO:01000229] + mediterranean shrubland biome [ENVO:01000217]: + text: mediterranean shrubland biome [ENVO:01000217] + mediterranean woodland biome [ENVO:01000208]: + text: mediterranean woodland biome [ENVO:01000208] + mixed forest biome [ENVO:01000198]: + text: mixed forest biome [ENVO:01000198] + montane grassland biome [ENVO:01000194]: + text: montane grassland biome [ENVO:01000194] + montane savanna biome [ENVO:01000223]: + text: montane savanna biome [ENVO:01000223] + montane shrubland biome [ENVO:01000216]: + text: montane shrubland biome [ENVO:01000216] + rangeland biome [ENVO:01000247]: + text: rangeland biome [ENVO:01000247] + savanna biome [ENVO:01000178]: + text: savanna biome [ENVO:01000178] + shrubland biome [ENVO:01000176]: + text: shrubland biome [ENVO:01000176] + subpolar coniferous forest biome [ENVO:01000250]: + text: subpolar coniferous forest biome [ENVO:01000250] + subtropical broadleaf forest biome [ENVO:01000201]: + text: subtropical broadleaf forest biome [ENVO:01000201] + subtropical coniferous forest biome [ENVO:01000209]: + text: subtropical coniferous forest biome [ENVO:01000209] + subtropical dry broadleaf forest biome [ENVO:01000225]: + text: subtropical dry broadleaf forest biome [ENVO:01000225] + subtropical grassland biome [ENVO:01000191]: + text: subtropical grassland biome [ENVO:01000191] + subtropical moist broadleaf forest biome [ENVO:01000226]: + text: subtropical moist broadleaf forest biome [ENVO:01000226] + subtropical savanna biome [ENVO:01000187]: + text: subtropical savanna biome [ENVO:01000187] + subtropical shrubland biome [ENVO:01000213]: + text: subtropical shrubland biome [ENVO:01000213] + subtropical woodland biome [ENVO:01000222]: + text: subtropical woodland biome [ENVO:01000222] + temperate broadleaf forest biome [ENVO:01000202]: + text: temperate broadleaf forest biome [ENVO:01000202] + temperate coniferous forest biome [ENVO:01000211]: + text: temperate coniferous forest biome [ENVO:01000211] + temperate grassland biome [ENVO:01000193]: + text: temperate grassland biome [ENVO:01000193] + temperate mixed forest biome [ENVO:01000212]: + text: temperate mixed forest biome [ENVO:01000212] + temperate savanna biome [ENVO:01000189]: + text: temperate savanna biome [ENVO:01000189] + temperate shrubland biome [ENVO:01000215]: + text: temperate shrubland biome [ENVO:01000215] + temperate woodland biome [ENVO:01000221]: + text: temperate woodland biome [ENVO:01000221] + terrestrial biome [ENVO:00000446]: + text: terrestrial biome [ENVO:00000446] + tidal mangrove shrubland [ENVO:01001369]: + text: tidal mangrove shrubland [ENVO:01001369] + tropical broadleaf forest biome [ENVO:01000200]: + text: tropical broadleaf forest biome [ENVO:01000200] + tropical coniferous forest biome [ENVO:01000210]: + text: tropical coniferous forest biome [ENVO:01000210] + tropical dry broadleaf forest biome [ENVO:01000227]: + text: tropical dry broadleaf forest biome [ENVO:01000227] + tropical grassland biome [ENVO:01000192]: + text: tropical grassland biome [ENVO:01000192] + tropical mixed forest biome [ENVO:01001798]: + text: tropical mixed forest biome [ENVO:01001798] + tropical moist broadleaf forest biome [ENVO:01000228]: + text: tropical moist broadleaf forest biome [ENVO:01000228] + tropical savanna biome [ENVO:01000188]: + text: tropical savanna biome [ENVO:01000188] + tropical shrubland biome [ENVO:01000214]: + text: tropical shrubland biome [ENVO:01000214] + tropical woodland biome [ENVO:01000220]: + text: tropical woodland biome [ENVO:01000220] + tundra biome [ENVO:01000180]: + text: tundra biome [ENVO:01000180] + woodland biome [ENVO:01000175]: + text: woodland biome [ENVO:01000175] + xeric shrubland biome [ENVO:01000218]: + text: xeric shrubland biome [ENVO:01000218] slots: air_data: name: air_data @@ -7066,7 +7364,8 @@ slots: inlined_as_list: true biofilm_data: name: biofilm_data - description: aggregation slot relating biofilm data collections to a SampleData container + description: aggregation slot relating biofilm data collections to a SampleData + container from_schema: https://example.com/nmdc_submission_schema range: BiofilmInterface multivalued: true @@ -7074,7 +7373,8 @@ slots: inlined_as_list: true built_env_data: name: built_env_data - description: aggregation slot relating built_env data collections to a SampleData container + description: aggregation slot relating built_env data collections to a SampleData + container from_schema: https://example.com/nmdc_submission_schema range: BuiltEnvInterface multivalued: true @@ -7090,7 +7390,8 @@ slots: inlined_as_list: true hcr_cores_data: name: hcr_cores_data - description: aggregation slot relating hcr_cores data collections to a SampleData container + description: aggregation slot relating hcr_cores data collections to a SampleData + container from_schema: https://example.com/nmdc_submission_schema range: HcrCoresInterface multivalued: true @@ -7098,7 +7399,8 @@ slots: 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 + description: aggregation slot relating hcr_fluids_swabs data collections to a + SampleData container from_schema: https://example.com/nmdc_submission_schema range: HcrFluidsSwabsInterface multivalued: true @@ -7106,7 +7408,8 @@ slots: inlined_as_list: true host_associated_data: name: host_associated_data - description: aggregation slot relating host_associated data collections to a SampleData container + description: aggregation slot relating host_associated data collections to a SampleData + container from_schema: https://example.com/nmdc_submission_schema range: HostAssociatedInterface multivalued: true @@ -7114,7 +7417,8 @@ slots: inlined_as_list: true jgi_mg_data: name: jgi_mg_data - description: aggregation slot relating jgi_mg data collections to a SampleData container + description: aggregation slot relating jgi_mg data collections to a SampleData + container from_schema: https://example.com/nmdc_submission_schema range: JgiMgInterface multivalued: true @@ -7122,7 +7426,8 @@ slots: inlined_as_list: true jgi_mg_lr_data: name: jgi_mg_lr_data - description: aggregation slot relating jgi_mg_lr data collections to a SampleData container + description: aggregation slot relating jgi_mg_lr data collections to a SampleData + container from_schema: https://example.com/nmdc_submission_schema range: JgiMgLrInterface multivalued: true @@ -7130,7 +7435,8 @@ slots: inlined_as_list: true jgi_mt_data: name: jgi_mt_data - description: aggregation slot relating jgi_mt data collections to a SampleData container + description: aggregation slot relating jgi_mt data collections to a SampleData + container from_schema: https://example.com/nmdc_submission_schema range: JgiMtInterface multivalued: true @@ -7138,7 +7444,8 @@ slots: inlined_as_list: true misc_envs_data: name: misc_envs_data - description: aggregation slot relating misc_envs data collections to a SampleData container + description: aggregation slot relating misc_envs data collections to a SampleData + container from_schema: https://example.com/nmdc_submission_schema range: MiscEnvsInterface multivalued: true @@ -7146,7 +7453,8 @@ slots: inlined_as_list: true plant_associated_data: name: plant_associated_data - description: aggregation slot relating plant_associated data collections to a SampleData container + description: aggregation slot relating plant_associated data collections to a + SampleData container from_schema: https://example.com/nmdc_submission_schema range: PlantAssociatedInterface multivalued: true @@ -7154,7 +7462,8 @@ slots: inlined_as_list: true sediment_data: name: sediment_data - description: aggregation slot relating sediment data collections to a SampleData container + description: aggregation slot relating sediment data collections to a SampleData + container from_schema: https://example.com/nmdc_submission_schema range: SedimentInterface multivalued: true @@ -7170,7 +7479,8 @@ slots: inlined_as_list: true wastewater_sludge_data: name: wastewater_sludge_data - description: aggregation slot relating wastewater_sludge data collections to a SampleData container + description: aggregation slot relating wastewater_sludge data collections to a + SampleData container from_schema: https://example.com/nmdc_submission_schema range: WastewaterSludgeInterface multivalued: true @@ -7178,7 +7488,8 @@ slots: inlined_as_list: true water_data: name: water_data - description: aggregation slot relating water data collections to a SampleData container + description: aggregation slot relating water data collections to a SampleData + container from_schema: https://example.com/nmdc_submission_schema range: WaterInterface multivalued: true @@ -7258,17 +7569,18 @@ slots: occurrence: tag: occurrence value: '1' - description: Actual mass of water vapor - mh20 - present in the air water vapor mixture + description: Actual mass of water vapor - mh20 - present in the air water vapor + mixture title: absolute air humidity examples: - - value: 9 gram per gram + - value: 9 gram per gram from_schema: https://example.com/nmdc_submission_schema aliases: - - absolute air humidity + - absolute air humidity is_a: core field slot_uri: MIXS:0000122 domain_of: - - Biosample + - Biosample range: string multivalued: false add_recov_method: @@ -7280,17 +7592,20 @@ slots: 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 + 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 + - value: Polymer Addition;2018-06-21T14:30Z from_schema: https://example.com/nmdc_submission_schema aliases: - - secondary and tertiary recovery methods and start date + - secondary and tertiary recovery methods and start date is_a: core field slot_uri: MIXS:0001009 domain_of: - - Biosample + - Biosample range: string multivalued: false additional_info: @@ -7302,18 +7617,19 @@ slots: 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 + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - additional info + - additional info is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000300 domain_of: - - Biosample + - Biosample range: string multivalued: false address: @@ -7328,15 +7644,15 @@ slots: description: The street name and building number where the sampling occurred. title: address examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - address + - address is_a: core field string_serialization: '{integer}{text}' slot_uri: MIXS:0000218 domain_of: - - Biosample + - Biosample range: string multivalued: false adj_room: @@ -7348,18 +7664,19 @@ slots: occurrence: tag: occurrence value: '1' - description: List of rooms (room number, room name) immediately adjacent to the sampling room + description: List of rooms (room number, room name) immediately adjacent to the + sampling room title: adjacent rooms examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - adjacent rooms + - adjacent rooms is_a: core field string_serialization: '{text};{integer}' slot_uri: MIXS:0000219 domain_of: - - Biosample + - Biosample range: string multivalued: false aero_struc: @@ -7371,18 +7688,20 @@ slots: 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 + 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 + - value: plane from_schema: https://example.com/nmdc_submission_schema aliases: - - aerospace structure + - aerospace structure is_a: core field string_serialization: '[plane|glider]' slot_uri: MIXS:0000773 domain_of: - - Biosample + - Biosample range: string multivalued: false agrochem_addition: @@ -7400,15 +7719,15 @@ slots: 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 + - value: roundup;5 milligram per liter;2018-06-21 from_schema: https://example.com/nmdc_submission_schema aliases: - - history/agrochemical additions + - history/agrochemical additions is_a: core field string_serialization: '{text};{float} {unit};{timestamp}' slot_uri: MIXS:0000639 domain_of: - - Biosample + - Biosample range: string multivalued: false air_PM_concen: @@ -7423,18 +7742,20 @@ slots: 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 + 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 + - value: PM2.5;10 microgram per cubic meter from_schema: https://example.com/nmdc_submission_schema aliases: - - air particulate matter concentration + - air particulate matter concentration is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000108 domain_of: - - Biosample + - Biosample range: string multivalued: false air_temp: @@ -7452,14 +7773,14 @@ slots: description: Temperature of the air at the time of sampling title: air temperature examples: - - value: 20 degree Celsius + - value: 20 degree Celsius from_schema: https://example.com/nmdc_submission_schema aliases: - - air temperature + - air temperature is_a: core field slot_uri: MIXS:0000124 domain_of: - - Biosample + - Biosample range: string multivalued: false air_temp_regm: @@ -7474,18 +7795,21 @@ slots: 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 + 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 + - 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 + - air temperature regimen is_a: core field string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000551 domain_of: - - Biosample + - Biosample range: string multivalued: false al_sat: @@ -7503,14 +7827,14 @@ slots: description: Aluminum saturation (esp. For tropical soils) title: extreme_unusual_properties/Al saturation examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - extreme_unusual_properties/Al saturation + - extreme_unusual_properties/Al saturation is_a: core field slot_uri: MIXS:0000607 domain_of: - - Biosample + - Biosample range: string multivalued: false al_sat_meth: @@ -7525,15 +7849,15 @@ slots: description: Reference or method used in determining Al saturation title: extreme_unusual_properties/Al saturation method examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - extreme_unusual_properties/Al saturation method + - extreme_unusual_properties/Al saturation method is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000324 domain_of: - - Biosample + - Biosample range: string multivalued: false alkalinity: @@ -7548,17 +7872,18 @@ slots: occurrence: tag: occurrence value: '1' - description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + 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 + - value: 50 milligram per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - alkalinity + - alkalinity is_a: core field slot_uri: MIXS:0000421 domain_of: - - Biosample + - Biosample range: string multivalued: false alkalinity_method: @@ -7573,15 +7898,15 @@ slots: description: Method used for alkalinity measurement title: alkalinity method examples: - - value: titration + - value: titration from_schema: https://example.com/nmdc_submission_schema aliases: - - alkalinity method + - alkalinity method is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000298 domain_of: - - Biosample + - Biosample range: string multivalued: false alkyl_diethers: @@ -7599,14 +7924,14 @@ slots: description: Concentration of alkyl diethers title: alkyl diethers examples: - - value: 0.005 mole per liter + - value: 0.005 mole per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - alkyl diethers + - alkyl diethers is_a: core field slot_uri: MIXS:0000490 domain_of: - - Biosample + - Biosample range: string multivalued: false alt: @@ -7615,41 +7940,46 @@ slots: 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 + 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 + - value: 100 meter from_schema: https://example.com/nmdc_submission_schema aliases: - - altitude + - altitude is_a: environment field slot_uri: MIXS:0000094 domain_of: - - agriculture - - air - - built environment - - core - - food-animal and animal feed - - food-farm environment - - food-food production facility - - food-human foods - - host-associated - - human-associated - - human-gut - - human-oral - - human-skin - - human-vaginal - - hydrocarbon resources-cores - - hydrocarbon resources-fluids_swabs - - microbial mat_biofilm - - miscellaneous natural or artificial environment - - plant-associated - - sediment - - soil - - symbiont-associated - - wastewater_sludge - - water - - Biosample + - agriculture + - air + - built environment + - core + - food-animal and animal feed + - food-farm environment + - food-food production facility + - food-human foods + - host-associated + - human-associated + - human-gut + - human-oral + - human-skin + - human-vaginal + - hydrocarbon resources-cores + - hydrocarbon resources-fluids_swabs + - microbial mat_biofilm + - miscellaneous natural or artificial environment + - plant-associated + - sediment + - soil + - symbiont-associated + - wastewater_sludge + - water + - Biosample range: string multivalued: false aminopept_act: @@ -7667,14 +7997,14 @@ slots: description: Measurement of aminopeptidase activity title: aminopeptidase activity examples: - - value: 0.269 mole per liter per hour + - value: 0.269 mole per liter per hour from_schema: https://example.com/nmdc_submission_schema aliases: - - aminopeptidase activity + - aminopeptidase activity is_a: core field slot_uri: MIXS:0000172 domain_of: - - Biosample + - Biosample range: string multivalued: false ammonium: @@ -7692,14 +8022,14 @@ slots: description: Concentration of ammonium in the sample title: ammonium examples: - - value: 1.5 milligram per liter + - value: 1.5 milligram per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - ammonium + - ammonium is_a: core field slot_uri: MIXS:0000427 domain_of: - - Biosample + - Biosample range: string multivalued: false ammonium_nitrogen: @@ -7717,15 +8047,15 @@ slots: description: Concentration of ammonium nitrogen in the sample title: ammonium nitrogen examples: - - value: 2.3 mg/kg + - value: 2.3 mg/kg from_schema: https://example.com/nmdc_submission_schema see_also: - - https://www.ornl.gov/content/bio-scales-0 + - https://www.ornl.gov/content/bio-scales-0 aliases: - - ammonium_nitrogen - - NH4-N + - ammonium_nitrogen + - NH4-N domain_of: - - Biosample + - Biosample range: string multivalued: false amount_light: @@ -7740,17 +8070,18 @@ slots: occurrence: tag: occurrence value: '1' - description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area + description: The unit of illuminance and luminous emittance, measuring luminous + flux per unit area title: amount of light examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - amount of light + - amount of light is_a: core field slot_uri: MIXS:0000140 domain_of: - - Biosample + - Biosample range: string multivalued: false analysis_type: @@ -7758,13 +8089,13 @@ slots: description: Select all the data types associated or available for this biosample title: analysis/data type examples: - - value: metagenomics; metabolomics; proteomics + - value: metagenomics; metabolomics; proteomics from_schema: https://example.com/nmdc_submission_schema see_also: - - MIxS:investigation_type + - MIxS:investigation_type rank: 3 domain_of: - - Biosample + - Biosample slot_group: Sample ID range: AnalysisTypeEnum recommended: true @@ -7778,18 +8109,20 @@ slots: 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) + 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 + - value: A/3*B from_schema: https://example.com/nmdc_submission_schema aliases: - - ancestral data + - ancestral data is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000247 domain_of: - - Biosample + - Biosample range: string multivalued: false annual_precpt: @@ -7804,17 +8137,18 @@ slots: 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. + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - mean annual precipitation + - mean annual precipitation is_a: core field slot_uri: MIXS:0000644 domain_of: - - Biosample + - Biosample range: string multivalued: false annual_temp: @@ -7832,14 +8166,14 @@ slots: description: Mean annual temperature title: mean annual temperature examples: - - value: 12.5 degree Celsius + - value: 12.5 degree Celsius from_schema: https://example.com/nmdc_submission_schema aliases: - - mean annual temperature + - mean annual temperature is_a: core field slot_uri: MIXS:0000642 domain_of: - - Biosample + - Biosample range: string multivalued: false antibiotic_regm: @@ -7854,18 +8188,22 @@ slots: 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 + 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 + - 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 + - antibiotic regimen is_a: core field string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000553 domain_of: - - Biosample + - Biosample range: string multivalued: false api: @@ -7880,17 +8218,19 @@ slots: 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)' + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - API gravity + - API gravity is_a: core field slot_uri: MIXS:0000157 domain_of: - - Biosample + - Biosample range: string multivalued: false arch_struc: @@ -7902,17 +8242,18 @@ slots: occurrence: tag: occurrence value: '1' - description: An architectural structure is a human-made, free-standing, immobile outdoor construction + description: An architectural structure is a human-made, free-standing, immobile + outdoor construction title: architectural structure examples: - - value: shed + - value: shed from_schema: https://example.com/nmdc_submission_schema aliases: - - architectural structure + - architectural structure is_a: core field slot_uri: MIXS:0000774 domain_of: - - Biosample + - Biosample range: arch_struc_enum multivalued: false aromatics_pc: @@ -7927,18 +8268,22 @@ slots: 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)' + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - aromatics wt% + - aromatics wt% is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000133 domain_of: - - Biosample + - Biosample range: string multivalued: false asphaltenes_pc: @@ -7953,18 +8298,22 @@ slots: 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)' + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - asphaltenes wt% + - asphaltenes wt% is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000135 domain_of: - - Biosample + - Biosample range: string multivalued: false atmospheric_data: @@ -7979,15 +8328,15 @@ slots: description: Measurement of atmospheric data; can include multiple data title: atmospheric data examples: - - value: wind speed;9 knots + - value: wind speed;9 knots from_schema: https://example.com/nmdc_submission_schema aliases: - - atmospheric data + - atmospheric data is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0001097 domain_of: - - Biosample + - Biosample range: string multivalued: false avg_dew_point: @@ -8002,17 +8351,18 @@ slots: 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 + 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 + - value: 25.5 degree Celsius from_schema: https://example.com/nmdc_submission_schema aliases: - - average dew point + - average dew point is_a: core field slot_uri: MIXS:0000141 domain_of: - - Biosample + - Biosample range: string multivalued: false avg_occup: @@ -8024,17 +8374,18 @@ slots: occurrence: tag: occurrence value: '1' - description: Daily average occupancy of room. Indicate the number of person(s) daily occupying the sampling room. + description: Daily average occupancy of room. Indicate the number of person(s) + daily occupying the sampling room. title: average daily occupancy examples: - - value: '2' + - value: '2' from_schema: https://example.com/nmdc_submission_schema aliases: - - average daily occupancy + - average daily occupancy is_a: core field slot_uri: MIXS:0000775 domain_of: - - Biosample + - Biosample range: string multivalued: false avg_temp: @@ -8049,17 +8400,18 @@ slots: 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 + 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 + - value: 12.5 degree Celsius from_schema: https://example.com/nmdc_submission_schema aliases: - - average temperature + - average temperature is_a: core field slot_uri: MIXS:0000142 domain_of: - - Biosample + - Biosample range: string multivalued: false bac_prod: @@ -8077,14 +8429,14 @@ slots: description: Bacterial production in the water column measured by isotope uptake title: bacterial production examples: - - value: 5 milligram per cubic meter per day + - value: 5 milligram per cubic meter per day from_schema: https://example.com/nmdc_submission_schema aliases: - - bacterial production + - bacterial production is_a: core field slot_uri: MIXS:0000683 domain_of: - - Biosample + - Biosample range: string multivalued: false bac_resp: @@ -8102,14 +8454,14 @@ slots: description: Measurement of bacterial respiration in the water column title: bacterial respiration examples: - - value: 300 micromole oxygen per liter per hour + - value: 300 micromole oxygen per liter per hour from_schema: https://example.com/nmdc_submission_schema aliases: - - bacterial respiration + - bacterial respiration is_a: core field slot_uri: MIXS:0000684 domain_of: - - Biosample + - Biosample range: string multivalued: false bacteria_carb_prod: @@ -8127,14 +8479,14 @@ slots: description: Measurement of bacterial carbon production title: bacterial carbon production examples: - - value: 2.53 microgram per liter per hour + - value: 2.53 microgram per liter per hour from_schema: https://example.com/nmdc_submission_schema aliases: - - bacterial carbon production + - bacterial carbon production is_a: core field slot_uri: MIXS:0000173 domain_of: - - Biosample + - Biosample range: string multivalued: false barometric_press: @@ -8149,17 +8501,18 @@ slots: occurrence: tag: occurrence value: '1' - description: Force per unit area exerted against a surface by the weight of air above that surface + description: Force per unit area exerted against a surface by the weight of air + above that surface title: barometric pressure examples: - - value: 5 millibar + - value: 5 millibar from_schema: https://example.com/nmdc_submission_schema aliases: - - barometric pressure + - barometric pressure is_a: core field slot_uri: MIXS:0000096 domain_of: - - Biosample + - Biosample range: string multivalued: false basin: @@ -8174,15 +8527,15 @@ slots: description: Name of the basin (e.g. Campos) title: basin name examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - basin name + - basin name is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000290 domain_of: - - Biosample + - Biosample range: string multivalued: false bathroom_count: @@ -8197,14 +8550,14 @@ slots: description: The number of bathrooms in the building title: bathroom count examples: - - value: '1' + - value: '1' from_schema: https://example.com/nmdc_submission_schema aliases: - - bathroom count + - bathroom count is_a: core field slot_uri: MIXS:0000776 domain_of: - - Biosample + - Biosample range: string multivalued: false bedroom_count: @@ -8219,14 +8572,14 @@ slots: description: The number of bedrooms in the building title: bedroom count examples: - - value: '2' + - value: '2' from_schema: https://example.com/nmdc_submission_schema aliases: - - bedroom count + - bedroom count is_a: core field slot_uri: MIXS:0000777 domain_of: - - Biosample + - Biosample range: string multivalued: false benzene: @@ -8244,14 +8597,14 @@ slots: description: Concentration of benzene in the sample title: benzene examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - benzene + - benzene is_a: core field slot_uri: MIXS:0000153 domain_of: - - Biosample + - Biosample range: string multivalued: false biochem_oxygen_dem: @@ -8266,17 +8619,19 @@ slots: 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 + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - biochemical oxygen demand + - biochemical oxygen demand is_a: core field slot_uri: MIXS:0000653 domain_of: - - Biosample + - Biosample range: string multivalued: false biocide: @@ -8288,18 +8643,19 @@ slots: occurrence: tag: occurrence value: '1' - description: List of biocides (commercial name of product and supplier) and date of administration + 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 + - value: ALPHA 1427;Baker Hughes;2008-01-23 from_schema: https://example.com/nmdc_submission_schema aliases: - - biocide administration + - biocide administration is_a: core field string_serialization: '{text};{text};{timestamp}' slot_uri: MIXS:0001011 domain_of: - - Biosample + - Biosample range: string multivalued: false biocide_admin_method: @@ -8314,18 +8670,20 @@ slots: 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) + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - biocide administration method + - biocide administration method is_a: core field string_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration}' slot_uri: MIXS:0000456 domain_of: - - Biosample + - Biosample range: string multivalued: false biol_stat: @@ -8340,14 +8698,14 @@ slots: description: The level of genome modification. title: biological status examples: - - value: natural + - value: natural from_schema: https://example.com/nmdc_submission_schema aliases: - - biological status + - biological status is_a: core field slot_uri: MIXS:0000858 domain_of: - - Biosample + - Biosample range: biol_stat_enum multivalued: false biomass: @@ -8362,18 +8720,19 @@ slots: 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 + 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 + - value: total;20 gram from_schema: https://example.com/nmdc_submission_schema aliases: - - biomass + - biomass is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000174 domain_of: - - Biosample + - Biosample range: string multivalued: false biotic_regm: @@ -8385,18 +8744,19 @@ slots: occurrence: tag: occurrence value: '1' - description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. + 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 + - value: sample inoculated with Rhizobium spp. Culture from_schema: https://example.com/nmdc_submission_schema aliases: - - biotic regimen + - biotic regimen is_a: core field string_serialization: '{text}' slot_uri: MIXS:0001038 domain_of: - - Biosample + - Biosample range: string multivalued: false biotic_relationship: @@ -8405,17 +8765,20 @@ slots: 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 + 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 + - value: free living from_schema: https://example.com/nmdc_submission_schema aliases: - - observed biotic relationship + - observed biotic relationship is_a: nucleic acid sequence source field slot_uri: MIXS:0000028 domain_of: - - Biosample + - Biosample range: biotic_relationship_enum multivalued: false bishomohopanol: @@ -8433,14 +8796,14 @@ slots: description: Concentration of bishomohopanol title: bishomohopanol examples: - - value: 14 microgram per liter + - value: 14 microgram per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - bishomohopanol + - bishomohopanol is_a: core field slot_uri: MIXS:0000175 domain_of: - - Biosample + - Biosample range: string multivalued: false blood_press_diast: @@ -8458,14 +8821,14 @@ slots: description: Resting diastolic blood pressure, measured as mm mercury title: host blood pressure diastolic examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - host blood pressure diastolic + - host blood pressure diastolic is_a: core field slot_uri: MIXS:0000258 domain_of: - - Biosample + - Biosample range: string multivalued: false blood_press_syst: @@ -8483,14 +8846,14 @@ slots: description: Resting systolic blood pressure, measured as mm mercury title: host blood pressure systolic examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - host blood pressure systolic + - host blood pressure systolic is_a: core field slot_uri: MIXS:0000259 domain_of: - - Biosample + - Biosample range: string multivalued: false bromide: @@ -8508,14 +8871,14 @@ slots: description: Concentration of bromide title: bromide examples: - - value: 0.05 parts per million + - value: 0.05 parts per million from_schema: https://example.com/nmdc_submission_schema aliases: - - bromide + - bromide is_a: core field slot_uri: MIXS:0000176 domain_of: - - Biosample + - Biosample range: string multivalued: false build_docs: @@ -8530,14 +8893,14 @@ slots: description: The building design, construction and operation documents title: design, construction, and operation documents examples: - - value: maintenance plans + - value: maintenance plans from_schema: https://example.com/nmdc_submission_schema aliases: - - design, construction, and operation documents + - design, construction, and operation documents is_a: core field slot_uri: MIXS:0000787 domain_of: - - Biosample + - Biosample range: build_docs_enum multivalued: false build_occup_type: @@ -8549,17 +8912,18 @@ slots: occurrence: tag: occurrence value: m - description: The primary function for which a building or discrete part of a building is intended to be used + 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 + - value: market from_schema: https://example.com/nmdc_submission_schema aliases: - - building occupancy type + - building occupancy type is_a: core field slot_uri: MIXS:0000761 domain_of: - - Biosample + - Biosample range: build_occup_type_enum multivalued: true building_setting: @@ -8574,14 +8938,14 @@ slots: description: A location (geography) where a building is set title: building setting examples: - - value: rural + - value: rural from_schema: https://example.com/nmdc_submission_schema aliases: - - building setting + - building setting is_a: core field slot_uri: MIXS:0000768 domain_of: - - Biosample + - Biosample range: building_setting_enum multivalued: false built_struc_age: @@ -8599,14 +8963,14 @@ slots: description: The age of the built structure since construction title: built structure age examples: - - value: '15' + - value: '15' from_schema: https://example.com/nmdc_submission_schema aliases: - - built structure age + - built structure age is_a: core field slot_uri: MIXS:0000145 domain_of: - - Biosample + - Biosample range: string multivalued: false built_struc_set: @@ -8618,18 +8982,19 @@ slots: occurrence: tag: occurrence value: '1' - description: The characterization of the location of the built structure as high or low human density + description: The characterization of the location of the built structure as high + or low human density title: built structure setting examples: - - value: rural + - value: rural from_schema: https://example.com/nmdc_submission_schema aliases: - - built structure setting + - built structure setting is_a: core field string_serialization: '[urban|rural]' slot_uri: MIXS:0000778 domain_of: - - Biosample + - Biosample range: string multivalued: false built_struc_type: @@ -8641,32 +9006,34 @@ slots: 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 + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - built structure type + - built structure type is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000721 domain_of: - - Biosample + - Biosample range: string multivalued: false bulk_elect_conductivity: name: bulk_elect_conductivity - description: Electrical conductivity is a measure of the ability to carry electric current, which is mostly dictated by the chemistry of and amount of water. + description: Electrical conductivity is a measure of the ability to carry electric + current, which is mostly dictated by the chemistry of and amount of water. title: bulk electrical conductivity comments: - - Provide the value output of the field instrument. + - Provide the value output of the field instrument. examples: - - value: JsonObj(has_raw_value='0.017 mS/cm', has_numeric_value=0.017, has_unit='mS/cm') - description: The conductivity measurement was 0.017 millisiemens per centimeter. + - value: JsonObj(has_raw_value='0.017 mS/cm', has_numeric_value=0.017, has_unit='mS/cm') + description: The conductivity measurement was 0.017 millisiemens per centimeter. from_schema: https://example.com/nmdc_submission_schema domain_of: - - Biosample + - Biosample range: string multivalued: false calcium: @@ -8684,14 +9051,14 @@ slots: description: Concentration of calcium in the sample title: calcium examples: - - value: 0.2 micromole per liter + - value: 0.2 micromole per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - calcium + - calcium is_a: core field slot_uri: MIXS:0000432 domain_of: - - Biosample + - Biosample range: string multivalued: false carb_dioxide: @@ -8709,14 +9076,14 @@ slots: description: Carbon dioxide (gas) amount or concentration at the time of sampling title: carbon dioxide examples: - - value: 410 parts per million + - value: 410 parts per million from_schema: https://example.com/nmdc_submission_schema aliases: - - carbon dioxide + - carbon dioxide is_a: core field slot_uri: MIXS:0000097 domain_of: - - Biosample + - Biosample range: string multivalued: false carb_monoxide: @@ -8734,14 +9101,14 @@ slots: description: Carbon monoxide (gas) amount or concentration at the time of sampling title: carbon monoxide examples: - - value: 0.1 parts per million + - value: 0.1 parts per million from_schema: https://example.com/nmdc_submission_schema aliases: - - carbon monoxide + - carbon monoxide is_a: core field slot_uri: MIXS:0000098 domain_of: - - Biosample + - Biosample range: string multivalued: false carb_nitro_ratio: @@ -8756,14 +9123,14 @@ slots: description: Ratio of amount or concentrations of carbon to nitrogen title: carbon/nitrogen ratio examples: - - value: '0.417361111' + - value: '0.417361111' from_schema: https://example.com/nmdc_submission_schema aliases: - - carbon/nitrogen ratio + - carbon/nitrogen ratio is_a: core field slot_uri: MIXS:0000310 domain_of: - - Biosample + - Biosample range: string multivalued: false ceil_area: @@ -8781,14 +9148,14 @@ slots: description: The area of the ceiling space within the room title: ceiling area examples: - - value: 25 square meter + - value: 25 square meter from_schema: https://example.com/nmdc_submission_schema aliases: - - ceiling area + - ceiling area is_a: core field slot_uri: MIXS:0000148 domain_of: - - Biosample + - Biosample range: string multivalued: false ceil_cond: @@ -8800,17 +9167,18 @@ slots: 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 + 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 + - value: damaged from_schema: https://example.com/nmdc_submission_schema aliases: - - ceiling condition + - ceiling condition is_a: core field slot_uri: MIXS:0000779 domain_of: - - Biosample + - Biosample range: ceil_cond_enum multivalued: false ceil_finish_mat: @@ -8825,14 +9193,14 @@ slots: description: The type of material used to finish a ceiling title: ceiling finish material examples: - - value: stucco + - value: stucco from_schema: https://example.com/nmdc_submission_schema aliases: - - ceiling finish material + - ceiling finish material is_a: core field slot_uri: MIXS:0000780 domain_of: - - Biosample + - Biosample range: ceil_finish_mat_enum multivalued: false ceil_struc: @@ -8847,15 +9215,15 @@ slots: description: The construction format of the ceiling title: ceiling structure examples: - - value: concrete + - value: concrete from_schema: https://example.com/nmdc_submission_schema aliases: - - ceiling structure + - ceiling structure is_a: core field string_serialization: '[wood frame|concrete]' slot_uri: MIXS:0000782 domain_of: - - Biosample + - Biosample range: string multivalued: false ceil_texture: @@ -8870,14 +9238,14 @@ slots: description: The feel, appearance, or consistency of a ceiling surface title: ceiling texture examples: - - value: popcorn + - value: popcorn from_schema: https://example.com/nmdc_submission_schema aliases: - - ceiling texture + - ceiling texture is_a: core field slot_uri: MIXS:0000783 domain_of: - - Biosample + - Biosample range: ceil_texture_enum multivalued: false ceil_thermal_mass: @@ -8892,17 +9260,20 @@ slots: 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 + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - ceiling thermal mass + - ceiling thermal mass is_a: core field slot_uri: MIXS:0000143 domain_of: - - Biosample + - Biosample range: string multivalued: false ceil_type: @@ -8917,14 +9288,14 @@ slots: description: The type of ceiling according to the ceiling's appearance or construction title: ceiling type examples: - - value: coffered + - value: coffered from_schema: https://example.com/nmdc_submission_schema aliases: - - ceiling type + - ceiling type is_a: core field slot_uri: MIXS:0000784 domain_of: - - Biosample + - Biosample range: ceil_type_enum multivalued: false ceil_water_mold: @@ -8939,15 +9310,15 @@ slots: description: Signs of the presence of mold or mildew on the ceiling title: ceiling signs of water/mold examples: - - value: presence of mold visible + - value: presence of mold visible from_schema: https://example.com/nmdc_submission_schema aliases: - - ceiling signs of water/mold + - ceiling signs of water/mold is_a: core field string_serialization: '[presence of mold visible|no presence of mold visible]' slot_uri: MIXS:0000781 domain_of: - - Biosample + - Biosample range: string multivalued: false chem_administration: @@ -8959,18 +9330,21 @@ slots: 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 + 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 + - value: agar [CHEBI:2509];2018-05-11T20:00Z from_schema: https://example.com/nmdc_submission_schema aliases: - - chemical administration + - chemical administration is_a: core field string_serialization: '{termLabel} {[termID]};{timestamp}' slot_uri: MIXS:0000751 domain_of: - - Biosample + - Biosample range: string multivalued: false chem_mutagen: @@ -8985,18 +9359,21 @@ slots: 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 + 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 + - 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 + - chemical mutagen is_a: core field string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000555 domain_of: - - Biosample + - Biosample range: string multivalued: false chem_oxygen_dem: @@ -9011,17 +9388,19 @@ slots: 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 + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - chemical oxygen demand + - chemical oxygen demand is_a: core field slot_uri: MIXS:0000656 domain_of: - - Biosample + - Biosample range: string multivalued: false chem_treat_method: @@ -9036,18 +9415,20 @@ slots: 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) + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - chemical treatment method + - chemical treatment method is_a: core field string_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration};{duration}' slot_uri: MIXS:0000457 domain_of: - - Biosample + - Biosample range: string multivalued: false chem_treatment: @@ -9059,18 +9440,22 @@ slots: 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 + 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 + - value: ACCENT 1125;DOW;2010-11-17 from_schema: https://example.com/nmdc_submission_schema aliases: - - chemical treatment + - chemical treatment is_a: core field string_serialization: '{text};{text};{timestamp}' slot_uri: MIXS:0001012 domain_of: - - Biosample + - Biosample range: string multivalued: false chloride: @@ -9088,14 +9473,14 @@ slots: description: Concentration of chloride in the sample title: chloride examples: - - value: 5000 milligram per liter + - value: 5000 milligram per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - chloride + - chloride is_a: core field slot_uri: MIXS:0000429 domain_of: - - Biosample + - Biosample range: string multivalued: false chlorophyll: @@ -9113,14 +9498,14 @@ slots: description: Concentration of chlorophyll title: chlorophyll examples: - - value: 5 milligram per cubic meter + - value: 5 milligram per cubic meter from_schema: https://example.com/nmdc_submission_schema aliases: - - chlorophyll + - chlorophyll is_a: core field slot_uri: MIXS:0000177 domain_of: - - Biosample + - Biosample range: string multivalued: false climate_environment: @@ -9132,18 +9517,21 @@ slots: 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 + 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 + - value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://example.com/nmdc_submission_schema aliases: - - climate environment + - climate environment is_a: core field string_serialization: '{text};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0001040 domain_of: - - Biosample + - Biosample range: string multivalued: false collection_date: @@ -9152,36 +9540,42 @@ slots: 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' + 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 + - value: 2018-05-11T10:00:00+01:00; 2018-05-11 from_schema: https://example.com/nmdc_submission_schema aliases: - - collection date + - collection date is_a: environment field slot_uri: MIXS:0000011 domain_of: - - Biosample + - Biosample range: string multivalued: false collection_date_inc: name: collection_date_inc - description: Date the incubation was harvested/collected/ended. Only relevant for incubation samples. + 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 + - 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. + - 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. + - value: 2021-04-15, 2021-04 and 2021 are all acceptable. from_schema: https://example.com/nmdc_submission_schema see_also: - - MIXS:0000011 + - MIXS:0000011 rank: 2 string_serialization: '{date, arbitrary precision}' domain_of: - - Biosample + - Biosample slot_group: MIxS Inspired recommended: true collection_time: @@ -9189,37 +9583,40 @@ slots: 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 + - 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' + - '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 + - value: 13:33 or 13:33:55 from_schema: https://example.com/nmdc_submission_schema see_also: - - MIXS:0000011 + - MIXS:0000011 rank: 1 string_serialization: '{time, seconds optional}' domain_of: - - Biosample + - Biosample 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. + 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 + - 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' + - '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 + - value: 13:33 or 13:33:55 from_schema: https://example.com/nmdc_submission_schema see_also: - - MIXS:0000011 + - MIXS:0000011 rank: 3 string_serialization: '{time, seconds optional}' domain_of: - - Biosample + - Biosample slot_group: MIxS Inspired recommended: true conduc: @@ -9237,14 +9634,14 @@ slots: description: Electrical conductivity of water title: conductivity examples: - - value: 10 milliSiemens per centimeter + - value: 10 milliSiemens per centimeter from_schema: https://example.com/nmdc_submission_schema aliases: - - conductivity + - conductivity is_a: core field slot_uri: MIXS:0000692 domain_of: - - Biosample + - Biosample range: string multivalued: false cool_syst_id: @@ -9259,14 +9656,14 @@ slots: description: The cooling system identifier title: cooling system identifier examples: - - value: '12345' + - value: '12345' from_schema: https://example.com/nmdc_submission_schema aliases: - - cooling system identifier + - cooling system identifier is_a: core field slot_uri: MIXS:0000785 domain_of: - - Biosample + - Biosample range: string multivalued: false crop_rotation: @@ -9281,15 +9678,15 @@ slots: 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 + - value: yes;R2/2017-01-01/2018-12-31/P6M from_schema: https://example.com/nmdc_submission_schema aliases: - - history/crop rotation + - history/crop rotation is_a: core field string_serialization: '{boolean};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000318 domain_of: - - Biosample + - Biosample range: string multivalued: false cult_root_med: @@ -9301,18 +9698,21 @@ slots: 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. + 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 + - value: http://himedialabs.com/TD/PT158.pdf from_schema: https://example.com/nmdc_submission_schema aliases: - - culture rooting medium + - culture rooting medium is_a: core field string_serialization: '{text}|{PMID}|{DOI}|{URL}' slot_uri: MIXS:0001041 domain_of: - - Biosample + - Biosample range: string multivalued: false cur_land_use: @@ -9327,14 +9727,14 @@ slots: description: Present state of sample site title: current land use examples: - - value: conifers + - value: conifers from_schema: https://example.com/nmdc_submission_schema aliases: - - current land use + - current land use is_a: core field slot_uri: MIXS:0001080 domain_of: - - Biosample + - Biosample range: cur_land_use_enum multivalued: false cur_vegetation: @@ -9346,19 +9746,20 @@ slots: occurrence: tag: occurrence value: '1' - description: Vegetation classification from one or more standard classification systems, or agricultural crop + description: Vegetation classification from one or more standard classification + systems, or agricultural crop title: current vegetation examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - current vegetation + - current vegetation is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000312 domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample range: string multivalued: false cur_vegetation_meth: @@ -9373,15 +9774,15 @@ slots: description: Reference or method used in vegetation classification title: current vegetation method examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - current vegetation method + - current vegetation method is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000314 domain_of: - - Biosample + - Biosample range: string multivalued: false date_last_rain: @@ -9396,14 +9797,14 @@ slots: description: The date of the last time it rained title: date last rain examples: - - value: 2018-05-11:T14:30Z + - value: 2018-05-11:T14:30Z from_schema: https://example.com/nmdc_submission_schema aliases: - - date last rain + - date last rain is_a: core field slot_uri: MIXS:0000786 domain_of: - - Biosample + - Biosample range: string multivalued: false density: @@ -9418,17 +9819,18 @@ slots: occurrence: tag: occurrence value: '1' - description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + 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 + - value: 1000 kilogram per cubic meter from_schema: https://example.com/nmdc_submission_schema aliases: - - density + - density is_a: core field slot_uri: MIXS:0000435 domain_of: - - Biosample + - Biosample range: string multivalued: false depos_env: @@ -9440,17 +9842,18 @@ slots: 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 + 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 + - value: Continental - Alluvial from_schema: https://example.com/nmdc_submission_schema aliases: - - depositional environment + - depositional environment is_a: core field slot_uri: MIXS:0000992 domain_of: - - Biosample + - Biosample range: depos_env_enum multivalued: false depth: @@ -9459,17 +9862,19 @@ slots: 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. + 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 + - value: 10 meter from_schema: https://example.com/nmdc_submission_schema aliases: - - depth + - depth is_a: environment field slot_uri: MIXS:0000018 domain_of: - - Biosample + - Biosample range: string multivalued: false dew_point: @@ -9484,17 +9889,18 @@ slots: 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. + 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 + - value: 22 degree Celsius from_schema: https://example.com/nmdc_submission_schema aliases: - - dew point + - dew point is_a: core field slot_uri: MIXS:0000129 domain_of: - - Biosample + - Biosample range: string multivalued: false diether_lipids: @@ -9509,18 +9915,19 @@ slots: occurrence: tag: occurrence value: m - description: Concentration of diether lipids; can include multiple types of diether lipids + description: Concentration of diether lipids; can include multiple types of diether + lipids title: diether lipids examples: - - value: 0.2 nanogram per liter + - value: 0.2 nanogram per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - diether lipids + - diether lipids is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000178 domain_of: - - Biosample + - Biosample range: string multivalued: false diss_carb_dioxide: @@ -9535,17 +9942,18 @@ slots: occurrence: tag: occurrence value: '1' - description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + 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 + - value: 5 milligram per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - dissolved carbon dioxide + - dissolved carbon dioxide is_a: core field slot_uri: MIXS:0000436 domain_of: - - Biosample + - Biosample range: string multivalued: false diss_hydrogen: @@ -9563,14 +9971,14 @@ slots: description: Concentration of dissolved hydrogen title: dissolved hydrogen examples: - - value: 0.3 micromole per liter + - value: 0.3 micromole per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - dissolved hydrogen + - dissolved hydrogen is_a: core field slot_uri: MIXS:0000179 domain_of: - - Biosample + - Biosample range: string multivalued: false diss_inorg_carb: @@ -9585,17 +9993,18 @@ slots: 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 + 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 + - value: 2059 micromole per kilogram from_schema: https://example.com/nmdc_submission_schema aliases: - - dissolved inorganic carbon + - dissolved inorganic carbon is_a: core field slot_uri: MIXS:0000434 domain_of: - - Biosample + - Biosample range: string multivalued: false diss_inorg_nitro: @@ -9613,14 +10022,14 @@ slots: description: Concentration of dissolved inorganic nitrogen title: dissolved inorganic nitrogen examples: - - value: 761 micromole per liter + - value: 761 micromole per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - dissolved inorganic nitrogen + - dissolved inorganic nitrogen is_a: core field slot_uri: MIXS:0000698 domain_of: - - Biosample + - Biosample range: string multivalued: false diss_inorg_phosp: @@ -9638,14 +10047,14 @@ slots: description: Concentration of dissolved inorganic phosphorus in the sample title: dissolved inorganic phosphorus examples: - - value: 56.5 micromole per liter + - value: 56.5 micromole per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - dissolved inorganic phosphorus + - dissolved inorganic phosphorus is_a: core field slot_uri: MIXS:0000106 domain_of: - - Biosample + - Biosample range: string multivalued: false diss_iron: @@ -9663,14 +10072,14 @@ slots: description: Concentration of dissolved iron in the sample title: dissolved iron examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - dissolved iron + - dissolved iron is_a: core field slot_uri: MIXS:0000139 domain_of: - - Biosample + - Biosample range: string multivalued: false diss_org_carb: @@ -9685,17 +10094,18 @@ slots: 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 + 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 + - value: 197 micromole per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - dissolved organic carbon + - dissolved organic carbon is_a: core field slot_uri: MIXS:0000433 domain_of: - - Biosample + - Biosample range: string multivalued: false diss_org_nitro: @@ -9710,17 +10120,18 @@ slots: occurrence: tag: occurrence value: '1' - description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + description: Dissolved organic nitrogen concentration measured as; total dissolved + nitrogen - NH4 - NO3 - NO2 title: dissolved organic nitrogen examples: - - value: 0.05 micromole per liter + - value: 0.05 micromole per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - dissolved organic nitrogen + - dissolved organic nitrogen is_a: core field slot_uri: MIXS:0000162 domain_of: - - Biosample + - Biosample range: string multivalued: false diss_oxygen: @@ -9738,14 +10149,14 @@ slots: description: Concentration of dissolved oxygen title: dissolved oxygen examples: - - value: 175 micromole per kilogram + - value: 175 micromole per kilogram from_schema: https://example.com/nmdc_submission_schema aliases: - - dissolved oxygen + - dissolved oxygen is_a: core field slot_uri: MIXS:0000119 domain_of: - - Biosample + - Biosample range: string multivalued: false diss_oxygen_fluid: @@ -9760,17 +10171,18 @@ slots: 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). + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - dissolved oxygen in fluids + - dissolved oxygen in fluids is_a: core field slot_uri: MIXS:0000438 domain_of: - - Biosample + - Biosample range: string multivalued: false dna_absorb1: @@ -9778,15 +10190,15 @@ slots: description: 260/280 measurement of DNA sample purity title: DNA absorbance 260/280 comments: - - Recommended value is between 1 and 3. + - Recommended value is between 1 and 3. examples: - - value: '2.02' + - value: '2.02' from_schema: https://example.com/nmdc_submission_schema rank: 7 is_a: biomaterial_purity domain_of: - - Biosample - - ProcessedSample + - Biosample + - ProcessedSample slot_group: JGI-Metagenomics range: float recommended: true @@ -9795,14 +10207,14 @@ slots: description: 260/230 measurement of DNA sample purity title: DNA absorbance 260/230 comments: - - Recommended value is between 1 and 3. + - Recommended value is between 1 and 3. examples: - - value: '2.02' + - value: '2.02' from_schema: https://example.com/nmdc_submission_schema rank: 8 is_a: biomaterial_purity domain_of: - - Biosample + - Biosample slot_group: JGI-Metagenomics range: float recommended: true @@ -9810,16 +10222,17 @@ slots: 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. + - 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' + - value: '100' from_schema: https://example.com/nmdc_submission_schema see_also: - - nmdc:nucleic_acid_concentration + - nmdc:nucleic_acid_concentration rank: 5 domain_of: - - Biosample - - ProcessedSample + - Biosample + - ProcessedSample slot_group: JGI-Metagenomics range: float recommended: true @@ -9830,11 +10243,11 @@ slots: description: Tube or plate (96-well) title: DNA container type examples: - - value: plate + - value: plate from_schema: https://example.com/nmdc_submission_schema rank: 10 domain_of: - - Biosample + - Biosample slot_group: JGI-Metagenomics range: JgiContTypeEnum recommended: true @@ -9842,17 +10255,18 @@ slots: 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). + - 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 + - value: B2 from_schema: https://example.com/nmdc_submission_schema rank: 11 string_serialization: '{96 well plate pos}' domain_of: - - Biosample + - Biosample slot_group: JGI-Metagenomics recommended: true pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$ @@ -9860,27 +10274,28 @@ slots: 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. + - 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 + - value: Pond_MT_041618 from_schema: https://example.com/nmdc_submission_schema rank: 9 string_serialization: '{text < 20 characters}' domain_of: - - Biosample + - Biosample 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. + - Note DNase treatment is required for all RNA samples. examples: - - value: 'no' + - value: 'no' from_schema: https://example.com/nmdc_submission_schema rank: 13 domain_of: - - Biosample + - Biosample slot_group: JGI-Metagenomics range: YesNoEnum recommended: true @@ -9889,44 +10304,48 @@ slots: description: Describe the method/protocol/kit used to extract DNA/RNA. title: DNA isolation method examples: - - value: phenol/chloroform extraction + - value: phenol/chloroform extraction from_schema: https://example.com/nmdc_submission_schema aliases: - - Sample Isolation Method + - Sample Isolation Method rank: 16 string_serialization: '{text}' domain_of: - - Biosample + - Biosample 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. + - Do not edit these values. A template will be provided by NMDC in which these + values have been pre-filled. examples: - - value: John Jones + - value: John Jones from_schema: https://example.com/nmdc_submission_schema rank: 18 string_serialization: '{text}' domain_of: - - Biosample + - Biosample 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? + - 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. + - Do not edit these values. A template will be provided by NMDC in which these + values have been pre-filled. examples: - - value: '187654' + - value: '187654' from_schema: https://example.com/nmdc_submission_schema rank: 3 string_serialization: '{text}' domain_of: - - Biosample + - Biosample slot_group: JGI-Metagenomics recommended: true dna_sample_format: @@ -9934,83 +10353,89 @@ slots: description: Solution in which the DNA sample has been suspended title: DNA sample format examples: - - value: Water + - value: Water from_schema: https://example.com/nmdc_submission_schema rank: 12 domain_of: - - Biosample + - Biosample slot_group: JGI-Metagenomics range: DNASampleFormatEnum 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. + 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 + - value: JGI_pond_041618 from_schema: https://example.com/nmdc_submission_schema rank: 4 string_serialization: '{text}' domain_of: - - Biosample + - Biosample 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. + - Do not edit these values. A template will be provided by NMDC in which these + values have been pre-filled. examples: - - value: '1191234' + - value: '1191234' from_schema: https://example.com/nmdc_submission_schema aliases: - - Seq Project ID + - Seq Project ID rank: 1 string_serialization: '{text}' domain_of: - - Biosample + - Biosample 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. + - 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 + - value: JGI Pond metagenomics from_schema: https://example.com/nmdc_submission_schema rank: 2 string_serialization: '{text}' domain_of: - - Biosample + - Biosample 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. + - Do not edit these values. A template will be provided by NMDC in which these + values have been pre-filled. examples: - - value: Jane Johnson + - value: Jane Johnson from_schema: https://example.com/nmdc_submission_schema rank: 17 string_serialization: '{text}' domain_of: - - Biosample + - Biosample 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 + - 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' + - value: '25' from_schema: https://example.com/nmdc_submission_schema rank: 6 string_serialization: '{float}' domain_of: - - Biosample + - Biosample slot_group: JGI-Metagenomics range: float recommended: true @@ -10020,15 +10445,15 @@ slots: name: dnase_rna title: DNase treated comments: - - Note DNase treatment is required for all RNA samples. + - Note DNase treatment is required for all RNA samples. examples: - - value: 'no' + - value: 'no' from_schema: https://example.com/nmdc_submission_schema aliases: - - Was Sample DNAse treated? + - Was Sample DNAse treated? rank: 13 domain_of: - - Biosample + - Biosample slot_group: JGI-Metatranscriptomics range: YesNoEnum recommended: true @@ -10044,14 +10469,14 @@ slots: description: The composite type of the door title: door type, composite examples: - - value: revolving + - value: revolving from_schema: https://example.com/nmdc_submission_schema aliases: - - door type, composite + - door type, composite is_a: core field slot_uri: MIXS:0000795 domain_of: - - Biosample + - Biosample range: door_comp_type_enum multivalued: false door_cond: @@ -10066,14 +10491,14 @@ slots: description: The phsical condition of the door title: door condition examples: - - value: new + - value: new from_schema: https://example.com/nmdc_submission_schema aliases: - - door condition + - door condition is_a: core field slot_uri: MIXS:0000788 domain_of: - - Biosample + - Biosample range: door_cond_enum multivalued: false door_direct: @@ -10088,14 +10513,14 @@ slots: description: The direction the door opens title: door direction of opening examples: - - value: inward + - value: inward from_schema: https://example.com/nmdc_submission_schema aliases: - - door direction of opening + - door direction of opening is_a: core field slot_uri: MIXS:0000789 domain_of: - - Biosample + - Biosample range: door_direct_enum multivalued: false door_loc: @@ -10110,14 +10535,14 @@ slots: description: The relative location of the door in the room title: door location examples: - - value: north + - value: north from_schema: https://example.com/nmdc_submission_schema aliases: - - door location + - door location is_a: core field slot_uri: MIXS:0000790 domain_of: - - Biosample + - Biosample range: door_loc_enum multivalued: false door_mat: @@ -10132,14 +10557,14 @@ slots: description: The material the door is composed of title: door material examples: - - value: wood + - value: wood from_schema: https://example.com/nmdc_submission_schema aliases: - - door material + - door material is_a: core field slot_uri: MIXS:0000791 domain_of: - - Biosample + - Biosample range: door_mat_enum multivalued: false door_move: @@ -10154,14 +10579,14 @@ slots: description: The type of movement of the door title: door movement examples: - - value: swinging + - value: swinging from_schema: https://example.com/nmdc_submission_schema aliases: - - door movement + - door movement is_a: core field slot_uri: MIXS:0000792 domain_of: - - Biosample + - Biosample range: door_move_enum multivalued: false door_size: @@ -10179,14 +10604,14 @@ slots: description: The size of the door title: door area or size examples: - - value: 2.5 square meter + - value: 2.5 square meter from_schema: https://example.com/nmdc_submission_schema aliases: - - door area or size + - door area or size is_a: core field slot_uri: MIXS:0000158 domain_of: - - Biosample + - Biosample range: string multivalued: false door_type: @@ -10201,14 +10626,14 @@ slots: description: The type of door material title: door type examples: - - value: wooden + - value: wooden from_schema: https://example.com/nmdc_submission_schema aliases: - - door type + - door type is_a: core field slot_uri: MIXS:0000794 domain_of: - - Biosample + - Biosample range: door_type_enum multivalued: false door_type_metal: @@ -10223,14 +10648,14 @@ slots: description: The type of metal door title: door type, metal examples: - - value: hollow + - value: hollow from_schema: https://example.com/nmdc_submission_schema aliases: - - door type, metal + - door type, metal is_a: core field slot_uri: MIXS:0000796 domain_of: - - Biosample + - Biosample range: door_type_metal_enum multivalued: false door_type_wood: @@ -10245,14 +10670,14 @@ slots: description: The type of wood door title: door type, wood examples: - - value: battened + - value: battened from_schema: https://example.com/nmdc_submission_schema aliases: - - door type, wood + - door type, wood is_a: core field slot_uri: MIXS:0000797 domain_of: - - Biosample + - Biosample range: door_type_wood_enum multivalued: false door_water_mold: @@ -10267,15 +10692,15 @@ slots: description: Signs of the presence of mold or mildew on a door title: door signs of water/mold examples: - - value: presence of mold visible + - value: presence of mold visible from_schema: https://example.com/nmdc_submission_schema aliases: - - door signs of water/mold + - door signs of water/mold is_a: core field string_serialization: '[presence of mold visible|no presence of mold visible]' slot_uri: MIXS:0000793 domain_of: - - Biosample + - Biosample range: string multivalued: false down_par: @@ -10286,21 +10711,23 @@ slots: value: measurement value preferred_unit: tag: preferred_unit - value: microEinstein per square meter per second, microEinstein per square centimeter per second + 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 + description: Visible waveband radiance and irradiance measurements in the water + column title: downward PAR examples: - - value: 28.71 microEinstein per square meter per second + - value: 28.71 microEinstein per square meter per second from_schema: https://example.com/nmdc_submission_schema aliases: - - downward PAR + - downward PAR is_a: core field slot_uri: MIXS:0000703 domain_of: - - Biosample + - Biosample range: string multivalued: false drainage_class: @@ -10315,14 +10742,14 @@ slots: description: Drainage classification from a standard system such as the USDA system title: drainage classification examples: - - value: well + - value: well from_schema: https://example.com/nmdc_submission_schema aliases: - - drainage classification + - drainage classification is_a: core field slot_uri: MIXS:0001085 domain_of: - - Biosample + - Biosample range: drainage_class_enum multivalued: false drawings: @@ -10334,67 +10761,91 @@ slots: occurrence: tag: occurrence value: '1' - description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents + description: The buildings architectural drawings; if design is chosen, indicate + phase-conceptual, schematic, design development, and construction documents title: drawings examples: - - value: sketch + - value: sketch from_schema: https://example.com/nmdc_submission_schema aliases: - - drawings + - drawings is_a: core field slot_uri: MIXS:0000798 domain_of: - - Biosample + - Biosample range: drawings_enum multivalued: false 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help is_a: gold_path_field domain_of: - - Biosample - - Study + - Biosample + - Study 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help is_a: gold_path_field domain_of: - - Biosample - - Study + - Biosample + - Study 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help is_a: gold_path_field domain_of: - - Biosample - - Study + - Biosample + - Study 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help is_a: gold_path_field domain_of: - - Biosample - - Study + - Biosample + - Study efficiency_percent: name: efficiency_percent annotations: @@ -10410,14 +10861,14 @@ slots: description: Percentage of volatile solids removed from the anaerobic digestor title: efficiency percent examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - efficiency percent + - efficiency percent is_a: core field slot_uri: MIXS:0000657 domain_of: - - Biosample + - Biosample range: string multivalued: false elev: @@ -10426,18 +10877,21 @@ slots: 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. + 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 + - value: 100 meter from_schema: https://example.com/nmdc_submission_schema aliases: - - elevation + - elevation is_a: environment field slot_uri: MIXS:0000093 domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample range: float multivalued: false elevator: @@ -10452,26 +10906,27 @@ slots: description: The number of elevators within the built structure title: elevator count examples: - - value: '2' + - value: '2' from_schema: https://example.com/nmdc_submission_schema aliases: - - elevator count + - elevator count is_a: core field slot_uri: MIXS:0000799 domain_of: - - Biosample + - Biosample range: string multivalued: false emsl_store_temp: name: emsl_store_temp - description: The temperature at which the sample should be stored upon delivery to EMSL + 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 + - add 'see_alsos' with link to NEXUS info comments: - - Enter a temperature in celsius. Numeric portion only. + - Enter a temperature in celsius. Numeric portion only. examples: - - value: '-80' + - value: '-80' from_schema: https://example.com/nmdc_submission_schema rank: 4 string_serialization: '{float}' @@ -10489,18 +10944,20 @@ slots: 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 + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - emulsions + - emulsions is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000660 domain_of: - - Biosample + - Biosample range: string multivalued: false env_broad_scale: @@ -10508,22 +10965,33 @@ slots: 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. + 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. tooltip: tag: tooltip - value: The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context - 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' + value: The biome or major environmental system where the sample or specimen + originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] + in the Environment Ontology (ENVO). For host-associated or plant-associated + samples, use terms from the UBERON or Plant Ontology to describe the broad + anatomical or morphological context + 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 + - 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 + - broad-scale environmental context is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000012 domain_of: - - Biosample + - Biosample range: string multivalued: false env_local_scale: @@ -10531,22 +10999,38 @@ slots: annotations: expected_value: tag: expected_value - value: Environmental entities having causal influences upon the entity at time of sampling. + value: Environmental entities having causal influences upon the entity at + time of sampling. tooltip: tag: tooltip - value: The specific environmental entities or features near the sample or specimen that significantly influence its characteristics or composition. These entities are typically smaller in scale than the broad environmental context. Values for this field should be countable, material nouns and must be chosen from subclasses of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe specific anatomical structures or plant parts. - 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.' + value: The specific environmental entities or features near the sample or + specimen that significantly influence its characteristics or composition. + These entities are typically smaller in scale than the broad environmental + context. Values for this field should be countable, material nouns and must + be chosen from subclasses of BFO:0000040 (material entity) that appear in + the Environment Ontology (ENVO). For host-associated or plant-associated + samples, use terms from the UBERON or Plant Ontology to describe specific + anatomical structures or plant parts. + 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].' + - 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 + - local environmental context is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000013 domain_of: - - Biosample + - Biosample range: string multivalued: false env_medium: @@ -10554,22 +11038,37 @@ slots: annotations: expected_value: tag: expected_value - value: The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]. + value: The material displaced by the entity at time of sampling. Recommend + subclasses of environmental material [ENVO:00010483]. tooltip: tag: tooltip - value: The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure - 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).' + value: The predominant environmental material or substrate that directly surrounds + or hosts the sample or specimen at the time of sampling. Choose values from + subclasses of the 'environmental material' class [ENVO:00010483] in the + Environment Ontology (ENVO). Values for this field should be measurable + or mass material nouns, representing continuous environmental materials. + For host-associated or plant-associated samples, use terms from the UBERON + or Plant Ontology to indicate a tissue, organ, or plant structure + 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]' + - 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 + - environmental medium is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000014 domain_of: - - Biosample + - Biosample range: string multivalued: false escalator: @@ -10584,14 +11083,14 @@ slots: description: The number of escalators within the built structure title: escalator count examples: - - value: '4' + - value: '4' from_schema: https://example.com/nmdc_submission_schema aliases: - - escalator count + - escalator count is_a: core field slot_uri: MIXS:0000800 domain_of: - - Biosample + - Biosample range: string multivalued: false ethylbenzene: @@ -10609,14 +11108,14 @@ slots: description: Concentration of ethylbenzene in the sample title: ethylbenzene examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - ethylbenzene + - ethylbenzene is_a: core field slot_uri: MIXS:0000155 domain_of: - - Biosample + - Biosample range: string multivalued: false exp_duct: @@ -10634,14 +11133,14 @@ slots: description: The amount of exposed ductwork in the room title: exposed ductwork examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - exposed ductwork + - exposed ductwork is_a: core field slot_uri: MIXS:0000144 domain_of: - - Biosample + - Biosample range: string multivalued: false exp_pipe: @@ -10656,14 +11155,14 @@ slots: description: The number of exposed pipes in the room title: exposed pipes examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - exposed pipes + - exposed pipes is_a: core field slot_uri: MIXS:0000220 domain_of: - - Biosample + - Biosample range: string multivalued: false experimental_factor: @@ -10672,38 +11171,45 @@ slots: 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 + 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] + - value: time series design [EFO:EFO_0001779] from_schema: https://example.com/nmdc_submission_schema aliases: - - experimental factor + - experimental factor is_a: investigation field string_serialization: '{termLabel} {[termID]}|{text}' slot_uri: MIXS:0000008 domain_of: - - Biosample + - Biosample range: string multivalued: false 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. + 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. + - 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' + - value: 'experimental treatment: value' from_schema: https://example.com/nmdc_submission_schema see_also: - - MIXS:0000008 - - MIXS:0000300 + - MIXS:0000008 + - MIXS:0000300 rank: 7 string_serialization: '{text}' domain_of: - - Biosample + - Biosample slot_group: MIxS Inspired recommended: true ext_door: @@ -10718,14 +11224,14 @@ slots: description: The number of exterior doors in the built structure title: exterior door count examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - exterior door count + - exterior door count is_a: core field slot_uri: MIXS:0000170 domain_of: - - Biosample + - Biosample range: string multivalued: false ext_wall_orient: @@ -10740,14 +11246,14 @@ slots: description: The orientation of the exterior wall title: orientations of exterior wall examples: - - value: northwest + - value: northwest from_schema: https://example.com/nmdc_submission_schema aliases: - - orientations of exterior wall + - orientations of exterior wall is_a: core field slot_uri: MIXS:0000817 domain_of: - - Biosample + - Biosample range: ext_wall_orient_enum multivalued: false ext_window_orient: @@ -10762,14 +11268,14 @@ slots: description: The compass direction the exterior window of the room is facing title: orientations of exterior window examples: - - value: southwest + - value: southwest from_schema: https://example.com/nmdc_submission_schema aliases: - - orientations of exterior window + - orientations of exterior window is_a: core field slot_uri: MIXS:0000818 domain_of: - - Biosample + - Biosample range: ext_window_orient_enum multivalued: false extreme_event: @@ -10784,14 +11290,14 @@ slots: description: Unusual physical events that may have affected microbial populations title: history/extreme events examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - history/extreme events + - history/extreme events is_a: core field slot_uri: MIXS:0000320 domain_of: - - Biosample + - Biosample range: string multivalued: false fao_class: @@ -10803,17 +11309,18 @@ slots: 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 + 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 + - value: Luvisols from_schema: https://example.com/nmdc_submission_schema aliases: - - soil_taxonomic/FAO classification + - soil_taxonomic/FAO classification is_a: core field slot_uri: MIXS:0001083 domain_of: - - Biosample + - Biosample range: fao_class_enum multivalued: false fertilizer_regm: @@ -10828,18 +11335,22 @@ slots: 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 + 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 + - 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 + - fertilizer regimen is_a: core field string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000556 domain_of: - - Biosample + - Biosample range: string multivalued: false field: @@ -10854,15 +11365,15 @@ slots: description: Name of the hydrocarbon field (e.g. Albacora) title: field name examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - field name + - field name is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000291 domain_of: - - Biosample + - Biosample range: string multivalued: false filter_method: @@ -10870,17 +11381,17 @@ slots: 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 + - describe the filter or provide a catalog number and manufacturer examples: - - value: C18 - - value: Basix PES, 13-100-106 FisherSci + - value: C18 + - value: Basix PES, 13-100-106 FisherSci from_schema: https://example.com/nmdc_submission_schema see_also: - - MIXS:0000765 + - MIXS:0000765 rank: 6 string_serialization: '{text}' domain_of: - - Biosample + - Biosample slot_group: MIxS Inspired recommended: true filter_type: @@ -10895,14 +11406,14 @@ slots: description: A device which removes solid particulates or airborne molecular contaminants title: filter type examples: - - value: HEPA + - value: HEPA from_schema: https://example.com/nmdc_submission_schema aliases: - - filter type + - filter type is_a: core field slot_uri: MIXS:0000765 domain_of: - - Biosample + - Biosample range: filter_type_enum multivalued: true fire: @@ -10917,14 +11428,14 @@ slots: description: Historical and/or physical evidence of fire title: history/fire examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - history/fire + - history/fire is_a: core field slot_uri: MIXS:0001086 domain_of: - - Biosample + - Biosample range: string multivalued: false fireplace_type: @@ -10939,15 +11450,15 @@ slots: description: A firebox with chimney title: fireplace type examples: - - value: wood burning + - value: wood burning from_schema: https://example.com/nmdc_submission_schema aliases: - - fireplace type + - fireplace type is_a: core field string_serialization: '[gas burning|wood burning]' slot_uri: MIXS:0000802 domain_of: - - Biosample + - Biosample range: string multivalued: false flooding: @@ -10962,14 +11473,14 @@ slots: description: Historical and/or physical evidence of flooding title: history/flooding examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - history/flooding + - history/flooding is_a: core field slot_uri: MIXS:0000319 domain_of: - - Biosample + - Biosample range: string multivalued: false floor_age: @@ -10987,14 +11498,14 @@ slots: description: The time period since installment of the carpet or flooring title: floor age examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - floor age + - floor age is_a: core field slot_uri: MIXS:0000164 domain_of: - - Biosample + - Biosample range: string multivalued: false floor_area: @@ -11012,14 +11523,14 @@ slots: description: The area of the floor space within the room title: floor area examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - floor area + - floor area is_a: core field slot_uri: MIXS:0000165 domain_of: - - Biosample + - Biosample range: string multivalued: false floor_cond: @@ -11031,17 +11542,18 @@ slots: 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 + 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 + - value: new from_schema: https://example.com/nmdc_submission_schema aliases: - - floor condition + - floor condition is_a: core field slot_uri: MIXS:0000803 domain_of: - - Biosample + - Biosample range: floor_cond_enum multivalued: false floor_count: @@ -11053,17 +11565,18 @@ slots: occurrence: tag: occurrence value: '1' - description: The number of floors in the building, including basements and mechanical penthouse + description: The number of floors in the building, including basements and mechanical + penthouse title: floor count examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - floor count + - floor count is_a: core field slot_uri: MIXS:0000225 domain_of: - - Biosample + - Biosample range: string multivalued: false floor_finish_mat: @@ -11078,14 +11591,14 @@ slots: description: The floor covering type; the finished surface that is walked on title: floor finish material examples: - - value: carpet + - value: carpet from_schema: https://example.com/nmdc_submission_schema aliases: - - floor finish material + - floor finish material is_a: core field slot_uri: MIXS:0000804 domain_of: - - Biosample + - Biosample range: floor_finish_mat_enum multivalued: false floor_struc: @@ -11097,17 +11610,18 @@ slots: occurrence: tag: occurrence value: '1' - description: Refers to the structural elements and subfloor upon which the finish flooring is installed + description: Refers to the structural elements and subfloor upon which the finish + flooring is installed title: floor structure examples: - - value: concrete + - value: concrete from_schema: https://example.com/nmdc_submission_schema aliases: - - floor structure + - floor structure is_a: core field slot_uri: MIXS:0000806 domain_of: - - Biosample + - Biosample range: floor_struc_enum multivalued: false floor_thermal_mass: @@ -11125,14 +11639,14 @@ slots: description: The ability of the floor to provide inertia against temperature fluctuations title: floor thermal mass examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - floor thermal mass + - floor thermal mass is_a: core field slot_uri: MIXS:0000166 domain_of: - - Biosample + - Biosample range: string multivalued: false floor_water_mold: @@ -11147,14 +11661,14 @@ slots: description: Signs of the presence of mold or mildew in a room title: floor signs of water/mold examples: - - value: ceiling discoloration + - value: ceiling discoloration from_schema: https://example.com/nmdc_submission_schema aliases: - - floor signs of water/mold + - floor signs of water/mold is_a: core field slot_uri: MIXS:0000805 domain_of: - - Biosample + - Biosample range: floor_water_mold_enum multivalued: false fluor: @@ -11172,14 +11686,14 @@ slots: description: Raw or converted fluorescence of water title: fluorescence examples: - - value: 2.5 volts + - value: 2.5 volts from_schema: https://example.com/nmdc_submission_schema aliases: - - fluorescence + - fluorescence is_a: core field slot_uri: MIXS:0000704 domain_of: - - Biosample + - Biosample range: string multivalued: false freq_clean: @@ -11191,17 +11705,18 @@ slots: 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. + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - frequency of cleaning + - frequency of cleaning is_a: core field slot_uri: MIXS:0000226 domain_of: - - Biosample + - Biosample range: string multivalued: false freq_cook: @@ -11216,14 +11731,14 @@ slots: description: The number of times a meal is cooked per week title: frequency of cooking examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - frequency of cooking + - frequency of cooking is_a: core field slot_uri: MIXS:0000227 domain_of: - - Biosample + - Biosample range: string multivalued: false fungicide_regm: @@ -11238,18 +11753,21 @@ slots: 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 + 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 + - 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 + - fungicide regimen is_a: core field string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000557 domain_of: - - Biosample + - Biosample range: string multivalued: false furniture: @@ -11264,14 +11782,14 @@ slots: description: The types of furniture present in the sampled room title: furniture examples: - - value: chair + - value: chair from_schema: https://example.com/nmdc_submission_schema aliases: - - furniture + - furniture is_a: core field slot_uri: MIXS:0000807 domain_of: - - Biosample + - Biosample range: furniture_enum multivalued: false gaseous_environment: @@ -11279,25 +11797,28 @@ slots: annotations: expected_value: tag: expected_value - value: gaseous compound name;gaseous compound amount;treatment interval and duration + 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 + 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 + - 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 + - gaseous environment is_a: core field string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000558 domain_of: - - Biosample + - Biosample range: string multivalued: false gaseous_substances: @@ -11312,18 +11833,19 @@ slots: occurrence: tag: occurrence value: m - description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances + description: Amount or concentration of substances such as hydrogen sulfide, carbon + dioxide, methane, etc.; can include multiple substances title: gaseous substances examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - gaseous substances + - gaseous substances is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000661 domain_of: - - Biosample + - Biosample range: string multivalued: false gender_restroom: @@ -11338,14 +11860,14 @@ slots: description: The gender type of the restroom title: gender of restroom examples: - - value: male + - value: male from_schema: https://example.com/nmdc_submission_schema aliases: - - gender of restroom + - gender of restroom is_a: core field slot_uri: MIXS:0000808 domain_of: - - Biosample + - Biosample range: gender_restroom_enum multivalued: false genetic_mod: @@ -11357,18 +11879,21 @@ slots: 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 + 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 + - value: aox1A transgenic from_schema: https://example.com/nmdc_submission_schema aliases: - - genetic modification + - genetic modification is_a: core field string_serialization: '{PMID}|{DOI}|{URL}|{text}' slot_uri: MIXS:0000859 domain_of: - - Biosample + - Biosample range: string multivalued: false geo_loc_name: @@ -11376,20 +11901,24 @@ slots: 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) + 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' + - value: 'USA: Maryland, Bethesda' from_schema: https://example.com/nmdc_submission_schema aliases: - - geographic location (country and/or sea,region) + - geographic location (country and/or sea,region) is_a: environment field string_serialization: '{term}: {term}, {text}' slot_uri: MIXS:0000010 domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample range: string multivalued: false glucosidase_act: @@ -11407,14 +11936,14 @@ slots: description: Measurement of glucosidase activity title: glucosidase activity examples: - - value: 5 mol per liter per hour + - value: 5 mol per liter per hour from_schema: https://example.com/nmdc_submission_schema aliases: - - glucosidase activity + - glucosidase activity is_a: core field slot_uri: MIXS:0000137 domain_of: - - Biosample + - Biosample range: string multivalued: false gravidity: @@ -11426,18 +11955,19 @@ slots: 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 + 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 + - value: yes;due date:2018-05-11 from_schema: https://example.com/nmdc_submission_schema aliases: - - gravidity + - gravidity is_a: core field string_serialization: '{boolean};{timestamp}' slot_uri: MIXS:0000875 domain_of: - - Biosample + - Biosample range: string multivalued: false gravity: @@ -11452,18 +11982,22 @@ slots: 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 + 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 + - value: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://example.com/nmdc_submission_schema aliases: - - gravity + - gravity is_a: core field string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000559 domain_of: - - Biosample + - Biosample range: string multivalued: false growth_facil: @@ -11475,18 +12009,20 @@ slots: 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' + 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] + - value: Growth chamber [CO_715:0000189] from_schema: https://example.com/nmdc_submission_schema aliases: - - growth facility + - growth facility is_a: core field string_serialization: '{text}|{termLabel} {[termID]}' slot_uri: MIXS:0001043 domain_of: - - Biosample + - Biosample range: string multivalued: false growth_habit: @@ -11501,14 +12037,14 @@ slots: description: Characteristic shape, appearance or growth form of a plant species title: growth habit examples: - - value: spreading + - value: spreading from_schema: https://example.com/nmdc_submission_schema aliases: - - growth habit + - growth habit is_a: core field slot_uri: MIXS:0001044 domain_of: - - Biosample + - Biosample range: growth_habit_enum multivalued: false growth_hormone_regm: @@ -11523,18 +12059,22 @@ slots: 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 + 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 + - 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 + - growth hormone regimen is_a: core field string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000560 domain_of: - - Biosample + - Biosample range: string multivalued: false hall_count: @@ -11549,14 +12089,14 @@ slots: description: The total count of hallways and cooridors in the built structure title: hallway/corridor count examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - hallway/corridor count + - hallway/corridor count is_a: core field slot_uri: MIXS:0000228 domain_of: - - Biosample + - Biosample range: string multivalued: false handidness: @@ -11571,14 +12111,14 @@ slots: description: The handidness of the individual sampled title: handidness examples: - - value: right handedness + - value: right handedness from_schema: https://example.com/nmdc_submission_schema aliases: - - handidness + - handidness is_a: core field slot_uri: MIXS:0000809 domain_of: - - Biosample + - Biosample range: handidness_enum multivalued: false hc_produced: @@ -11590,17 +12130,18 @@ slots: 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 + 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 + - value: Gas from_schema: https://example.com/nmdc_submission_schema aliases: - - hydrocarbon type produced + - hydrocarbon type produced is_a: core field slot_uri: MIXS:0000989 domain_of: - - Biosample + - Biosample range: hc_produced_enum multivalued: false hcr: @@ -11612,17 +12153,23 @@ slots: 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 + 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 + - value: Oil Sand from_schema: https://example.com/nmdc_submission_schema aliases: - - hydrocarbon resource type + - hydrocarbon resource type is_a: core field slot_uri: MIXS:0000988 domain_of: - - Biosample + - Biosample range: hcr_enum multivalued: false hcr_fw_salinity: @@ -11637,17 +12184,18 @@ slots: occurrence: tag: occurrence value: '1' - description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + description: Original formation water salinity (prior to secondary recovery e.g. + Waterflooding) expressed as TDS title: formation water salinity examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - formation water salinity + - formation water salinity is_a: core field slot_uri: MIXS:0000406 domain_of: - - Biosample + - Biosample range: string multivalued: false hcr_geol_age: @@ -11659,17 +12207,18 @@ slots: 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' + 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 + - value: Silurian from_schema: https://example.com/nmdc_submission_schema aliases: - - hydrocarbon resource geological age + - hydrocarbon resource geological age is_a: core field slot_uri: MIXS:0000993 domain_of: - - Biosample + - Biosample range: hcr_geol_age_enum multivalued: false hcr_pressure: @@ -11687,15 +12236,15 @@ slots: description: Original pressure of the hydrocarbon resource title: hydrocarbon resource original pressure examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - hydrocarbon resource original pressure + - hydrocarbon resource original pressure is_a: core field string_serialization: '{float} - {float} {unit}' slot_uri: MIXS:0000395 domain_of: - - Biosample + - Biosample range: string multivalued: false hcr_temp: @@ -11713,15 +12262,15 @@ slots: description: Original temperature of the hydrocarbon resource title: hydrocarbon resource original temperature examples: - - value: 150-295 degree Celsius + - value: 150-295 degree Celsius from_schema: https://example.com/nmdc_submission_schema aliases: - - hydrocarbon resource original temperature + - hydrocarbon resource original temperature is_a: core field string_serialization: '{float} - {float} {unit}' slot_uri: MIXS:0000393 domain_of: - - Biosample + - Biosample range: string multivalued: false heat_cool_type: @@ -11736,14 +12285,14 @@ slots: description: Methods of conditioning or heating a room or building title: heating and cooling system type examples: - - value: heat pump + - value: heat pump from_schema: https://example.com/nmdc_submission_schema aliases: - - heating and cooling system type + - heating and cooling system type is_a: core field slot_uri: MIXS:0000766 domain_of: - - Biosample + - Biosample range: heat_cool_type_enum multivalued: true heat_deliv_loc: @@ -11758,14 +12307,14 @@ slots: description: The location of heat delivery within the room title: heating delivery locations examples: - - value: north + - value: north from_schema: https://example.com/nmdc_submission_schema aliases: - - heating delivery locations + - heating delivery locations is_a: core field slot_uri: MIXS:0000810 domain_of: - - Biosample + - Biosample range: heat_deliv_loc_enum multivalued: false heat_sys_deliv_meth: @@ -11780,15 +12329,15 @@ slots: description: The method by which the heat is delivered through the system title: heating system delivery method examples: - - value: radiant + - value: radiant from_schema: https://example.com/nmdc_submission_schema aliases: - - heating system delivery method + - heating system delivery method is_a: core field string_serialization: '[conductive|radiant]' slot_uri: MIXS:0000812 domain_of: - - Biosample + - Biosample range: string multivalued: false heat_system_id: @@ -11803,14 +12352,14 @@ slots: description: The heating system identifier title: heating system identifier examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - heating system identifier + - heating system identifier is_a: core field slot_uri: MIXS:0000833 domain_of: - - Biosample + - Biosample range: string multivalued: false heavy_metals: @@ -11825,18 +12374,19 @@ slots: 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. + 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 + - value: mercury;0.09 micrograms per gram from_schema: https://example.com/nmdc_submission_schema aliases: - - extreme_unusual_properties/heavy metals + - extreme_unusual_properties/heavy metals is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000652 domain_of: - - Biosample + - Biosample range: string multivalued: false heavy_metals_meth: @@ -11851,15 +12401,15 @@ slots: description: Reference or method used in determining heavy metals title: extreme_unusual_properties/heavy metals method examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - extreme_unusual_properties/heavy metals method + - extreme_unusual_properties/heavy metals method is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000343 domain_of: - - Biosample + - Biosample range: string multivalued: false height_carper_fiber: @@ -11877,14 +12427,14 @@ slots: description: The average carpet fiber height in the indoor environment title: height carpet fiber mat examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - height carpet fiber mat + - height carpet fiber mat is_a: core field slot_uri: MIXS:0000167 domain_of: - - Biosample + - Biosample range: string multivalued: false herbicide_regm: @@ -11899,18 +12449,22 @@ slots: 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 + 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 + - 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 + - herbicide regimen is_a: core field string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000561 domain_of: - - Biosample + - Biosample range: string multivalued: false horizon_meth: @@ -11925,15 +12479,15 @@ slots: description: Reference or method used in determining the horizon title: soil horizon method examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - soil horizon method + - soil horizon method is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000321 domain_of: - - Biosample + - Biosample range: string multivalued: false host_age: @@ -11948,17 +12502,18 @@ slots: 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 + 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 + - value: 10 days from_schema: https://example.com/nmdc_submission_schema aliases: - - host age + - host age is_a: core field slot_uri: MIXS:0000255 domain_of: - - Biosample + - Biosample range: string multivalued: false host_body_habitat: @@ -11973,15 +12528,15 @@ slots: description: Original body habitat where the sample was obtained from title: host body habitat examples: - - value: nasopharynx + - value: nasopharynx from_schema: https://example.com/nmdc_submission_schema aliases: - - host body habitat + - host body habitat is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000866 domain_of: - - Biosample + - Biosample range: string multivalued: false host_body_product: @@ -11993,18 +12548,21 @@ slots: 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 + 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] + - value: Portion of mucus [fma66938] from_schema: https://example.com/nmdc_submission_schema aliases: - - host body product + - host body product is_a: core field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000888 domain_of: - - Biosample + - Biosample range: string multivalued: false host_body_site: @@ -12016,18 +12574,21 @@ slots: 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 + 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] + - value: gill [UBERON:0002535] from_schema: https://example.com/nmdc_submission_schema aliases: - - host body site + - host body site is_a: core field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000867 domain_of: - - Biosample + - Biosample range: string multivalued: false host_body_temp: @@ -12045,14 +12606,14 @@ slots: description: Core body temperature of the host when sample was collected title: host body temperature examples: - - value: 15 degree Celsius + - value: 15 degree Celsius from_schema: https://example.com/nmdc_submission_schema aliases: - - host body temperature + - host body temperature is_a: core field slot_uri: MIXS:0000274 domain_of: - - Biosample + - Biosample range: string multivalued: false host_color: @@ -12067,15 +12628,15 @@ slots: description: The color of host title: host color examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - host color + - host color is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000260 domain_of: - - Biosample + - Biosample range: string multivalued: false host_common_name: @@ -12090,15 +12651,15 @@ slots: description: Common name of the host. title: host common name examples: - - value: human + - value: human from_schema: https://example.com/nmdc_submission_schema aliases: - - host common name + - host common name is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000248 domain_of: - - Biosample + - Biosample range: string multivalued: false host_diet: @@ -12110,18 +12671,19 @@ slots: 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 + 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 + - value: herbivore from_schema: https://example.com/nmdc_submission_schema aliases: - - host diet + - host diet is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000869 domain_of: - - Biosample + - Biosample range: string multivalued: false host_disease_stat: @@ -12130,18 +12692,21 @@ slots: expected_value: tag: expected_value value: disease name or Disease Ontology term - description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + description: List of diseases with which the host has been diagnosed; can include + multiple diagnoses. The value of the field depends on host; for humans the terms + should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, + non-human host diseases are free text title: host disease status examples: - - value: rabies [DOID:11260] + - value: rabies [DOID:11260] from_schema: https://example.com/nmdc_submission_schema aliases: - - host disease status + - host disease status is_a: nucleic acid sequence source field string_serialization: '{termLabel} {[termID]}|{text}' slot_uri: MIXS:0000031 domain_of: - - Biosample + - Biosample range: string multivalued: false host_dry_mass: @@ -12159,14 +12724,14 @@ slots: description: Measurement of dry mass title: host dry mass examples: - - value: 500 gram + - value: 500 gram from_schema: https://example.com/nmdc_submission_schema aliases: - - host dry mass + - host dry mass is_a: core field slot_uri: MIXS:0000257 domain_of: - - Biosample + - Biosample range: string multivalued: false host_family_relation: @@ -12178,18 +12743,19 @@ slots: occurrence: tag: occurrence value: m - description: Familial relationships to other hosts in the same study; can include multiple relationships + description: Familial relationships to other hosts in the same study; can include + multiple relationships title: host family relationship examples: - - value: offspring;Mussel25 + - value: offspring;Mussel25 from_schema: https://example.com/nmdc_submission_schema aliases: - - host family relationship + - host family relationship is_a: core field string_serialization: '{text};{text}' slot_uri: MIXS:0000872 domain_of: - - Biosample + - Biosample range: string multivalued: false host_genotype: @@ -12204,15 +12770,15 @@ slots: description: Observed genotype title: host genotype examples: - - value: C57BL/6 + - value: C57BL/6 from_schema: https://example.com/nmdc_submission_schema aliases: - - host genotype + - host genotype is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000365 domain_of: - - Biosample + - Biosample range: string multivalued: false host_growth_cond: @@ -12227,15 +12793,15 @@ slots: 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 + - value: https://academic.oup.com/icesjms/article/68/2/349/617247 from_schema: https://example.com/nmdc_submission_schema aliases: - - host growth conditions + - host growth conditions is_a: core field string_serialization: '{PMID}|{DOI}|{URL}|{text}' slot_uri: MIXS:0000871 domain_of: - - Biosample + - Biosample range: string multivalued: false host_height: @@ -12253,14 +12819,14 @@ slots: description: The height of subject title: host height examples: - - value: 0.1 meter + - value: 0.1 meter from_schema: https://example.com/nmdc_submission_schema aliases: - - host height + - host height is_a: core field slot_uri: MIXS:0000264 domain_of: - - Biosample + - Biosample range: string multivalued: false host_last_meal: @@ -12272,18 +12838,19 @@ slots: occurrence: tag: occurrence value: m - description: Content of last meal and time since feeding; can include multiple values + description: Content of last meal and time since feeding; can include multiple + values title: host last meal examples: - - value: corn feed;P2H + - value: corn feed;P2H from_schema: https://example.com/nmdc_submission_schema aliases: - - host last meal + - host last meal is_a: core field string_serialization: '{text};{duration}' slot_uri: MIXS:0000870 domain_of: - - Biosample + - Biosample range: string multivalued: false host_length: @@ -12301,14 +12868,14 @@ slots: description: The length of subject title: host length examples: - - value: 1 meter + - value: 1 meter from_schema: https://example.com/nmdc_submission_schema aliases: - - host length + - host length is_a: core field slot_uri: MIXS:0000256 domain_of: - - Biosample + - Biosample range: string multivalued: false host_life_stage: @@ -12323,15 +12890,15 @@ slots: description: Description of life stage of host title: host life stage examples: - - value: adult + - value: adult from_schema: https://example.com/nmdc_submission_schema aliases: - - host life stage + - host life stage is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000251 domain_of: - - Biosample + - Biosample range: string multivalued: false host_phenotype: @@ -12343,18 +12910,20 @@ slots: 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 + 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] + - value: elongated [PATO:0001154] from_schema: https://example.com/nmdc_submission_schema aliases: - - host phenotype + - host phenotype is_a: core field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000874 domain_of: - - Biosample + - Biosample range: string multivalued: false host_sex: @@ -12369,14 +12938,14 @@ slots: description: Gender or physical sex of the host. title: host sex examples: - - value: non-binary + - value: non-binary from_schema: https://example.com/nmdc_submission_schema aliases: - - host sex + - host sex is_a: core field slot_uri: MIXS:0000811 domain_of: - - Biosample + - Biosample range: host_sex_enum multivalued: false host_shape: @@ -12391,15 +12960,15 @@ slots: description: Morphological shape of host title: host shape examples: - - value: round + - value: round from_schema: https://example.com/nmdc_submission_schema aliases: - - host shape + - host shape is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000261 domain_of: - - Biosample + - Biosample range: string multivalued: false host_subject_id: @@ -12414,15 +12983,15 @@ slots: description: A unique identifier by which each subject can be referred to, de-identified. title: host subject id examples: - - value: MPI123 + - value: MPI123 from_schema: https://example.com/nmdc_submission_schema aliases: - - host subject id + - host subject id is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000861 domain_of: - - Biosample + - Biosample range: string multivalued: false host_subspecf_genlin: @@ -12430,22 +12999,27 @@ slots: 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. + 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. + 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' + - value: 'serovar:Newport, variety:glabrum, cultivar: Red Delicious' from_schema: https://example.com/nmdc_submission_schema aliases: - - host subspecific genetic lineage + - host subspecific genetic lineage is_a: core field string_serialization: '{rank name}:{text}' slot_uri: MIXS:0001318 domain_of: - - Biosample + - Biosample range: string multivalued: false host_substrate: @@ -12460,15 +13034,15 @@ slots: description: The growth substrate of the host. title: host substrate examples: - - value: rock + - value: rock from_schema: https://example.com/nmdc_submission_schema aliases: - - host substrate + - host substrate is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000252 domain_of: - - Biosample + - Biosample range: string multivalued: false host_symbiont: @@ -12480,18 +13054,19 @@ slots: 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. + 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 + - value: flukeworms from_schema: https://example.com/nmdc_submission_schema aliases: - - observed host symbionts + - observed host symbionts is_a: core field string_serialization: '{text}' slot_uri: MIXS:0001298 domain_of: - - Biosample + - Biosample range: string multivalued: false host_taxid: @@ -12506,14 +13081,14 @@ slots: 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 + - Homo sapiens [NCBITaxon:9606] would be a reasonable has_raw_value from_schema: https://example.com/nmdc_submission_schema aliases: - - host taxid + - host taxid is_a: core field slot_uri: MIXS:0000250 domain_of: - - Biosample + - Biosample range: string multivalued: false host_tot_mass: @@ -12531,14 +13106,14 @@ slots: description: Total mass of the host at collection, the unit depends on host title: host total mass examples: - - value: 2500 gram + - value: 2500 gram from_schema: https://example.com/nmdc_submission_schema aliases: - - host total mass + - host total mass is_a: core field slot_uri: MIXS:0000263 domain_of: - - Biosample + - Biosample range: string multivalued: false host_wet_mass: @@ -12556,14 +13131,14 @@ slots: description: Measurement of wet mass title: host wet mass examples: - - value: 1500 gram + - value: 1500 gram from_schema: https://example.com/nmdc_submission_schema aliases: - - host wet mass + - host wet mass is_a: core field slot_uri: MIXS:0000567 domain_of: - - Biosample + - Biosample range: string multivalued: false humidity: @@ -12581,14 +13156,14 @@ slots: description: Amount of water vapour in the air, at the time of sampling title: humidity examples: - - value: 25 gram per cubic meter + - value: 25 gram per cubic meter from_schema: https://example.com/nmdc_submission_schema aliases: - - humidity + - humidity is_a: core field slot_uri: MIXS:0000100 domain_of: - - Biosample + - Biosample range: string multivalued: false humidity_regm: @@ -12603,18 +13178,22 @@ slots: 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 + 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 + - 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 + - humidity regimen is_a: core field string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000568 domain_of: - - Biosample + - Biosample range: string multivalued: false indoor_space: @@ -12626,17 +13205,18 @@ slots: occurrence: tag: occurrence value: '1' - description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used + description: A distinguishable space within a structure, the purpose for which + discrete areas of a building is used title: indoor space examples: - - value: foyer + - value: foyer from_schema: https://example.com/nmdc_submission_schema aliases: - - indoor space + - indoor space is_a: core field slot_uri: MIXS:0000763 domain_of: - - Biosample + - Biosample range: indoor_space_enum multivalued: false indoor_surf: @@ -12651,14 +13231,14 @@ slots: description: Type of indoor surface title: indoor surface examples: - - value: wall + - value: wall from_schema: https://example.com/nmdc_submission_schema aliases: - - indoor surface + - indoor surface is_a: core field slot_uri: MIXS:0000764 domain_of: - - Biosample + - Biosample range: indoor_surf_enum multivalued: false indust_eff_percent: @@ -12673,33 +13253,34 @@ slots: occurrence: tag: occurrence value: '1' - description: Percentage of industrial effluents received by wastewater treatment plant + description: Percentage of industrial effluents received by wastewater treatment + plant title: industrial effluent percent examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - industrial effluent percent + - industrial effluent percent is_a: core field slot_uri: MIXS:0000662 domain_of: - - Biosample + - Biosample range: string multivalued: false infiltrations: name: infiltrations description: The amount of time it takes to complete each infiltration activity examples: - - value: '[''00:01:32'', ''00:00:53'']' + - value: '[''00:01:32'', ''00:00:53'']' from_schema: https://example.com/nmdc_submission_schema see_also: - - https://www.protocols.io/view/field-sampling-protocol-kqdg3962pg25/v1 + - https://www.protocols.io/view/field-sampling-protocol-kqdg3962pg25/v1 aliases: - - infiltration_1 - - infiltration_2 + - infiltration_1 + - infiltration_2 list_elements_ordered: true domain_of: - - Biosample + - Biosample range: string multivalued: false pattern: ^(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9]$ @@ -12715,18 +13296,19 @@ slots: occurrence: tag: occurrence value: m - description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles + description: Concentration of particles such as sand, grit, metal particles, ceramics, + etc.; can include multiple particles title: inorganic particles examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - inorganic particles + - inorganic particles is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000664 domain_of: - - Biosample + - Biosample range: string multivalued: false inside_lux: @@ -12744,14 +13326,14 @@ slots: description: The recorded value at sampling time (power density) title: inside lux light examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - inside lux light + - inside lux light is_a: core field slot_uri: MIXS:0000168 domain_of: - - Biosample + - Biosample range: string multivalued: false int_wall_cond: @@ -12763,17 +13345,18 @@ slots: 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 + 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 + - value: damaged from_schema: https://example.com/nmdc_submission_schema aliases: - - interior wall condition + - interior wall condition is_a: core field slot_uri: MIXS:0000813 domain_of: - - Biosample + - Biosample range: int_wall_cond_enum multivalued: false isotope_exposure: @@ -12781,19 +13364,20 @@ slots: description: List isotope exposure or addition applied to your sample. title: isotope exposure/addition todos: - - Can we make the H218O correctly super and subscripted? + - Can we make the H218O correctly super and subscripted? comments: - - This is required when your experimental design includes the use of isotopically labeled compounds + - This is required when your experimental design includes the use of isotopically + labeled compounds examples: - - value: 13C glucose - - value: H218O + - value: 13C glucose + - value: H218O from_schema: https://example.com/nmdc_submission_schema see_also: - - MIXS:0000751 + - MIXS:0000751 rank: 16 string_serialization: '{termLabel} {[termID]}; {timestamp}' domain_of: - - Biosample + - Biosample slot_group: MIxS Inspired recommended: true iw_bt_date_well: @@ -12805,17 +13389,18 @@ slots: occurrence: tag: occurrence value: '1' - description: Injection water breakthrough date per well following a secondary and/or tertiary recovery + 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' + - value: '2018-05-11' from_schema: https://example.com/nmdc_submission_schema aliases: - - injection water breakthrough date of specific well + - injection water breakthrough date of specific well is_a: core field slot_uri: MIXS:0001010 domain_of: - - Biosample + - Biosample range: string multivalued: false iwf: @@ -12830,17 +13415,18 @@ slots: occurrence: tag: occurrence value: '1' - description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) + description: Proportion of the produced fluids derived from injected water at + the time of sampling. (e.g. 87%) title: injection water fraction examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - injection water fraction + - injection water fraction is_a: core field slot_uri: MIXS:0000455 domain_of: - - Biosample + - Biosample range: string multivalued: false last_clean: @@ -12855,14 +13441,14 @@ slots: description: The last time the floor was cleaned (swept, mopped, vacuumed) title: last time swept/mopped/vacuumed examples: - - value: 2018-05-11:T14:30Z + - value: 2018-05-11:T14:30Z from_schema: https://example.com/nmdc_submission_schema aliases: - - last time swept/mopped/vacuumed + - last time swept/mopped/vacuumed is_a: core field slot_uri: MIXS:0000814 domain_of: - - Biosample + - Biosample range: string multivalued: false lat_lon: @@ -12871,19 +13457,20 @@ slots: 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 + 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 + - value: 50.586825 6.408977 from_schema: https://example.com/nmdc_submission_schema aliases: - - geographic location (latitude and longitude) + - geographic location (latitude and longitude) is_a: environment field string_serialization: '{float} {float}' slot_uri: MIXS:0000009 domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample range: string multivalued: false lbc_thirty: @@ -12901,19 +13488,20 @@ slots: 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 + - 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 + - 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 + - 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) + - lbc_thirty + - lbc30 + - lime buffer capacity (at 30 minutes) domain_of: - - Biosample + - Biosample range: string multivalued: false lbceq: @@ -12931,17 +13519,18 @@ slots: 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 + - 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 + - value: 1575 mg/kg from_schema: https://example.com/nmdc_submission_schema see_also: - - https://www.ornl.gov/content/bio-scales-0 + - https://www.ornl.gov/content/bio-scales-0 aliases: - - lbceq - - lime buffer capacity (at 5-day equilibrium) + - lbceq + - lime buffer capacity (at 5-day equilibrium) domain_of: - - Biosample + - Biosample range: string multivalued: false light_intensity: @@ -12959,14 +13548,14 @@ slots: description: Measurement of light intensity title: light intensity examples: - - value: 0.3 lux + - value: 0.3 lux from_schema: https://example.com/nmdc_submission_schema aliases: - - light intensity + - light intensity is_a: core field slot_uri: MIXS:0000706 domain_of: - - Biosample + - Biosample range: string multivalued: false light_regm: @@ -12981,18 +13570,19 @@ slots: occurrence: tag: occurrence value: '1' - description: Information about treatment(s) involving exposure to light, including both light intensity and quality. + 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 + - value: incandescant light;10 lux;450 nanometer from_schema: https://example.com/nmdc_submission_schema aliases: - - light regimen + - light regimen is_a: core field string_serialization: '{text};{float} {unit};{float} {unit}' slot_uri: MIXS:0000569 domain_of: - - Biosample + - Biosample range: string multivalued: false light_type: @@ -13004,17 +13594,20 @@ slots: 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 + 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 + - value: desk lamp from_schema: https://example.com/nmdc_submission_schema aliases: - - light type + - light type is_a: core field slot_uri: MIXS:0000769 domain_of: - - Biosample + - Biosample range: light_type_enum multivalued: true link_addit_analys: @@ -13029,15 +13622,15 @@ slots: description: Link to additional analysis results performed on the sample title: links to additional analysis examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - links to additional analysis + - links to additional analysis is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000340 domain_of: - - Biosample + - Biosample range: string multivalued: false link_class_info: @@ -13052,15 +13645,15 @@ slots: description: Link to digitized soil maps or other soil classification information title: link to classification information examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - link to classification information + - link to classification information is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000329 domain_of: - - Biosample + - Biosample range: string multivalued: false link_climate_info: @@ -13075,15 +13668,15 @@ slots: description: Link to climate resource title: link to climate information examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - link to climate information + - link to climate information is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000328 domain_of: - - Biosample + - Biosample range: string multivalued: false lithology: @@ -13095,17 +13688,18 @@ slots: 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' + 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 + - value: Volcanic from_schema: https://example.com/nmdc_submission_schema aliases: - - lithology + - lithology is_a: core field slot_uri: MIXS:0000990 domain_of: - - Biosample + - Biosample range: lithology_enum multivalued: false local_class: @@ -13120,16 +13714,16 @@ slots: description: Soil classification based on local soil classification system title: soil_taxonomic/local classification examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - soil_taxonomic/local classification + - soil_taxonomic/local classification is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000330 domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample range: string multivalued: false local_class_meth: @@ -13144,15 +13738,15 @@ slots: description: Reference or method used in determining the local soil classification title: soil_taxonomic/local classification method examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - soil_taxonomic/local classification method + - soil_taxonomic/local classification method is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000331 domain_of: - - Biosample + - Biosample range: string multivalued: false magnesium: @@ -13163,21 +13757,22 @@ slots: value: measurement value preferred_unit: tag: preferred_unit - value: mole per liter, milligram per liter, parts per million, micromole per kilogram + 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 + - value: 52.8 micromole per kilogram from_schema: https://example.com/nmdc_submission_schema aliases: - - magnesium + - magnesium is_a: core field slot_uri: MIXS:0000431 domain_of: - - Biosample + - Biosample range: string multivalued: false manganese: @@ -13195,14 +13790,14 @@ slots: description: Concentration of manganese in the sample title: manganese examples: - - value: 24.7 mg/kg + - value: 24.7 mg/kg from_schema: https://example.com/nmdc_submission_schema see_also: - - https://www.ornl.gov/content/bio-scales-0 + - https://www.ornl.gov/content/bio-scales-0 aliases: - - manganese + - manganese domain_of: - - Biosample + - Biosample range: string multivalued: false max_occup: @@ -13217,14 +13812,14 @@ slots: description: The maximum amount of people allowed in the indoor environment title: maximum occupancy examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - maximum occupancy + - maximum occupancy is_a: core field slot_uri: MIXS:0000229 domain_of: - - Biosample + - Biosample range: string multivalued: false mean_frict_vel: @@ -13242,14 +13837,14 @@ slots: description: Measurement of mean friction velocity title: mean friction velocity examples: - - value: 0.5 meter per second + - value: 0.5 meter per second from_schema: https://example.com/nmdc_submission_schema aliases: - - mean friction velocity + - mean friction velocity is_a: core field slot_uri: MIXS:0000498 domain_of: - - Biosample + - Biosample range: string multivalued: false mean_peak_frict_vel: @@ -13267,14 +13862,14 @@ slots: description: Measurement of mean peak friction velocity title: mean peak friction velocity examples: - - value: 1 meter per second + - value: 1 meter per second from_schema: https://example.com/nmdc_submission_schema aliases: - - mean peak friction velocity + - mean peak friction velocity is_a: core field slot_uri: MIXS:0000502 domain_of: - - Biosample + - Biosample range: string multivalued: false mech_struc: @@ -13289,14 +13884,14 @@ slots: description: 'mechanical structure: a moving structure' title: mechanical structure examples: - - value: elevator + - value: elevator from_schema: https://example.com/nmdc_submission_schema aliases: - - mechanical structure + - mechanical structure is_a: core field slot_uri: MIXS:0000815 domain_of: - - Biosample + - Biosample range: mech_struc_enum multivalued: false mechanical_damage: @@ -13308,18 +13903,19 @@ slots: occurrence: tag: occurrence value: m - description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites + description: Information about any mechanical damage exerted on the plant; can + include multiple damages and sites title: mechanical damage examples: - - value: pruning;bark + - value: pruning;bark from_schema: https://example.com/nmdc_submission_schema aliases: - - mechanical damage + - mechanical damage is_a: core field string_serialization: '{text};{text}' slot_uri: MIXS:0001052 domain_of: - - Biosample + - Biosample range: string multivalued: false methane: @@ -13337,14 +13933,14 @@ slots: description: Methane (gas) amount or concentration at the time of sampling title: methane examples: - - value: 1800 parts per billion + - value: 1800 parts per billion from_schema: https://example.com/nmdc_submission_schema aliases: - - methane + - methane is_a: core field slot_uri: MIXS:0000101 domain_of: - - Biosample + - Biosample range: string multivalued: false micro_biomass_c_meth: @@ -13352,19 +13948,19 @@ slots: 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 + - How should we separate values? | or ;? lets be consistent comments: - - required if "microbial_biomass_c" is provided + - 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 + - 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:0000339 + - MIXS:0000339 rank: 11 string_serialization: '{PMID}|{DOI}|{URL}' domain_of: - - Biosample + - Biosample slot_group: MIxS Inspired recommended: true micro_biomass_meth: @@ -13379,15 +13975,15 @@ slots: description: Reference or method used in determining microbial biomass title: microbial biomass method examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - microbial biomass method + - microbial biomass method is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000339 domain_of: - - Biosample + - Biosample range: string multivalued: false micro_biomass_n_meth: @@ -13395,17 +13991,17 @@ slots: description: Reference or method used in determining microbial biomass nitrogen title: microbial biomass nitrogen method comments: - - required if "microbial_biomass_n" is provided + - 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 + - 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:0000339 + - MIXS:0000339 rank: 13 string_serialization: '{PMID}|{DOI}|{URL}' domain_of: - - Biosample + - Biosample slot_group: MIxS Inspired microbial_biomass: name: microbial_biomass @@ -13419,75 +14015,86 @@ slots: 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 + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - microbial biomass + - microbial biomass is_a: core field slot_uri: MIXS:0000650 domain_of: - - Biosample + - Biosample range: string multivalued: false 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. + 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 + - 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 + - value: 0.05 ug C/g dry soil from_schema: https://example.com/nmdc_submission_schema see_also: - - MIXS:0000650 + - MIXS:0000650 rank: 10 string_serialization: '{float} {unit}' domain_of: - - Biosample + - Biosample 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. + 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 + - 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 + - value: 0.05 ug N/g dry soil from_schema: https://example.com/nmdc_submission_schema see_also: - - MIXS:0000650 + - MIXS:0000650 rank: 12 string_serialization: '{float} {unit}' domain_of: - - Biosample + - Biosample 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 + 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 + 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 + - 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 + - mineral nutrient regimen is_a: core field string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000570 domain_of: - - Biosample + - Biosample range: string multivalued: false misc_param: @@ -13499,18 +14106,19 @@ slots: occurrence: tag: occurrence value: m - description: Any other measurement performed or parameter collected, that is not listed here + 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 + - value: Bicarbonate ion concentration;2075 micromole per kilogram from_schema: https://example.com/nmdc_submission_schema aliases: - - miscellaneous parameter + - miscellaneous parameter is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000752 domain_of: - - Biosample + - Biosample range: string multivalued: false n_alkanes: @@ -13528,15 +14136,15 @@ slots: description: Concentration of n-alkanes; can include multiple n-alkanes title: n-alkanes examples: - - value: n-hexadecane;100 milligram per liter + - value: n-hexadecane;100 milligram per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - n-alkanes + - n-alkanes is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000503 domain_of: - - Biosample + - Biosample range: string multivalued: false nitrate: @@ -13554,14 +14162,14 @@ slots: description: Concentration of nitrate in the sample title: nitrate examples: - - value: 65 micromole per liter + - value: 65 micromole per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - nitrate + - nitrate is_a: core field slot_uri: MIXS:0000425 domain_of: - - Biosample + - Biosample range: string multivalued: false nitrate_nitrogen: @@ -13579,17 +14187,17 @@ slots: description: Concentration of nitrate nitrogen in the sample title: nitrate_nitrogen comments: - - often below some specified limit of detection + - often below some specified limit of detection examples: - - value: 0.29 mg/kg + - value: 0.29 mg/kg from_schema: https://example.com/nmdc_submission_schema see_also: - - https://www.ornl.gov/content/bio-scales-0 + - https://www.ornl.gov/content/bio-scales-0 aliases: - - nitrate_nitrogen - - NO3-N + - nitrate_nitrogen + - NO3-N domain_of: - - Biosample + - Biosample range: string multivalued: false nitrite: @@ -13607,14 +14215,14 @@ slots: description: Concentration of nitrite in the sample title: nitrite examples: - - value: 0.5 micromole per liter + - value: 0.5 micromole per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - nitrite + - nitrite is_a: core field slot_uri: MIXS:0000426 domain_of: - - Biosample + - Biosample range: string multivalued: false nitrite_nitrogen: @@ -13632,15 +14240,15 @@ slots: description: Concentration of nitrite nitrogen in the sample title: nitrite_nitrogen examples: - - value: 1.2 mg/kg + - value: 1.2 mg/kg from_schema: https://example.com/nmdc_submission_schema see_also: - - https://www.ornl.gov/content/bio-scales-0 + - https://www.ornl.gov/content/bio-scales-0 aliases: - - nitrite_nitrogen - - NO2-N + - nitrite_nitrogen + - NO2-N domain_of: - - Biosample + - Biosample range: string multivalued: false nitro: @@ -13658,71 +14266,78 @@ slots: description: Concentration of nitrogen (total) title: nitrogen examples: - - value: 4.2 micromole per liter + - value: 4.2 micromole per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - nitrogen + - nitrogen is_a: core field slot_uri: MIXS:0000504 domain_of: - - Biosample + - Biosample range: string multivalued: false 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 ; + 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 + - value: insect 0.23 ug; plant 1g from_schema: https://example.com/nmdc_submission_schema see_also: - - MIXS:0000174 - - MIXS:0000650 + - MIXS:0000174 + - MIXS:0000650 rank: 8 string_serialization: '{text};{float} {unit}' domain_of: - - Biosample + - Biosample 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 + - required if "non-microbial biomass" is provided examples: - - value: https://doi.org/10.1038/s41467-021-26181-3 + - value: https://doi.org/10.1038/s41467-021-26181-3 from_schema: https://example.com/nmdc_submission_schema see_also: - - MIXS:0000650 + - MIXS:0000650 rank: 9 string_serialization: '{PMID}|{DOI}|{URL}' domain_of: - - Biosample + - Biosample 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 + 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 + 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 + - 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 + - non-mineral nutrient regimen is_a: core field string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000571 domain_of: - - Biosample + - Biosample range: string multivalued: false number_pets: @@ -13737,14 +14352,14 @@ slots: description: The number of pets residing in the sampled space title: number of pets examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - number of pets + - number of pets is_a: core field slot_uri: MIXS:0000231 domain_of: - - Biosample + - Biosample range: string multivalued: false number_plants: @@ -13759,14 +14374,14 @@ slots: description: The number of plant(s) in the sampling space title: number of houseplants examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - number of houseplants + - number of houseplants is_a: core field slot_uri: MIXS:0000230 domain_of: - - Biosample + - Biosample range: string multivalued: false number_resident: @@ -13781,14 +14396,14 @@ slots: description: The number of individuals currently occupying in the sampling location title: number of residents examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - number of residents + - number of residents is_a: core field slot_uri: MIXS:0000232 domain_of: - - Biosample + - Biosample range: string multivalued: false occup_density_samp: @@ -13803,14 +14418,14 @@ slots: description: Average number of occupants at time of sampling per square footage title: occupant density at sampling examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - occupant density at sampling + - occupant density at sampling is_a: core field slot_uri: MIXS:0000217 domain_of: - - Biosample + - Biosample range: string multivalued: false occup_document: @@ -13825,14 +14440,14 @@ slots: description: The type of documentation of occupancy title: occupancy documentation examples: - - value: estimate + - value: estimate from_schema: https://example.com/nmdc_submission_schema aliases: - - occupancy documentation + - occupancy documentation is_a: core field slot_uri: MIXS:0000816 domain_of: - - Biosample + - Biosample range: occup_document_enum multivalued: false occup_samp: @@ -13847,14 +14462,14 @@ slots: description: Number of occupants present at time of sample within the given space title: occupancy at sampling examples: - - value: '10' + - value: '10' from_schema: https://example.com/nmdc_submission_schema aliases: - - occupancy at sampling + - occupancy at sampling is_a: core field slot_uri: MIXS:0000772 domain_of: - - Biosample + - Biosample range: string multivalued: false org_carb: @@ -13872,14 +14487,14 @@ slots: description: Concentration of organic carbon title: organic carbon examples: - - value: 1.5 microgram per liter + - value: 1.5 microgram per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - organic carbon + - organic carbon is_a: core field slot_uri: MIXS:0000508 domain_of: - - Biosample + - Biosample range: string multivalued: false org_count_qpcr_info: @@ -13887,25 +14502,32 @@ slots: 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 + 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)' + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - organism count qPCR information + - 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' + 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 domain_of: - - Biosample + - Biosample range: string multivalued: false org_matter: @@ -13923,14 +14545,14 @@ slots: description: Concentration of organic matter title: organic matter examples: - - value: 1.75 milligram per cubic meter + - value: 1.75 milligram per cubic meter from_schema: https://example.com/nmdc_submission_schema aliases: - - organic matter + - organic matter is_a: core field slot_uri: MIXS:0000204 domain_of: - - Biosample + - Biosample range: string multivalued: false org_nitro: @@ -13948,14 +14570,14 @@ slots: description: Concentration of organic nitrogen title: organic nitrogen examples: - - value: 4 micromole per liter + - value: 4 micromole per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - organic nitrogen + - organic nitrogen is_a: core field slot_uri: MIXS:0000205 domain_of: - - Biosample + - Biosample range: string multivalued: false org_nitro_method: @@ -13963,17 +14585,17 @@ slots: description: Method used for obtaining organic nitrogen title: organic nitrogen method comments: - - required if "org_nitro" is provided + - required if "org_nitro" is provided examples: - - value: https://doi.org/10.1016/0038-0717(85)90144-0 + - value: https://doi.org/10.1016/0038-0717(85)90144-0 from_schema: https://example.com/nmdc_submission_schema see_also: - - MIXS:0000338 - - MIXS:0000205 + - MIXS:0000338 + - MIXS:0000205 rank: 14 string_serialization: '{PMID}|{DOI}|{URL}' domain_of: - - Biosample + - Biosample slot_group: MIxS Inspired org_particles: name: org_particles @@ -13987,18 +14609,19 @@ slots: occurrence: tag: occurrence value: m - description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. + description: Concentration of particles such as faeces, hairs, food, vomit, paper + fibers, plant material, humus, etc. title: organic particles examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - organic particles + - organic particles is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000665 domain_of: - - Biosample + - Biosample range: string multivalued: false organism_count: @@ -14009,38 +14632,44 @@ slots: 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 + 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)' + 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 + - value: total prokaryotes;3.5e7 cells per milliliter;qPCR from_schema: https://example.com/nmdc_submission_schema aliases: - - organism count + - organism count is_a: core field slot_uri: MIXS:0000103 domain_of: - - Biosample + - Biosample range: string multivalued: false other_treatment: name: other_treatment - description: Other treatments applied to your samples that are not applicable to the provided fields + description: Other treatments applied to your samples that are not applicable + to the provided fields title: other treatments notes: - - Values entered here will be used to determine potential new slots. + - Values entered here will be used to determine potential new slots. comments: - - This is an open text field to provide any treatments that cannot be captured in the provided slots. + - 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:0000300 + - MIXS:0000300 rank: 15 string_serialization: '{text}' domain_of: - - Biosample + - Biosample slot_group: MIxS Inspired recommended: true owc_tvdss: @@ -14058,14 +14687,14 @@ slots: description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) title: oil water contact depth examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - oil water contact depth + - oil water contact depth is_a: core field slot_uri: MIXS:0000405 domain_of: - - Biosample + - Biosample range: string multivalued: false oxy_stat_samp: @@ -14080,14 +14709,14 @@ slots: description: Oxygenation status of sample title: oxygenation status of sample examples: - - value: aerobic + - value: aerobic from_schema: https://example.com/nmdc_submission_schema aliases: - - oxygenation status of sample + - oxygenation status of sample is_a: core field slot_uri: MIXS:0000753 domain_of: - - Biosample + - Biosample range: OxyStatSampEnum multivalued: false oxygen: @@ -14105,14 +14734,14 @@ slots: description: Oxygen (gas) amount or concentration at the time of sampling title: oxygen examples: - - value: 600 parts per million + - value: 600 parts per million from_schema: https://example.com/nmdc_submission_schema aliases: - - oxygen + - oxygen is_a: core field slot_uri: MIXS:0000104 domain_of: - - Biosample + - Biosample range: string multivalued: false part_org_carb: @@ -14130,14 +14759,14 @@ slots: description: Concentration of particulate organic carbon title: particulate organic carbon examples: - - value: 1.92 micromole per liter + - value: 1.92 micromole per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - particulate organic carbon + - particulate organic carbon is_a: core field slot_uri: MIXS:0000515 domain_of: - - Biosample + - Biosample range: string multivalued: false part_org_nitro: @@ -14155,14 +14784,14 @@ slots: description: Concentration of particulate organic nitrogen title: particulate organic nitrogen examples: - - value: 0.3 micromole per liter + - value: 0.3 micromole per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - particulate organic nitrogen + - particulate organic nitrogen is_a: core field slot_uri: MIXS:0000719 domain_of: - - Biosample + - Biosample range: string multivalued: false particle_class: @@ -14177,18 +14806,20 @@ slots: 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 + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - particle classification + - particle classification is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000206 domain_of: - - Biosample + - Biosample range: string multivalued: false permeability: @@ -14203,18 +14834,19 @@ slots: 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))' + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - permeability + - permeability is_a: core field string_serialization: '{integer} - {integer} {unit}' slot_uri: MIXS:0000404 domain_of: - - Biosample + - Biosample range: string multivalued: false perturbation: @@ -14226,18 +14858,21 @@ slots: 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 + 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 + - value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M from_schema: https://example.com/nmdc_submission_schema aliases: - - perturbation + - perturbation is_a: core field string_serialization: '{text};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000754 domain_of: - - Biosample + - Biosample range: string multivalued: false pesticide_regm: @@ -14252,18 +14887,22 @@ slots: 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 + 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 + - 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 + - pesticide regimen is_a: core field string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000573 domain_of: - - Biosample + - Biosample range: string multivalued: false petroleum_hydrocarb: @@ -14281,14 +14920,14 @@ slots: description: Concentration of petroleum hydrocarbon title: petroleum hydrocarbon examples: - - value: 0.05 micromole per liter + - value: 0.05 micromole per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - petroleum hydrocarbon + - petroleum hydrocarbon is_a: core field slot_uri: MIXS:0000516 domain_of: - - Biosample + - Biosample range: string multivalued: false ph: @@ -14300,17 +14939,18 @@ slots: occurrence: tag: occurrence value: '1' - description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + description: Ph measurement of the sample, or liquid portion of sample, or aqueous + phase of the fluid title: pH examples: - - value: '7.2' + - value: '7.2' from_schema: https://example.com/nmdc_submission_schema aliases: - - pH + - pH is_a: core field slot_uri: MIXS:0001001 domain_of: - - Biosample + - Biosample range: double multivalued: false ph_meth: @@ -14325,15 +14965,15 @@ slots: description: Reference or method used in determining ph title: pH method examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - pH method + - pH method is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0001106 domain_of: - - Biosample + - Biosample range: string multivalued: false ph_regm: @@ -14345,18 +14985,21 @@ slots: 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 + 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 + - 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 + - pH regimen is_a: core field string_serialization: '{float};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0001056 domain_of: - - Biosample + - Biosample range: string multivalued: false phaeopigments: @@ -14374,15 +15017,15 @@ slots: description: Concentration of phaeopigments; can include multiple phaeopigments title: phaeopigments examples: - - value: 2.5 milligram per cubic meter + - value: 2.5 milligram per cubic meter from_schema: https://example.com/nmdc_submission_schema aliases: - - phaeopigments + - phaeopigments is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000180 domain_of: - - Biosample + - Biosample range: string multivalued: false phosphate: @@ -14400,14 +15043,14 @@ slots: description: Concentration of phosphate title: phosphate examples: - - value: 0.7 micromole per liter + - value: 0.7 micromole per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - phosphate + - phosphate is_a: core field slot_uri: MIXS:0000505 domain_of: - - Biosample + - Biosample range: string multivalued: false phosplipid_fatt_acid: @@ -14425,15 +15068,15 @@ slots: description: Concentration of phospholipid fatty acids; can include multiple values title: phospholipid fatty acid examples: - - value: 2.98 milligram per liter + - value: 2.98 milligram per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - phospholipid fatty acid + - phospholipid fatty acid is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000181 domain_of: - - Biosample + - Biosample range: string multivalued: false photon_flux: @@ -14451,14 +15094,14 @@ slots: description: Measurement of photon flux title: photon flux examples: - - value: 3.926 micromole photons per second per square meter + - value: 3.926 micromole photons per second per square meter from_schema: https://example.com/nmdc_submission_schema aliases: - - photon flux + - photon flux is_a: core field slot_uri: MIXS:0000725 domain_of: - - Biosample + - Biosample range: string multivalued: false plant_growth_med: @@ -14470,17 +15113,21 @@ slots: 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 + 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] + - value: hydroponic plant culture media [EO:0007067] from_schema: https://example.com/nmdc_submission_schema aliases: - - plant growth medium + - plant growth medium is_a: core field slot_uri: MIXS:0001057 domain_of: - - Biosample + - Biosample range: string multivalued: false plant_product: @@ -14495,15 +15142,15 @@ slots: description: Substance produced by the plant, where the sample was obtained from title: plant product examples: - - value: xylem sap [PO:0025539] + - value: xylem sap [PO:0025539] from_schema: https://example.com/nmdc_submission_schema aliases: - - plant product + - plant product is_a: core field string_serialization: '{text}' slot_uri: MIXS:0001058 domain_of: - - Biosample + - Biosample range: string multivalued: false plant_sex: @@ -14515,17 +15162,18 @@ slots: occurrence: tag: occurrence value: '1' - description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. + description: Sex of the reproductive parts on the whole plant, e.g. pistillate, + staminate, monoecieous, hermaphrodite. title: plant sex examples: - - value: Hermaphroditic + - value: Hermaphroditic from_schema: https://example.com/nmdc_submission_schema aliases: - - plant sex + - plant sex is_a: core field slot_uri: MIXS:0001059 domain_of: - - Biosample + - Biosample range: plant_sex_enum multivalued: false plant_struc: @@ -14537,18 +15185,21 @@ slots: 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. + 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] + - value: epidermis [PO:0005679] from_schema: https://example.com/nmdc_submission_schema aliases: - - plant structure + - plant structure is_a: core field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0001060 domain_of: - - Biosample + - Biosample range: string multivalued: false pollutants: @@ -14563,18 +15214,20 @@ slots: 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 + 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 + - value: lead;0.15 microgram per cubic meter from_schema: https://example.com/nmdc_submission_schema aliases: - - pollutants + - pollutants is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000107 domain_of: - - Biosample + - Biosample range: string multivalued: false porosity: @@ -14589,18 +15242,19 @@ slots: occurrence: tag: occurrence value: '1' - description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + description: Porosity of deposited sediment is volume of voids divided by the + total volume of sample title: porosity examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - porosity + - porosity is_a: core field string_serialization: '{float} - {float} {unit}' slot_uri: MIXS:0000211 domain_of: - - Biosample + - Biosample range: string multivalued: false potassium: @@ -14618,14 +15272,14 @@ slots: description: Concentration of potassium in the sample title: potassium examples: - - value: 463 milligram per liter + - value: 463 milligram per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - potassium + - potassium is_a: core field slot_uri: MIXS:0000430 domain_of: - - Biosample + - Biosample range: string multivalued: false pour_point: @@ -14640,17 +15294,20 @@ slots: 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)' + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - pour point + - pour point is_a: core field slot_uri: MIXS:0000127 domain_of: - - Biosample + - Biosample range: string multivalued: false pre_treatment: @@ -14662,18 +15319,19 @@ slots: occurrence: tag: occurrence value: '1' - description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater + description: The process of pre-treatment removes materials that can be easily + collected from the raw wastewater title: pre-treatment examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - pre-treatment + - pre-treatment is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000348 domain_of: - - Biosample + - Biosample range: string multivalued: false pres_animal_insect: @@ -14685,17 +15343,18 @@ slots: occurrence: tag: occurrence value: '1' - description: The type and number of animals or insects present in the sampling space. + 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 + - value: cat;5 from_schema: https://example.com/nmdc_submission_schema aliases: - - presence of pets, animals, or insects + - presence of pets, animals, or insects is_a: core field slot_uri: MIXS:0000819 domain_of: - - Biosample + - Biosample range: string multivalued: false pattern: ^(cat|dog|rodent|snake|other);\d+$ @@ -14714,14 +15373,14 @@ slots: description: Pressure to which the sample is subject to, in atmospheres title: pressure examples: - - value: 50 atmosphere + - value: 50 atmosphere from_schema: https://example.com/nmdc_submission_schema aliases: - - pressure + - pressure is_a: core field slot_uri: MIXS:0000412 domain_of: - - Biosample + - Biosample range: string multivalued: false prev_land_use_meth: @@ -14736,15 +15395,15 @@ slots: description: Reference or method used in determining previous land use and dates title: history/previous land use method examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - history/previous land use method + - history/previous land use method is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000316 domain_of: - - Biosample + - Biosample range: string multivalued: false previous_land_use: @@ -14759,15 +15418,15 @@ slots: description: Previous land use and dates title: history/previous land use examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - history/previous land use + - history/previous land use is_a: core field string_serialization: '{text};{timestamp}' slot_uri: MIXS:0000315 domain_of: - - Biosample + - Biosample range: string multivalued: false primary_prod: @@ -14782,17 +15441,18 @@ slots: occurrence: tag: occurrence value: '1' - description: Measurement of primary production, generally measured as isotope uptake + description: Measurement of primary production, generally measured as isotope + uptake title: primary production examples: - - value: 100 milligram per cubic meter per day + - value: 100 milligram per cubic meter per day from_schema: https://example.com/nmdc_submission_schema aliases: - - primary production + - primary production is_a: core field slot_uri: MIXS:0000728 domain_of: - - Biosample + - Biosample range: string multivalued: false primary_treatment: @@ -14804,18 +15464,20 @@ slots: 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 + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - primary treatment + - primary treatment is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000349 domain_of: - - Biosample + - Biosample range: string multivalued: false prod_rate: @@ -14833,14 +15495,14 @@ slots: description: Oil and/or gas production rates per well (e.g. 524 m3 / day) title: production rate examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - production rate + - production rate is_a: core field slot_uri: MIXS:0000452 domain_of: - - Biosample + - Biosample range: string multivalued: false prod_start_date: @@ -14855,14 +15517,14 @@ slots: description: Date of field's first production title: production start date examples: - - value: '2018-05-11' + - value: '2018-05-11' from_schema: https://example.com/nmdc_submission_schema aliases: - - production start date + - production start date is_a: core field slot_uri: MIXS:0001008 domain_of: - - Biosample + - Biosample range: string multivalued: false profile_position: @@ -14874,17 +15536,18 @@ slots: occurrence: tag: occurrence value: '1' - description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas + 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 + - value: summit from_schema: https://example.com/nmdc_submission_schema aliases: - - profile position + - profile position is_a: core field slot_uri: MIXS:0001084 domain_of: - - Biosample + - Biosample range: profile_position_enum multivalued: false project_id: @@ -14895,35 +15558,37 @@ slots: rank: 1 string_serialization: '{text}' domain_of: - - Biosample + - Biosample 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. + - Do not edit these values. A template will be provided by NMDC in which these + values have been pre-filled. examples: - - value: '504000' + - value: '504000' from_schema: https://example.com/nmdc_submission_schema rank: 19 string_serialization: '{text}' domain_of: - - Biosample + - Biosample 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. + - Do not edit these values. A template will be provided by NMDC in which these + values have been pre-filled. examples: - - value: '504000' + - value: '504000' from_schema: https://example.com/nmdc_submission_schema rank: 19 string_serialization: '{text}' domain_of: - - Biosample + - Biosample slot_group: JGI-Metatranscriptomics recommended: true quad_pos: @@ -14938,14 +15603,14 @@ slots: description: The quadrant position of the sampling room within the building title: quadrant position examples: - - value: West side + - value: West side from_schema: https://example.com/nmdc_submission_schema aliases: - - quadrant position + - quadrant position is_a: core field slot_uri: MIXS:0000820 domain_of: - - Biosample + - Biosample range: quad_pos_enum multivalued: false radiation_regm: @@ -14960,18 +15625,22 @@ slots: 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 + 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 + - 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 + - radiation regimen is_a: core field string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000575 domain_of: - - Biosample + - Biosample range: string multivalued: false rainfall_regm: @@ -14986,18 +15655,21 @@ slots: 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 + 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 + - value: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://example.com/nmdc_submission_schema aliases: - - rainfall regimen + - rainfall regimen is_a: core field string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000576 domain_of: - - Biosample + - Biosample range: string multivalued: false reactor_type: @@ -15009,18 +15681,20 @@ slots: 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 + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - reactor type + - reactor type is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000350 domain_of: - - Biosample + - Biosample range: string multivalued: false redox_potential: @@ -15035,17 +15709,18 @@ slots: occurrence: tag: occurrence value: '1' - description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + description: Redox potential, measured relative to a hydrogen cell, indicating + oxidation or reduction potential title: redox potential examples: - - value: 300 millivolt + - value: 300 millivolt from_schema: https://example.com/nmdc_submission_schema aliases: - - redox potential + - redox potential is_a: core field slot_uri: MIXS:0000182 domain_of: - - Biosample + - Biosample range: string multivalued: false rel_air_humidity: @@ -15060,17 +15735,18 @@ slots: 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 + 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% + - value: 80% from_schema: https://example.com/nmdc_submission_schema aliases: - - relative air humidity + - relative air humidity is_a: core field slot_uri: MIXS:0000121 domain_of: - - Biosample + - Biosample range: string multivalued: false rel_humidity_out: @@ -15088,14 +15764,14 @@ slots: description: The recorded outside relative humidity value at the time of sampling title: outside relative humidity examples: - - value: 12 per kilogram of air + - value: 12 per kilogram of air from_schema: https://example.com/nmdc_submission_schema aliases: - - outside relative humidity + - outside relative humidity is_a: core field slot_uri: MIXS:0000188 domain_of: - - Biosample + - Biosample range: string multivalued: false rel_samp_loc: @@ -15110,14 +15786,14 @@ slots: description: The sampling location within the train car title: relative sampling location examples: - - value: center of car + - value: center of car from_schema: https://example.com/nmdc_submission_schema aliases: - - relative sampling location + - relative sampling location is_a: core field slot_uri: MIXS:0000821 domain_of: - - Biosample + - Biosample range: rel_samp_loc_enum multivalued: false replicate_number: @@ -15125,12 +15801,12 @@ slots: 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 + - 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}' domain_of: - - Biosample + - Biosample slot_group: EMSL recommended: true reservoir: @@ -15145,15 +15821,15 @@ slots: description: Name of the reservoir (e.g. Carapebus) title: reservoir name examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - reservoir name + - reservoir name is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000303 domain_of: - - Biosample + - Biosample range: string multivalued: false resins_pc: @@ -15168,18 +15844,22 @@ slots: 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)' + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - resins wt% + - resins wt% is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000134 domain_of: - - Biosample + - Biosample range: string multivalued: false rna_absorb1: @@ -15187,14 +15867,14 @@ slots: description: 260/280 measurement of RNA sample purity title: RNA absorbance 260/280 comments: - - Recommended value is between 1 and 3. + - Recommended value is between 1 and 3. examples: - - value: '2.02' + - value: '2.02' from_schema: https://example.com/nmdc_submission_schema rank: 7 string_serialization: '{float}' domain_of: - - Biosample + - Biosample slot_group: JGI-Metatranscriptomics range: float recommended: true @@ -15203,14 +15883,14 @@ slots: description: 260/230 measurement of RNA sample purity title: RNA absorbance 260/230 comments: - - Recommended value is between 1 and 3. + - Recommended value is between 1 and 3. examples: - - value: '2.02' + - value: '2.02' from_schema: https://example.com/nmdc_submission_schema rank: 8 string_serialization: '{float}' domain_of: - - Biosample + - Biosample slot_group: JGI-Metatranscriptomics range: float recommended: true @@ -15218,16 +15898,17 @@ slots: 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. + - 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' + - value: '100' from_schema: https://example.com/nmdc_submission_schema see_also: - - nmdc:nucleic_acid_concentration + - nmdc:nucleic_acid_concentration rank: 5 string_serialization: '{float}' domain_of: - - Biosample + - Biosample slot_group: JGI-Metatranscriptomics range: float recommended: true @@ -15238,11 +15919,11 @@ slots: description: Tube or plate (96-well) title: RNA container type examples: - - value: plate + - value: plate from_schema: https://example.com/nmdc_submission_schema rank: 10 domain_of: - - Biosample + - Biosample slot_group: JGI-Metatranscriptomics range: JgiContTypeEnum recommended: true @@ -15250,17 +15931,18 @@ slots: 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). + - 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 + - value: B2 from_schema: https://example.com/nmdc_submission_schema rank: 11 string_serialization: '{96 well plate pos}' domain_of: - - Biosample + - Biosample slot_group: JGI-Metatranscriptomics recommended: true pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$ @@ -15268,14 +15950,15 @@ slots: 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. + - 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 + - value: Pond_MT_041618 from_schema: https://example.com/nmdc_submission_schema rank: 9 string_serialization: '{text < 20 characters}' domain_of: - - Biosample + - Biosample slot_group: JGI-Metatranscriptomics recommended: true rna_isolate_meth: @@ -15283,42 +15966,44 @@ slots: description: Describe the method/protocol/kit used to extract DNA/RNA. title: RNA isolation method examples: - - value: phenol/chloroform extraction + - value: phenol/chloroform extraction from_schema: https://example.com/nmdc_submission_schema aliases: - - Sample Isolation Method + - Sample Isolation Method rank: 16 string_serialization: '{text}' domain_of: - - Biosample + - Biosample 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. + - Do not edit these values. A template will be provided by NMDC in which these + values have been pre-filled. examples: - - value: John Jones + - value: John Jones from_schema: https://example.com/nmdc_submission_schema rank: 18 string_serialization: '{text}' domain_of: - - Biosample + - Biosample 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. + - Do not edit these values. A template will be provided by NMDC in which these + values have been pre-filled. examples: - - value: '187654' + - value: '187654' from_schema: https://example.com/nmdc_submission_schema rank: 3 string_serialization: '{text}' domain_of: - - Biosample + - Biosample slot_group: JGI-Metatranscriptomics recommended: true rna_sample_format: @@ -15326,25 +16011,26 @@ slots: description: Solution in which the RNA sample has been suspended title: RNA sample format examples: - - value: Water + - value: Water from_schema: https://example.com/nmdc_submission_schema rank: 12 domain_of: - - Biosample + - Biosample slot_group: JGI-Metatranscriptomics range: RNASampleFormatEnum 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. + 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 + - value: JGI_pond_041618 from_schema: https://example.com/nmdc_submission_schema rank: 4 string_serialization: '{text}' domain_of: - - Biosample + - Biosample slot_group: JGI-Metatranscriptomics recommended: true minimum_value: 0 @@ -15353,58 +16039,63 @@ slots: 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. + - Do not edit these values. A template will be provided by NMDC in which these + values have been pre-filled. examples: - - value: '1191234' + - value: '1191234' from_schema: https://example.com/nmdc_submission_schema aliases: - - Seq Project ID + - Seq Project ID rank: 1 string_serialization: '{text}' domain_of: - - Biosample + - Biosample 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. + - 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 + - value: JGI Pond metatranscriptomics from_schema: https://example.com/nmdc_submission_schema rank: 2 string_serialization: '{text}' domain_of: - - Biosample + - Biosample 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. + - Do not edit these values. A template will be provided by NMDC in which these + values have been pre-filled. examples: - - value: Jane Johnson + - value: Jane Johnson from_schema: https://example.com/nmdc_submission_schema rank: 17 string_serialization: '{text}' domain_of: - - Biosample + - Biosample 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 + - 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' + - value: '25' from_schema: https://example.com/nmdc_submission_schema rank: 6 string_serialization: '{float}' domain_of: - - Biosample + - Biosample slot_group: JGI-Metatranscriptomics range: float recommended: true @@ -15425,14 +16116,14 @@ slots: description: The rate at which outside air replaces indoor air in a given space title: room air exchange rate examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - room air exchange rate + - room air exchange rate is_a: core field slot_uri: MIXS:0000169 domain_of: - - Biosample + - Biosample range: string multivalued: false room_architec_elem: @@ -15444,18 +16135,19 @@ slots: 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 + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - room architectural elements + - room architectural elements is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000233 domain_of: - - Biosample + - Biosample range: string multivalued: false room_condt: @@ -15470,14 +16162,14 @@ slots: description: The condition of the room at the time of sampling title: room condition examples: - - value: new + - value: new from_schema: https://example.com/nmdc_submission_schema aliases: - - room condition + - room condition is_a: core field slot_uri: MIXS:0000822 domain_of: - - Biosample + - Biosample range: room_condt_enum multivalued: false room_connected: @@ -15492,14 +16184,14 @@ slots: description: List of rooms connected to the sampling room by a doorway title: rooms connected by a doorway examples: - - value: office + - value: office from_schema: https://example.com/nmdc_submission_schema aliases: - - rooms connected by a doorway + - rooms connected by a doorway is_a: core field slot_uri: MIXS:0000826 domain_of: - - Biosample + - Biosample range: room_connected_enum multivalued: false room_count: @@ -15511,17 +16203,18 @@ slots: occurrence: tag: occurrence value: '1' - description: The total count of rooms in the built structure including all room types + description: The total count of rooms in the built structure including all room + types title: room count examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - room count + - room count is_a: core field slot_uri: MIXS:0000234 domain_of: - - Biosample + - Biosample range: string multivalued: false room_dim: @@ -15539,15 +16232,15 @@ slots: description: The length, width and height of sampling room title: room dimensions examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - room dimensions + - room dimensions is_a: core field string_serialization: '{integer} {unit} x {integer} {unit} x {integer} {unit}' slot_uri: MIXS:0000192 domain_of: - - Biosample + - Biosample range: string multivalued: false room_door_dist: @@ -15562,18 +16255,19 @@ slots: occurrence: tag: occurrence value: '1' - description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms + description: Distance between doors (meters) in the hallway between the sampling + room and adjacent rooms title: room door distance examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - room door distance + - room door distance is_a: core field string_serialization: '{integer} {unit}' slot_uri: MIXS:0000193 domain_of: - - Biosample + - Biosample range: string multivalued: false room_door_share: @@ -15585,18 +16279,19 @@ slots: occurrence: tag: occurrence value: '1' - description: List of room(s) (room number, room name) sharing a door with the sampling room + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - rooms that share a door with sampling room + - rooms that share a door with sampling room is_a: core field string_serialization: '{text};{integer}' slot_uri: MIXS:0000242 domain_of: - - Biosample + - Biosample range: string multivalued: false room_hallway: @@ -15608,18 +16303,19 @@ slots: occurrence: tag: occurrence value: '1' - description: List of room(s) (room number, room name) located in the same hallway as sampling room + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - rooms that are on the same hallway + - rooms that are on the same hallway is_a: core field string_serialization: '{text};{integer}' slot_uri: MIXS:0000238 domain_of: - - Biosample + - Biosample range: string multivalued: false room_loc: @@ -15634,14 +16330,14 @@ slots: description: The position of the room within the building title: room location in building examples: - - value: interior room + - value: interior room from_schema: https://example.com/nmdc_submission_schema aliases: - - room location in building + - room location in building is_a: core field slot_uri: MIXS:0000823 domain_of: - - Biosample + - Biosample range: room_loc_enum multivalued: false room_moist_dam_hist: @@ -15653,17 +16349,18 @@ slots: 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 + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - room moisture damage or mold history + - room moisture damage or mold history is_a: core field slot_uri: MIXS:0000235 domain_of: - - Biosample + - Biosample range: integer multivalued: false room_net_area: @@ -15681,15 +16378,15 @@ slots: description: The net floor area of sampling room. Net area excludes wall thicknesses title: room net area examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - room net area + - room net area is_a: core field string_serialization: '{integer} {unit}' slot_uri: MIXS:0000194 domain_of: - - Biosample + - Biosample range: string multivalued: false room_occup: @@ -15704,14 +16401,14 @@ slots: description: Count of room occupancy at time of sampling title: room occupancy examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - room occupancy + - room occupancy is_a: core field slot_uri: MIXS:0000236 domain_of: - - Biosample + - Biosample range: string multivalued: false room_samp_pos: @@ -15723,17 +16420,18 @@ slots: occurrence: tag: occurrence value: '1' - description: The horizontal sampling position in the room relative to architectural elements + description: The horizontal sampling position in the room relative to architectural + elements title: room sampling position examples: - - value: south corner + - value: south corner from_schema: https://example.com/nmdc_submission_schema aliases: - - room sampling position + - room sampling position is_a: core field slot_uri: MIXS:0000824 domain_of: - - Biosample + - Biosample range: room_samp_pos_enum multivalued: false room_type: @@ -15745,17 +16443,18 @@ slots: occurrence: tag: occurrence value: '1' - description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure + 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 + - value: bathroom from_schema: https://example.com/nmdc_submission_schema aliases: - - room type + - room type is_a: core field slot_uri: MIXS:0000825 domain_of: - - Biosample + - Biosample range: room_type_enum multivalued: false room_vol: @@ -15773,15 +16472,15 @@ slots: description: Volume of sampling room title: room volume examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - room volume + - room volume is_a: core field string_serialization: '{integer} {unit}' slot_uri: MIXS:0000195 domain_of: - - Biosample + - Biosample range: string multivalued: false room_wall_share: @@ -15793,18 +16492,19 @@ slots: occurrence: tag: occurrence value: '1' - description: List of room(s) (room number, room name) sharing a wall with the sampling room + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - rooms that share a wall with sampling room + - rooms that share a wall with sampling room is_a: core field string_serialization: '{text};{integer}' slot_uri: MIXS:0000243 domain_of: - - Biosample + - Biosample range: string multivalued: false room_window_count: @@ -15819,14 +16519,14 @@ slots: description: Number of windows in the room title: room window count examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - room window count + - room window count is_a: core field slot_uri: MIXS:0000237 domain_of: - - Biosample + - Biosample range: integer multivalued: false root_cond: @@ -15838,18 +16538,19 @@ slots: occurrence: tag: occurrence value: '1' - description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. + 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 + - value: http://himedialabs.com/TD/PT158.pdf from_schema: https://example.com/nmdc_submission_schema aliases: - - rooting conditions + - rooting conditions is_a: core field string_serialization: '{PMID}|{DOI}|{URL}|{text}' slot_uri: MIXS:0001061 domain_of: - - Biosample + - Biosample range: string multivalued: false root_med_carbon: @@ -15867,15 +16568,15 @@ slots: description: Source of organic carbon in the culture rooting medium; e.g. sucrose. title: rooting medium carbon examples: - - value: sucrose + - value: sucrose from_schema: https://example.com/nmdc_submission_schema aliases: - - rooting medium carbon + - rooting medium carbon is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000577 domain_of: - - Biosample + - Biosample range: string multivalued: false root_med_macronutr: @@ -15890,18 +16591,19 @@ slots: 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). + 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 + - value: KH2PO4;170¬†milligram per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - rooting medium macronutrients + - rooting medium macronutrients is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000578 domain_of: - - Biosample + - Biosample range: string multivalued: false root_med_micronutr: @@ -15916,18 +16618,19 @@ slots: 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). + 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 + - value: H3BO3;6.2¬†milligram per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - rooting medium micronutrients + - rooting medium micronutrients is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000579 domain_of: - - Biosample + - Biosample range: string multivalued: false root_med_ph: @@ -15942,14 +16645,14 @@ slots: description: pH measurement of the culture rooting medium; e.g. 5.5. title: rooting medium pH examples: - - value: '7.5' + - value: '7.5' from_schema: https://example.com/nmdc_submission_schema aliases: - - rooting medium pH + - rooting medium pH is_a: core field slot_uri: MIXS:0001062 domain_of: - - Biosample + - Biosample range: string multivalued: false root_med_regl: @@ -15964,18 +16667,19 @@ slots: 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. + 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 + - value: abscisic acid;0.75 milligram per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - rooting medium regulators + - rooting medium regulators is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000581 domain_of: - - Biosample + - Biosample range: string multivalued: false root_med_solid: @@ -15987,18 +16691,19 @@ slots: occurrence: tag: occurrence value: '1' - description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. + description: Specification of the solidifying agent in the culture rooting medium; + e.g. agar. title: rooting medium solidifier examples: - - value: agar + - value: agar from_schema: https://example.com/nmdc_submission_schema aliases: - - rooting medium solidifier + - rooting medium solidifier is_a: core field string_serialization: '{text}' slot_uri: MIXS:0001063 domain_of: - - Biosample + - Biosample range: string multivalued: false root_med_suppl: @@ -16013,18 +16718,20 @@ slots: 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). + 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 + - value: nicotinic acid;0.5 milligram per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - rooting medium organic supplements + - rooting medium organic supplements is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000580 domain_of: - - Biosample + - Biosample range: string multivalued: false salinity: @@ -16039,17 +16746,22 @@ slots: 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. + 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 + - value: 25 practical salinity unit from_schema: https://example.com/nmdc_submission_schema aliases: - - salinity + - salinity is_a: core field slot_uri: MIXS:0000183 domain_of: - - Biosample + - Biosample range: string multivalued: false salinity_meth: @@ -16064,15 +16776,15 @@ slots: description: Reference or method used in determining salinity title: salinity method examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - salinity method + - salinity method is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000341 domain_of: - - Biosample + - Biosample range: string multivalued: false salt_regm: @@ -16087,18 +16799,22 @@ slots: 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 + 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 + - 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 + - salt regimen is_a: core field string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000582 domain_of: - - Biosample + - Biosample range: string multivalued: false samp_capt_status: @@ -16113,14 +16829,14 @@ slots: description: Reason for the sample title: sample capture status examples: - - value: farm sample + - value: farm sample from_schema: https://example.com/nmdc_submission_schema aliases: - - sample capture status + - sample capture status is_a: core field slot_uri: MIXS:0000860 domain_of: - - Biosample + - Biosample range: samp_capt_status_enum multivalued: false samp_collec_device: @@ -16129,18 +16845,20 @@ slots: 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). + 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] + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] from_schema: https://example.com/nmdc_submission_schema aliases: - - sample collection device + - sample collection device is_a: nucleic acid sequence source field string_serialization: '{termLabel} {[termID]}|{text}' slot_uri: MIXS:0000002 domain_of: - - Biosample + - Biosample range: string multivalued: false samp_collec_method: @@ -16152,15 +16870,15 @@ slots: description: The method employed for collecting the sample. title: sample collection method examples: - - value: swabbing + - value: swabbing from_schema: https://example.com/nmdc_submission_schema aliases: - - sample collection method + - sample collection method is_a: nucleic acid sequence source field string_serialization: '{PMID}|{DOI}|{URL}|{text}' slot_uri: MIXS:0001225 domain_of: - - Biosample + - Biosample range: string multivalued: false samp_collect_point: @@ -16172,17 +16890,19 @@ slots: 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 + 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 + - value: well from_schema: https://example.com/nmdc_submission_schema aliases: - - sample collection point + - sample collection point is_a: core field slot_uri: MIXS:0001015 domain_of: - - Biosample + - Biosample range: samp_collect_point_enum multivalued: false samp_dis_stage: @@ -16194,17 +16914,18 @@ slots: 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. + 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 + - value: infection from_schema: https://example.com/nmdc_submission_schema aliases: - - sample disease stage + - sample disease stage is_a: core field slot_uri: MIXS:0000249 domain_of: - - Biosample + - Biosample range: samp_dis_stage_enum multivalued: false samp_floor: @@ -16219,14 +16940,14 @@ slots: description: The floor of the building, where the sampling room is located title: sampling floor examples: - - value: 4th floor + - value: 4th floor from_schema: https://example.com/nmdc_submission_schema aliases: - - sampling floor + - sampling floor is_a: core field slot_uri: MIXS:0000828 domain_of: - - Biosample + - Biosample range: samp_floor_enum multivalued: false samp_loc_corr_rate: @@ -16241,18 +16962,24 @@ slots: 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 + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - corrosion rate at sample location + - corrosion rate at sample location is_a: core field string_serialization: '{float} - {float} {unit}' slot_uri: MIXS:0000136 domain_of: - - Biosample + - Biosample range: string multivalued: false samp_mat_process: @@ -16261,18 +16988,20 @@ slots: 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. + 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 + - value: filtering of seawater, storing samples in ethanol from_schema: https://example.com/nmdc_submission_schema aliases: - - sample material processing + - sample material processing is_a: nucleic acid sequence source field string_serialization: '{text}' slot_uri: MIXS:0000016 domain_of: - - Biosample + - Biosample range: string multivalued: false samp_md: @@ -16287,17 +17016,22 @@ slots: 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 + 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 + - value: 1534 meter;MSL from_schema: https://example.com/nmdc_submission_schema aliases: - - sample measured depth + - sample measured depth is_a: core field slot_uri: MIXS:0000413 domain_of: - - Biosample + - Biosample range: string multivalued: false samp_name: @@ -16306,18 +17040,24 @@ slots: 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. + 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 + - value: ISDsoil1 from_schema: https://example.com/nmdc_submission_schema aliases: - - sample name + - sample name is_a: investigation field string_serialization: '{text}' slot_uri: MIXS:0001107 domain_of: - - Biosample + - Biosample range: string multivalued: false samp_preserv: @@ -16332,18 +17072,19 @@ slots: 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) + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - preservative added to sample + - preservative added to sample is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000463 domain_of: - - Biosample + - Biosample range: string multivalued: false samp_room_id: @@ -16355,17 +17096,18 @@ slots: occurrence: tag: occurrence value: '1' - description: Sampling room number. This ID should be consistent with the designations on the building floor plans + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - sampling room ID or name + - sampling room ID or name is_a: core field slot_uri: MIXS:0000244 domain_of: - - Biosample + - Biosample range: string multivalued: false samp_size: @@ -16377,17 +17119,18 @@ slots: 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. + 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 + - value: 5 liter from_schema: https://example.com/nmdc_submission_schema aliases: - - amount or size of sample collected + - amount or size of sample collected is_a: nucleic acid sequence source field slot_uri: MIXS:0000001 domain_of: - - Biosample + - Biosample range: string multivalued: false samp_sort_meth: @@ -16399,18 +17142,21 @@ slots: 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. + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - sample size sorting method + - sample size sorting method is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000216 domain_of: - - Biosample + - Biosample range: string multivalued: false samp_store_dur: @@ -16425,15 +17171,15 @@ slots: description: Duration for which the sample was stored title: sample storage duration examples: - - value: P1Y6M + - value: P1Y6M from_schema: https://example.com/nmdc_submission_schema aliases: - - sample storage duration + - sample storage duration is_a: core field string_serialization: '{duration}' slot_uri: MIXS:0000116 domain_of: - - Biosample + - Biosample range: string multivalued: false samp_store_loc: @@ -16448,15 +17194,15 @@ slots: description: Location at which sample was stored, usually name of a specific freezer/room title: sample storage location examples: - - value: Freezer no:5 + - value: Freezer no:5 from_schema: https://example.com/nmdc_submission_schema aliases: - - sample storage location + - sample storage location is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000755 domain_of: - - Biosample + - Biosample range: string multivalued: false samp_store_temp: @@ -16474,14 +17220,14 @@ slots: description: Temperature at which sample was stored, e.g. -80 degree Celsius title: sample storage temperature examples: - - value: -80 degree Celsius + - value: -80 degree Celsius from_schema: https://example.com/nmdc_submission_schema aliases: - - sample storage temperature + - sample storage temperature is_a: core field slot_uri: MIXS:0000110 domain_of: - - Biosample + - Biosample range: string multivalued: false samp_subtype: @@ -16493,17 +17239,19 @@ slots: 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 + 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 + - value: biofilm from_schema: https://example.com/nmdc_submission_schema aliases: - - sample subtype + - sample subtype is_a: core field slot_uri: MIXS:0000999 domain_of: - - Biosample + - Biosample range: samp_subtype_enum multivalued: false samp_time_out: @@ -16521,14 +17269,14 @@ slots: description: The recent and long term history of outside sampling title: sampling time outside examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - sampling time outside + - sampling time outside is_a: core field slot_uri: MIXS:0000196 domain_of: - - Biosample + - Biosample range: string multivalued: false samp_transport_cond: @@ -16543,18 +17291,19 @@ slots: 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) + 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 + - value: 5 days;-20 degree Celsius from_schema: https://example.com/nmdc_submission_schema aliases: - - sample transport conditions + - sample transport conditions is_a: core field string_serialization: '{float} {unit};{float} {unit}' slot_uri: MIXS:0000410 domain_of: - - Biosample + - Biosample range: string multivalued: false samp_tvdss: @@ -16569,18 +17318,20 @@ slots: 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 + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - sample true vertical depth subsea + - sample true vertical depth subsea is_a: core field string_serialization: '{float}-{float} {unit}' slot_uri: MIXS:0000409 domain_of: - - Biosample + - Biosample range: string multivalued: false samp_type: @@ -16592,18 +17343,23 @@ slots: 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). + 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] + - value: built environment sample [GENEPIO:0001248] from_schema: https://example.com/nmdc_submission_schema aliases: - - sample type + - sample type is_a: core field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000998 domain_of: - - Biosample + - Biosample range: string multivalued: false samp_weather: @@ -16618,14 +17374,14 @@ slots: description: The weather on the sampling day title: sampling day weather examples: - - value: foggy + - value: foggy from_schema: https://example.com/nmdc_submission_schema aliases: - - sampling day weather + - sampling day weather is_a: core field slot_uri: MIXS:0000827 domain_of: - - Biosample + - Biosample range: samp_weather_enum multivalued: false samp_well_name: @@ -16640,49 +17396,56 @@ slots: description: Name of the well (e.g. BXA1123) where sample was taken title: sample well name examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - sample well name + - sample well name is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000296 domain_of: - - Biosample + - Biosample range: string multivalued: false 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. + 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)' + - '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 + - value: IGSN:DSJ0284 from_schema: https://example.com/nmdc_submission_schema rank: 5 string_serialization: '{text}:{text}' domain_of: - - Biosample + - Biosample slot_group: Sample ID + range: string recommended: true multivalued: false - range: string sample_shipped: name: sample_shipped - description: The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent to EMSL. + 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. + - 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 + - value: 15 g + - value: 100 uL + - value: 5 mL from_schema: https://example.com/nmdc_submission_schema rank: 3 string_serialization: '{float} {unit}' domain_of: - - Biosample + - Biosample slot_group: EMSL recommended: true sample_type: @@ -16690,13 +17453,13 @@ slots: description: Type of sample being submitted title: sample type comments: - - This can vary from 'environmental package' if the sample is an extraction. + - This can vary from 'environmental package' if the sample is an extraction. examples: - - value: water extracted soil + - value: water extracted soil from_schema: https://example.com/nmdc_submission_schema rank: 2 domain_of: - - Biosample + - Biosample slot_group: EMSL range: SampleTypeEnum recommended: true @@ -16712,18 +17475,22 @@ slots: 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)' + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - saturates wt% + - saturates wt% is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000131 domain_of: - - Biosample + - Biosample range: string multivalued: false season: @@ -16735,18 +17502,20 @@ slots: 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). + 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] + - value: autumn [NCIT:C94733] from_schema: https://example.com/nmdc_submission_schema aliases: - - season + - season is_a: core field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000829 domain_of: - - Biosample + - Biosample range: string multivalued: false season_environment: @@ -16758,18 +17527,21 @@ slots: 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 + 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 + - value: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://example.com/nmdc_submission_schema aliases: - - seasonal environment + - seasonal environment is_a: core field string_serialization: '{text};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0001068 domain_of: - - Biosample + - Biosample range: string multivalued: false season_precpt: @@ -16784,17 +17556,18 @@ slots: 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. + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - mean seasonal precipitation + - mean seasonal precipitation is_a: core field slot_uri: MIXS:0000645 domain_of: - - Biosample + - Biosample range: string multivalued: false season_temp: @@ -16812,14 +17585,14 @@ slots: description: Mean seasonal temperature title: mean seasonal temperature examples: - - value: 18 degree Celsius + - value: 18 degree Celsius from_schema: https://example.com/nmdc_submission_schema aliases: - - mean seasonal temperature + - mean seasonal temperature is_a: core field slot_uri: MIXS:0000643 domain_of: - - Biosample + - Biosample range: string multivalued: false season_use: @@ -16834,14 +17607,14 @@ slots: description: The seasons the space is occupied title: seasonal use examples: - - value: Winter + - value: Winter from_schema: https://example.com/nmdc_submission_schema aliases: - - seasonal use + - seasonal use is_a: core field slot_uri: MIXS:0000830 domain_of: - - Biosample + - Biosample range: season_use_enum multivalued: false secondary_treatment: @@ -16853,18 +17626,19 @@ slots: occurrence: tag: occurrence value: '1' - description: The process for substantially degrading the biological content of the sewage + description: The process for substantially degrading the biological content of + the sewage title: secondary treatment examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - secondary treatment + - secondary treatment is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000351 domain_of: - - Biosample + - Biosample range: string multivalued: false sediment_type: @@ -16879,14 +17653,14 @@ slots: description: Information about the sediment type based on major constituents title: sediment type examples: - - value: biogenous + - value: biogenous from_schema: https://example.com/nmdc_submission_schema aliases: - - sediment type + - sediment type is_a: core field slot_uri: MIXS:0001078 domain_of: - - Biosample + - Biosample range: sediment_type_enum multivalued: false sewage_type: @@ -16901,15 +17675,15 @@ slots: description: Type of wastewater treatment plant as municipial or industrial title: sewage type examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - sewage type + - sewage type is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000215 domain_of: - - Biosample + - Biosample range: string multivalued: false shad_dev_water_mold: @@ -16924,15 +17698,15 @@ slots: 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 + - value: no presence of mold visible from_schema: https://example.com/nmdc_submission_schema aliases: - - shading device signs of water/mold + - 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 domain_of: - - Biosample + - Biosample range: string multivalued: false shading_device_cond: @@ -16947,14 +17721,14 @@ slots: description: The physical condition of the shading device at the time of sampling title: shading device condition examples: - - value: new + - value: new from_schema: https://example.com/nmdc_submission_schema aliases: - - shading device condition + - shading device condition is_a: core field slot_uri: MIXS:0000831 domain_of: - - Biosample + - Biosample range: shading_device_cond_enum multivalued: false shading_device_loc: @@ -16969,15 +17743,15 @@ slots: description: The location of the shading device in relation to the built structure title: shading device location examples: - - value: exterior + - value: exterior from_schema: https://example.com/nmdc_submission_schema aliases: - - shading device location + - shading device location is_a: core field string_serialization: '[exterior|interior]' slot_uri: MIXS:0000832 domain_of: - - Biosample + - Biosample range: string multivalued: false shading_device_mat: @@ -16992,15 +17766,15 @@ slots: description: The material the shading device is composed of title: shading device material examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - shading device material + - shading device material is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000245 domain_of: - - Biosample + - Biosample range: string multivalued: false shading_device_type: @@ -17015,14 +17789,14 @@ slots: description: The type of shading device title: shading device type examples: - - value: slatted aluminum awning + - value: slatted aluminum awning from_schema: https://example.com/nmdc_submission_schema aliases: - - shading device type + - shading device type is_a: core field slot_uri: MIXS:0000835 domain_of: - - Biosample + - Biosample range: shading_device_type_enum multivalued: false sieving: @@ -17034,18 +17808,19 @@ slots: occurrence: tag: occurrence value: '1' - description: Collection design of pooled samples and/or sieve size and amount of sample sieved + description: Collection design of pooled samples and/or sieve size and amount + of sample sieved title: composite design/sieving examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - composite design/sieving + - composite design/sieving is_a: core field string_serialization: '{{text}|{float} {unit}};{float} {unit}' slot_uri: MIXS:0000322 domain_of: - - Biosample + - Biosample range: string multivalued: false silicate: @@ -17063,14 +17838,14 @@ slots: description: Concentration of silicate title: silicate examples: - - value: 0.05 micromole per liter + - value: 0.05 micromole per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - silicate + - silicate is_a: core field slot_uri: MIXS:0000184 domain_of: - - Biosample + - Biosample range: string multivalued: false size_frac: @@ -17082,15 +17857,15 @@ slots: description: Filtering pore size used in sample preparation title: size fraction selected examples: - - value: 0-0.22 micrometer + - value: 0-0.22 micrometer from_schema: https://example.com/nmdc_submission_schema aliases: - - size fraction selected + - size fraction selected is_a: nucleic acid sequence source field string_serialization: '{float}-{float} {unit}' slot_uri: MIXS:0000017 domain_of: - - Biosample + - Biosample range: string multivalued: false size_frac_low: @@ -17105,17 +17880,18 @@ slots: 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 + 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 + - value: 0.2 micrometer from_schema: https://example.com/nmdc_submission_schema aliases: - - size-fraction lower threshold + - size-fraction lower threshold is_a: core field slot_uri: MIXS:0000735 domain_of: - - Biosample + - Biosample range: string multivalued: false size_frac_up: @@ -17130,17 +17906,18 @@ slots: 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 + 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 + - value: 20 micrometer from_schema: https://example.com/nmdc_submission_schema aliases: - - size-fraction upper threshold + - size-fraction upper threshold is_a: core field slot_uri: MIXS:0000736 domain_of: - - Biosample + - Biosample range: string multivalued: false slope_aspect: @@ -17155,17 +17932,20 @@ slots: 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. + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - slope aspect + - slope aspect is_a: core field slot_uri: MIXS:0000647 domain_of: - - Biosample + - Biosample range: string multivalued: false slope_gradient: @@ -17180,17 +17960,19 @@ slots: 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 + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - slope gradient + - slope gradient is_a: core field slot_uri: MIXS:0000646 domain_of: - - Biosample + - Biosample range: string multivalued: false sludge_retent_time: @@ -17208,14 +17990,14 @@ slots: description: The time activated sludge remains in reactor title: sludge retention time examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - sludge retention time + - sludge retention time is_a: core field slot_uri: MIXS:0000669 domain_of: - - Biosample + - Biosample range: string multivalued: false sodium: @@ -17233,14 +18015,14 @@ slots: description: Sodium concentration in the sample title: sodium examples: - - value: 10.5 milligram per liter + - value: 10.5 milligram per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - sodium + - sodium is_a: core field slot_uri: MIXS:0000428 domain_of: - - Biosample + - Biosample range: string multivalued: false soil_horizon: @@ -17252,17 +18034,19 @@ slots: 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 + 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 + - value: A horizon from_schema: https://example.com/nmdc_submission_schema aliases: - - soil horizon + - soil horizon is_a: core field slot_uri: MIXS:0001082 domain_of: - - Biosample + - Biosample range: soil_horizon_enum multivalued: false soil_text_measure: @@ -17274,17 +18058,20 @@ slots: 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. + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - soil texture measurement + - soil texture measurement is_a: core field slot_uri: MIXS:0000335 domain_of: - - Biosample + - Biosample range: string multivalued: false soil_texture_meth: @@ -17299,15 +18086,15 @@ slots: description: Reference or method used in determining soil texture title: soil texture method examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - soil texture method + - soil texture method is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000336 domain_of: - - Biosample + - Biosample range: string multivalued: false soil_type: @@ -17319,19 +18106,21 @@ slots: 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. + 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] + - value: plinthosol [ENVO:00002250] from_schema: https://example.com/nmdc_submission_schema aliases: - - soil type + - soil type is_a: core field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000332 domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample range: string multivalued: false soil_type_meth: @@ -17343,18 +18132,19 @@ slots: occurrence: tag: occurrence value: '1' - description: Reference or method used in determining soil series name or other lower-level classification + description: Reference or method used in determining soil series name or other + lower-level classification title: soil type method examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - soil type method + - soil type method is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000334 domain_of: - - Biosample + - Biosample range: string multivalued: false solar_irradiance: @@ -17365,21 +18155,23 @@ slots: value: measurement value preferred_unit: tag: preferred_unit - value: kilowatts per square meter per day, ergs per square centimeter per second + 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 + 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 + - value: 1.36 kilowatts per square meter per day from_schema: https://example.com/nmdc_submission_schema aliases: - - solar irradiance + - solar irradiance is_a: core field slot_uri: MIXS:0000112 domain_of: - - Biosample + - Biosample range: string multivalued: false soluble_inorg_mat: @@ -17394,18 +18186,19 @@ slots: occurrence: tag: occurrence value: m - description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. + description: Concentration of substances such as ammonia, road-salt, sea-salt, + cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. title: soluble inorganic material examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - soluble inorganic material + - soluble inorganic material is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000672 domain_of: - - Biosample + - Biosample range: string multivalued: false soluble_org_mat: @@ -17420,18 +18213,19 @@ slots: occurrence: tag: occurrence value: m - description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. + description: Concentration of substances such as urea, fruit sugars, soluble proteins, + drugs, pharmaceuticals, etc. title: soluble organic material examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - soluble organic material + - soluble organic material is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000673 domain_of: - - Biosample + - Biosample range: string multivalued: false soluble_react_phosp: @@ -17449,14 +18243,14 @@ slots: description: Concentration of soluble reactive phosphorus title: soluble reactive phosphorus examples: - - value: 0.1 milligram per liter + - value: 0.1 milligram per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - soluble reactive phosphorus + - soluble reactive phosphorus is_a: core field slot_uri: MIXS:0000738 domain_of: - - Biosample + - Biosample range: string multivalued: false source_mat_id: @@ -17464,19 +18258,31 @@ slots: 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). + 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 + - value: MPI012345 from_schema: https://example.com/nmdc_submission_schema aliases: - - source material identifiers + - source material identifiers is_a: nucleic acid sequence source field string_serialization: '{text}' slot_uri: MIXS:0000026 domain_of: - - Biosample + - Biosample range: string multivalued: false space_typ_state: @@ -17491,15 +18297,15 @@ slots: description: Customary or normal state of the space title: space typical state examples: - - value: typically occupied + - value: typically occupied from_schema: https://example.com/nmdc_submission_schema aliases: - - space typical state + - space typical state is_a: core field string_serialization: '[typically occupied|typically unoccupied]' slot_uri: MIXS:0000770 domain_of: - - Biosample + - Biosample range: string multivalued: false specific: @@ -17511,31 +18317,35 @@ slots: occurrence: tag: occurrence value: '1' - description: 'The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents' + description: 'The building specifications. If design is chosen, indicate phase: + conceptual, schematic, design development, construction documents' title: specifications examples: - - value: construction + - value: construction from_schema: https://example.com/nmdc_submission_schema aliases: - - specifications + - specifications is_a: core field slot_uri: MIXS:0000836 domain_of: - - Biosample + - Biosample range: specific_enum multivalued: false 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help is_a: gold_path_field domain_of: - - Biosample - - Study + - Biosample + - Study specific_humidity: name: specific_humidity annotations: @@ -17548,17 +18358,19 @@ slots: 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. + 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 + - value: 15 per kilogram of air from_schema: https://example.com/nmdc_submission_schema aliases: - - specific humidity + - specific humidity is_a: core field slot_uri: MIXS:0000214 domain_of: - - Biosample + - Biosample range: string multivalued: false sr_dep_env: @@ -17570,17 +18382,18 @@ slots: 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 + 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 + - value: Marine from_schema: https://example.com/nmdc_submission_schema aliases: - - source rock depositional environment + - source rock depositional environment is_a: core field slot_uri: MIXS:0000996 domain_of: - - Biosample + - Biosample range: sr_dep_env_enum multivalued: false sr_geol_age: @@ -17592,17 +18405,18 @@ slots: 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' + 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 + - value: Silurian from_schema: https://example.com/nmdc_submission_schema aliases: - - source rock geological age + - source rock geological age is_a: core field slot_uri: MIXS:0000997 domain_of: - - Biosample + - Biosample range: sr_geol_age_enum multivalued: false sr_kerog_type: @@ -17614,17 +18428,21 @@ slots: 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' + 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 + - value: Type IV from_schema: https://example.com/nmdc_submission_schema aliases: - - source rock kerogen type + - source rock kerogen type is_a: core field slot_uri: MIXS:0000994 domain_of: - - Biosample + - Biosample range: sr_kerog_type_enum multivalued: false sr_lithology: @@ -17636,17 +18454,18 @@ slots: 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 + 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 + - value: Coal from_schema: https://example.com/nmdc_submission_schema aliases: - - source rock lithology + - source rock lithology is_a: core field slot_uri: MIXS:0000995 domain_of: - - Biosample + - Biosample range: sr_lithology_enum multivalued: false standing_water_regm: @@ -17658,18 +18477,21 @@ slots: 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 + 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 + - 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 + - standing water regimen is_a: core field string_serialization: '{text};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0001069 domain_of: - - Biosample + - Biosample range: string multivalued: false start_date_inc: @@ -17677,18 +18499,20 @@ slots: 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 + - 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. + - 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. + - value: 2021-04-15, 2021-04 and 2021 are all acceptable. from_schema: https://example.com/nmdc_submission_schema see_also: - - MIXS:0000011 + - MIXS:0000011 rank: 4 string_serialization: '{date, arbitrary precision}' domain_of: - - Biosample + - Biosample slot_group: MIxS Inspired recommended: true start_time_inc: @@ -17696,18 +18520,19 @@ slots: 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 + - 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' + - '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 + - value: 13:33 or 13:33:55 from_schema: https://example.com/nmdc_submission_schema see_also: - - MIXS:0000011 + - MIXS:0000011 rank: 5 string_serialization: '{time, seconds optional}' domain_of: - - Biosample + - Biosample slot_group: MIxS Inspired recommended: true store_cond: @@ -17719,18 +18544,19 @@ slots: occurrence: tag: occurrence value: '1' - description: Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other). + 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 + - value: -20 degree Celsius freezer;P2Y10D from_schema: https://example.com/nmdc_submission_schema aliases: - - storage conditions + - storage conditions is_a: core field string_serialization: '{text};{duration}' slot_uri: MIXS:0000327 domain_of: - - Biosample + - Biosample range: string multivalued: false substructure_type: @@ -17742,17 +18568,18 @@ slots: 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 + 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 + - value: basement from_schema: https://example.com/nmdc_submission_schema aliases: - - substructure type + - substructure type is_a: core field slot_uri: MIXS:0000767 domain_of: - - Biosample + - Biosample range: substructure_type_enum multivalued: true sulfate: @@ -17770,14 +18597,14 @@ slots: description: Concentration of sulfate in the sample title: sulfate examples: - - value: 5 micromole per liter + - value: 5 micromole per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - sulfate + - sulfate is_a: core field slot_uri: MIXS:0000423 domain_of: - - Biosample + - Biosample range: string multivalued: false sulfate_fw: @@ -17795,14 +18622,14 @@ slots: description: Original sulfate concentration in the hydrocarbon resource title: sulfate in formation water examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - sulfate in formation water + - sulfate in formation water is_a: core field slot_uri: MIXS:0000407 domain_of: - - Biosample + - Biosample range: string multivalued: false sulfide: @@ -17820,14 +18647,14 @@ slots: description: Concentration of sulfide in the sample title: sulfide examples: - - value: 2 micromole per liter + - value: 2 micromole per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - sulfide + - sulfide is_a: core field slot_uri: MIXS:0000424 domain_of: - - Biosample + - Biosample range: string multivalued: false surf_air_cont: @@ -17842,14 +18669,14 @@ slots: description: Contaminant identified on surface title: surface-air contaminant examples: - - value: radon + - value: radon from_schema: https://example.com/nmdc_submission_schema aliases: - - surface-air contaminant + - surface-air contaminant is_a: core field slot_uri: MIXS:0000759 domain_of: - - Biosample + - Biosample range: surf_air_cont_enum multivalued: true surf_humidity: @@ -17867,14 +18694,14 @@ slots: description: 'Surfaces: water activity as a function of air and material moisture' title: surface humidity examples: - - value: 10% + - value: 10% from_schema: https://example.com/nmdc_submission_schema aliases: - - surface humidity + - surface humidity is_a: core field slot_uri: MIXS:0000123 domain_of: - - Biosample + - Biosample range: string multivalued: false surf_material: @@ -17889,14 +18716,14 @@ slots: description: Surface materials at the point of sampling title: surface material examples: - - value: wood + - value: wood from_schema: https://example.com/nmdc_submission_schema aliases: - - surface material + - surface material is_a: core field slot_uri: MIXS:0000758 domain_of: - - Biosample + - Biosample range: surf_material_enum multivalued: false surf_moisture: @@ -17914,14 +18741,14 @@ slots: description: Water held on a surface title: surface moisture examples: - - value: 0.01 gram per square meter + - value: 0.01 gram per square meter from_schema: https://example.com/nmdc_submission_schema aliases: - - surface moisture + - surface moisture is_a: core field slot_uri: MIXS:0000128 domain_of: - - Biosample + - Biosample range: string multivalued: false surf_moisture_ph: @@ -17936,14 +18763,14 @@ slots: description: ph measurement of surface title: surface moisture pH examples: - - value: '7' + - value: '7' from_schema: https://example.com/nmdc_submission_schema aliases: - - surface moisture pH + - surface moisture pH is_a: core field slot_uri: MIXS:0000760 domain_of: - - Biosample + - Biosample range: double multivalued: false surf_temp: @@ -17961,14 +18788,14 @@ slots: description: Temperature of the surface at the time of sampling title: surface temperature examples: - - value: 15 degree Celsius + - value: 15 degree Celsius from_schema: https://example.com/nmdc_submission_schema aliases: - - surface temperature + - surface temperature is_a: core field slot_uri: MIXS:0000125 domain_of: - - Biosample + - Biosample range: string multivalued: false suspend_part_matter: @@ -17986,14 +18813,14 @@ slots: description: Concentration of suspended particulate matter title: suspended particulate matter examples: - - value: 0.5 milligram per liter + - value: 0.5 milligram per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - suspended particulate matter + - suspended particulate matter is_a: core field slot_uri: MIXS:0000741 domain_of: - - Biosample + - Biosample range: string multivalued: false suspend_solids: @@ -18004,22 +18831,24 @@ slots: 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 + 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 + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - suspended solids + - suspended solids is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000150 domain_of: - - Biosample + - Biosample range: string multivalued: false tan: @@ -18034,32 +18863,37 @@ slots: 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)' + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - total acid number + - total acid number is_a: core field slot_uri: MIXS:0000120 domain_of: - - Biosample + - Biosample range: string multivalued: false technical_reps: name: technical_reps - description: If sending technical replicates of the same sample, indicate the replicate count. + 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. + - This field is only required when completing metadata for samples being submitted + to EMSL for analyses. examples: - - value: '2' + - value: '2' from_schema: https://example.com/nmdc_submission_schema rank: 5 string_serialization: '{integer}' domain_of: - - Biosample + - Biosample slot_group: EMSL recommended: true temp: @@ -18074,14 +18908,14 @@ slots: description: Temperature of the sample at the time of sampling. title: temperature examples: - - value: 25 degree Celsius + - value: 25 degree Celsius from_schema: https://example.com/nmdc_submission_schema aliases: - - temperature + - temperature is_a: environment field slot_uri: MIXS:0000113 domain_of: - - Biosample + - Biosample range: string multivalued: false temp_out: @@ -18099,14 +18933,14 @@ slots: description: The recorded temperature value at sampling time outside title: temperature outside house examples: - - value: 5 degree Celsius + - value: 5 degree Celsius from_schema: https://example.com/nmdc_submission_schema aliases: - - temperature outside house + - temperature outside house is_a: core field slot_uri: MIXS:0000197 domain_of: - - Biosample + - Biosample range: string multivalued: false tertiary_treatment: @@ -18118,18 +18952,19 @@ slots: 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 + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - tertiary treatment + - tertiary treatment is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000352 domain_of: - - Biosample + - Biosample range: string multivalued: false tidal_stage: @@ -18144,14 +18979,14 @@ slots: description: Stage of tide title: tidal stage examples: - - value: high tide + - value: high tide from_schema: https://example.com/nmdc_submission_schema aliases: - - tidal stage + - tidal stage is_a: core field slot_uri: MIXS:0000750 domain_of: - - Biosample + - Biosample range: tidal_stage_enum multivalued: false tillage: @@ -18166,14 +19001,14 @@ slots: description: Note method(s) used for tilling title: history/tillage examples: - - value: chisel + - value: chisel from_schema: https://example.com/nmdc_submission_schema aliases: - - history/tillage + - history/tillage is_a: core field slot_uri: MIXS:0001081 domain_of: - - Biosample + - Biosample range: tillage_enum multivalued: true tiss_cult_growth_med: @@ -18188,15 +19023,15 @@ slots: 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 + - value: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf from_schema: https://example.com/nmdc_submission_schema aliases: - - tissue culture growth media + - tissue culture growth media is_a: core field string_serialization: '{PMID}|{DOI}|{URL}|{text}' slot_uri: MIXS:0001070 domain_of: - - Biosample + - Biosample range: string multivalued: false toluene: @@ -18214,14 +19049,14 @@ slots: description: Concentration of toluene in the sample title: toluene examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - toluene + - toluene is_a: core field slot_uri: MIXS:0000154 domain_of: - - Biosample + - Biosample range: string multivalued: false tot_carb: @@ -18239,14 +19074,14 @@ slots: description: Total carbon content title: total carbon examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - total carbon + - total carbon is_a: core field slot_uri: MIXS:0000525 domain_of: - - Biosample + - Biosample range: string multivalued: false tot_depth_water_col: @@ -18264,14 +19099,14 @@ slots: description: Measurement of total depth of water column title: total depth of water column examples: - - value: 500 meter + - value: 500 meter from_schema: https://example.com/nmdc_submission_schema aliases: - - total depth of water column + - total depth of water column is_a: core field slot_uri: MIXS:0000634 domain_of: - - Biosample + - Biosample range: string multivalued: false tot_diss_nitro: @@ -18286,17 +19121,18 @@ slots: occurrence: tag: occurrence value: '1' - description: 'Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen' + 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 + - value: 40 microgram per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - total dissolved nitrogen + - total dissolved nitrogen is_a: core field slot_uri: MIXS:0000744 domain_of: - - Biosample + - Biosample range: string multivalued: false tot_inorg_nitro: @@ -18314,14 +19150,14 @@ slots: description: Total inorganic nitrogen content title: total inorganic nitrogen examples: - - value: 40 microgram per liter + - value: 40 microgram per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - total inorganic nitrogen + - total inorganic nitrogen is_a: core field slot_uri: MIXS:0000745 domain_of: - - Biosample + - Biosample range: string multivalued: false tot_iron: @@ -18339,14 +19175,14 @@ slots: description: Concentration of total iron in the sample title: total iron examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - total iron + - total iron is_a: core field slot_uri: MIXS:0000105 domain_of: - - Biosample + - Biosample range: string multivalued: false tot_nitro: @@ -18361,17 +19197,19 @@ slots: 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' + 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 + - value: 50 micromole per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - total nitrogen concentration + - total nitrogen concentration is_a: core field slot_uri: MIXS:0000102 domain_of: - - Biosample + - Biosample range: string multivalued: false tot_nitro_cont_meth: @@ -18386,15 +19224,15 @@ slots: description: Reference or method used in determining the total nitrogen title: total nitrogen content method examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - total nitrogen content method + - total nitrogen content method is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000338 domain_of: - - Biosample + - Biosample range: string multivalued: false tot_nitro_content: @@ -18412,14 +19250,14 @@ slots: description: Total nitrogen content of the sample title: total nitrogen content examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - total nitrogen content + - total nitrogen content is_a: core field slot_uri: MIXS:0000530 domain_of: - - Biosample + - Biosample range: string multivalued: false tot_org_c_meth: @@ -18434,15 +19272,15 @@ slots: description: Reference or method used in determining total organic carbon title: total organic carbon method examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - total organic carbon method + - total organic carbon method is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000337 domain_of: - - Biosample + - Biosample range: string multivalued: false tot_org_carb: @@ -18457,17 +19295,18 @@ slots: occurrence: tag: occurrence value: '1' - description: 'Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content' + description: 'Definition for soil: total organic carbon content of the soil, definition + otherwise: total organic carbon content' title: total organic carbon examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - total organic carbon + - total organic carbon is_a: core field slot_uri: MIXS:0000533 domain_of: - - Biosample + - Biosample range: string multivalued: false tot_part_carb: @@ -18485,14 +19324,14 @@ slots: description: Total particulate carbon content title: total particulate carbon examples: - - value: 35 micromole per liter + - value: 35 micromole per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - total particulate carbon + - total particulate carbon is_a: core field slot_uri: MIXS:0000747 domain_of: - - Biosample + - Biosample range: string multivalued: false tot_phosp: @@ -18507,17 +19346,18 @@ slots: occurrence: tag: occurrence value: '1' - description: 'Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus' + 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 + - value: 0.03 milligram per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - total phosphorus + - total phosphorus is_a: core field slot_uri: MIXS:0000117 domain_of: - - Biosample + - Biosample range: string multivalued: false tot_phosphate: @@ -18535,14 +19375,14 @@ slots: description: Total amount or concentration of phosphate title: total phosphate examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - total phosphate + - total phosphate is_a: core field slot_uri: MIXS:0000689 domain_of: - - Biosample + - Biosample range: string multivalued: false tot_sulfur: @@ -18560,14 +19400,14 @@ slots: description: Concentration of total sulfur in the sample title: total sulfur examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - total sulfur + - total sulfur is_a: core field slot_uri: MIXS:0000419 domain_of: - - Biosample + - Biosample range: string multivalued: false train_line: @@ -18582,14 +19422,14 @@ slots: description: The subway line name title: train line examples: - - value: red + - value: red from_schema: https://example.com/nmdc_submission_schema aliases: - - train line + - train line is_a: core field slot_uri: MIXS:0000837 domain_of: - - Biosample + - Biosample range: train_line_enum multivalued: false train_stat_loc: @@ -18604,14 +19444,14 @@ slots: description: The train station collection location title: train station collection location examples: - - value: forest hills + - value: forest hills from_schema: https://example.com/nmdc_submission_schema aliases: - - train station collection location + - train station collection location is_a: core field slot_uri: MIXS:0000838 domain_of: - - Biosample + - Biosample range: train_stat_loc_enum multivalued: false train_stop_loc: @@ -18626,14 +19466,14 @@ slots: description: The train stop collection location title: train stop collection location examples: - - value: end + - value: end from_schema: https://example.com/nmdc_submission_schema aliases: - - train stop collection location + - train stop collection location is_a: core field slot_uri: MIXS:0000839 domain_of: - - Biosample + - Biosample range: train_stop_loc_enum multivalued: false turbidity: @@ -18648,17 +19488,18 @@ slots: occurrence: tag: occurrence value: '1' - description: Measure of the amount of cloudiness or haziness in water caused by individual particles + description: Measure of the amount of cloudiness or haziness in water caused by + individual particles title: turbidity examples: - - value: 0.3 nephelometric turbidity units + - value: 0.3 nephelometric turbidity units from_schema: https://example.com/nmdc_submission_schema aliases: - - turbidity + - turbidity is_a: core field slot_uri: MIXS:0000191 domain_of: - - Biosample + - Biosample range: string multivalued: false tvdss_of_hcr_press: @@ -18673,17 +19514,18 @@ slots: 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). + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - depth (TVDSS) of hydrocarbon resource pressure + - depth (TVDSS) of hydrocarbon resource pressure is_a: core field slot_uri: MIXS:0000397 domain_of: - - Biosample + - Biosample range: string multivalued: false tvdss_of_hcr_temp: @@ -18698,17 +19540,18 @@ slots: 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). + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - depth (TVDSS) of hydrocarbon resource temperature + - depth (TVDSS) of hydrocarbon resource temperature is_a: core field slot_uri: MIXS:0000394 domain_of: - - Biosample + - Biosample range: string multivalued: false typ_occup_density: @@ -18723,14 +19566,14 @@ slots: description: Customary or normal density of occupants title: typical occupant density examples: - - value: '25' + - value: '25' from_schema: https://example.com/nmdc_submission_schema aliases: - - typical occupant density + - typical occupant density is_a: core field slot_uri: MIXS:0000771 domain_of: - - Biosample + - Biosample range: double multivalued: false ventilation_rate: @@ -18748,14 +19591,14 @@ slots: description: Ventilation rate of the system in the sampled premises title: ventilation rate examples: - - value: 750 cubic meter per minute + - value: 750 cubic meter per minute from_schema: https://example.com/nmdc_submission_schema aliases: - - ventilation rate + - ventilation rate is_a: core field slot_uri: MIXS:0000114 domain_of: - - Biosample + - Biosample range: string multivalued: false ventilation_type: @@ -18770,15 +19613,15 @@ slots: description: Ventilation system used in the sampled premises title: ventilation type examples: - - value: Operable windows + - value: Operable windows from_schema: https://example.com/nmdc_submission_schema aliases: - - ventilation type + - ventilation type is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000756 domain_of: - - Biosample + - Biosample range: string multivalued: false vfa: @@ -18796,14 +19639,14 @@ slots: description: Concentration of Volatile Fatty Acids in the sample title: volatile fatty acids examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - volatile fatty acids + - volatile fatty acids is_a: core field slot_uri: MIXS:0000152 domain_of: - - Biosample + - Biosample range: string multivalued: false vfa_fw: @@ -18821,14 +19664,14 @@ slots: description: Original volatile fatty acid concentration in the hydrocarbon resource title: vfa in formation water examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - vfa in formation water + - vfa in formation water is_a: core field slot_uri: MIXS:0000408 domain_of: - - Biosample + - Biosample range: string multivalued: false vis_media: @@ -18843,14 +19686,14 @@ slots: description: The building visual media title: visual media examples: - - value: 3D scans + - value: 3D scans from_schema: https://example.com/nmdc_submission_schema aliases: - - visual media + - visual media is_a: core field slot_uri: MIXS:0000840 domain_of: - - Biosample + - Biosample range: vis_media_enum multivalued: false viscosity: @@ -18865,18 +19708,19 @@ slots: 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) + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - viscosity + - viscosity is_a: core field string_serialization: '{float} {unit};{float} {unit}' slot_uri: MIXS:0000126 domain_of: - - Biosample + - Biosample range: string multivalued: false volatile_org_comp: @@ -18891,18 +19735,20 @@ slots: 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 + 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 + - value: formaldehyde;500 nanogram per liter from_schema: https://example.com/nmdc_submission_schema aliases: - - volatile organic compounds + - volatile organic compounds is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000115 domain_of: - - Biosample + - Biosample range: string multivalued: false wall_area: @@ -18920,14 +19766,14 @@ slots: description: The total area of the sampled room's walls title: wall area examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - wall area + - wall area is_a: core field slot_uri: MIXS:0000198 domain_of: - - Biosample + - Biosample range: string multivalued: false wall_const_type: @@ -18939,17 +19785,18 @@ slots: occurrence: tag: occurrence value: '1' - description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. + 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 + - value: fire resistive from_schema: https://example.com/nmdc_submission_schema aliases: - - wall construction type + - wall construction type is_a: core field slot_uri: MIXS:0000841 domain_of: - - Biosample + - Biosample range: wall_const_type_enum multivalued: false wall_finish_mat: @@ -18964,14 +19811,14 @@ slots: description: The material utilized to finish the outer most layer of the wall title: wall finish material examples: - - value: wood + - value: wood from_schema: https://example.com/nmdc_submission_schema aliases: - - wall finish material + - wall finish material is_a: core field slot_uri: MIXS:0000842 domain_of: - - Biosample + - Biosample range: wall_finish_mat_enum multivalued: false wall_height: @@ -18989,14 +19836,14 @@ slots: description: The average height of the walls in the sampled room title: wall height examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - wall height + - wall height is_a: core field slot_uri: MIXS:0000221 domain_of: - - Biosample + - Biosample range: string multivalued: false wall_loc: @@ -19011,14 +19858,14 @@ slots: description: The relative location of the wall within the room title: wall location examples: - - value: north + - value: north from_schema: https://example.com/nmdc_submission_schema aliases: - - wall location + - wall location is_a: core field slot_uri: MIXS:0000843 domain_of: - - Biosample + - Biosample range: wall_loc_enum multivalued: false wall_surf_treatment: @@ -19033,14 +19880,14 @@ slots: description: The surface treatment of interior wall title: wall surface treatment examples: - - value: paneling + - value: paneling from_schema: https://example.com/nmdc_submission_schema aliases: - - wall surface treatment + - wall surface treatment is_a: core field slot_uri: MIXS:0000845 domain_of: - - Biosample + - Biosample range: wall_surf_treatment_enum multivalued: false wall_texture: @@ -19055,14 +19902,14 @@ slots: description: The feel, appearance, or consistency of a wall surface title: wall texture examples: - - value: popcorn + - value: popcorn from_schema: https://example.com/nmdc_submission_schema aliases: - - wall texture + - wall texture is_a: core field slot_uri: MIXS:0000846 domain_of: - - Biosample + - Biosample range: wall_texture_enum multivalued: false wall_thermal_mass: @@ -19077,17 +19924,19 @@ slots: 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 + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - wall thermal mass + - wall thermal mass is_a: core field slot_uri: MIXS:0000222 domain_of: - - Biosample + - Biosample range: string multivalued: false wall_water_mold: @@ -19102,15 +19951,15 @@ slots: 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 + - value: no presence of mold visible from_schema: https://example.com/nmdc_submission_schema aliases: - - wall signs of water/mold + - wall signs of water/mold is_a: core field string_serialization: '[presence of mold visible|no presence of mold visible]' slot_uri: MIXS:0000844 domain_of: - - Biosample + - Biosample range: string multivalued: false wastewater_type: @@ -19122,18 +19971,19 @@ slots: occurrence: tag: occurrence value: '1' - description: The origin of wastewater such as human waste, rainfall, storm drains, etc. + description: The origin of wastewater such as human waste, rainfall, storm drains, + etc. title: wastewater type examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - wastewater type + - wastewater type is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000353 domain_of: - - Biosample + - Biosample range: string multivalued: false water_cont_soil_meth: @@ -19148,15 +19998,15 @@ slots: description: Reference or method used in determining the water content of soil title: water content method examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - water content method + - water content method is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000323 domain_of: - - Biosample + - Biosample range: string multivalued: false water_content: @@ -19174,14 +20024,14 @@ slots: description: Water content measurement title: water content examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - water content + - water content is_a: core field slot_uri: MIXS:0000185 domain_of: - - Biosample + - Biosample range: string multivalued: false water_current: @@ -19199,14 +20049,14 @@ slots: description: Measurement of magnitude and direction of flow within a fluid title: water current examples: - - value: 10 cubic meter per second + - value: 10 cubic meter per second from_schema: https://example.com/nmdc_submission_schema aliases: - - water current + - water current is_a: core field slot_uri: MIXS:0000203 domain_of: - - Biosample + - Biosample range: string multivalued: false water_cut: @@ -19221,17 +20071,18 @@ slots: occurrence: tag: occurrence value: '1' - description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams + description: Current amount of water (%) in a produced fluid stream; or the average + of the combined streams title: water cut examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - water cut + - water cut is_a: core field slot_uri: MIXS:0000454 domain_of: - - Biosample + - Biosample range: string multivalued: false water_feat_size: @@ -19249,14 +20100,14 @@ slots: description: The size of the water feature title: water feature size examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - water feature size + - water feature size is_a: core field slot_uri: MIXS:0000223 domain_of: - - Biosample + - Biosample range: string multivalued: false water_feat_type: @@ -19271,14 +20122,14 @@ slots: description: The type of water feature present within the building being sampled title: water feature type examples: - - value: stream + - value: stream from_schema: https://example.com/nmdc_submission_schema aliases: - - water feature type + - water feature type is_a: core field slot_uri: MIXS:0000847 domain_of: - - Biosample + - Biosample range: water_feat_type_enum multivalued: false water_prod_rate: @@ -19296,14 +20147,14 @@ slots: description: Water production rates per well (e.g. 987 m3 / day) title: water production rate examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - water production rate + - water production rate is_a: core field slot_uri: MIXS:0000453 domain_of: - - Biosample + - Biosample range: string multivalued: false water_temp_regm: @@ -19318,18 +20169,21 @@ slots: 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 + 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 + - 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 + - water temperature regimen is_a: core field string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000590 domain_of: - - Biosample + - Biosample range: string multivalued: false watering_regm: @@ -19344,18 +20198,21 @@ slots: 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 + 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: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://example.com/nmdc_submission_schema aliases: - - watering regimen + - watering regimen is_a: core field string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000591 domain_of: - - Biosample + - Biosample range: string multivalued: false weekday: @@ -19370,14 +20227,14 @@ slots: description: The day of the week when sampling occurred title: weekday examples: - - value: Sunday + - value: Sunday from_schema: https://example.com/nmdc_submission_schema aliases: - - weekday + - weekday is_a: core field slot_uri: MIXS:0000848 domain_of: - - Biosample + - Biosample range: weekday_enum multivalued: false win: @@ -19389,18 +20246,21 @@ slots: 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)' + 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: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - well identification number + - well identification number is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000297 domain_of: - - Biosample + - Biosample range: string multivalued: false wind_direction: @@ -19415,15 +20275,15 @@ slots: description: Wind direction is the direction from which a wind originates title: wind direction examples: - - value: Northwest + - value: Northwest from_schema: https://example.com/nmdc_submission_schema aliases: - - wind direction + - wind direction is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000757 domain_of: - - Biosample + - Biosample range: string multivalued: false wind_speed: @@ -19441,14 +20301,14 @@ slots: description: Speed of wind measured at the time of sampling title: wind speed examples: - - value: 21 kilometer per hour + - value: 21 kilometer per hour from_schema: https://example.com/nmdc_submission_schema aliases: - - wind speed + - wind speed is_a: core field slot_uri: MIXS:0000118 domain_of: - - Biosample + - Biosample range: string multivalued: false window_cond: @@ -19463,14 +20323,14 @@ slots: description: The physical condition of the window at the time of sampling title: window condition examples: - - value: rupture + - value: rupture from_schema: https://example.com/nmdc_submission_schema aliases: - - window condition + - window condition is_a: core field slot_uri: MIXS:0000849 domain_of: - - Biosample + - Biosample range: window_cond_enum multivalued: false window_cover: @@ -19485,14 +20345,14 @@ slots: description: The type of window covering title: window covering examples: - - value: curtains + - value: curtains from_schema: https://example.com/nmdc_submission_schema aliases: - - window covering + - window covering is_a: core field slot_uri: MIXS:0000850 domain_of: - - Biosample + - Biosample range: window_cover_enum multivalued: false window_horiz_pos: @@ -19507,14 +20367,14 @@ slots: description: The horizontal position of the window on the wall title: window horizontal position examples: - - value: middle + - value: middle from_schema: https://example.com/nmdc_submission_schema aliases: - - window horizontal position + - window horizontal position is_a: core field slot_uri: MIXS:0000851 domain_of: - - Biosample + - Biosample range: window_horiz_pos_enum multivalued: false window_loc: @@ -19529,14 +20389,14 @@ slots: description: The relative location of the window within the room title: window location examples: - - value: west + - value: west from_schema: https://example.com/nmdc_submission_schema aliases: - - window location + - window location is_a: core field slot_uri: MIXS:0000852 domain_of: - - Biosample + - Biosample range: window_loc_enum multivalued: false window_mat: @@ -19551,14 +20411,14 @@ slots: description: The type of material used to finish a window title: window material examples: - - value: wood + - value: wood from_schema: https://example.com/nmdc_submission_schema aliases: - - window material + - window material is_a: core field slot_uri: MIXS:0000853 domain_of: - - Biosample + - Biosample range: window_mat_enum multivalued: false window_open_freq: @@ -19573,14 +20433,14 @@ slots: description: The number of times windows are opened per week title: window open frequency examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - window open frequency + - window open frequency is_a: core field slot_uri: MIXS:0000246 domain_of: - - Biosample + - Biosample range: string multivalued: false window_size: @@ -19598,15 +20458,15 @@ slots: description: The window's length and width title: window area/size examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - window area/size + - window area/size is_a: core field string_serialization: '{float} {unit} x {float} {unit}' slot_uri: MIXS:0000224 domain_of: - - Biosample + - Biosample range: string multivalued: false window_status: @@ -19618,18 +20478,19 @@ slots: occurrence: tag: occurrence value: '1' - description: Defines whether the windows were open or closed during environmental testing + description: Defines whether the windows were open or closed during environmental + testing title: window status examples: - - value: open + - value: open from_schema: https://example.com/nmdc_submission_schema aliases: - - window status + - window status is_a: core field string_serialization: '[closed|open]' slot_uri: MIXS:0000855 domain_of: - - Biosample + - Biosample range: string multivalued: false window_type: @@ -19644,14 +20505,14 @@ slots: description: The type of windows title: window type examples: - - value: fixed window + - value: fixed window from_schema: https://example.com/nmdc_submission_schema aliases: - - window type + - window type is_a: core field slot_uri: MIXS:0000856 domain_of: - - Biosample + - Biosample range: window_type_enum multivalued: false window_vert_pos: @@ -19666,14 +20527,14 @@ slots: description: The vertical position of the window on the wall title: window vertical position examples: - - value: middle + - value: middle from_schema: https://example.com/nmdc_submission_schema aliases: - - window vertical position + - window vertical position is_a: core field slot_uri: MIXS:0000857 domain_of: - - Biosample + - Biosample range: window_vert_pos_enum multivalued: false window_water_mold: @@ -19688,15 +20549,15 @@ slots: 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 + - value: no presence of mold visible from_schema: https://example.com/nmdc_submission_schema aliases: - - window signs of water/mold + - window signs of water/mold is_a: core field string_serialization: '[presence of mold visible|no presence of mold visible]' slot_uri: MIXS:0000854 domain_of: - - Biosample + - Biosample range: string multivalued: false xylene: @@ -19714,14 +20575,14 @@ slots: description: Concentration of xylene in the sample title: xylene examples: - - value: '' + - value: '' from_schema: https://example.com/nmdc_submission_schema aliases: - - xylene + - xylene is_a: core field slot_uri: MIXS:0000156 domain_of: - - Biosample + - Biosample range: string multivalued: false zinc: @@ -19739,14 +20600,14 @@ slots: description: Concentration of zinc in the sample title: zinc examples: - - value: 2.5 mg/kg + - value: 2.5 mg/kg from_schema: https://example.com/nmdc_submission_schema see_also: - - https://www.ornl.gov/content/bio-scales-0 + - https://www.ornl.gov/content/bio-scales-0 aliases: - - zinc + - zinc domain_of: - - Biosample + - Biosample range: string multivalued: false alternative_identifiers: @@ -19754,8 +20615,8 @@ slots: description: A list of alternative identifiers for the entity. from_schema: https://example.com/nmdc_submission_schema domain_of: - - MetaboliteIdentification - - NamedThing + - MetaboliteIdentification + - NamedThing range: uriorcurie multivalued: true pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$ @@ -19765,15 +20626,15 @@ slots: from_schema: https://example.com/nmdc_submission_schema abstract: true domain_of: - - Biosample + - Biosample description: name: description description: a human-readable description of a thing from_schema: https://example.com/nmdc_submission_schema slot_uri: dcterms:description domain_of: - - ImageValue - - NamedThing + - ImageValue + - NamedThing range: string multivalued: false environment field: @@ -19782,13 +20643,14 @@ slots: from_schema: https://example.com/nmdc_submission_schema abstract: true domain_of: - - Biosample + - Biosample gold_path_field: name: gold_path_field annotations: tooltip: tag: tooltip - value: GOLD Ecosystem Classification paths describe the surroundings from which an environmental sample or an organism is collected. + value: GOLD Ecosystem Classification paths describe the surroundings from + which an environmental sample or an organism is collected. annotations: source: tag: source @@ -19800,44 +20662,49 @@ slots: multivalued: false id: name: id - description: A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI + 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 + - '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 + - 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 domain_of: - - NamedThing + - NamedThing range: uriorcurie required: true 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 + description: field describing aspect of the investigation/study to which the sample + belongs from_schema: https://example.com/nmdc_submission_schema abstract: true domain_of: - - Biosample + - Biosample language: name: language description: Should use ISO 639-1 code e.g. "en", "fr" from_schema: https://example.com/nmdc_submission_schema domain_of: - - TextValue + - TextValue range: language code name: name: name description: A human readable label for an entity from_schema: https://example.com/nmdc_submission_schema domain_of: - - PersonValue - - NamedThing - - Protocol + - PersonValue + - NamedThing + - Protocol range: string multivalued: false nucleic acid sequence source field: @@ -19845,41 +20712,41 @@ slots: from_schema: https://example.com/nmdc_submission_schema abstract: true domain_of: - - Biosample + - Biosample type: name: type description: the class_uri of the class that has been instantiated notes: - - replaces legacy nmdc:type slot - - makes it easier to read example data files - - required for polymorphic MongoDB collections + - replaces legacy nmdc:type slot + - makes it easier to read example data files + - required for polymorphic MongoDB collections examples: - - value: nmdc:Biosample - - value: nmdc:Study + - value: nmdc:Biosample + - value: nmdc:Study from_schema: https://example.com/nmdc_submission_schema see_also: - - https://github.com/microbiomedata/nmdc-schema/issues/1048 - - https://github.com/microbiomedata/nmdc-schema/issues/1233 - - https://github.com/microbiomedata/nmdc-schema/issues/248 + - https://github.com/microbiomedata/nmdc-schema/issues/1048 + - https://github.com/microbiomedata/nmdc-schema/issues/1233 + - https://github.com/microbiomedata/nmdc-schema/issues/248 slot_uri: rdf:type designates_type: true domain_of: - - EukEval - - FunctionalAnnotationAggMember - - MobilePhaseSegment - - PortionOfSubstance - - MagBin - - MetaboliteIdentification - - PeptideQuantification - - ProteinQuantification - - GenomeFeature - - FunctionalAnnotation - - AttributeValue - - NamedThing - - FailureCategorization - - Protocol - - CreditAssociation - - Doi + - EukEval + - FunctionalAnnotationAggMember + - MobilePhaseSegment + - PortionOfSubstance + - MagBin + - MetaboliteIdentification + - PeptideQuantification + - ProteinQuantification + - GenomeFeature + - FunctionalAnnotation + - AttributeValue + - NamedThing + - FailureCategorization + - Protocol + - CreditAssociation + - Doi range: uriorcurie required: true biomaterial_purity: @@ -19899,54 +20766,54 @@ classes: from_schema: https://example.com/nmdc_submission_schema is_a: DhInterface mixins: - - DhMultiviewCommonColumnsMixin - - SampIdNewTermsMixin + - 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 - - 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 + - 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 + - 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 slot_usage: air_PM_concen: name: air_PM_concen @@ -19960,67 +20827,76 @@ classes: 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 + 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 + - value: PM2.5;10 microgram per cubic meter from_schema: https://w3id.org/nmdc/nmdc aliases: - - air particulate matter concentration + - air particulate matter concentration rank: 48 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000108 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false - 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]+)$ + 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 + 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 + - value: 100 meter from_schema: https://w3id.org/nmdc/nmdc aliases: - - altitude + - altitude rank: 26 is_a: environment field slot_uri: MIXS:0000094 owner: Biosample domain_of: - - agriculture - - air - - built environment - - core - - food-animal and animal feed - - food-farm environment - - food-food production facility - - food-human foods - - host-associated - - human-associated - - human-gut - - human-oral - - human-skin - - human-vaginal - - hydrocarbon resources-cores - - hydrocarbon resources-fluids_swabs - - microbial mat_biofilm - - miscellaneous natural or artificial environment - - plant-associated - - sediment - - soil - - symbiont-associated - - wastewater_sludge - - water - - Biosample + - agriculture + - air + - built environment + - core + - food-animal and animal feed + - food-farm environment + - food-food production facility + - food-human foods + - host-associated + - human-associated + - human-gut + - human-oral + - human-skin + - human-vaginal + - hydrocarbon resources-cores + - hydrocarbon resources-fluids_swabs + - microbial mat_biofilm + - miscellaneous natural or artificial environment + - plant-associated + - sediment + - soil + - symbiont-associated + - wastewater_sludge + - water + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -20038,19 +20914,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Force per unit area exerted against a surface by the weight of air above that surface + description: Force per unit area exerted against a surface by the weight of + air above that surface title: barometric pressure examples: - - value: 5 millibar + - value: 5 millibar from_schema: https://w3id.org/nmdc/nmdc aliases: - - barometric pressure + - barometric pressure rank: 49 is_a: core field slot_uri: MIXS:0000096 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -20070,16 +20947,16 @@ classes: description: Carbon dioxide (gas) amount or concentration at the time of sampling title: carbon dioxide examples: - - value: 410 parts per million + - value: 410 parts per million from_schema: https://w3id.org/nmdc/nmdc aliases: - - carbon dioxide + - carbon dioxide rank: 50 is_a: core field slot_uri: MIXS:0000097 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -20096,19 +20973,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Carbon monoxide (gas) amount or concentration at the time of sampling + description: Carbon monoxide (gas) amount or concentration at the time of + sampling title: carbon monoxide examples: - - value: 0.1 parts per million + - value: 0.1 parts per million from_schema: https://w3id.org/nmdc/nmdc aliases: - - carbon monoxide + - carbon monoxide rank: 51 is_a: core field slot_uri: MIXS:0000098 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -20122,21 +21000,24 @@ classes: 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 + 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 + - 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 + - chemical administration rank: 17 is_a: core field string_serialization: '{termLabel} {[termID]};{timestamp}' slot_uri: MIXS:0000751 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -20151,22 +21032,23 @@ classes: 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) + - 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' + - value: '2021-04-15' + - value: 2021-04 + - value: '2021' from_schema: https://w3id.org/nmdc/nmdc aliases: - - collection date + - collection date rank: 3 is_a: environment field string_serialization: '{date, arbitrary precision}' slot_uri: MIXS:0000011 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string required: true @@ -20178,25 +21060,27 @@ classes: 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. + 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 + - Use modified term comments: - - All depths must be reported in meters. Provide the numerical portion only. + - All depths must be reported in meters. Provide the numerical portion only. examples: - - value: 0 - 0.1 - - value: '1' + - value: 0 - 0.1 + - value: '1' from_schema: https://w3id.org/nmdc/nmdc aliases: - - depth + - depth rank: 9 is_a: environment field string_serialization: '{float}|{float}-{float}' slot_uri: MIXS:0000018 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -20204,69 +21088,93 @@ classes: 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 9 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 10 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 12 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 11 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study slot_group: sample_id_section range: EcosystemTypeEnum recommended: true @@ -20276,25 +21184,31 @@ classes: 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. + 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. + - 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' + - value: '225' + - value: '0' + - value: '1250' from_schema: https://w3id.org/nmdc/nmdc aliases: - - elevation + - elevation rank: 6 is_a: environment field slot_uri: MIXS:0000093 owner: Biosample domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample slot_group: mixs_modified_section range: float required: true @@ -20304,26 +21218,44 @@ classes: 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. + 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. tooltip: tag: tooltip - value: The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context - 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' + value: The biome or major environmental system where the sample or specimen + originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] + in the Environment Ontology (ENVO). For host-associated or plant-associated + samples, use terms from the UBERON or Plant Ontology to describe the + broad anatomical or morphological context + 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) + - range changed to enumeration late in makefile, so this is modified (but + "sample ID" anyway) examples: - - value: oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean + - 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://w3id.org/nmdc/nmdc aliases: - - broad-scale environmental context + - broad-scale environmental context rank: 6 is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000012 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string required: true @@ -20334,30 +21266,45 @@ classes: annotations: expected_value: tag: expected_value - value: Environmental entities having causal influences upon the entity at time of sampling. + value: Environmental entities having causal influences upon the entity + at time of sampling. tooltip: tag: tooltip - value: The specific environmental entities or features near the sample or specimen that significantly influence its characteristics or composition. These entities are typically smaller in scale than the broad environmental context. Values for this field should be countable, material nouns and must be chosen from subclasses of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe specific anatomical structures or plant parts. - 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.' + value: The specific environmental entities or features near the sample + or specimen that significantly influence its characteristics or composition. + These entities are typically smaller in scale than the broad environmental + context. Values for this field should be countable, material nouns and + must be chosen from subclasses of BFO:0000040 (material entity) that + appear in the Environment Ontology (ENVO). For host-associated or plant-associated + samples, use terms from the UBERON or Plant Ontology to describe specific + anatomical structures or plant parts. + 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) + - 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] + - 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 aliases: - - local environmental context + - local environmental context rank: 7 is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000013 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string required: true @@ -20368,26 +21315,41 @@ classes: annotations: expected_value: tag: expected_value - value: The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]. + value: The material displaced by the entity at time of sampling. Recommend + subclasses of environmental material [ENVO:00010483]. tooltip: tag: tooltip - value: The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure - 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).' + value: The predominant environmental material or substrate that directly + surrounds or hosts the sample or specimen at the time of sampling. Choose + values from subclasses of the 'environmental material' class [ENVO:00010483] + in the Environment Ontology (ENVO). Values for this field should be + measurable or mass material nouns, representing continuous environmental + materials. For host-associated or plant-associated samples, use terms + from the UBERON or Plant Ontology to indicate a tissue, organ, or plant + structure + 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) + - range changed to enumeration late in makefile, so this is modified (but + "sample ID" anyway) examples: - - value: soil [ENVO:00001998] + - value: soil [ENVO:00001998] from_schema: https://w3id.org/nmdc/nmdc aliases: - - environmental medium + - environmental medium rank: 8 is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000014 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string required: true @@ -20399,20 +21361,25 @@ classes: 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 + 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] + - value: time series design [EFO:EFO_0001779] from_schema: https://w3id.org/nmdc/nmdc aliases: - - experimental factor + - experimental factor rank: 12 is_a: investigation field string_serialization: '{termLabel} {[termID]}|{text}' slot_uri: MIXS:0000008 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -20421,22 +21388,24 @@ classes: 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. + 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' + - value: 'USA: Maryland, Bethesda' from_schema: https://w3id.org/nmdc/nmdc aliases: - - geographic location (country and/or sea,region) + - geographic location (country and/or sea,region) rank: 4 is_a: environment field string_serialization: '{text}: {text}, {text}' slot_uri: MIXS:0000010 owner: Biosample domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample slot_group: mixs_modified_section range: string required: true @@ -20457,16 +21426,16 @@ classes: description: Amount of water vapour in the air, at the time of sampling title: humidity examples: - - value: 25 gram per cubic meter + - value: 25 gram per cubic meter from_schema: https://w3id.org/nmdc/nmdc aliases: - - humidity + - humidity rank: 52 is_a: core field slot_uri: MIXS:0000100 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -20477,23 +21446,26 @@ classes: 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 + 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) notes: - - This is currently a required field but it's not clear if this should be required for human hosts + - This is currently a required field but it's not clear if this should be + required for human hosts examples: - - value: 50.586825 6.408977 + - value: 50.586825 6.408977 from_schema: https://w3id.org/nmdc/nmdc aliases: - - geographic location (latitude and longitude) + - geographic location (latitude and longitude) rank: 5 is_a: environment field string_serialization: '{lat lon}' slot_uri: MIXS:0000009 owner: Biosample domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample slot_group: mixs_modified_section range: string required: true @@ -20514,16 +21486,16 @@ classes: description: Methane (gas) amount or concentration at the time of sampling title: methane examples: - - value: 1800 parts per billion + - value: 1800 parts per billion from_schema: https://w3id.org/nmdc/nmdc aliases: - - methane + - methane rank: 24 is_a: core field slot_uri: MIXS:0000101 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -20537,24 +21509,26 @@ classes: occurrence: tag: occurrence value: m - description: Any other measurement performed or parameter collected, that is not listed here + 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 + - value: Bicarbonate ion concentration;2075 micromole per kilogram from_schema: https://w3id.org/nmdc/nmdc aliases: - - miscellaneous parameter + - miscellaneous parameter rank: 23 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000752 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false - 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]+)$ + 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: @@ -20563,23 +21537,28 @@ classes: 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 + 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)' + 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 + - value: total prokaryotes;3.5e7 cells per milliliter;qPCR from_schema: https://w3id.org/nmdc/nmdc aliases: - - organism count + - organism count rank: 30 is_a: core field slot_uri: MIXS:0000103 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -20596,16 +21575,16 @@ classes: description: Oxygenation status of sample title: oxygenation status of sample examples: - - value: aerobic + - value: aerobic from_schema: https://w3id.org/nmdc/nmdc aliases: - - oxygenation status of sample + - oxygenation status of sample rank: 25 is_a: core field slot_uri: MIXS:0000753 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: OxyStatSampEnum multivalued: false @@ -20624,16 +21603,16 @@ classes: description: Oxygen (gas) amount or concentration at the time of sampling title: oxygen examples: - - value: 600 parts per million + - value: 600 parts per million from_schema: https://w3id.org/nmdc/nmdc aliases: - - oxygen + - oxygen rank: 53 is_a: core field slot_uri: MIXS:0000104 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -20647,20 +21626,24 @@ classes: 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 + 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 + - value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - - perturbation + - perturbation rank: 33 is_a: core field string_serialization: '{text};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000754 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -20672,28 +21655,32 @@ classes: value: pollutant name;measurement value preferred_unit: tag: preferred_unit - value: gram, mole per liter, milligram per liter, microgram per cubic meter + 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 + 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 + - value: lead;0.15 microgram per cubic meter from_schema: https://w3id.org/nmdc/nmdc aliases: - - pollutants + - pollutants rank: 54 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000107 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false - 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]+)$ + 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: @@ -20706,19 +21693,24 @@ classes: 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. + 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 + - value: 25 practical salinity unit from_schema: https://w3id.org/nmdc/nmdc aliases: - - salinity + - salinity rank: 54 is_a: core field slot_uri: MIXS:0000183 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -20729,22 +21721,24 @@ classes: 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). + 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 + - Report dimensions and details when applicable examples: - - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample collection device + - sample collection device rank: 14 is_a: nucleic acid sequence source field string_serialization: '{termLabel} {[termID]}|{text}' slot_uri: MIXS:0000002 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -20758,19 +21752,19 @@ classes: description: The method employed for collecting the sample. title: sample collection method comments: - - This can be a citation or description + - This can be a citation or description examples: - - value: swabbing + - value: swabbing from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample collection method + - sample collection method rank: 15 is_a: nucleic acid sequence source field string_serialization: '{PMID}|{DOI}|{URL}|{text}' slot_uri: MIXS:0001225 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -20780,21 +21774,23 @@ classes: 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. + 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 + - value: filtering of seawater + - value: storing samples in ethanol from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample material processing + - sample material processing rank: 12 is_a: nucleic acid sequence source field string_serialization: '{text}' slot_uri: MIXS:0000016 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -20807,23 +21803,25 @@ classes: 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. + 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. + - 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 + - value: 5 grams + - value: 10 mL from_schema: https://w3id.org/nmdc/nmdc aliases: - - amount or size of sample collected + - amount or size of sample collected rank: 18 is_a: nucleic acid sequence source field string_serialization: '{float} {unit}' slot_uri: MIXS:0000001 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -20840,17 +21838,17 @@ classes: description: Duration for which the sample was stored title: sample storage duration examples: - - value: P1Y6M + - value: P1Y6M from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample storage duration + - sample storage duration rank: 353 is_a: core field string_serialization: '{duration}' slot_uri: MIXS:0000116 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -20863,20 +21861,21 @@ classes: occurrence: tag: occurrence value: '1' - description: Location at which sample was stored, usually name of a specific freezer/room + description: Location at which sample was stored, usually name of a specific + freezer/room title: sample storage location examples: - - value: Freezer no:5 + - value: Freezer no:5 from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample storage location + - sample storage location rank: 41 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000755 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -20895,16 +21894,16 @@ classes: description: Temperature at which the sample was stored (degrees are assumed) title: sample storage temperature examples: - - value: -80 Celsius + - value: -80 Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample storage temperature + - sample storage temperature rank: 7 is_a: core field slot_uri: MIXS:0000110 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string required: true @@ -20912,20 +21911,27 @@ classes: 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. + 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''' + - '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)' + - '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 + - value: IGSN:DSJ0284 from_schema: https://w3id.org/nmdc/nmdc rank: 5 string_serialization: '{text}:{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string recommended: true @@ -20940,17 +21946,17 @@ classes: description: Filtering pore size used in sample preparation title: size fraction selected examples: - - value: 0-0.22 micrometer + - value: 0-0.22 micrometer from_schema: https://w3id.org/nmdc/nmdc aliases: - - size fraction selected + - size fraction selected rank: 285 is_a: nucleic acid sequence source field string_serialization: '{float}-{float} {unit}' slot_uri: MIXS:0000017 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -20962,41 +21968,46 @@ classes: value: measurement value preferred_unit: tag: preferred_unit - value: kilowatts per square meter per day, ergs per square centimeter per second + 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 + 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 + - value: 1.36 kilowatts per square meter per day from_schema: https://w3id.org/nmdc/nmdc aliases: - - solar irradiance + - solar irradiance rank: 55 is_a: core field slot_uri: MIXS:0000112 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 13 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study slot_group: sample_id_section range: SpecificEcosystemEnum recommended: true @@ -21012,16 +22023,16 @@ classes: description: Temperature of the sample at the time of sampling. title: temperature examples: - - value: 25 degree Celsius + - value: 25 degree Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - - temperature + - temperature rank: 37 is_a: environment field slot_uri: MIXS:0000113 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -21041,16 +22052,16 @@ classes: description: Ventilation rate of the system in the sampled premises title: ventilation rate examples: - - value: 750 cubic meter per minute + - value: 750 cubic meter per minute from_schema: https://w3id.org/nmdc/nmdc aliases: - - ventilation rate + - ventilation rate rank: 56 is_a: core field slot_uri: MIXS:0000114 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -21067,17 +22078,17 @@ classes: description: Ventilation system used in the sampled premises title: ventilation type examples: - - value: Operable windows + - value: Operable windows from_schema: https://w3id.org/nmdc/nmdc aliases: - - ventilation type + - ventilation type rank: 57 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000756 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -21093,24 +22104,27 @@ classes: 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 + 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 + - value: formaldehyde;500 nanogram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - volatile organic compounds + - volatile organic compounds rank: 58 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000115 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false - 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]+)$ + 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: @@ -21123,17 +22137,17 @@ classes: description: Wind direction is the direction from which a wind originates title: wind direction examples: - - value: Northwest + - value: Northwest from_schema: https://w3id.org/nmdc/nmdc aliases: - - wind direction + - wind direction rank: 59 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000757 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -21152,16 +22166,16 @@ classes: description: Speed of wind measured at the time of sampling title: wind speed examples: - - value: 21 kilometer per hour + - value: 21 kilometer per hour from_schema: https://w3id.org/nmdc/nmdc aliases: - - wind speed + - wind speed rank: 60 is_a: core field slot_uri: MIXS:0000118 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -21180,90 +22194,90 @@ classes: from_schema: https://example.com/nmdc_submission_schema is_a: DhInterface mixins: - - DhMultiviewCommonColumnsMixin - - SampIdNewTermsMixin + - 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 - - 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 + - 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 + - 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 slot_usage: alkalinity: name: alkalinity @@ -21277,19 +22291,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + 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 + - value: 50 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - alkalinity + - alkalinity rank: 1 is_a: core field slot_uri: MIXS:0000421 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -21309,16 +22324,16 @@ classes: description: Concentration of alkyl diethers title: alkyl diethers examples: - - value: 0.005 mole per liter + - value: 0.005 mole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - alkyl diethers + - alkyl diethers rank: 2 is_a: core field slot_uri: MIXS:0000490 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -21329,43 +22344,48 @@ classes: 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 + 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 + - value: 100 meter from_schema: https://w3id.org/nmdc/nmdc aliases: - - altitude + - altitude rank: 26 is_a: environment field slot_uri: MIXS:0000094 owner: Biosample domain_of: - - agriculture - - air - - built environment - - core - - food-animal and animal feed - - food-farm environment - - food-food production facility - - food-human foods - - host-associated - - human-associated - - human-gut - - human-oral - - human-skin - - human-vaginal - - hydrocarbon resources-cores - - hydrocarbon resources-fluids_swabs - - microbial mat_biofilm - - miscellaneous natural or artificial environment - - plant-associated - - sediment - - soil - - symbiont-associated - - wastewater_sludge - - water - - Biosample + - agriculture + - air + - built environment + - core + - food-animal and animal feed + - food-farm environment + - food-food production facility + - food-human foods + - host-associated + - human-associated + - human-gut + - human-oral + - human-skin + - human-vaginal + - hydrocarbon resources-cores + - hydrocarbon resources-fluids_swabs + - microbial mat_biofilm + - miscellaneous natural or artificial environment + - plant-associated + - sediment + - soil + - symbiont-associated + - wastewater_sludge + - water + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -21386,16 +22406,16 @@ classes: description: Measurement of aminopeptidase activity title: aminopeptidase activity examples: - - value: 0.269 mole per liter per hour + - value: 0.269 mole per liter per hour from_schema: https://w3id.org/nmdc/nmdc aliases: - - aminopeptidase activity + - aminopeptidase activity rank: 3 is_a: core field slot_uri: MIXS:0000172 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -21415,16 +22435,16 @@ classes: description: Concentration of ammonium in the sample title: ammonium examples: - - value: 1.5 milligram per liter + - value: 1.5 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - ammonium + - ammonium rank: 4 is_a: core field slot_uri: MIXS:0000427 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -21444,16 +22464,16 @@ classes: description: Measurement of bacterial carbon production title: bacterial carbon production examples: - - value: 2.53 microgram per liter per hour + - value: 2.53 microgram per liter per hour from_schema: https://w3id.org/nmdc/nmdc aliases: - - bacterial carbon production + - bacterial carbon production rank: 5 is_a: core field slot_uri: MIXS:0000173 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -21470,24 +22490,26 @@ classes: 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 + 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 + - value: total;20 gram from_schema: https://w3id.org/nmdc/nmdc aliases: - - biomass + - biomass rank: 6 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000174 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false - 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]+)$ + 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: @@ -21503,16 +22525,16 @@ classes: description: Concentration of bishomohopanol title: bishomohopanol examples: - - value: 14 microgram per liter + - value: 14 microgram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - bishomohopanol + - bishomohopanol rank: 7 is_a: core field slot_uri: MIXS:0000175 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -21532,16 +22554,16 @@ classes: description: Concentration of bromide title: bromide examples: - - value: 0.05 parts per million + - value: 0.05 parts per million from_schema: https://w3id.org/nmdc/nmdc aliases: - - bromide + - bromide rank: 8 is_a: core field slot_uri: MIXS:0000176 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -21561,16 +22583,16 @@ classes: description: Concentration of calcium in the sample title: calcium examples: - - value: 0.2 micromole per liter + - value: 0.2 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - calcium + - calcium rank: 9 is_a: core field slot_uri: MIXS:0000432 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -21587,16 +22609,16 @@ classes: description: Ratio of amount or concentrations of carbon to nitrogen title: carbon/nitrogen ratio examples: - - value: '0.417361111' + - value: '0.417361111' from_schema: https://w3id.org/nmdc/nmdc aliases: - - carbon/nitrogen ratio + - carbon/nitrogen ratio rank: 44 is_a: core field slot_uri: MIXS:0000310 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: float multivalued: false @@ -21610,21 +22632,24 @@ classes: 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 + 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 + - 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 + - chemical administration rank: 17 is_a: core field string_serialization: '{termLabel} {[termID]};{timestamp}' slot_uri: MIXS:0000751 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -21645,16 +22670,16 @@ classes: description: Concentration of chloride in the sample title: chloride examples: - - value: 5000 milligram per liter + - value: 5000 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - chloride + - chloride rank: 10 is_a: core field slot_uri: MIXS:0000429 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -21674,16 +22699,16 @@ classes: description: Concentration of chlorophyll title: chlorophyll examples: - - value: 5 milligram per cubic meter + - value: 5 milligram per cubic meter from_schema: https://w3id.org/nmdc/nmdc aliases: - - chlorophyll + - chlorophyll rank: 11 is_a: core field slot_uri: MIXS:0000177 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -21697,22 +22722,23 @@ classes: 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) + - 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' + - value: '2021-04-15' + - value: 2021-04 + - value: '2021' from_schema: https://w3id.org/nmdc/nmdc aliases: - - collection date + - collection date rank: 3 is_a: environment field string_serialization: '{date, arbitrary precision}' slot_uri: MIXS:0000011 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string required: true @@ -21724,25 +22750,27 @@ classes: 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. + 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 + - Use modified term comments: - - All depths must be reported in meters. Provide the numerical portion only. + - All depths must be reported in meters. Provide the numerical portion only. examples: - - value: 0 - 0.1 - - value: '1' + - value: 0 - 0.1 + - value: '1' from_schema: https://w3id.org/nmdc/nmdc aliases: - - depth + - depth rank: 9 is_a: environment field string_serialization: '{float}|{float}-{float}' slot_uri: MIXS:0000018 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -21760,24 +22788,26 @@ classes: occurrence: tag: occurrence value: m - description: Concentration of diether lipids; can include multiple types of diether lipids + description: Concentration of diether lipids; can include multiple types of + diether lipids title: diether lipids examples: - - value: 0.2 nanogram per liter + - value: 0.2 nanogram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - diether lipids + - diether lipids rank: 13 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000178 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false - 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]+)$ + 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: @@ -21790,19 +22820,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + 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 + - value: 5 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - dissolved carbon dioxide + - dissolved carbon dioxide rank: 14 is_a: core field slot_uri: MIXS:0000436 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -21822,16 +22853,16 @@ classes: description: Concentration of dissolved hydrogen title: dissolved hydrogen examples: - - value: 0.3 micromole per liter + - value: 0.3 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - dissolved hydrogen + - dissolved hydrogen rank: 15 is_a: core field slot_uri: MIXS:0000179 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -21848,19 +22879,20 @@ classes: 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 + 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 + - value: 2059 micromole per kilogram from_schema: https://w3id.org/nmdc/nmdc aliases: - - dissolved inorganic carbon + - dissolved inorganic carbon rank: 16 is_a: core field slot_uri: MIXS:0000434 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -21877,19 +22909,20 @@ classes: 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 + 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 + - value: 197 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - dissolved organic carbon + - dissolved organic carbon rank: 17 is_a: core field slot_uri: MIXS:0000433 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -21906,19 +22939,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + description: Dissolved organic nitrogen concentration measured as; total dissolved + nitrogen - NH4 - NO3 - NO2 title: dissolved organic nitrogen examples: - - value: 0.05 micromole per liter + - value: 0.05 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - dissolved organic nitrogen + - dissolved organic nitrogen rank: 18 is_a: core field slot_uri: MIXS:0000162 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -21938,85 +22972,109 @@ classes: description: Concentration of dissolved oxygen title: dissolved oxygen examples: - - value: 175 micromole per kilogram + - value: 175 micromole per kilogram from_schema: https://w3id.org/nmdc/nmdc aliases: - - dissolved oxygen + - dissolved oxygen rank: 19 is_a: core field slot_uri: MIXS:0000119 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 9 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 10 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 12 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 11 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study slot_group: sample_id_section range: EcosystemTypeEnum recommended: true @@ -22026,25 +23084,31 @@ classes: 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. + 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. + - 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' + - value: '225' + - value: '0' + - value: '1250' from_schema: https://w3id.org/nmdc/nmdc aliases: - - elevation + - elevation rank: 6 is_a: environment field slot_uri: MIXS:0000093 owner: Biosample domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample slot_group: mixs_modified_section range: float required: true @@ -22054,26 +23118,44 @@ classes: 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. + 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. tooltip: tag: tooltip - value: The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context - 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' + value: The biome or major environmental system where the sample or specimen + originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] + in the Environment Ontology (ENVO). For host-associated or plant-associated + samples, use terms from the UBERON or Plant Ontology to describe the + broad anatomical or morphological context + 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) + - range changed to enumeration late in makefile, so this is modified (but + "sample ID" anyway) examples: - - value: oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean + - 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://w3id.org/nmdc/nmdc aliases: - - broad-scale environmental context + - broad-scale environmental context rank: 6 is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000012 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string required: true @@ -22084,30 +23166,45 @@ classes: annotations: expected_value: tag: expected_value - value: Environmental entities having causal influences upon the entity at time of sampling. + value: Environmental entities having causal influences upon the entity + at time of sampling. tooltip: tag: tooltip - value: The specific environmental entities or features near the sample or specimen that significantly influence its characteristics or composition. These entities are typically smaller in scale than the broad environmental context. Values for this field should be countable, material nouns and must be chosen from subclasses of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe specific anatomical structures or plant parts. - 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.' + value: The specific environmental entities or features near the sample + or specimen that significantly influence its characteristics or composition. + These entities are typically smaller in scale than the broad environmental + context. Values for this field should be countable, material nouns and + must be chosen from subclasses of BFO:0000040 (material entity) that + appear in the Environment Ontology (ENVO). For host-associated or plant-associated + samples, use terms from the UBERON or Plant Ontology to describe specific + anatomical structures or plant parts. + 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) + - 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] + - 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 aliases: - - local environmental context + - local environmental context rank: 7 is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000013 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string required: true @@ -22118,26 +23215,41 @@ classes: annotations: expected_value: tag: expected_value - value: The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]. + value: The material displaced by the entity at time of sampling. Recommend + subclasses of environmental material [ENVO:00010483]. tooltip: tag: tooltip - value: The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure - 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).' + value: The predominant environmental material or substrate that directly + surrounds or hosts the sample or specimen at the time of sampling. Choose + values from subclasses of the 'environmental material' class [ENVO:00010483] + in the Environment Ontology (ENVO). Values for this field should be + measurable or mass material nouns, representing continuous environmental + materials. For host-associated or plant-associated samples, use terms + from the UBERON or Plant Ontology to indicate a tissue, organ, or plant + structure + 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) + - range changed to enumeration late in makefile, so this is modified (but + "sample ID" anyway) examples: - - value: soil [ENVO:00001998] + - value: soil [ENVO:00001998] from_schema: https://w3id.org/nmdc/nmdc aliases: - - environmental medium + - environmental medium rank: 8 is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000014 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string required: true @@ -22149,20 +23261,25 @@ classes: 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 + 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] + - value: time series design [EFO:EFO_0001779] from_schema: https://w3id.org/nmdc/nmdc aliases: - - experimental factor + - experimental factor rank: 12 is_a: investigation field string_serialization: '{termLabel} {[termID]}|{text}' slot_uri: MIXS:0000008 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -22171,22 +23288,24 @@ classes: 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. + 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' + - value: 'USA: Maryland, Bethesda' from_schema: https://w3id.org/nmdc/nmdc aliases: - - geographic location (country and/or sea,region) + - geographic location (country and/or sea,region) rank: 4 is_a: environment field string_serialization: '{text}: {text}, {text}' slot_uri: MIXS:0000010 owner: Biosample domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample slot_group: mixs_modified_section range: string required: true @@ -22207,16 +23326,16 @@ classes: description: Measurement of glucosidase activity title: glucosidase activity examples: - - value: 5 mol per liter per hour + - value: 5 mol per liter per hour from_schema: https://w3id.org/nmdc/nmdc aliases: - - glucosidase activity + - glucosidase activity rank: 20 is_a: core field slot_uri: MIXS:0000137 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -22227,23 +23346,26 @@ classes: 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 + 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) notes: - - This is currently a required field but it's not clear if this should be required for human hosts + - This is currently a required field but it's not clear if this should be + required for human hosts examples: - - value: 50.586825 6.408977 + - value: 50.586825 6.408977 from_schema: https://w3id.org/nmdc/nmdc aliases: - - geographic location (latitude and longitude) + - geographic location (latitude and longitude) rank: 5 is_a: environment field string_serialization: '{lat lon}' slot_uri: MIXS:0000009 owner: Biosample domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample slot_group: mixs_modified_section range: string required: true @@ -22257,23 +23379,24 @@ classes: value: measurement value preferred_unit: tag: preferred_unit - value: mole per liter, milligram per liter, parts per million, micromole per kilogram + 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 + - value: 52.8 micromole per kilogram from_schema: https://w3id.org/nmdc/nmdc aliases: - - magnesium + - magnesium rank: 21 is_a: core field slot_uri: MIXS:0000431 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -22293,16 +23416,16 @@ classes: description: Measurement of mean friction velocity title: mean friction velocity examples: - - value: 0.5 meter per second + - value: 0.5 meter per second from_schema: https://w3id.org/nmdc/nmdc aliases: - - mean friction velocity + - mean friction velocity rank: 22 is_a: core field slot_uri: MIXS:0000498 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -22322,16 +23445,16 @@ classes: description: Measurement of mean peak friction velocity title: mean peak friction velocity examples: - - value: 1 meter per second + - value: 1 meter per second from_schema: https://w3id.org/nmdc/nmdc aliases: - - mean peak friction velocity + - mean peak friction velocity rank: 23 is_a: core field slot_uri: MIXS:0000502 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -22351,16 +23474,16 @@ classes: description: Methane (gas) amount or concentration at the time of sampling title: methane examples: - - value: 1800 parts per billion + - value: 1800 parts per billion from_schema: https://w3id.org/nmdc/nmdc aliases: - - methane + - methane rank: 24 is_a: core field slot_uri: MIXS:0000101 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -22374,24 +23497,26 @@ classes: occurrence: tag: occurrence value: m - description: Any other measurement performed or parameter collected, that is not listed here + 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 + - value: Bicarbonate ion concentration;2075 micromole per kilogram from_schema: https://w3id.org/nmdc/nmdc aliases: - - miscellaneous parameter + - miscellaneous parameter rank: 23 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000752 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false - 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]+)$ + 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: @@ -22407,21 +23532,22 @@ classes: description: Concentration of n-alkanes; can include multiple n-alkanes title: n-alkanes examples: - - value: n-hexadecane;100 milligram per liter + - value: n-hexadecane;100 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - n-alkanes + - n-alkanes rank: 25 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000503 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false - 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]+)$ + 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: @@ -22437,16 +23563,16 @@ classes: description: Concentration of nitrate in the sample title: nitrate examples: - - value: 65 micromole per liter + - value: 65 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - nitrate + - nitrate rank: 26 is_a: core field slot_uri: MIXS:0000425 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -22466,16 +23592,16 @@ classes: description: Concentration of nitrite in the sample title: nitrite examples: - - value: 0.5 micromole per liter + - value: 0.5 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - nitrite + - nitrite rank: 27 is_a: core field slot_uri: MIXS:0000426 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -22495,16 +23621,16 @@ classes: description: Concentration of nitrogen (total) title: nitrogen examples: - - value: 4.2 micromole per liter + - value: 4.2 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - nitrogen + - nitrogen rank: 28 is_a: core field slot_uri: MIXS:0000504 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -22524,16 +23650,16 @@ classes: description: Concentration of organic carbon title: organic carbon examples: - - value: 1.5 microgram per liter + - value: 1.5 microgram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - organic carbon + - organic carbon rank: 29 is_a: core field slot_uri: MIXS:0000508 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -22553,16 +23679,16 @@ classes: description: Concentration of organic matter title: organic matter examples: - - value: 1.75 milligram per cubic meter + - value: 1.75 milligram per cubic meter from_schema: https://w3id.org/nmdc/nmdc aliases: - - organic matter + - organic matter rank: 45 is_a: core field slot_uri: MIXS:0000204 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -22582,16 +23708,16 @@ classes: description: Concentration of organic nitrogen title: organic nitrogen examples: - - value: 4 micromole per liter + - value: 4 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - organic nitrogen + - organic nitrogen rank: 46 is_a: core field slot_uri: MIXS:0000205 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -22604,23 +23730,28 @@ classes: 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 + 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)' + 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 + - value: total prokaryotes;3.5e7 cells per milliliter;qPCR from_schema: https://w3id.org/nmdc/nmdc aliases: - - organism count + - organism count rank: 30 is_a: core field slot_uri: MIXS:0000103 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -22637,16 +23768,16 @@ classes: description: Oxygenation status of sample title: oxygenation status of sample examples: - - value: aerobic + - value: aerobic from_schema: https://w3id.org/nmdc/nmdc aliases: - - oxygenation status of sample + - oxygenation status of sample rank: 25 is_a: core field slot_uri: MIXS:0000753 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: OxyStatSampEnum multivalued: false @@ -22665,16 +23796,16 @@ classes: description: Concentration of particulate organic carbon title: particulate organic carbon examples: - - value: 1.92 micromole per liter + - value: 1.92 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - particulate organic carbon + - particulate organic carbon rank: 31 is_a: core field slot_uri: MIXS:0000515 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -22688,20 +23819,24 @@ classes: 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 + 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 + - value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - - perturbation + - perturbation rank: 33 is_a: core field string_serialization: '{text};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000754 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -22720,16 +23855,16 @@ classes: description: Concentration of petroleum hydrocarbon title: petroleum hydrocarbon examples: - - value: 0.05 micromole per liter + - value: 0.05 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - petroleum hydrocarbon + - petroleum hydrocarbon rank: 34 is_a: core field slot_uri: MIXS:0000516 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -22743,22 +23878,23 @@ classes: occurrence: tag: occurrence value: '1' - description: pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + description: pH measurement of the sample, or liquid portion of sample, or + aqueous phase of the fluid title: pH notes: - - Use modified term + - Use modified term examples: - - value: '7.2' + - value: '7.2' from_schema: https://w3id.org/nmdc/nmdc aliases: - - pH + - pH rank: 27 is_a: core field string_serialization: '{float}' slot_uri: MIXS:0001001 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: float recommended: true @@ -22777,20 +23913,20 @@ classes: 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. + - 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 + - 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 aliases: - - pH method + - pH method rank: 41 is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0001106 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -22809,21 +23945,22 @@ classes: description: Concentration of phaeopigments; can include multiple phaeopigments title: phaeopigments examples: - - value: 2.5 milligram per cubic meter + - value: 2.5 milligram per cubic meter from_schema: https://w3id.org/nmdc/nmdc aliases: - - phaeopigments + - phaeopigments rank: 35 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000180 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false - 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]+)$ + 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: @@ -22839,16 +23976,16 @@ classes: description: Concentration of phosphate title: phosphate examples: - - value: 0.7 micromole per liter + - value: 0.7 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - phosphate + - phosphate rank: 53 is_a: core field slot_uri: MIXS:0000505 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -22865,24 +24002,26 @@ classes: occurrence: tag: occurrence value: m - description: Concentration of phospholipid fatty acids; can include multiple values + description: Concentration of phospholipid fatty acids; can include multiple + values title: phospholipid fatty acid examples: - - value: 2.98 milligram per liter + - value: 2.98 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - phospholipid fatty acid + - phospholipid fatty acid rank: 36 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000181 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false - 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]+)$ + 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: @@ -22898,16 +24037,16 @@ classes: description: Concentration of potassium in the sample title: potassium examples: - - value: 463 milligram per liter + - value: 463 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - potassium + - potassium rank: 38 is_a: core field slot_uri: MIXS:0000430 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -22927,16 +24066,16 @@ classes: description: Pressure to which the sample is subject to, in atmospheres title: pressure examples: - - value: 50 atmosphere + - value: 50 atmosphere from_schema: https://w3id.org/nmdc/nmdc aliases: - - pressure + - pressure rank: 39 is_a: core field slot_uri: MIXS:0000412 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -22953,19 +24092,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + description: Redox potential, measured relative to a hydrogen cell, indicating + oxidation or reduction potential title: redox potential examples: - - value: 300 millivolt + - value: 300 millivolt from_schema: https://w3id.org/nmdc/nmdc aliases: - - redox potential + - redox potential rank: 40 is_a: core field slot_uri: MIXS:0000182 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -22982,19 +24122,24 @@ classes: 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. + 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 + - value: 25 practical salinity unit from_schema: https://w3id.org/nmdc/nmdc aliases: - - salinity + - salinity rank: 54 is_a: core field slot_uri: MIXS:0000183 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -23005,22 +24150,24 @@ classes: 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). + 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 + - Report dimensions and details when applicable examples: - - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample collection device + - sample collection device rank: 14 is_a: nucleic acid sequence source field string_serialization: '{termLabel} {[termID]}|{text}' slot_uri: MIXS:0000002 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -23034,19 +24181,19 @@ classes: description: The method employed for collecting the sample. title: sample collection method comments: - - This can be a citation or description + - This can be a citation or description examples: - - value: swabbing + - value: swabbing from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample collection method + - sample collection method rank: 15 is_a: nucleic acid sequence source field string_serialization: '{PMID}|{DOI}|{URL}|{text}' slot_uri: MIXS:0001225 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -23056,21 +24203,23 @@ classes: 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. + 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 + - value: filtering of seawater + - value: storing samples in ethanol from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample material processing + - sample material processing rank: 12 is_a: nucleic acid sequence source field string_serialization: '{text}' slot_uri: MIXS:0000016 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -23083,23 +24232,25 @@ classes: 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. + 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. + - 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 + - value: 5 grams + - value: 10 mL from_schema: https://w3id.org/nmdc/nmdc aliases: - - amount or size of sample collected + - amount or size of sample collected rank: 18 is_a: nucleic acid sequence source field string_serialization: '{float} {unit}' slot_uri: MIXS:0000001 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -23116,17 +24267,17 @@ classes: description: Duration for which the sample was stored title: sample storage duration examples: - - value: P1Y6M + - value: P1Y6M from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample storage duration + - sample storage duration rank: 353 is_a: core field string_serialization: '{duration}' slot_uri: MIXS:0000116 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -23139,20 +24290,21 @@ classes: occurrence: tag: occurrence value: '1' - description: Location at which sample was stored, usually name of a specific freezer/room + description: Location at which sample was stored, usually name of a specific + freezer/room title: sample storage location examples: - - value: Freezer no:5 + - value: Freezer no:5 from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample storage location + - sample storage location rank: 41 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000755 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -23171,16 +24323,16 @@ classes: description: Temperature at which the sample was stored (degrees are assumed) title: sample storage temperature examples: - - value: -80 Celsius + - value: -80 Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample storage temperature + - sample storage temperature rank: 7 is_a: core field slot_uri: MIXS:0000110 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string required: true @@ -23188,20 +24340,27 @@ classes: 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. + 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''' + - '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)' + - '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 + - value: IGSN:DSJ0284 from_schema: https://w3id.org/nmdc/nmdc rank: 5 string_serialization: '{text}:{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string recommended: true @@ -23222,16 +24381,16 @@ classes: description: Concentration of silicate title: silicate examples: - - value: 0.05 micromole per liter + - value: 0.05 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - silicate + - silicate rank: 43 is_a: core field slot_uri: MIXS:0000184 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -23245,17 +24404,17 @@ classes: description: Filtering pore size used in sample preparation title: size fraction selected examples: - - value: 0-0.22 micrometer + - value: 0-0.22 micrometer from_schema: https://w3id.org/nmdc/nmdc aliases: - - size fraction selected + - size fraction selected rank: 285 is_a: nucleic acid sequence source field string_serialization: '{float}-{float} {unit}' slot_uri: MIXS:0000017 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -23274,34 +24433,37 @@ classes: description: Sodium concentration in the sample title: sodium examples: - - value: 10.5 milligram per liter + - value: 10.5 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - sodium + - sodium rank: 363 is_a: core field slot_uri: MIXS:0000428 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 13 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study slot_group: sample_id_section range: SpecificEcosystemEnum recommended: true @@ -23320,16 +24482,16 @@ classes: description: Concentration of sulfate in the sample title: sulfate examples: - - value: 5 micromole per liter + - value: 5 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - sulfate + - sulfate rank: 44 is_a: core field slot_uri: MIXS:0000423 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -23349,16 +24511,16 @@ classes: description: Concentration of sulfide in the sample title: sulfide examples: - - value: 2 micromole per liter + - value: 2 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - sulfide + - sulfide rank: 371 is_a: core field slot_uri: MIXS:0000424 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -23375,16 +24537,16 @@ classes: description: Temperature of the sample at the time of sampling. title: temperature examples: - - value: 25 degree Celsius + - value: 25 degree Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - - temperature + - temperature rank: 37 is_a: environment field slot_uri: MIXS:0000113 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -23404,21 +24566,25 @@ classes: 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 + - 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 + - value: 1 ug/L from_schema: https://w3id.org/nmdc/nmdc aliases: - - total carbon + - total carbon rank: 47 is_a: core field slot_uri: MIXS:0000525 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -23438,16 +24604,16 @@ classes: description: Total nitrogen content of the sample title: total nitrogen content examples: - - value: 5 mg N/ L + - value: 5 mg N/ L from_schema: https://w3id.org/nmdc/nmdc aliases: - - total nitrogen content + - total nitrogen content rank: 48 is_a: core field slot_uri: MIXS:0000530 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -23464,22 +24630,23 @@ classes: occurrence: tag: occurrence value: '1' - description: 'Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content' + 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? + - check description. How are they different? + - check description. How are they different? examples: - - value: 5 mg N/ L + - value: 5 mg N/ L from_schema: https://w3id.org/nmdc/nmdc aliases: - - total organic carbon + - total organic carbon rank: 50 is_a: core field slot_uri: MIXS:0000533 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -23496,19 +24663,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Measure of the amount of cloudiness or haziness in water caused by individual particles + description: Measure of the amount of cloudiness or haziness in water caused + by individual particles title: turbidity examples: - - value: 0.3 nephelometric turbidity units + - value: 0.3 nephelometric turbidity units from_schema: https://w3id.org/nmdc/nmdc aliases: - - turbidity + - turbidity rank: 47 is_a: core field slot_uri: MIXS:0000191 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -23525,24 +24693,24 @@ classes: 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 - - 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 + - how to manage multiple water content methods? examples: - - 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 + - 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 aliases: - - water content + - water content rank: 39 is_a: core field string_serialization: '{float or pct} {unit}' slot_uri: MIXS:0000185 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -23561,187 +24729,187 @@ classes: from_schema: https://example.com/nmdc_submission_schema is_a: DhInterface mixins: - - DhMultiviewCommonColumnsMixin - - SampIdNewTermsMixin + - 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 - - 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 + - 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 + - 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 slot_usage: abs_air_humidity: name: abs_air_humidity @@ -23755,19 +24923,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Actual mass of water vapor - mh20 - present in the air water vapor mixture + description: Actual mass of water vapor - mh20 - present in the air water + vapor mixture title: absolute air humidity examples: - - value: 9 gram per gram + - value: 9 gram per gram from_schema: https://w3id.org/nmdc/nmdc aliases: - - absolute air humidity + - absolute air humidity rank: 61 is_a: core field slot_uri: MIXS:0000122 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -23784,17 +24953,17 @@ classes: description: The street name and building number where the sampling occurred. title: address examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - address + - address rank: 62 is_a: core field string_serialization: '{integer}{text}' slot_uri: MIXS:0000218 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -23807,20 +24976,21 @@ classes: occurrence: tag: occurrence value: '1' - description: List of rooms (room number, room name) immediately adjacent to the sampling room + description: List of rooms (room number, room name) immediately adjacent to + the sampling room title: adjacent rooms examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - adjacent rooms + - adjacent rooms rank: 63 is_a: core field string_serialization: '{text};{integer}' slot_uri: MIXS:0000219 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -23833,20 +25003,23 @@ classes: 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 + 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 + - value: plane from_schema: https://w3id.org/nmdc/nmdc aliases: - - aerospace structure + - aerospace structure rank: 64 is_a: core field string_serialization: '[plane|glider]' slot_uri: MIXS:0000773 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -23865,16 +25038,16 @@ classes: description: Temperature of the air at the time of sampling title: air temperature examples: - - value: 20 degree Celsius + - value: 20 degree Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - - air temperature + - air temperature rank: 65 is_a: core field slot_uri: MIXS:0000124 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -23885,43 +25058,48 @@ classes: 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 + 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 + - value: 100 meter from_schema: https://w3id.org/nmdc/nmdc aliases: - - altitude + - altitude rank: 26 is_a: environment field slot_uri: MIXS:0000094 owner: Biosample domain_of: - - agriculture - - air - - built environment - - core - - food-animal and animal feed - - food-farm environment - - food-food production facility - - food-human foods - - host-associated - - human-associated - - human-gut - - human-oral - - human-skin - - human-vaginal - - hydrocarbon resources-cores - - hydrocarbon resources-fluids_swabs - - microbial mat_biofilm - - miscellaneous natural or artificial environment - - plant-associated - - sediment - - soil - - symbiont-associated - - wastewater_sludge - - water - - Biosample + - agriculture + - air + - built environment + - core + - food-animal and animal feed + - food-farm environment + - food-food production facility + - food-human foods + - host-associated + - human-associated + - human-gut + - human-oral + - human-skin + - human-vaginal + - hydrocarbon resources-cores + - hydrocarbon resources-fluids_swabs + - microbial mat_biofilm + - miscellaneous natural or artificial environment + - plant-associated + - sediment + - soil + - symbiont-associated + - wastewater_sludge + - water + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -23939,19 +25117,20 @@ classes: occurrence: tag: occurrence value: '1' - description: The unit of illuminance and luminous emittance, measuring luminous flux per unit area + description: The unit of illuminance and luminous emittance, measuring luminous + flux per unit area title: amount of light examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - amount of light + - amount of light rank: 66 is_a: core field slot_uri: MIXS:0000140 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -23965,19 +25144,20 @@ classes: occurrence: tag: occurrence value: '1' - description: An architectural structure is a human-made, free-standing, immobile outdoor construction + description: An architectural structure is a human-made, free-standing, immobile + outdoor construction title: architectural structure examples: - - value: shed + - value: shed from_schema: https://w3id.org/nmdc/nmdc aliases: - - architectural structure + - architectural structure rank: 67 is_a: core field slot_uri: MIXS:0000774 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: arch_struc_enum multivalued: false @@ -23993,19 +25173,20 @@ classes: 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 + 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 + - value: 25.5 degree Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - - average dew point + - average dew point rank: 68 is_a: core field slot_uri: MIXS:0000141 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -24019,19 +25200,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Daily average occupancy of room. Indicate the number of person(s) daily occupying the sampling room. + description: Daily average occupancy of room. Indicate the number of person(s) + daily occupying the sampling room. title: average daily occupancy examples: - - value: '2' + - value: '2' from_schema: https://w3id.org/nmdc/nmdc aliases: - - average daily occupancy + - average daily occupancy rank: 69 is_a: core field slot_uri: MIXS:0000775 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -24047,19 +25229,20 @@ classes: 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 + 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 + - value: 12.5 degree Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - - average temperature + - average temperature rank: 70 is_a: core field slot_uri: MIXS:0000142 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -24076,16 +25259,16 @@ classes: description: The number of bathrooms in the building title: bathroom count examples: - - value: '1' + - value: '1' from_schema: https://w3id.org/nmdc/nmdc aliases: - - bathroom count + - bathroom count rank: 71 is_a: core field slot_uri: MIXS:0000776 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -24101,16 +25284,16 @@ classes: description: The number of bedrooms in the building title: bedroom count examples: - - value: '2' + - value: '2' from_schema: https://w3id.org/nmdc/nmdc aliases: - - bedroom count + - bedroom count rank: 72 is_a: core field slot_uri: MIXS:0000777 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -24126,16 +25309,16 @@ classes: description: The building design, construction and operation documents title: design, construction, and operation documents examples: - - value: maintenance plans + - value: maintenance plans from_schema: https://w3id.org/nmdc/nmdc aliases: - - design, construction, and operation documents + - design, construction, and operation documents rank: 73 is_a: core field slot_uri: MIXS:0000787 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: build_docs_enum multivalued: false @@ -24148,19 +25331,20 @@ classes: occurrence: tag: occurrence value: m - description: The primary function for which a building or discrete part of a building is intended to be used + 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 + - value: market from_schema: https://w3id.org/nmdc/nmdc aliases: - - building occupancy type + - building occupancy type rank: 74 is_a: core field slot_uri: MIXS:0000761 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: build_occup_type_enum multivalued: true @@ -24176,16 +25360,16 @@ classes: description: A location (geography) where a building is set title: building setting examples: - - value: rural + - value: rural from_schema: https://w3id.org/nmdc/nmdc aliases: - - building setting + - building setting rank: 75 is_a: core field slot_uri: MIXS:0000768 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: building_setting_enum multivalued: false @@ -24204,16 +25388,16 @@ classes: description: The age of the built structure since construction title: built structure age examples: - - value: '15' + - value: '15' from_schema: https://w3id.org/nmdc/nmdc aliases: - - built structure age + - built structure age rank: 76 is_a: core field slot_uri: MIXS:0000145 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -24227,20 +25411,21 @@ classes: occurrence: tag: occurrence value: '1' - description: The characterization of the location of the built structure as high or low human density + description: The characterization of the location of the built structure as + high or low human density title: built structure setting examples: - - value: rural + - value: rural from_schema: https://w3id.org/nmdc/nmdc aliases: - - built structure setting + - built structure setting rank: 77 is_a: core field string_serialization: '[urban|rural]' slot_uri: MIXS:0000778 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -24253,20 +25438,21 @@ classes: 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 + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - built structure type + - built structure type rank: 78 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000721 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -24285,16 +25471,16 @@ classes: description: Carbon dioxide (gas) amount or concentration at the time of sampling title: carbon dioxide examples: - - value: 410 parts per million + - value: 410 parts per million from_schema: https://w3id.org/nmdc/nmdc aliases: - - carbon dioxide + - carbon dioxide rank: 50 is_a: core field slot_uri: MIXS:0000097 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -24314,16 +25500,16 @@ classes: description: The area of the ceiling space within the room title: ceiling area examples: - - value: 25 square meter + - value: 25 square meter from_schema: https://w3id.org/nmdc/nmdc aliases: - - ceiling area + - ceiling area rank: 79 is_a: core field slot_uri: MIXS:0000148 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -24337,19 +25523,21 @@ classes: 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 + 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 + - value: damaged from_schema: https://w3id.org/nmdc/nmdc aliases: - - ceiling condition + - ceiling condition rank: 80 is_a: core field slot_uri: MIXS:0000779 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: ceil_cond_enum multivalued: false @@ -24365,16 +25553,16 @@ classes: description: The type of material used to finish a ceiling title: ceiling finish material examples: - - value: stucco + - value: stucco from_schema: https://w3id.org/nmdc/nmdc aliases: - - ceiling finish material + - ceiling finish material rank: 81 is_a: core field slot_uri: MIXS:0000780 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: ceil_finish_mat_enum multivalued: false @@ -24390,17 +25578,17 @@ classes: description: The construction format of the ceiling title: ceiling structure examples: - - value: concrete + - value: concrete from_schema: https://w3id.org/nmdc/nmdc aliases: - - ceiling structure + - ceiling structure rank: 82 is_a: core field string_serialization: '[wood frame|concrete]' slot_uri: MIXS:0000782 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -24416,16 +25604,16 @@ classes: description: The feel, appearance, or consistency of a ceiling surface title: ceiling texture examples: - - value: popcorn + - value: popcorn from_schema: https://w3id.org/nmdc/nmdc aliases: - - ceiling texture + - ceiling texture rank: 83 is_a: core field slot_uri: MIXS:0000783 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: ceil_texture_enum multivalued: false @@ -24441,19 +25629,22 @@ classes: 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 + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - ceiling thermal mass + - ceiling thermal mass rank: 84 is_a: core field slot_uri: MIXS:0000143 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -24467,19 +25658,20 @@ classes: occurrence: tag: occurrence value: '1' - description: The type of ceiling according to the ceiling's appearance or construction + description: The type of ceiling according to the ceiling's appearance or + construction title: ceiling type examples: - - value: coffered + - value: coffered from_schema: https://w3id.org/nmdc/nmdc aliases: - - ceiling type + - ceiling type rank: 85 is_a: core field slot_uri: MIXS:0000784 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: ceil_type_enum multivalued: false @@ -24495,17 +25687,17 @@ classes: description: Signs of the presence of mold or mildew on the ceiling title: ceiling signs of water/mold examples: - - value: presence of mold visible + - value: presence of mold visible from_schema: https://w3id.org/nmdc/nmdc aliases: - - ceiling signs of water/mold + - 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 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -24518,22 +25710,23 @@ classes: 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) + - 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' + - value: '2021-04-15' + - value: 2021-04 + - value: '2021' from_schema: https://w3id.org/nmdc/nmdc aliases: - - collection date + - collection date rank: 3 is_a: environment field string_serialization: '{date, arbitrary precision}' slot_uri: MIXS:0000011 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string required: true @@ -24551,16 +25744,16 @@ classes: description: The cooling system identifier title: cooling system identifier examples: - - value: '12345' + - value: '12345' from_schema: https://w3id.org/nmdc/nmdc aliases: - - cooling system identifier + - cooling system identifier rank: 87 is_a: core field slot_uri: MIXS:0000785 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -24576,16 +25769,16 @@ classes: description: The date of the last time it rained title: date last rain examples: - - value: 2018-05-11:T14:30Z + - value: 2018-05-11:T14:30Z from_schema: https://w3id.org/nmdc/nmdc aliases: - - date last rain + - date last rain rank: 88 is_a: core field slot_uri: MIXS:0000786 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -24595,25 +25788,27 @@ classes: 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. + 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 + - Use modified term comments: - - All depths must be reported in meters. Provide the numerical portion only. + - All depths must be reported in meters. Provide the numerical portion only. examples: - - value: 0 - 0.1 - - value: '1' + - value: 0 - 0.1 + - value: '1' from_schema: https://w3id.org/nmdc/nmdc aliases: - - depth + - depth rank: 9 is_a: environment field string_serialization: '{float}|{float}-{float}' slot_uri: MIXS:0000018 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -24631,19 +25826,21 @@ classes: 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. + 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 + - value: 22 degree Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - - dew point + - dew point rank: 89 is_a: core field slot_uri: MIXS:0000129 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -24660,16 +25857,16 @@ classes: description: The composite type of the door title: door type, composite examples: - - value: revolving + - value: revolving from_schema: https://w3id.org/nmdc/nmdc aliases: - - door type, composite + - door type, composite rank: 90 is_a: core field slot_uri: MIXS:0000795 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: door_comp_type_enum multivalued: false @@ -24685,16 +25882,16 @@ classes: description: The phsical condition of the door title: door condition examples: - - value: new + - value: new from_schema: https://w3id.org/nmdc/nmdc aliases: - - door condition + - door condition rank: 91 is_a: core field slot_uri: MIXS:0000788 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: door_cond_enum multivalued: false @@ -24710,16 +25907,16 @@ classes: description: The direction the door opens title: door direction of opening examples: - - value: inward + - value: inward from_schema: https://w3id.org/nmdc/nmdc aliases: - - door direction of opening + - door direction of opening rank: 92 is_a: core field slot_uri: MIXS:0000789 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: door_direct_enum multivalued: false @@ -24735,16 +25932,16 @@ classes: description: The relative location of the door in the room title: door location examples: - - value: north + - value: north from_schema: https://w3id.org/nmdc/nmdc aliases: - - door location + - door location rank: 93 is_a: core field slot_uri: MIXS:0000790 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: door_loc_enum multivalued: false @@ -24760,16 +25957,16 @@ classes: description: The material the door is composed of title: door material examples: - - value: wood + - value: wood from_schema: https://w3id.org/nmdc/nmdc aliases: - - door material + - door material rank: 94 is_a: core field slot_uri: MIXS:0000791 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: door_mat_enum multivalued: false @@ -24785,16 +25982,16 @@ classes: description: The type of movement of the door title: door movement examples: - - value: swinging + - value: swinging from_schema: https://w3id.org/nmdc/nmdc aliases: - - door movement + - door movement rank: 95 is_a: core field slot_uri: MIXS:0000792 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: door_move_enum multivalued: false @@ -24813,16 +26010,16 @@ classes: description: The size of the door title: door area or size examples: - - value: 2.5 square meter + - value: 2.5 square meter from_schema: https://w3id.org/nmdc/nmdc aliases: - - door area or size + - door area or size rank: 96 is_a: core field slot_uri: MIXS:0000158 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -24839,16 +26036,16 @@ classes: description: The type of door material title: door type examples: - - value: wooden + - value: wooden from_schema: https://w3id.org/nmdc/nmdc aliases: - - door type + - door type rank: 97 is_a: core field slot_uri: MIXS:0000794 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: door_type_enum multivalued: false @@ -24864,16 +26061,16 @@ classes: description: The type of metal door title: door type, metal examples: - - value: hollow + - value: hollow from_schema: https://w3id.org/nmdc/nmdc aliases: - - door type, metal + - door type, metal rank: 98 is_a: core field slot_uri: MIXS:0000796 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: door_type_metal_enum multivalued: false @@ -24889,16 +26086,16 @@ classes: description: The type of wood door title: door type, wood examples: - - value: battened + - value: battened from_schema: https://w3id.org/nmdc/nmdc aliases: - - door type, wood + - door type, wood rank: 99 is_a: core field slot_uri: MIXS:0000797 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: door_type_wood_enum multivalued: false @@ -24914,17 +26111,17 @@ classes: description: Signs of the presence of mold or mildew on a door title: door signs of water/mold examples: - - value: presence of mold visible + - value: presence of mold visible from_schema: https://w3id.org/nmdc/nmdc aliases: - - door signs of water/mold + - 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 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -24937,87 +26134,112 @@ classes: occurrence: tag: occurrence value: '1' - description: The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents + description: The buildings architectural drawings; if design is chosen, indicate + phase-conceptual, schematic, design development, and construction documents title: drawings examples: - - value: sketch + - value: sketch from_schema: https://w3id.org/nmdc/nmdc aliases: - - drawings + - drawings rank: 101 is_a: core field slot_uri: MIXS:0000798 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: drawings_enum multivalued: false 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 9 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 10 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 12 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 11 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study slot_group: sample_id_section range: EcosystemTypeEnum recommended: true @@ -25027,25 +26249,31 @@ classes: 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. + 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. + - 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' + - value: '225' + - value: '0' + - value: '1250' from_schema: https://w3id.org/nmdc/nmdc aliases: - - elevation + - elevation rank: 6 is_a: environment field slot_uri: MIXS:0000093 owner: Biosample domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample slot_group: mixs_modified_section range: float required: true @@ -25062,16 +26290,16 @@ classes: description: The number of elevators within the built structure title: elevator count examples: - - value: '2' + - value: '2' from_schema: https://w3id.org/nmdc/nmdc aliases: - - elevator count + - elevator count rank: 102 is_a: core field slot_uri: MIXS:0000799 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -25080,26 +26308,44 @@ classes: 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. + 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. tooltip: tag: tooltip - value: The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context - 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' + value: The biome or major environmental system where the sample or specimen + originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] + in the Environment Ontology (ENVO). For host-associated or plant-associated + samples, use terms from the UBERON or Plant Ontology to describe the + broad anatomical or morphological context + 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) + - range changed to enumeration late in makefile, so this is modified (but + "sample ID" anyway) examples: - - value: oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean + - 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://w3id.org/nmdc/nmdc aliases: - - broad-scale environmental context + - broad-scale environmental context rank: 6 is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000012 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string required: true @@ -25110,30 +26356,45 @@ classes: annotations: expected_value: tag: expected_value - value: Environmental entities having causal influences upon the entity at time of sampling. + value: Environmental entities having causal influences upon the entity + at time of sampling. tooltip: tag: tooltip - value: The specific environmental entities or features near the sample or specimen that significantly influence its characteristics or composition. These entities are typically smaller in scale than the broad environmental context. Values for this field should be countable, material nouns and must be chosen from subclasses of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe specific anatomical structures or plant parts. - 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.' + value: The specific environmental entities or features near the sample + or specimen that significantly influence its characteristics or composition. + These entities are typically smaller in scale than the broad environmental + context. Values for this field should be countable, material nouns and + must be chosen from subclasses of BFO:0000040 (material entity) that + appear in the Environment Ontology (ENVO). For host-associated or plant-associated + samples, use terms from the UBERON or Plant Ontology to describe specific + anatomical structures or plant parts. + 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) + - 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] + - 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 aliases: - - local environmental context + - local environmental context rank: 7 is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000013 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string required: true @@ -25144,26 +26405,41 @@ classes: annotations: expected_value: tag: expected_value - value: The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]. + value: The material displaced by the entity at time of sampling. Recommend + subclasses of environmental material [ENVO:00010483]. tooltip: tag: tooltip - value: The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure - 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).' + value: The predominant environmental material or substrate that directly + surrounds or hosts the sample or specimen at the time of sampling. Choose + values from subclasses of the 'environmental material' class [ENVO:00010483] + in the Environment Ontology (ENVO). Values for this field should be + measurable or mass material nouns, representing continuous environmental + materials. For host-associated or plant-associated samples, use terms + from the UBERON or Plant Ontology to indicate a tissue, organ, or plant + structure + 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) + - range changed to enumeration late in makefile, so this is modified (but + "sample ID" anyway) examples: - - value: soil [ENVO:00001998] + - value: soil [ENVO:00001998] from_schema: https://w3id.org/nmdc/nmdc aliases: - - environmental medium + - environmental medium rank: 8 is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000014 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string required: true @@ -25181,16 +26457,16 @@ classes: description: The number of escalators within the built structure title: escalator count examples: - - value: '4' + - value: '4' from_schema: https://w3id.org/nmdc/nmdc aliases: - - escalator count + - escalator count rank: 103 is_a: core field slot_uri: MIXS:0000800 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -25209,16 +26485,16 @@ classes: description: The amount of exposed ductwork in the room title: exposed ductwork examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - exposed ductwork + - exposed ductwork rank: 104 is_a: core field slot_uri: MIXS:0000144 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -25235,16 +26511,16 @@ classes: description: The number of exposed pipes in the room title: exposed pipes examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - exposed pipes + - exposed pipes rank: 105 is_a: core field slot_uri: MIXS:0000220 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -25255,20 +26531,25 @@ classes: 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 + 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] + - value: time series design [EFO:EFO_0001779] from_schema: https://w3id.org/nmdc/nmdc aliases: - - experimental factor + - experimental factor rank: 12 is_a: investigation field string_serialization: '{termLabel} {[termID]}|{text}' slot_uri: MIXS:0000008 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -25284,16 +26565,16 @@ classes: description: The number of exterior doors in the built structure title: exterior door count examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - exterior door count + - exterior door count rank: 106 is_a: core field slot_uri: MIXS:0000170 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -25309,16 +26590,16 @@ classes: description: The orientation of the exterior wall title: orientations of exterior wall examples: - - value: northwest + - value: northwest from_schema: https://w3id.org/nmdc/nmdc aliases: - - orientations of exterior wall + - orientations of exterior wall rank: 107 is_a: core field slot_uri: MIXS:0000817 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: ext_wall_orient_enum multivalued: false @@ -25334,16 +26615,16 @@ classes: description: The compass direction the exterior window of the room is facing title: orientations of exterior window examples: - - value: southwest + - value: southwest from_schema: https://w3id.org/nmdc/nmdc aliases: - - orientations of exterior window + - orientations of exterior window rank: 108 is_a: core field slot_uri: MIXS:0000818 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: ext_window_orient_enum multivalued: false @@ -25356,19 +26637,20 @@ classes: occurrence: tag: occurrence value: m - description: A device which removes solid particulates or airborne molecular contaminants + description: A device which removes solid particulates or airborne molecular + contaminants title: filter type examples: - - value: HEPA + - value: HEPA from_schema: https://w3id.org/nmdc/nmdc aliases: - - filter type + - filter type rank: 109 is_a: core field slot_uri: MIXS:0000765 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: filter_type_enum multivalued: true @@ -25384,17 +26666,17 @@ classes: description: A firebox with chimney title: fireplace type examples: - - value: wood burning + - value: wood burning from_schema: https://w3id.org/nmdc/nmdc aliases: - - fireplace type + - fireplace type rank: 110 is_a: core field string_serialization: '[gas burning|wood burning]' slot_uri: MIXS:0000802 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -25413,16 +26695,16 @@ classes: description: The time period since installment of the carpet or flooring title: floor age examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - floor age + - floor age rank: 111 is_a: core field slot_uri: MIXS:0000164 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -25442,16 +26724,16 @@ classes: description: The area of the floor space within the room title: floor area examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - floor area + - floor area rank: 112 is_a: core field slot_uri: MIXS:0000165 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -25465,19 +26747,21 @@ classes: 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 + 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 + - value: new from_schema: https://w3id.org/nmdc/nmdc aliases: - - floor condition + - floor condition rank: 113 is_a: core field slot_uri: MIXS:0000803 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: floor_cond_enum multivalued: false @@ -25490,19 +26774,20 @@ classes: occurrence: tag: occurrence value: '1' - description: The number of floors in the building, including basements and mechanical penthouse + description: The number of floors in the building, including basements and + mechanical penthouse title: floor count examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - floor count + - floor count rank: 114 is_a: core field slot_uri: MIXS:0000225 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -25515,19 +26800,20 @@ classes: occurrence: tag: occurrence value: '1' - description: The floor covering type; the finished surface that is walked on + description: The floor covering type; the finished surface that is walked + on title: floor finish material examples: - - value: carpet + - value: carpet from_schema: https://w3id.org/nmdc/nmdc aliases: - - floor finish material + - floor finish material rank: 115 is_a: core field slot_uri: MIXS:0000804 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: floor_finish_mat_enum multivalued: false @@ -25540,19 +26826,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Refers to the structural elements and subfloor upon which the finish flooring is installed + description: Refers to the structural elements and subfloor upon which the + finish flooring is installed title: floor structure examples: - - value: concrete + - value: concrete from_schema: https://w3id.org/nmdc/nmdc aliases: - - floor structure + - floor structure rank: 116 is_a: core field slot_uri: MIXS:0000806 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: floor_struc_enum multivalued: false @@ -25568,19 +26855,20 @@ classes: occurrence: tag: occurrence value: '1' - description: The ability of the floor to provide inertia against temperature fluctuations + description: The ability of the floor to provide inertia against temperature + fluctuations title: floor thermal mass examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - floor thermal mass + - floor thermal mass rank: 117 is_a: core field slot_uri: MIXS:0000166 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -25597,16 +26885,16 @@ classes: description: Signs of the presence of mold or mildew in a room title: floor signs of water/mold examples: - - value: ceiling discoloration + - value: ceiling discoloration from_schema: https://w3id.org/nmdc/nmdc aliases: - - floor signs of water/mold + - floor signs of water/mold rank: 118 is_a: core field slot_uri: MIXS:0000805 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: floor_water_mold_enum multivalued: false @@ -25619,19 +26907,20 @@ classes: 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. + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - frequency of cleaning + - frequency of cleaning rank: 119 is_a: core field slot_uri: MIXS:0000226 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -25648,16 +26937,16 @@ classes: description: The number of times a meal is cooked per week title: frequency of cooking examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - frequency of cooking + - frequency of cooking rank: 120 is_a: core field slot_uri: MIXS:0000227 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -25674,16 +26963,16 @@ classes: description: The types of furniture present in the sampled room title: furniture examples: - - value: chair + - value: chair from_schema: https://w3id.org/nmdc/nmdc aliases: - - furniture + - furniture rank: 121 is_a: core field slot_uri: MIXS:0000807 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: furniture_enum multivalued: false @@ -25699,16 +26988,16 @@ classes: description: The gender type of the restroom title: gender of restroom examples: - - value: male + - value: male from_schema: https://w3id.org/nmdc/nmdc aliases: - - gender of restroom + - gender of restroom rank: 122 is_a: core field slot_uri: MIXS:0000808 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: gender_restroom_enum multivalued: false @@ -25717,22 +27006,24 @@ classes: 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. + 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' + - value: 'USA: Maryland, Bethesda' from_schema: https://w3id.org/nmdc/nmdc aliases: - - geographic location (country and/or sea,region) + - geographic location (country and/or sea,region) rank: 4 is_a: environment field string_serialization: '{text}: {text}, {text}' slot_uri: MIXS:0000010 owner: Biosample domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample slot_group: mixs_modified_section range: string required: true @@ -25750,16 +27041,16 @@ classes: description: The total count of hallways and cooridors in the built structure title: hallway/corridor count examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - hallway/corridor count + - hallway/corridor count rank: 123 is_a: core field slot_uri: MIXS:0000228 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -25775,16 +27066,16 @@ classes: description: The handidness of the individual sampled title: handidness examples: - - value: right handedness + - value: right handedness from_schema: https://w3id.org/nmdc/nmdc aliases: - - handidness + - handidness rank: 124 is_a: core field slot_uri: MIXS:0000809 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: handidness_enum multivalued: false @@ -25800,16 +27091,16 @@ classes: description: Methods of conditioning or heating a room or building title: heating and cooling system type examples: - - value: heat pump + - value: heat pump from_schema: https://w3id.org/nmdc/nmdc aliases: - - heating and cooling system type + - heating and cooling system type rank: 125 is_a: core field slot_uri: MIXS:0000766 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: heat_cool_type_enum multivalued: true @@ -25825,16 +27116,16 @@ classes: description: The location of heat delivery within the room title: heating delivery locations examples: - - value: north + - value: north from_schema: https://w3id.org/nmdc/nmdc aliases: - - heating delivery locations + - heating delivery locations rank: 126 is_a: core field slot_uri: MIXS:0000810 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: heat_deliv_loc_enum multivalued: false @@ -25850,17 +27141,17 @@ classes: description: The method by which the heat is delivered through the system title: heating system delivery method examples: - - value: radiant + - value: radiant from_schema: https://w3id.org/nmdc/nmdc aliases: - - heating system delivery method + - heating system delivery method rank: 127 is_a: core field string_serialization: '[conductive|radiant]' slot_uri: MIXS:0000812 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -25876,16 +27167,16 @@ classes: description: The heating system identifier title: heating system identifier examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - heating system identifier + - heating system identifier rank: 128 is_a: core field slot_uri: MIXS:0000833 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -25904,16 +27195,16 @@ classes: description: The average carpet fiber height in the indoor environment title: height carpet fiber mat examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - height carpet fiber mat + - height carpet fiber mat rank: 129 is_a: core field slot_uri: MIXS:0000167 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -25927,19 +27218,20 @@ classes: occurrence: tag: occurrence value: '1' - description: A distinguishable space within a structure, the purpose for which discrete areas of a building is used + description: A distinguishable space within a structure, the purpose for which + discrete areas of a building is used title: indoor space examples: - - value: foyer + - value: foyer from_schema: https://w3id.org/nmdc/nmdc aliases: - - indoor space + - indoor space rank: 130 is_a: core field slot_uri: MIXS:0000763 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: indoor_space_enum multivalued: false @@ -25955,16 +27247,16 @@ classes: description: Type of indoor surface title: indoor surface examples: - - value: wall + - value: wall from_schema: https://w3id.org/nmdc/nmdc aliases: - - indoor surface + - indoor surface rank: 131 is_a: core field slot_uri: MIXS:0000764 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: indoor_surf_enum multivalued: false @@ -25983,16 +27275,16 @@ classes: description: The recorded value at sampling time (power density) title: inside lux light examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - inside lux light + - inside lux light rank: 132 is_a: core field slot_uri: MIXS:0000168 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -26006,19 +27298,20 @@ classes: 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 + 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 + - value: damaged from_schema: https://w3id.org/nmdc/nmdc aliases: - - interior wall condition + - interior wall condition rank: 133 is_a: core field slot_uri: MIXS:0000813 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: int_wall_cond_enum multivalued: false @@ -26034,16 +27327,16 @@ classes: description: The last time the floor was cleaned (swept, mopped, vacuumed) title: last time swept/mopped/vacuumed examples: - - value: 2018-05-11:T14:30Z + - value: 2018-05-11:T14:30Z from_schema: https://w3id.org/nmdc/nmdc aliases: - - last time swept/mopped/vacuumed + - last time swept/mopped/vacuumed rank: 134 is_a: core field slot_uri: MIXS:0000814 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -26053,23 +27346,26 @@ classes: 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 + 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) notes: - - This is currently a required field but it's not clear if this should be required for human hosts + - This is currently a required field but it's not clear if this should be + required for human hosts examples: - - value: 50.586825 6.408977 + - value: 50.586825 6.408977 from_schema: https://w3id.org/nmdc/nmdc aliases: - - geographic location (latitude and longitude) + - geographic location (latitude and longitude) rank: 5 is_a: environment field string_serialization: '{lat lon}' slot_uri: MIXS:0000009 owner: Biosample domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample slot_group: mixs_modified_section range: string required: true @@ -26084,19 +27380,22 @@ classes: 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 + 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 + - value: desk lamp from_schema: https://w3id.org/nmdc/nmdc aliases: - - light type + - light type rank: 135 is_a: core field slot_uri: MIXS:0000769 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: light_type_enum multivalued: true @@ -26112,16 +27411,16 @@ classes: description: The maximum amount of people allowed in the indoor environment title: maximum occupancy examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - maximum occupancy + - maximum occupancy rank: 136 is_a: core field slot_uri: MIXS:0000229 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -26138,16 +27437,16 @@ classes: description: 'mechanical structure: a moving structure' title: mechanical structure examples: - - value: elevator + - value: elevator from_schema: https://w3id.org/nmdc/nmdc aliases: - - mechanical structure + - mechanical structure rank: 137 is_a: core field slot_uri: MIXS:0000815 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: mech_struc_enum multivalued: false @@ -26163,16 +27462,16 @@ classes: description: The number of pets residing in the sampled space title: number of pets examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - number of pets + - number of pets rank: 138 is_a: core field slot_uri: MIXS:0000231 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -26189,16 +27488,16 @@ classes: description: The number of plant(s) in the sampling space title: number of houseplants examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - number of houseplants + - number of houseplants rank: 139 is_a: core field slot_uri: MIXS:0000230 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -26212,19 +27511,20 @@ classes: occurrence: tag: occurrence value: '1' - description: The number of individuals currently occupying in the sampling location + description: The number of individuals currently occupying in the sampling + location title: number of residents examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - number of residents + - number of residents rank: 140 is_a: core field slot_uri: MIXS:0000232 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -26241,16 +27541,16 @@ classes: description: Average number of occupants at time of sampling per square footage title: occupant density at sampling examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - occupant density at sampling + - occupant density at sampling rank: 141 is_a: core field slot_uri: MIXS:0000217 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -26267,16 +27567,16 @@ classes: description: The type of documentation of occupancy title: occupancy documentation examples: - - value: estimate + - value: estimate from_schema: https://w3id.org/nmdc/nmdc aliases: - - occupancy documentation + - occupancy documentation rank: 142 is_a: core field slot_uri: MIXS:0000816 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: occup_document_enum multivalued: false @@ -26289,19 +27589,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Number of occupants present at time of sample within the given space + description: Number of occupants present at time of sample within the given + space title: occupancy at sampling examples: - - value: '10' + - value: '10' from_schema: https://w3id.org/nmdc/nmdc aliases: - - occupancy at sampling + - occupancy at sampling rank: 143 is_a: core field slot_uri: MIXS:0000772 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -26314,23 +27615,28 @@ classes: 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 + 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)' + 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 + - value: total prokaryotes;3.5e7 cells per milliliter;qPCR from_schema: https://w3id.org/nmdc/nmdc aliases: - - organism count + - organism count rank: 30 is_a: core field slot_uri: MIXS:0000103 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -26344,19 +27650,20 @@ classes: occurrence: tag: occurrence value: '1' - description: The type and number of animals or insects present in the sampling space. + 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 + - value: cat;5 from_schema: https://w3id.org/nmdc/nmdc aliases: - - presence of pets, animals, or insects + - presence of pets, animals, or insects rank: 144 is_a: core field slot_uri: MIXS:0000819 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -26373,16 +27680,16 @@ classes: description: The quadrant position of the sampling room within the building title: quadrant position examples: - - value: West side + - value: West side from_schema: https://w3id.org/nmdc/nmdc aliases: - - quadrant position + - quadrant position rank: 145 is_a: core field slot_uri: MIXS:0000820 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: quad_pos_enum multivalued: false @@ -26398,19 +27705,20 @@ classes: 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 + 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% + - value: 80% from_schema: https://w3id.org/nmdc/nmdc aliases: - - relative air humidity + - relative air humidity rank: 146 is_a: core field slot_uri: MIXS:0000121 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -26430,16 +27738,16 @@ classes: description: The recorded outside relative humidity value at the time of sampling title: outside relative humidity examples: - - value: 12 per kilogram of air + - value: 12 per kilogram of air from_schema: https://w3id.org/nmdc/nmdc aliases: - - outside relative humidity + - outside relative humidity rank: 147 is_a: core field slot_uri: MIXS:0000188 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -26456,16 +27764,16 @@ classes: description: The sampling location within the train car title: relative sampling location examples: - - value: center of car + - value: center of car from_schema: https://w3id.org/nmdc/nmdc aliases: - - relative sampling location + - relative sampling location rank: 148 is_a: core field slot_uri: MIXS:0000821 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: rel_samp_loc_enum multivalued: false @@ -26481,19 +27789,20 @@ classes: occurrence: tag: occurrence value: '1' - description: The rate at which outside air replaces indoor air in a given space + description: The rate at which outside air replaces indoor air in a given + space title: room air exchange rate examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - room air exchange rate + - room air exchange rate rank: 149 is_a: core field slot_uri: MIXS:0000169 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -26507,20 +27816,21 @@ classes: 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 + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - room architectural elements + - room architectural elements rank: 150 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000233 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -26536,16 +27846,16 @@ classes: description: The condition of the room at the time of sampling title: room condition examples: - - value: new + - value: new from_schema: https://w3id.org/nmdc/nmdc aliases: - - room condition + - room condition rank: 151 is_a: core field slot_uri: MIXS:0000822 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: room_condt_enum multivalued: false @@ -26561,16 +27871,16 @@ classes: description: List of rooms connected to the sampling room by a doorway title: rooms connected by a doorway examples: - - value: office + - value: office from_schema: https://w3id.org/nmdc/nmdc aliases: - - rooms connected by a doorway + - rooms connected by a doorway rank: 152 is_a: core field slot_uri: MIXS:0000826 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: room_connected_enum multivalued: false @@ -26583,19 +27893,20 @@ classes: occurrence: tag: occurrence value: '1' - description: The total count of rooms in the built structure including all room types + description: The total count of rooms in the built structure including all + room types title: room count examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - room count + - room count rank: 153 is_a: core field slot_uri: MIXS:0000234 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -26614,17 +27925,17 @@ classes: description: The length, width and height of sampling room title: room dimensions examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - room dimensions + - room dimensions rank: 154 is_a: core field string_serialization: '{integer} {unit} x {integer} {unit} x {integer} {unit}' slot_uri: MIXS:0000192 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -26640,20 +27951,21 @@ classes: occurrence: tag: occurrence value: '1' - description: Distance between doors (meters) in the hallway between the sampling room and adjacent rooms + description: Distance between doors (meters) in the hallway between the sampling + room and adjacent rooms title: room door distance examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - room door distance + - room door distance rank: 155 is_a: core field string_serialization: '{integer} {unit}' slot_uri: MIXS:0000193 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -26666,20 +27978,21 @@ classes: occurrence: tag: occurrence value: '1' - description: List of room(s) (room number, room name) sharing a door with the sampling room + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - rooms that share a door with sampling room + - rooms that share a door with sampling room rank: 156 is_a: core field string_serialization: '{text};{integer}' slot_uri: MIXS:0000242 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -26692,20 +28005,21 @@ classes: occurrence: tag: occurrence value: '1' - description: List of room(s) (room number, room name) located in the same hallway as sampling room + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - rooms that are on the same hallway + - rooms that are on the same hallway rank: 157 is_a: core field string_serialization: '{text};{integer}' slot_uri: MIXS:0000238 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -26721,16 +28035,16 @@ classes: description: The position of the room within the building title: room location in building examples: - - value: interior room + - value: interior room from_schema: https://w3id.org/nmdc/nmdc aliases: - - room location in building + - room location in building rank: 158 is_a: core field slot_uri: MIXS:0000823 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: room_loc_enum multivalued: false @@ -26743,19 +28057,20 @@ classes: 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 + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - room moisture damage or mold history + - room moisture damage or mold history rank: 159 is_a: core field slot_uri: MIXS:0000235 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: integer multivalued: false @@ -26774,17 +28089,17 @@ classes: description: The net floor area of sampling room. Net area excludes wall thicknesses title: room net area examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - room net area + - room net area rank: 160 is_a: core field string_serialization: '{integer} {unit}' slot_uri: MIXS:0000194 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -26800,16 +28115,16 @@ classes: description: Count of room occupancy at time of sampling title: room occupancy examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - room occupancy + - room occupancy rank: 161 is_a: core field slot_uri: MIXS:0000236 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -26823,19 +28138,20 @@ classes: occurrence: tag: occurrence value: '1' - description: The horizontal sampling position in the room relative to architectural elements + description: The horizontal sampling position in the room relative to architectural + elements title: room sampling position examples: - - value: south corner + - value: south corner from_schema: https://w3id.org/nmdc/nmdc aliases: - - room sampling position + - room sampling position rank: 162 is_a: core field slot_uri: MIXS:0000824 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: room_samp_pos_enum multivalued: false @@ -26848,19 +28164,20 @@ classes: occurrence: tag: occurrence value: '1' - description: The main purpose or activity of the sampling room. A room is any distinguishable space within a structure + 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 + - value: bathroom from_schema: https://w3id.org/nmdc/nmdc aliases: - - room type + - room type rank: 163 is_a: core field slot_uri: MIXS:0000825 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: room_type_enum multivalued: false @@ -26879,17 +28196,17 @@ classes: description: Volume of sampling room title: room volume examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - room volume + - room volume rank: 164 is_a: core field string_serialization: '{integer} {unit}' slot_uri: MIXS:0000195 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -26902,20 +28219,21 @@ classes: occurrence: tag: occurrence value: '1' - description: List of room(s) (room number, room name) sharing a wall with the sampling room + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - rooms that share a wall with sampling room + - rooms that share a wall with sampling room rank: 165 is_a: core field string_serialization: '{text};{integer}' slot_uri: MIXS:0000243 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -26931,16 +28249,16 @@ classes: description: Number of windows in the room title: room window count examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - room window count + - room window count rank: 166 is_a: core field slot_uri: MIXS:0000237 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: integer multivalued: false @@ -26956,16 +28274,16 @@ classes: description: The floor of the building, where the sampling room is located title: sampling floor examples: - - value: 4th floor + - value: 4th floor from_schema: https://w3id.org/nmdc/nmdc aliases: - - sampling floor + - sampling floor rank: 167 is_a: core field slot_uri: MIXS:0000828 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: samp_floor_enum multivalued: false @@ -26978,19 +28296,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Sampling room number. This ID should be consistent with the designations on the building floor plans + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - sampling room ID or name + - sampling room ID or name rank: 168 is_a: core field slot_uri: MIXS:0000244 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -27003,20 +28322,23 @@ classes: 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. + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample size sorting method + - sample size sorting method rank: 169 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000216 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -27035,16 +28357,16 @@ classes: description: The recent and long term history of outside sampling title: sampling time outside examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - sampling time outside + - sampling time outside rank: 170 is_a: core field slot_uri: MIXS:0000196 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -27060,35 +28382,42 @@ classes: description: The weather on the sampling day title: sampling day weather examples: - - value: foggy + - value: foggy from_schema: https://w3id.org/nmdc/nmdc aliases: - - sampling day weather + - sampling day weather rank: 171 is_a: core field slot_uri: MIXS:0000827 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: samp_weather_enum multivalued: false 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. + 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''' + - '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)' + - '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 + - value: IGSN:DSJ0284 from_schema: https://w3id.org/nmdc/nmdc rank: 5 string_serialization: '{text}:{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string recommended: true @@ -27103,20 +28432,22 @@ classes: 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). + 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] + - value: autumn [NCIT:C94733] from_schema: https://w3id.org/nmdc/nmdc aliases: - - season + - season rank: 172 is_a: core field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000829 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -27133,16 +28464,16 @@ classes: description: The seasons the space is occupied title: seasonal use examples: - - value: Winter + - value: Winter from_schema: https://w3id.org/nmdc/nmdc aliases: - - seasonal use + - seasonal use rank: 173 is_a: core field slot_uri: MIXS:0000830 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: season_use_enum multivalued: false @@ -27158,17 +28489,17 @@ classes: 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 + - value: no presence of mold visible from_schema: https://w3id.org/nmdc/nmdc aliases: - - shading device signs of water/mold + - 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 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -27184,16 +28515,16 @@ classes: description: The physical condition of the shading device at the time of sampling title: shading device condition examples: - - value: new + - value: new from_schema: https://w3id.org/nmdc/nmdc aliases: - - shading device condition + - shading device condition rank: 175 is_a: core field slot_uri: MIXS:0000831 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: shading_device_cond_enum multivalued: false @@ -27209,17 +28540,17 @@ classes: description: The location of the shading device in relation to the built structure title: shading device location examples: - - value: exterior + - value: exterior from_schema: https://w3id.org/nmdc/nmdc aliases: - - shading device location + - shading device location rank: 176 is_a: core field string_serialization: '[exterior|interior]' slot_uri: MIXS:0000832 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -27235,17 +28566,17 @@ classes: description: The material the shading device is composed of title: shading device material examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - shading device material + - shading device material rank: 177 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000245 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -27261,16 +28592,16 @@ classes: description: The type of shading device title: shading device type examples: - - value: slatted aluminum awning + - value: slatted aluminum awning from_schema: https://w3id.org/nmdc/nmdc aliases: - - shading device type + - shading device type rank: 178 is_a: core field slot_uri: MIXS:0000835 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: shading_device_type_enum multivalued: false @@ -27283,17 +28614,17 @@ classes: description: Filtering pore size used in sample preparation title: size fraction selected examples: - - value: 0-0.22 micrometer + - value: 0-0.22 micrometer from_schema: https://w3id.org/nmdc/nmdc aliases: - - size fraction selected + - size fraction selected rank: 285 is_a: nucleic acid sequence source field string_serialization: '{float}-{float} {unit}' slot_uri: MIXS:0000017 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -27309,17 +28640,17 @@ classes: description: Customary or normal state of the space title: space typical state examples: - - value: typically occupied + - value: typically occupied from_schema: https://w3id.org/nmdc/nmdc aliases: - - space typical state + - space typical state rank: 179 is_a: core field string_serialization: '[typically occupied|typically unoccupied]' slot_uri: MIXS:0000770 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -27332,36 +28663,40 @@ classes: occurrence: tag: occurrence value: '1' - description: 'The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents' + description: 'The building specifications. If design is chosen, indicate phase: + conceptual, schematic, design development, construction documents' title: specifications examples: - - value: construction + - value: construction from_schema: https://w3id.org/nmdc/nmdc aliases: - - specifications + - specifications rank: 180 is_a: core field slot_uri: MIXS:0000836 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: specific_enum multivalued: false 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 13 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study slot_group: sample_id_section range: SpecificEcosystemEnum recommended: true @@ -27377,19 +28712,21 @@ classes: 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. + 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 + - value: 15 per kilogram of air from_schema: https://w3id.org/nmdc/nmdc aliases: - - specific humidity + - specific humidity rank: 181 is_a: core field slot_uri: MIXS:0000214 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -27403,19 +28740,20 @@ classes: 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 + 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 + - value: basement from_schema: https://w3id.org/nmdc/nmdc aliases: - - substructure type + - substructure type rank: 182 is_a: core field slot_uri: MIXS:0000767 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: substructure_type_enum multivalued: true @@ -27431,16 +28769,16 @@ classes: description: Contaminant identified on surface title: surface-air contaminant examples: - - value: radon + - value: radon from_schema: https://w3id.org/nmdc/nmdc aliases: - - surface-air contaminant + - surface-air contaminant rank: 183 is_a: core field slot_uri: MIXS:0000759 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: surf_air_cont_enum multivalued: true @@ -27459,16 +28797,16 @@ classes: description: 'Surfaces: water activity as a function of air and material moisture' title: surface humidity examples: - - value: 10% + - value: 10% from_schema: https://w3id.org/nmdc/nmdc aliases: - - surface humidity + - surface humidity rank: 184 is_a: core field slot_uri: MIXS:0000123 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -27485,16 +28823,16 @@ classes: description: Surface materials at the point of sampling title: surface material examples: - - value: wood + - value: wood from_schema: https://w3id.org/nmdc/nmdc aliases: - - surface material + - surface material rank: 185 is_a: core field slot_uri: MIXS:0000758 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: surf_material_enum multivalued: false @@ -27513,16 +28851,16 @@ classes: description: Water held on a surface title: surface moisture examples: - - value: 0.01 gram per square meter + - value: 0.01 gram per square meter from_schema: https://w3id.org/nmdc/nmdc aliases: - - surface moisture + - surface moisture rank: 186 is_a: core field slot_uri: MIXS:0000128 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -27539,16 +28877,16 @@ classes: description: ph measurement of surface title: surface moisture pH examples: - - value: '7' + - value: '7' from_schema: https://w3id.org/nmdc/nmdc aliases: - - surface moisture pH + - surface moisture pH rank: 187 is_a: core field slot_uri: MIXS:0000760 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: double multivalued: false @@ -27567,16 +28905,16 @@ classes: description: Temperature of the surface at the time of sampling title: surface temperature examples: - - value: 15 degree Celsius + - value: 15 degree Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - - surface temperature + - surface temperature rank: 188 is_a: core field slot_uri: MIXS:0000125 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -27593,16 +28931,16 @@ classes: description: Temperature of the sample at the time of sampling. title: temperature examples: - - value: 25 degree Celsius + - value: 25 degree Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - - temperature + - temperature rank: 37 is_a: environment field slot_uri: MIXS:0000113 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -27622,16 +28960,16 @@ classes: description: The recorded temperature value at sampling time outside title: temperature outside house examples: - - value: 5 degree Celsius + - value: 5 degree Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - - temperature outside house + - temperature outside house rank: 189 is_a: core field slot_uri: MIXS:0000197 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -27648,16 +28986,16 @@ classes: description: The subway line name title: train line examples: - - value: red + - value: red from_schema: https://w3id.org/nmdc/nmdc aliases: - - train line + - train line rank: 190 is_a: core field slot_uri: MIXS:0000837 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: train_line_enum multivalued: false @@ -27673,16 +29011,16 @@ classes: description: The train station collection location title: train station collection location examples: - - value: forest hills + - value: forest hills from_schema: https://w3id.org/nmdc/nmdc aliases: - - train station collection location + - train station collection location rank: 191 is_a: core field slot_uri: MIXS:0000838 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: train_stat_loc_enum multivalued: false @@ -27698,16 +29036,16 @@ classes: description: The train stop collection location title: train stop collection location examples: - - value: end + - value: end from_schema: https://w3id.org/nmdc/nmdc aliases: - - train stop collection location + - train stop collection location rank: 192 is_a: core field slot_uri: MIXS:0000839 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: train_stop_loc_enum multivalued: false @@ -27723,16 +29061,16 @@ classes: description: Customary or normal density of occupants title: typical occupant density examples: - - value: '25' + - value: '25' from_schema: https://w3id.org/nmdc/nmdc aliases: - - typical occupant density + - typical occupant density rank: 193 is_a: core field slot_uri: MIXS:0000771 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: double multivalued: false @@ -27748,17 +29086,17 @@ classes: description: Ventilation system used in the sampled premises title: ventilation type examples: - - value: Operable windows + - value: Operable windows from_schema: https://w3id.org/nmdc/nmdc aliases: - - ventilation type + - ventilation type rank: 57 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000756 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -27774,16 +29112,16 @@ classes: description: The building visual media title: visual media examples: - - value: 3D scans + - value: 3D scans from_schema: https://w3id.org/nmdc/nmdc aliases: - - visual media + - visual media rank: 194 is_a: core field slot_uri: MIXS:0000840 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: vis_media_enum multivalued: false @@ -27802,16 +29140,16 @@ classes: description: The total area of the sampled room's walls title: wall area examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - wall area + - wall area rank: 195 is_a: core field slot_uri: MIXS:0000198 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -27825,19 +29163,20 @@ classes: occurrence: tag: occurrence value: '1' - description: The building class of the wall defined by the composition of the building elements and fire-resistance rating. + 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 + - value: fire resistive from_schema: https://w3id.org/nmdc/nmdc aliases: - - wall construction type + - wall construction type rank: 196 is_a: core field slot_uri: MIXS:0000841 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: wall_const_type_enum multivalued: false @@ -27853,16 +29192,16 @@ classes: description: The material utilized to finish the outer most layer of the wall title: wall finish material examples: - - value: wood + - value: wood from_schema: https://w3id.org/nmdc/nmdc aliases: - - wall finish material + - wall finish material rank: 197 is_a: core field slot_uri: MIXS:0000842 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: wall_finish_mat_enum multivalued: false @@ -27881,16 +29220,16 @@ classes: description: The average height of the walls in the sampled room title: wall height examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - wall height + - wall height rank: 198 is_a: core field slot_uri: MIXS:0000221 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -27907,16 +29246,16 @@ classes: description: The relative location of the wall within the room title: wall location examples: - - value: north + - value: north from_schema: https://w3id.org/nmdc/nmdc aliases: - - wall location + - wall location rank: 199 is_a: core field slot_uri: MIXS:0000843 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: wall_loc_enum multivalued: false @@ -27932,16 +29271,16 @@ classes: description: The surface treatment of interior wall title: wall surface treatment examples: - - value: paneling + - value: paneling from_schema: https://w3id.org/nmdc/nmdc aliases: - - wall surface treatment + - wall surface treatment rank: 200 is_a: core field slot_uri: MIXS:0000845 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: wall_surf_treatment_enum multivalued: false @@ -27957,16 +29296,16 @@ classes: description: The feel, appearance, or consistency of a wall surface title: wall texture examples: - - value: popcorn + - value: popcorn from_schema: https://w3id.org/nmdc/nmdc aliases: - - wall texture + - wall texture rank: 201 is_a: core field slot_uri: MIXS:0000846 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: wall_texture_enum multivalued: false @@ -27982,19 +29321,21 @@ classes: 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 + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - wall thermal mass + - wall thermal mass rank: 202 is_a: core field slot_uri: MIXS:0000222 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -28011,17 +29352,17 @@ classes: 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 + - value: no presence of mold visible from_schema: https://w3id.org/nmdc/nmdc aliases: - - wall signs of water/mold + - 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 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -28040,16 +29381,16 @@ classes: description: The size of the water feature title: water feature size examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - water feature size + - water feature size rank: 204 is_a: core field slot_uri: MIXS:0000223 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -28066,16 +29407,16 @@ classes: description: The type of water feature present within the building being sampled title: water feature type examples: - - value: stream + - value: stream from_schema: https://w3id.org/nmdc/nmdc aliases: - - water feature type + - water feature type rank: 205 is_a: core field slot_uri: MIXS:0000847 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: water_feat_type_enum multivalued: false @@ -28091,16 +29432,16 @@ classes: description: The day of the week when sampling occurred title: weekday examples: - - value: Sunday + - value: Sunday from_schema: https://w3id.org/nmdc/nmdc aliases: - - weekday + - weekday rank: 206 is_a: core field slot_uri: MIXS:0000848 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: weekday_enum multivalued: false @@ -28116,16 +29457,16 @@ classes: description: The physical condition of the window at the time of sampling title: window condition examples: - - value: rupture + - value: rupture from_schema: https://w3id.org/nmdc/nmdc aliases: - - window condition + - window condition rank: 207 is_a: core field slot_uri: MIXS:0000849 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: window_cond_enum multivalued: false @@ -28141,16 +29482,16 @@ classes: description: The type of window covering title: window covering examples: - - value: curtains + - value: curtains from_schema: https://w3id.org/nmdc/nmdc aliases: - - window covering + - window covering rank: 208 is_a: core field slot_uri: MIXS:0000850 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: window_cover_enum multivalued: false @@ -28166,16 +29507,16 @@ classes: description: The horizontal position of the window on the wall title: window horizontal position examples: - - value: middle + - value: middle from_schema: https://w3id.org/nmdc/nmdc aliases: - - window horizontal position + - window horizontal position rank: 209 is_a: core field slot_uri: MIXS:0000851 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: window_horiz_pos_enum multivalued: false @@ -28191,16 +29532,16 @@ classes: description: The relative location of the window within the room title: window location examples: - - value: west + - value: west from_schema: https://w3id.org/nmdc/nmdc aliases: - - window location + - window location rank: 210 is_a: core field slot_uri: MIXS:0000852 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: window_loc_enum multivalued: false @@ -28216,16 +29557,16 @@ classes: description: The type of material used to finish a window title: window material examples: - - value: wood + - value: wood from_schema: https://w3id.org/nmdc/nmdc aliases: - - window material + - window material rank: 211 is_a: core field slot_uri: MIXS:0000853 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: window_mat_enum multivalued: false @@ -28241,16 +29582,16 @@ classes: description: The number of times windows are opened per week title: window open frequency examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - window open frequency + - window open frequency rank: 212 is_a: core field slot_uri: MIXS:0000246 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -28269,17 +29610,17 @@ classes: description: The window's length and width title: window area/size examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - window area/size + - window area/size rank: 213 is_a: core field string_serialization: '{float} {unit} x {float} {unit}' slot_uri: MIXS:0000224 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -28292,20 +29633,21 @@ classes: occurrence: tag: occurrence value: '1' - description: Defines whether the windows were open or closed during environmental testing + description: Defines whether the windows were open or closed during environmental + testing title: window status examples: - - value: open + - value: open from_schema: https://w3id.org/nmdc/nmdc aliases: - - window status + - window status rank: 214 is_a: core field string_serialization: '[closed|open]' slot_uri: MIXS:0000855 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -28321,16 +29663,16 @@ classes: description: The type of windows title: window type examples: - - value: fixed window + - value: fixed window from_schema: https://w3id.org/nmdc/nmdc aliases: - - window type + - window type rank: 215 is_a: core field slot_uri: MIXS:0000856 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: window_type_enum multivalued: false @@ -28346,16 +29688,16 @@ classes: description: The vertical position of the window on the wall title: window vertical position examples: - - value: middle + - value: middle from_schema: https://w3id.org/nmdc/nmdc aliases: - - window vertical position + - window vertical position rank: 216 is_a: core field slot_uri: MIXS:0000857 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: window_vert_pos_enum multivalued: false @@ -28371,17 +29713,17 @@ classes: 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 + - value: no presence of mold visible from_schema: https://w3id.org/nmdc/nmdc aliases: - - window signs of water/mold + - 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 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -28402,31 +29744,32 @@ classes: from_schema: https://example.com/nmdc_submission_schema is_a: DhInterface mixins: - - DhMultiviewCommonColumnsMixin + - 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 + - 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 + 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 + - add 'see_alsos' with link to NEXUS info comments: - - Enter a temperature in celsius. Numeric portion only. + - Enter a temperature in celsius. Numeric portion only. examples: - - value: '-80' + - value: '-80' from_schema: https://w3id.org/nmdc/nmdc rank: 4 string_serialization: '{float}' @@ -28444,7 +29787,7 @@ classes: string_serialization: '{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: emsl_section range: string required: true @@ -28455,69 +29798,74 @@ classes: 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 + - 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 + - Biosample 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. + 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. + - 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 + - value: 15 g + - value: 100 uL + - value: 5 mL from_schema: https://w3id.org/nmdc/nmdc rank: 3 string_serialization: '{float} {unit}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: emsl_section range: string required: true recommended: false - pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ multivalued: false + 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. + - This can vary from 'environmental package' if the sample is an extraction. examples: - - value: water extracted soil + - value: water extracted soil from_schema: https://w3id.org/nmdc/nmdc rank: 2 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: emsl_section range: SampleTypeEnum required: true recommended: false technical_reps: name: technical_reps - description: If sending technical replicates of the same sample, indicate the replicate count. + 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. + - This field is only required when completing metadata for samples being submitted + to EMSL for analyses. examples: - - value: '2' + - value: '2' from_schema: https://w3id.org/nmdc/nmdc rank: 5 string_serialization: '{integer}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: emsl_section range: integer recommended: true @@ -28535,108 +29883,108 @@ classes: from_schema: https://example.com/nmdc_submission_schema is_a: DhInterface mixins: - - DhMultiviewCommonColumnsMixin + - 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 - - 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 + - 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 + - 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 slot_usage: additional_info: name: additional_info @@ -28647,20 +29995,21 @@ classes: 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 + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - additional info + - additional info rank: 290 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000300 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -28676,19 +30025,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + 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 + - value: 50 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - alkalinity + - alkalinity rank: 1 is_a: core field slot_uri: MIXS:0000421 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -28705,17 +30055,17 @@ classes: description: Method used for alkalinity measurement title: alkalinity method examples: - - value: titration + - value: titration from_schema: https://w3id.org/nmdc/nmdc aliases: - - alkalinity method + - alkalinity method rank: 218 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000298 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -28734,16 +30084,16 @@ classes: description: Concentration of ammonium in the sample title: ammonium examples: - - value: 1.5 milligram per liter + - value: 1.5 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - ammonium + - ammonium rank: 4 is_a: core field slot_uri: MIXS:0000427 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -28760,19 +30110,21 @@ classes: 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)' + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - API gravity + - API gravity rank: 291 is_a: core field slot_uri: MIXS:0000157 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -28789,20 +30141,24 @@ classes: 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)' + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - aromatics wt% + - aromatics wt% rank: 292 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000133 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -28819,20 +30175,24 @@ classes: 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)' + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - asphaltenes wt% + - asphaltenes wt% rank: 293 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000135 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -28849,17 +30209,17 @@ classes: description: Name of the basin (e.g. Campos) title: basin name examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - basin name + - basin name rank: 294 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000290 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -28878,16 +30238,16 @@ classes: description: Concentration of benzene in the sample title: benzene examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - benzene + - benzene rank: 295 is_a: core field slot_uri: MIXS:0000153 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -28907,16 +30267,16 @@ classes: description: Concentration of calcium in the sample title: calcium examples: - - value: 0.2 micromole per liter + - value: 0.2 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - calcium + - calcium rank: 9 is_a: core field slot_uri: MIXS:0000432 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -28930,21 +30290,24 @@ classes: 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 + 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 + - 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 + - chemical administration rank: 17 is_a: core field string_serialization: '{termLabel} {[termID]};{timestamp}' slot_uri: MIXS:0000751 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -28965,16 +30328,16 @@ classes: description: Concentration of chloride in the sample title: chloride examples: - - value: 5000 milligram per liter + - value: 5000 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - chloride + - chloride rank: 10 is_a: core field slot_uri: MIXS:0000429 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -28988,22 +30351,23 @@ classes: 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) + - 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' + - value: '2021-04-15' + - value: 2021-04 + - value: '2021' from_schema: https://w3id.org/nmdc/nmdc aliases: - - collection date + - collection date rank: 3 is_a: environment field string_serialization: '{date, arbitrary precision}' slot_uri: MIXS:0000011 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string required: true @@ -29021,19 +30385,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + 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 + - value: 1000 kilogram per cubic meter from_schema: https://w3id.org/nmdc/nmdc aliases: - - density + - density rank: 12 is_a: core field slot_uri: MIXS:0000435 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -29047,19 +30412,20 @@ classes: 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 + 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 + - value: Continental - Alluvial from_schema: https://w3id.org/nmdc/nmdc aliases: - - depositional environment + - depositional environment rank: 304 is_a: core field slot_uri: MIXS:0000992 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: depos_env_enum multivalued: false @@ -29069,25 +30435,27 @@ classes: 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. + 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 + - Use modified term comments: - - All depths must be reported in meters. Provide the numerical portion only. + - All depths must be reported in meters. Provide the numerical portion only. examples: - - value: 0 - 0.1 - - value: '1' + - value: 0 - 0.1 + - value: '1' from_schema: https://w3id.org/nmdc/nmdc aliases: - - depth + - depth rank: 9 is_a: environment field string_serialization: '{float}|{float}-{float}' slot_uri: MIXS:0000018 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -29105,19 +30473,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + 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 + - value: 5 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - dissolved carbon dioxide + - dissolved carbon dioxide rank: 14 is_a: core field slot_uri: MIXS:0000436 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -29134,19 +30503,20 @@ classes: 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 + 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 + - value: 2059 micromole per kilogram from_schema: https://w3id.org/nmdc/nmdc aliases: - - dissolved inorganic carbon + - dissolved inorganic carbon rank: 16 is_a: core field slot_uri: MIXS:0000434 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -29166,16 +30536,16 @@ classes: description: Concentration of dissolved inorganic phosphorus in the sample title: dissolved inorganic phosphorus examples: - - value: 56.5 micromole per liter + - value: 56.5 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - dissolved inorganic phosphorus + - dissolved inorganic phosphorus rank: 224 is_a: core field slot_uri: MIXS:0000106 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -29195,16 +30565,16 @@ classes: description: Concentration of dissolved iron in the sample title: dissolved iron examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - dissolved iron + - dissolved iron rank: 305 is_a: core field slot_uri: MIXS:0000139 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -29221,19 +30591,20 @@ classes: 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 + 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 + - value: 197 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - dissolved organic carbon + - dissolved organic carbon rank: 17 is_a: core field slot_uri: MIXS:0000433 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -29250,88 +30621,113 @@ classes: 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). + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - dissolved oxygen in fluids + - dissolved oxygen in fluids rank: 306 is_a: core field slot_uri: MIXS:0000438 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 9 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 10 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 12 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 11 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study slot_group: sample_id_section range: EcosystemTypeEnum recommended: true @@ -29341,25 +30737,31 @@ classes: 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. + 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. + - 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' + - value: '225' + - value: '0' + - value: '1250' from_schema: https://w3id.org/nmdc/nmdc aliases: - - elevation + - elevation rank: 6 is_a: environment field slot_uri: MIXS:0000093 owner: Biosample domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample slot_group: mixs_modified_section range: float required: true @@ -29369,26 +30771,44 @@ classes: 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. + 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. tooltip: tag: tooltip - value: The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context - 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' + value: The biome or major environmental system where the sample or specimen + originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] + in the Environment Ontology (ENVO). For host-associated or plant-associated + samples, use terms from the UBERON or Plant Ontology to describe the + broad anatomical or morphological context + 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) + - range changed to enumeration late in makefile, so this is modified (but + "sample ID" anyway) examples: - - value: oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean + - 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://w3id.org/nmdc/nmdc aliases: - - broad-scale environmental context + - broad-scale environmental context rank: 6 is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000012 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string required: true @@ -29399,30 +30819,45 @@ classes: annotations: expected_value: tag: expected_value - value: Environmental entities having causal influences upon the entity at time of sampling. + value: Environmental entities having causal influences upon the entity + at time of sampling. tooltip: tag: tooltip - value: The specific environmental entities or features near the sample or specimen that significantly influence its characteristics or composition. These entities are typically smaller in scale than the broad environmental context. Values for this field should be countable, material nouns and must be chosen from subclasses of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe specific anatomical structures or plant parts. - 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.' + value: The specific environmental entities or features near the sample + or specimen that significantly influence its characteristics or composition. + These entities are typically smaller in scale than the broad environmental + context. Values for this field should be countable, material nouns and + must be chosen from subclasses of BFO:0000040 (material entity) that + appear in the Environment Ontology (ENVO). For host-associated or plant-associated + samples, use terms from the UBERON or Plant Ontology to describe specific + anatomical structures or plant parts. + 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) + - 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] + - 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 aliases: - - local environmental context + - local environmental context rank: 7 is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000013 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string required: true @@ -29433,26 +30868,41 @@ classes: annotations: expected_value: tag: expected_value - value: The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]. + value: The material displaced by the entity at time of sampling. Recommend + subclasses of environmental material [ENVO:00010483]. tooltip: tag: tooltip - value: The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure - 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).' + value: The predominant environmental material or substrate that directly + surrounds or hosts the sample or specimen at the time of sampling. Choose + values from subclasses of the 'environmental material' class [ENVO:00010483] + in the Environment Ontology (ENVO). Values for this field should be + measurable or mass material nouns, representing continuous environmental + materials. For host-associated or plant-associated samples, use terms + from the UBERON or Plant Ontology to indicate a tissue, organ, or plant + structure + 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) + - range changed to enumeration late in makefile, so this is modified (but + "sample ID" anyway) examples: - - value: soil [ENVO:00001998] + - value: soil [ENVO:00001998] from_schema: https://w3id.org/nmdc/nmdc aliases: - - environmental medium + - environmental medium rank: 8 is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000014 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string required: true @@ -29473,16 +30923,16 @@ classes: description: Concentration of ethylbenzene in the sample title: ethylbenzene examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - ethylbenzene + - ethylbenzene rank: 309 is_a: core field slot_uri: MIXS:0000155 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -29493,20 +30943,25 @@ classes: 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 + 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] + - value: time series design [EFO:EFO_0001779] from_schema: https://w3id.org/nmdc/nmdc aliases: - - experimental factor + - experimental factor rank: 12 is_a: investigation field string_serialization: '{termLabel} {[termID]}|{text}' slot_uri: MIXS:0000008 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -29522,17 +30977,17 @@ classes: description: Name of the hydrocarbon field (e.g. Albacora) title: field name examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - field name + - field name rank: 310 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000291 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -29541,22 +30996,24 @@ classes: 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. + 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' + - value: 'USA: Maryland, Bethesda' from_schema: https://w3id.org/nmdc/nmdc aliases: - - geographic location (country and/or sea,region) + - geographic location (country and/or sea,region) rank: 4 is_a: environment field string_serialization: '{text}: {text}, {text}' slot_uri: MIXS:0000010 owner: Biosample domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample slot_group: mixs_modified_section range: string required: true @@ -29571,19 +31028,21 @@ classes: 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 + 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 + - value: Gas from_schema: https://w3id.org/nmdc/nmdc aliases: - - hydrocarbon type produced + - hydrocarbon type produced rank: 313 is_a: core field slot_uri: MIXS:0000989 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: hc_produced_enum multivalued: false @@ -29596,19 +31055,25 @@ classes: 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 + 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 + - value: Oil Sand from_schema: https://w3id.org/nmdc/nmdc aliases: - - hydrocarbon resource type + - hydrocarbon resource type rank: 314 is_a: core field slot_uri: MIXS:0000988 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: hcr_enum multivalued: false @@ -29624,19 +31089,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + description: Original formation water salinity (prior to secondary recovery + e.g. Waterflooding) expressed as TDS title: formation water salinity examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - formation water salinity + - formation water salinity rank: 315 is_a: core field slot_uri: MIXS:0000406 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -29650,19 +31116,20 @@ classes: 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' + 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 + - value: Silurian from_schema: https://w3id.org/nmdc/nmdc aliases: - - hydrocarbon resource geological age + - hydrocarbon resource geological age rank: 316 is_a: core field slot_uri: MIXS:0000993 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: hcr_geol_age_enum multivalued: false @@ -29681,17 +31148,17 @@ classes: description: Original pressure of the hydrocarbon resource title: hydrocarbon resource original pressure examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - hydrocarbon resource original pressure + - hydrocarbon resource original pressure rank: 317 is_a: core field string_serialization: '{float} - {float} {unit}' slot_uri: MIXS:0000395 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -29710,17 +31177,17 @@ classes: description: Original temperature of the hydrocarbon resource title: hydrocarbon resource original temperature examples: - - value: 150-295 degree Celsius + - value: 150-295 degree Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - - hydrocarbon resource original temperature + - hydrocarbon resource original temperature rank: 318 is_a: core field string_serialization: '{float} - {float} {unit}' slot_uri: MIXS:0000393 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -29730,23 +31197,26 @@ classes: 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 + 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) notes: - - This is currently a required field but it's not clear if this should be required for human hosts + - This is currently a required field but it's not clear if this should be + required for human hosts examples: - - value: 50.586825 6.408977 + - value: 50.586825 6.408977 from_schema: https://w3id.org/nmdc/nmdc aliases: - - geographic location (latitude and longitude) + - geographic location (latitude and longitude) rank: 5 is_a: environment field string_serialization: '{lat lon}' slot_uri: MIXS:0000009 owner: Biosample domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample slot_group: mixs_modified_section range: string required: true @@ -29761,19 +31231,21 @@ classes: 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' + 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 + - value: Volcanic from_schema: https://w3id.org/nmdc/nmdc aliases: - - lithology + - lithology rank: 336 is_a: core field slot_uri: MIXS:0000990 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: lithology_enum multivalued: false @@ -29785,23 +31257,24 @@ classes: value: measurement value preferred_unit: tag: preferred_unit - value: mole per liter, milligram per liter, parts per million, micromole per kilogram + 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 + - value: 52.8 micromole per kilogram from_schema: https://w3id.org/nmdc/nmdc aliases: - - magnesium + - magnesium rank: 21 is_a: core field slot_uri: MIXS:0000431 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -29815,24 +31288,26 @@ classes: occurrence: tag: occurrence value: m - description: Any other measurement performed or parameter collected, that is not listed here + 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 + - value: Bicarbonate ion concentration;2075 micromole per kilogram from_schema: https://w3id.org/nmdc/nmdc aliases: - - miscellaneous parameter + - miscellaneous parameter rank: 23 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000752 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false - 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]+)$ + 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: @@ -29848,16 +31323,16 @@ classes: description: Concentration of nitrate in the sample title: nitrate examples: - - value: 65 micromole per liter + - value: 65 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - nitrate + - nitrate rank: 26 is_a: core field slot_uri: MIXS:0000425 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -29877,16 +31352,16 @@ classes: description: Concentration of nitrite in the sample title: nitrite examples: - - value: 0.5 micromole per liter + - value: 0.5 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - nitrite + - nitrite rank: 27 is_a: core field slot_uri: MIXS:0000426 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -29896,27 +31371,34 @@ classes: 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 + 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)' + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - organism count qPCR information + - 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' + 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 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -29928,23 +31410,28 @@ classes: 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 + 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)' + 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 + - value: total prokaryotes;3.5e7 cells per milliliter;qPCR from_schema: https://w3id.org/nmdc/nmdc aliases: - - organism count + - organism count rank: 30 is_a: core field slot_uri: MIXS:0000103 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -29961,19 +31448,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS) + description: Depth of the original oil water contact (OWC) zone (average) + (m TVDSS) title: oil water contact depth examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - oil water contact depth + - oil water contact depth rank: 339 is_a: core field slot_uri: MIXS:0000405 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -29990,16 +31478,16 @@ classes: description: Oxygenation status of sample title: oxygenation status of sample examples: - - value: aerobic + - value: aerobic from_schema: https://w3id.org/nmdc/nmdc aliases: - - oxygenation status of sample + - oxygenation status of sample rank: 25 is_a: core field slot_uri: MIXS:0000753 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: OxyStatSampEnum multivalued: false @@ -30015,20 +31503,21 @@ classes: 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))' + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - permeability + - permeability rank: 340 is_a: core field string_serialization: '{integer} - {integer} {unit}' slot_uri: MIXS:0000404 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -30041,22 +31530,23 @@ classes: occurrence: tag: occurrence value: '1' - description: pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + description: pH measurement of the sample, or liquid portion of sample, or + aqueous phase of the fluid title: pH notes: - - Use modified term + - Use modified term examples: - - value: '7.2' + - value: '7.2' from_schema: https://w3id.org/nmdc/nmdc aliases: - - pH + - pH rank: 27 is_a: core field string_serialization: '{float}' slot_uri: MIXS:0001001 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: float recommended: true @@ -30075,20 +31565,20 @@ classes: 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. + - 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 + - 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 aliases: - - pH method + - pH method rank: 41 is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0001106 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -30104,20 +31594,21 @@ classes: occurrence: tag: occurrence value: '1' - description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + description: Porosity of deposited sediment is volume of voids divided by + the total volume of sample title: porosity examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - porosity + - porosity rank: 37 is_a: core field string_serialization: '{float} - {float} {unit}' slot_uri: MIXS:0000211 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -30136,16 +31627,16 @@ classes: description: Concentration of potassium in the sample title: potassium examples: - - value: 463 milligram per liter + - value: 463 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - potassium + - potassium rank: 38 is_a: core field slot_uri: MIXS:0000430 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -30162,19 +31653,22 @@ classes: 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)' + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - pour point + - pour point rank: 341 is_a: core field slot_uri: MIXS:0000127 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -30194,16 +31688,16 @@ classes: description: Pressure to which the sample is subject to, in atmospheres title: pressure examples: - - value: 50 atmosphere + - value: 50 atmosphere from_schema: https://w3id.org/nmdc/nmdc aliases: - - pressure + - pressure rank: 39 is_a: core field slot_uri: MIXS:0000412 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -30220,17 +31714,17 @@ classes: description: Name of the reservoir (e.g. Carapebus) title: reservoir name examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - reservoir name + - reservoir name rank: 347 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000303 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -30246,20 +31740,24 @@ classes: 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)' + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - resins wt% + - resins wt% rank: 348 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000134 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -30276,19 +31774,24 @@ classes: 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. + 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 + - value: 25 practical salinity unit from_schema: https://w3id.org/nmdc/nmdc aliases: - - salinity + - salinity rank: 54 is_a: core field slot_uri: MIXS:0000183 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -30299,22 +31802,24 @@ classes: 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). + 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 + - Report dimensions and details when applicable examples: - - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample collection device + - sample collection device rank: 14 is_a: nucleic acid sequence source field string_serialization: '{termLabel} {[termID]}|{text}' slot_uri: MIXS:0000002 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -30328,19 +31833,19 @@ classes: description: The method employed for collecting the sample. title: sample collection method comments: - - This can be a citation or description + - This can be a citation or description examples: - - value: swabbing + - value: swabbing from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample collection method + - sample collection method rank: 15 is_a: nucleic acid sequence source field string_serialization: '{PMID}|{DOI}|{URL}|{text}' slot_uri: MIXS:0001225 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -30350,21 +31855,23 @@ classes: 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. + 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 + - value: filtering of seawater + - value: storing samples in ethanol from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample material processing + - sample material processing rank: 12 is_a: nucleic acid sequence source field string_serialization: '{text}' slot_uri: MIXS:0000016 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -30380,19 +31887,25 @@ classes: 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 + 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 + - value: 1534 meter;MSL from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample measured depth + - sample measured depth rank: 351 is_a: core field slot_uri: MIXS:0000413 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -30406,23 +31919,25 @@ classes: 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. + 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. + - 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 + - value: 5 grams + - value: 10 mL from_schema: https://w3id.org/nmdc/nmdc aliases: - - amount or size of sample collected + - amount or size of sample collected rank: 18 is_a: nucleic acid sequence source field string_serialization: '{float} {unit}' slot_uri: MIXS:0000001 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -30439,17 +31954,17 @@ classes: description: Duration for which the sample was stored title: sample storage duration examples: - - value: P1Y6M + - value: P1Y6M from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample storage duration + - sample storage duration rank: 353 is_a: core field string_serialization: '{duration}' slot_uri: MIXS:0000116 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -30462,20 +31977,21 @@ classes: occurrence: tag: occurrence value: '1' - description: Location at which sample was stored, usually name of a specific freezer/room + description: Location at which sample was stored, usually name of a specific + freezer/room title: sample storage location examples: - - value: Freezer no:5 + - value: Freezer no:5 from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample storage location + - sample storage location rank: 41 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000755 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -30494,16 +32010,16 @@ classes: description: Temperature at which the sample was stored (degrees are assumed) title: sample storage temperature examples: - - value: -80 Celsius + - value: -80 Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample storage temperature + - sample storage temperature rank: 7 is_a: core field slot_uri: MIXS:0000110 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string required: true @@ -30518,19 +32034,21 @@ classes: 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 + 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 + - value: biofilm from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample subtype + - sample subtype rank: 354 is_a: core field slot_uri: MIXS:0000999 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: samp_subtype_enum multivalued: false @@ -30546,20 +32064,21 @@ classes: 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) + 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 + - value: 5 days;-20 degree Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample transport conditions + - sample transport conditions rank: 355 is_a: core field string_serialization: '{float} {unit};{float} {unit}' slot_uri: MIXS:0000410 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -30575,20 +32094,22 @@ classes: 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 + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample true vertical depth subsea + - sample true vertical depth subsea rank: 356 is_a: core field string_serialization: '{float}-{float} {unit}' slot_uri: MIXS:0000409 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -30601,20 +32122,25 @@ classes: 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). + 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] + - value: built environment sample [GENEPIO:0001248] from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample type + - sample type rank: 357 is_a: core field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000998 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -30631,36 +32157,43 @@ classes: description: Name of the well (e.g. BXA1123) where sample was taken title: sample well name examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample well name + - sample well name rank: 358 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000296 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false 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. + 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''' + - '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)' + - '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 + - value: IGSN:DSJ0284 from_schema: https://w3id.org/nmdc/nmdc rank: 5 string_serialization: '{text}:{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string recommended: true @@ -30678,20 +32211,24 @@ classes: 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)' + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - saturates wt% + - saturates wt% rank: 359 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000131 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -30705,17 +32242,17 @@ classes: description: Filtering pore size used in sample preparation title: size fraction selected examples: - - value: 0-0.22 micrometer + - value: 0-0.22 micrometer from_schema: https://w3id.org/nmdc/nmdc aliases: - - size fraction selected + - size fraction selected rank: 285 is_a: nucleic acid sequence source field string_serialization: '{float}-{float} {unit}' slot_uri: MIXS:0000017 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -30734,34 +32271,37 @@ classes: description: Sodium concentration in the sample title: sodium examples: - - value: 10.5 milligram per liter + - value: 10.5 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - sodium + - sodium rank: 363 is_a: core field slot_uri: MIXS:0000428 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 13 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study slot_group: sample_id_section range: SpecificEcosystemEnum recommended: true @@ -30774,19 +32314,20 @@ classes: 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 + 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 + - value: Marine from_schema: https://w3id.org/nmdc/nmdc aliases: - - source rock depositional environment + - source rock depositional environment rank: 366 is_a: core field slot_uri: MIXS:0000996 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: sr_dep_env_enum multivalued: false @@ -30799,19 +32340,20 @@ classes: 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' + 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 + - value: Silurian from_schema: https://w3id.org/nmdc/nmdc aliases: - - source rock geological age + - source rock geological age rank: 367 is_a: core field slot_uri: MIXS:0000997 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: sr_geol_age_enum multivalued: false @@ -30824,19 +32366,23 @@ classes: 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' + 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 + - value: Type IV from_schema: https://w3id.org/nmdc/nmdc aliases: - - source rock kerogen type + - source rock kerogen type rank: 368 is_a: core field slot_uri: MIXS:0000994 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: sr_kerog_type_enum multivalued: false @@ -30849,19 +32395,20 @@ classes: 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 + 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 + - value: Coal from_schema: https://w3id.org/nmdc/nmdc aliases: - - source rock lithology + - source rock lithology rank: 369 is_a: core field slot_uri: MIXS:0000995 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: sr_lithology_enum multivalued: false @@ -30880,16 +32427,16 @@ classes: description: Concentration of sulfate in the sample title: sulfate examples: - - value: 5 micromole per liter + - value: 5 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - sulfate + - sulfate rank: 44 is_a: core field slot_uri: MIXS:0000423 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -30909,16 +32456,16 @@ classes: description: Original sulfate concentration in the hydrocarbon resource title: sulfate in formation water examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - sulfate in formation water + - sulfate in formation water rank: 370 is_a: core field slot_uri: MIXS:0000407 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -30938,16 +32485,16 @@ classes: description: Concentration of sulfide in the sample title: sulfide examples: - - value: 2 micromole per liter + - value: 2 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - sulfide + - sulfide rank: 371 is_a: core field slot_uri: MIXS:0000424 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -30960,28 +32507,31 @@ classes: 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 + 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 + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - suspended solids + - suspended solids rank: 372 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000150 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false - 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]+)$ + 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: @@ -30994,19 +32544,22 @@ classes: 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)' + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - total acid number + - total acid number rank: 373 is_a: core field slot_uri: MIXS:0000120 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -31023,16 +32576,16 @@ classes: description: Temperature of the sample at the time of sampling. title: temperature examples: - - value: 25 degree Celsius + - value: 25 degree Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - - temperature + - temperature rank: 37 is_a: environment field slot_uri: MIXS:0000113 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -31052,16 +32605,16 @@ classes: description: Concentration of toluene in the sample title: toluene examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - toluene + - toluene rank: 375 is_a: core field slot_uri: MIXS:0000154 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -31081,16 +32634,16 @@ classes: description: Concentration of total iron in the sample title: total iron examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - total iron + - total iron rank: 376 is_a: core field slot_uri: MIXS:0000105 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -31107,19 +32660,21 @@ classes: 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' + 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 + - value: 50 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - total nitrogen concentration + - total nitrogen concentration rank: 377 is_a: core field slot_uri: MIXS:0000102 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -31136,19 +32691,20 @@ classes: occurrence: tag: occurrence value: '1' - description: 'Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus' + 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 + - value: 0.03 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - total phosphorus + - total phosphorus rank: 52 is_a: core field slot_uri: MIXS:0000117 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -31168,16 +32724,16 @@ classes: description: Concentration of total sulfur in the sample title: total sulfur examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - total sulfur + - total sulfur rank: 379 is_a: core field slot_uri: MIXS:0000419 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -31194,19 +32750,20 @@ classes: 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). + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - depth (TVDSS) of hydrocarbon resource pressure + - depth (TVDSS) of hydrocarbon resource pressure rank: 380 is_a: core field slot_uri: MIXS:0000397 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -31223,19 +32780,20 @@ classes: 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). + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - depth (TVDSS) of hydrocarbon resource temperature + - depth (TVDSS) of hydrocarbon resource temperature rank: 381 is_a: core field slot_uri: MIXS:0000394 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -31255,16 +32813,16 @@ classes: description: Concentration of Volatile Fatty Acids in the sample title: volatile fatty acids examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - volatile fatty acids + - volatile fatty acids rank: 382 is_a: core field slot_uri: MIXS:0000152 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -31281,19 +32839,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Original volatile fatty acid concentration in the hydrocarbon resource + description: Original volatile fatty acid concentration in the hydrocarbon + resource title: vfa in formation water examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - vfa in formation water + - vfa in formation water rank: 383 is_a: core field slot_uri: MIXS:0000408 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -31310,20 +32869,21 @@ classes: 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) + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - viscosity + - viscosity rank: 384 is_a: core field string_serialization: '{float} {unit};{float} {unit}' slot_uri: MIXS:0000126 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -31336,20 +32896,24 @@ classes: 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)' + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - well identification number + - well identification number rank: 388 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000297 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -31368,16 +32932,16 @@ classes: description: Concentration of xylene in the sample title: xylene examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - xylene + - xylene rank: 389 is_a: core field slot_uri: MIXS:0000156 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -31396,113 +32960,113 @@ classes: from_schema: https://example.com/nmdc_submission_schema is_a: DhInterface mixins: - - DhMultiviewCommonColumnsMixin + - 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 - - 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 + - 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 + - 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 slot_usage: add_recov_method: name: add_recov_method @@ -31513,19 +33077,22 @@ classes: 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 + 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 + - value: Polymer Addition;2018-06-21T14:30Z from_schema: https://w3id.org/nmdc/nmdc aliases: - - secondary and tertiary recovery methods and start date + - secondary and tertiary recovery methods and start date rank: 289 is_a: core field slot_uri: MIXS:0001009 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -31538,20 +33105,21 @@ classes: 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 + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - additional info + - additional info rank: 290 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000300 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -31567,19 +33135,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + 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 + - value: 50 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - alkalinity + - alkalinity rank: 1 is_a: core field slot_uri: MIXS:0000421 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -31596,17 +33165,17 @@ classes: description: Method used for alkalinity measurement title: alkalinity method examples: - - value: titration + - value: titration from_schema: https://w3id.org/nmdc/nmdc aliases: - - alkalinity method + - alkalinity method rank: 218 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000298 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -31625,16 +33194,16 @@ classes: description: Concentration of ammonium in the sample title: ammonium examples: - - value: 1.5 milligram per liter + - value: 1.5 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - ammonium + - ammonium rank: 4 is_a: core field slot_uri: MIXS:0000427 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -31651,19 +33220,21 @@ classes: 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)' + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - API gravity + - API gravity rank: 291 is_a: core field slot_uri: MIXS:0000157 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -31680,20 +33251,24 @@ classes: 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)' + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - aromatics wt% + - aromatics wt% rank: 292 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000133 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -31710,20 +33285,24 @@ classes: 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)' + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - asphaltenes wt% + - asphaltenes wt% rank: 293 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000135 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -31740,17 +33319,17 @@ classes: description: Name of the basin (e.g. Campos) title: basin name examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - basin name + - basin name rank: 294 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000290 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -31769,16 +33348,16 @@ classes: description: Concentration of benzene in the sample title: benzene examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - benzene + - benzene rank: 295 is_a: core field slot_uri: MIXS:0000153 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -31792,20 +33371,21 @@ classes: occurrence: tag: occurrence value: '1' - description: List of biocides (commercial name of product and supplier) and date of administration + 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 + - value: ALPHA 1427;Baker Hughes;2008-01-23 from_schema: https://w3id.org/nmdc/nmdc aliases: - - biocide administration + - biocide administration rank: 297 is_a: core field string_serialization: '{text};{text};{timestamp}' slot_uri: MIXS:0001011 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -31821,20 +33401,22 @@ classes: 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) + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - biocide administration method + - biocide administration method rank: 298 is_a: core field string_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration}' slot_uri: MIXS:0000456 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -31853,16 +33435,16 @@ classes: description: Concentration of calcium in the sample title: calcium examples: - - value: 0.2 micromole per liter + - value: 0.2 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - calcium + - calcium rank: 9 is_a: core field slot_uri: MIXS:0000432 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -31876,21 +33458,24 @@ classes: 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 + 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 + - 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 + - chemical administration rank: 17 is_a: core field string_serialization: '{termLabel} {[termID]};{timestamp}' slot_uri: MIXS:0000751 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -31908,20 +33493,22 @@ classes: 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) + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - chemical treatment method + - 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 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -31934,20 +33521,24 @@ classes: 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 + 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 + - value: ACCENT 1125;DOW;2010-11-17 from_schema: https://w3id.org/nmdc/nmdc aliases: - - chemical treatment + - chemical treatment rank: 303 is_a: core field string_serialization: '{text};{text};{timestamp}' slot_uri: MIXS:0001012 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -31966,16 +33557,16 @@ classes: description: Concentration of chloride in the sample title: chloride examples: - - value: 5000 milligram per liter + - value: 5000 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - chloride + - chloride rank: 10 is_a: core field slot_uri: MIXS:0000429 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -31989,22 +33580,23 @@ classes: 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) + - 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' + - value: '2021-04-15' + - value: 2021-04 + - value: '2021' from_schema: https://w3id.org/nmdc/nmdc aliases: - - collection date + - collection date rank: 3 is_a: environment field string_serialization: '{date, arbitrary precision}' slot_uri: MIXS:0000011 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string required: true @@ -32022,19 +33614,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + 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 + - value: 1000 kilogram per cubic meter from_schema: https://w3id.org/nmdc/nmdc aliases: - - density + - density rank: 12 is_a: core field slot_uri: MIXS:0000435 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -32048,19 +33641,20 @@ classes: 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 + 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 + - value: Continental - Alluvial from_schema: https://w3id.org/nmdc/nmdc aliases: - - depositional environment + - depositional environment rank: 304 is_a: core field slot_uri: MIXS:0000992 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: depos_env_enum multivalued: false @@ -32070,25 +33664,27 @@ classes: 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. + 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 + - Use modified term comments: - - All depths must be reported in meters. Provide the numerical portion only. + - All depths must be reported in meters. Provide the numerical portion only. examples: - - value: 0 - 0.1 - - value: '1' + - value: 0 - 0.1 + - value: '1' from_schema: https://w3id.org/nmdc/nmdc aliases: - - depth + - depth rank: 9 is_a: environment field string_serialization: '{float}|{float}-{float}' slot_uri: MIXS:0000018 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -32106,19 +33702,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + 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 + - value: 5 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - dissolved carbon dioxide + - dissolved carbon dioxide rank: 14 is_a: core field slot_uri: MIXS:0000436 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -32135,19 +33732,20 @@ classes: 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 + 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 + - value: 2059 micromole per kilogram from_schema: https://w3id.org/nmdc/nmdc aliases: - - dissolved inorganic carbon + - dissolved inorganic carbon rank: 16 is_a: core field slot_uri: MIXS:0000434 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -32167,16 +33765,16 @@ classes: description: Concentration of dissolved inorganic phosphorus in the sample title: dissolved inorganic phosphorus examples: - - value: 56.5 micromole per liter + - value: 56.5 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - dissolved inorganic phosphorus + - dissolved inorganic phosphorus rank: 224 is_a: core field slot_uri: MIXS:0000106 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -32196,16 +33794,16 @@ classes: description: Concentration of dissolved iron in the sample title: dissolved iron examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - dissolved iron + - dissolved iron rank: 305 is_a: core field slot_uri: MIXS:0000139 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -32222,19 +33820,20 @@ classes: 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 + 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 + - value: 197 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - dissolved organic carbon + - dissolved organic carbon rank: 17 is_a: core field slot_uri: MIXS:0000433 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -32251,88 +33850,113 @@ classes: 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). + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - dissolved oxygen in fluids + - dissolved oxygen in fluids rank: 306 is_a: core field slot_uri: MIXS:0000438 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 9 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 10 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 12 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 11 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study slot_group: sample_id_section range: EcosystemTypeEnum recommended: true @@ -32342,25 +33966,31 @@ classes: 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. + 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. + - 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' + - value: '225' + - value: '0' + - value: '1250' from_schema: https://w3id.org/nmdc/nmdc aliases: - - elevation + - elevation rank: 6 is_a: environment field slot_uri: MIXS:0000093 owner: Biosample domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample slot_group: mixs_modified_section range: float required: true @@ -32370,26 +34000,44 @@ classes: 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. + 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. tooltip: tag: tooltip - value: The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context - 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' + value: The biome or major environmental system where the sample or specimen + originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] + in the Environment Ontology (ENVO). For host-associated or plant-associated + samples, use terms from the UBERON or Plant Ontology to describe the + broad anatomical or morphological context + 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) + - range changed to enumeration late in makefile, so this is modified (but + "sample ID" anyway) examples: - - value: oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean + - 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://w3id.org/nmdc/nmdc aliases: - - broad-scale environmental context + - broad-scale environmental context rank: 6 is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000012 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string required: true @@ -32400,30 +34048,45 @@ classes: annotations: expected_value: tag: expected_value - value: Environmental entities having causal influences upon the entity at time of sampling. + value: Environmental entities having causal influences upon the entity + at time of sampling. tooltip: tag: tooltip - value: The specific environmental entities or features near the sample or specimen that significantly influence its characteristics or composition. These entities are typically smaller in scale than the broad environmental context. Values for this field should be countable, material nouns and must be chosen from subclasses of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe specific anatomical structures or plant parts. - 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.' + value: The specific environmental entities or features near the sample + or specimen that significantly influence its characteristics or composition. + These entities are typically smaller in scale than the broad environmental + context. Values for this field should be countable, material nouns and + must be chosen from subclasses of BFO:0000040 (material entity) that + appear in the Environment Ontology (ENVO). For host-associated or plant-associated + samples, use terms from the UBERON or Plant Ontology to describe specific + anatomical structures or plant parts. + 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) + - 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] + - 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 aliases: - - local environmental context + - local environmental context rank: 7 is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000013 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string required: true @@ -32434,26 +34097,41 @@ classes: annotations: expected_value: tag: expected_value - value: The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]. + value: The material displaced by the entity at time of sampling. Recommend + subclasses of environmental material [ENVO:00010483]. tooltip: tag: tooltip - value: The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure - 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).' + value: The predominant environmental material or substrate that directly + surrounds or hosts the sample or specimen at the time of sampling. Choose + values from subclasses of the 'environmental material' class [ENVO:00010483] + in the Environment Ontology (ENVO). Values for this field should be + measurable or mass material nouns, representing continuous environmental + materials. For host-associated or plant-associated samples, use terms + from the UBERON or Plant Ontology to indicate a tissue, organ, or plant + structure + 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) + - range changed to enumeration late in makefile, so this is modified (but + "sample ID" anyway) examples: - - value: soil [ENVO:00001998] + - value: soil [ENVO:00001998] from_schema: https://w3id.org/nmdc/nmdc aliases: - - environmental medium + - environmental medium rank: 8 is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000014 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string required: true @@ -32474,16 +34152,16 @@ classes: description: Concentration of ethylbenzene in the sample title: ethylbenzene examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - ethylbenzene + - ethylbenzene rank: 309 is_a: core field slot_uri: MIXS:0000155 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -32494,20 +34172,25 @@ classes: 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 + 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] + - value: time series design [EFO:EFO_0001779] from_schema: https://w3id.org/nmdc/nmdc aliases: - - experimental factor + - experimental factor rank: 12 is_a: investigation field string_serialization: '{termLabel} {[termID]}|{text}' slot_uri: MIXS:0000008 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -32523,17 +34206,17 @@ classes: description: Name of the hydrocarbon field (e.g. Albacora) title: field name examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - field name + - field name rank: 310 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000291 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -32542,22 +34225,24 @@ classes: 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. + 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' + - value: 'USA: Maryland, Bethesda' from_schema: https://w3id.org/nmdc/nmdc aliases: - - geographic location (country and/or sea,region) + - geographic location (country and/or sea,region) rank: 4 is_a: environment field string_serialization: '{text}: {text}, {text}' slot_uri: MIXS:0000010 owner: Biosample domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample slot_group: mixs_modified_section range: string required: true @@ -32572,19 +34257,21 @@ classes: 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 + 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 + - value: Gas from_schema: https://w3id.org/nmdc/nmdc aliases: - - hydrocarbon type produced + - hydrocarbon type produced rank: 313 is_a: core field slot_uri: MIXS:0000989 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: hc_produced_enum multivalued: false @@ -32597,19 +34284,25 @@ classes: 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 + 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 + - value: Oil Sand from_schema: https://w3id.org/nmdc/nmdc aliases: - - hydrocarbon resource type + - hydrocarbon resource type rank: 314 is_a: core field slot_uri: MIXS:0000988 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: hcr_enum multivalued: false @@ -32625,19 +34318,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS + description: Original formation water salinity (prior to secondary recovery + e.g. Waterflooding) expressed as TDS title: formation water salinity examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - formation water salinity + - formation water salinity rank: 315 is_a: core field slot_uri: MIXS:0000406 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -32651,19 +34345,20 @@ classes: 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' + 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 + - value: Silurian from_schema: https://w3id.org/nmdc/nmdc aliases: - - hydrocarbon resource geological age + - hydrocarbon resource geological age rank: 316 is_a: core field slot_uri: MIXS:0000993 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: hcr_geol_age_enum multivalued: false @@ -32682,17 +34377,17 @@ classes: description: Original pressure of the hydrocarbon resource title: hydrocarbon resource original pressure examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - hydrocarbon resource original pressure + - hydrocarbon resource original pressure rank: 317 is_a: core field string_serialization: '{float} - {float} {unit}' slot_uri: MIXS:0000395 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -32711,17 +34406,17 @@ classes: description: Original temperature of the hydrocarbon resource title: hydrocarbon resource original temperature examples: - - value: 150-295 degree Celsius + - value: 150-295 degree Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - - hydrocarbon resource original temperature + - hydrocarbon resource original temperature rank: 318 is_a: core field string_serialization: '{float} - {float} {unit}' slot_uri: MIXS:0000393 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -32734,19 +34429,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Injection water breakthrough date per well following a secondary and/or tertiary recovery + 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' + - value: '2018-05-11' from_schema: https://w3id.org/nmdc/nmdc aliases: - - injection water breakthrough date of specific well + - injection water breakthrough date of specific well rank: 334 is_a: core field slot_uri: MIXS:0001010 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -32762,19 +34458,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) + description: Proportion of the produced fluids derived from injected water + at the time of sampling. (e.g. 87%) title: injection water fraction examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - injection water fraction + - injection water fraction rank: 335 is_a: core field slot_uri: MIXS:0000455 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -32785,23 +34482,26 @@ classes: 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 + 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) notes: - - This is currently a required field but it's not clear if this should be required for human hosts + - This is currently a required field but it's not clear if this should be + required for human hosts examples: - - value: 50.586825 6.408977 + - value: 50.586825 6.408977 from_schema: https://w3id.org/nmdc/nmdc aliases: - - geographic location (latitude and longitude) + - geographic location (latitude and longitude) rank: 5 is_a: environment field string_serialization: '{lat lon}' slot_uri: MIXS:0000009 owner: Biosample domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample slot_group: mixs_modified_section range: string required: true @@ -32816,19 +34516,21 @@ classes: 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' + 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 + - value: Volcanic from_schema: https://w3id.org/nmdc/nmdc aliases: - - lithology + - lithology rank: 336 is_a: core field slot_uri: MIXS:0000990 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: lithology_enum multivalued: false @@ -32840,23 +34542,24 @@ classes: value: measurement value preferred_unit: tag: preferred_unit - value: mole per liter, milligram per liter, parts per million, micromole per kilogram + 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 + - value: 52.8 micromole per kilogram from_schema: https://w3id.org/nmdc/nmdc aliases: - - magnesium + - magnesium rank: 21 is_a: core field slot_uri: MIXS:0000431 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -32870,24 +34573,26 @@ classes: occurrence: tag: occurrence value: m - description: Any other measurement performed or parameter collected, that is not listed here + 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 + - value: Bicarbonate ion concentration;2075 micromole per kilogram from_schema: https://w3id.org/nmdc/nmdc aliases: - - miscellaneous parameter + - miscellaneous parameter rank: 23 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000752 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false - 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]+)$ + 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: @@ -32903,16 +34608,16 @@ classes: description: Concentration of nitrate in the sample title: nitrate examples: - - value: 65 micromole per liter + - value: 65 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - nitrate + - nitrate rank: 26 is_a: core field slot_uri: MIXS:0000425 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -32932,16 +34637,16 @@ classes: description: Concentration of nitrite in the sample title: nitrite examples: - - value: 0.5 micromole per liter + - value: 0.5 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - nitrite + - nitrite rank: 27 is_a: core field slot_uri: MIXS:0000426 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -32951,27 +34656,34 @@ classes: 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 + 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)' + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - organism count qPCR information + - 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' + 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 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -32983,23 +34695,28 @@ classes: 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 + 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)' + 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 + - value: total prokaryotes;3.5e7 cells per milliliter;qPCR from_schema: https://w3id.org/nmdc/nmdc aliases: - - organism count + - organism count rank: 30 is_a: core field slot_uri: MIXS:0000103 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -33016,16 +34733,16 @@ classes: description: Oxygenation status of sample title: oxygenation status of sample examples: - - value: aerobic + - value: aerobic from_schema: https://w3id.org/nmdc/nmdc aliases: - - oxygenation status of sample + - oxygenation status of sample rank: 25 is_a: core field slot_uri: MIXS:0000753 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: OxyStatSampEnum multivalued: false @@ -33038,22 +34755,23 @@ classes: occurrence: tag: occurrence value: '1' - description: pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + description: pH measurement of the sample, or liquid portion of sample, or + aqueous phase of the fluid title: pH notes: - - Use modified term + - Use modified term examples: - - value: '7.2' + - value: '7.2' from_schema: https://w3id.org/nmdc/nmdc aliases: - - pH + - pH rank: 27 is_a: core field string_serialization: '{float}' slot_uri: MIXS:0001001 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: float recommended: true @@ -33072,20 +34790,20 @@ classes: 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. + - 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 + - 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 aliases: - - pH method + - pH method rank: 41 is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0001106 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -33104,16 +34822,16 @@ classes: description: Concentration of potassium in the sample title: potassium examples: - - value: 463 milligram per liter + - value: 463 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - potassium + - potassium rank: 38 is_a: core field slot_uri: MIXS:0000430 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -33130,19 +34848,22 @@ classes: 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)' + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - pour point + - pour point rank: 341 is_a: core field slot_uri: MIXS:0000127 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -33162,16 +34883,16 @@ classes: description: Pressure to which the sample is subject to, in atmospheres title: pressure examples: - - value: 50 atmosphere + - value: 50 atmosphere from_schema: https://w3id.org/nmdc/nmdc aliases: - - pressure + - pressure rank: 39 is_a: core field slot_uri: MIXS:0000412 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -33191,16 +34912,16 @@ classes: description: Oil and/or gas production rates per well (e.g. 524 m3 / day) title: production rate examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - production rate + - production rate rank: 344 is_a: core field slot_uri: MIXS:0000452 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -33217,16 +34938,16 @@ classes: description: Date of field's first production title: production start date examples: - - value: '2018-05-11' + - value: '2018-05-11' from_schema: https://w3id.org/nmdc/nmdc aliases: - - production start date + - production start date rank: 345 is_a: core field slot_uri: MIXS:0001008 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -33242,17 +34963,17 @@ classes: description: Name of the reservoir (e.g. Carapebus) title: reservoir name examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - reservoir name + - reservoir name rank: 347 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000303 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -33268,20 +34989,24 @@ classes: 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)' + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - resins wt% + - resins wt% rank: 348 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000134 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -33298,19 +35023,24 @@ classes: 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. + 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 + - value: 25 practical salinity unit from_schema: https://w3id.org/nmdc/nmdc aliases: - - salinity + - salinity rank: 54 is_a: core field slot_uri: MIXS:0000183 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -33321,22 +35051,24 @@ classes: 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). + 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 + - Report dimensions and details when applicable examples: - - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample collection device + - sample collection device rank: 14 is_a: nucleic acid sequence source field string_serialization: '{termLabel} {[termID]}|{text}' slot_uri: MIXS:0000002 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -33350,19 +35082,19 @@ classes: description: The method employed for collecting the sample. title: sample collection method comments: - - This can be a citation or description + - This can be a citation or description examples: - - value: swabbing + - value: swabbing from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample collection method + - sample collection method rank: 15 is_a: nucleic acid sequence source field string_serialization: '{PMID}|{DOI}|{URL}|{text}' slot_uri: MIXS:0001225 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -33375,19 +35107,21 @@ classes: 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 + 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 + - value: well from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample collection point + - sample collection point rank: 349 is_a: core field slot_uri: MIXS:0001015 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: samp_collect_point_enum multivalued: false @@ -33403,20 +35137,26 @@ classes: 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 + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - corrosion rate at sample location + - corrosion rate at sample location rank: 350 is_a: core field string_serialization: '{float} - {float} {unit}' slot_uri: MIXS:0000136 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -33426,21 +35166,23 @@ classes: 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. + 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 + - value: filtering of seawater + - value: storing samples in ethanol from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample material processing + - sample material processing rank: 12 is_a: nucleic acid sequence source field string_serialization: '{text}' slot_uri: MIXS:0000016 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -33456,20 +35198,21 @@ classes: 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) + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - preservative added to sample + - preservative added to sample rank: 352 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000463 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -33483,23 +35226,25 @@ classes: 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. + 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. + - 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 + - value: 5 grams + - value: 10 mL from_schema: https://w3id.org/nmdc/nmdc aliases: - - amount or size of sample collected + - amount or size of sample collected rank: 18 is_a: nucleic acid sequence source field string_serialization: '{float} {unit}' slot_uri: MIXS:0000001 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -33516,17 +35261,17 @@ classes: description: Duration for which the sample was stored title: sample storage duration examples: - - value: P1Y6M + - value: P1Y6M from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample storage duration + - sample storage duration rank: 353 is_a: core field string_serialization: '{duration}' slot_uri: MIXS:0000116 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -33539,20 +35284,21 @@ classes: occurrence: tag: occurrence value: '1' - description: Location at which sample was stored, usually name of a specific freezer/room + description: Location at which sample was stored, usually name of a specific + freezer/room title: sample storage location examples: - - value: Freezer no:5 + - value: Freezer no:5 from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample storage location + - sample storage location rank: 41 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000755 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -33571,16 +35317,16 @@ classes: description: Temperature at which the sample was stored (degrees are assumed) title: sample storage temperature examples: - - value: -80 Celsius + - value: -80 Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample storage temperature + - sample storage temperature rank: 7 is_a: core field slot_uri: MIXS:0000110 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string required: true @@ -33595,19 +35341,21 @@ classes: 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 + 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 + - value: biofilm from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample subtype + - sample subtype rank: 354 is_a: core field slot_uri: MIXS:0000999 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: samp_subtype_enum multivalued: false @@ -33623,20 +35371,21 @@ classes: 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) + 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 + - value: 5 days;-20 degree Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample transport conditions + - sample transport conditions rank: 355 is_a: core field string_serialization: '{float} {unit};{float} {unit}' slot_uri: MIXS:0000410 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -33649,20 +35398,25 @@ classes: 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). + 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] + - value: built environment sample [GENEPIO:0001248] from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample type + - sample type rank: 357 is_a: core field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000998 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -33679,36 +35433,43 @@ classes: description: Name of the well (e.g. BXA1123) where sample was taken title: sample well name examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample well name + - sample well name rank: 358 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000296 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false 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. + 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''' + - '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)' + - '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 + - value: IGSN:DSJ0284 from_schema: https://w3id.org/nmdc/nmdc rank: 5 string_serialization: '{text}:{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string recommended: true @@ -33726,20 +35487,24 @@ classes: 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)' + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - saturates wt% + - saturates wt% rank: 359 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000131 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -33753,17 +35518,17 @@ classes: description: Filtering pore size used in sample preparation title: size fraction selected examples: - - value: 0-0.22 micrometer + - value: 0-0.22 micrometer from_schema: https://w3id.org/nmdc/nmdc aliases: - - size fraction selected + - size fraction selected rank: 285 is_a: nucleic acid sequence source field string_serialization: '{float}-{float} {unit}' slot_uri: MIXS:0000017 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -33782,34 +35547,37 @@ classes: description: Sodium concentration in the sample title: sodium examples: - - value: 10.5 milligram per liter + - value: 10.5 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - sodium + - sodium rank: 363 is_a: core field slot_uri: MIXS:0000428 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 13 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study slot_group: sample_id_section range: SpecificEcosystemEnum recommended: true @@ -33828,16 +35596,16 @@ classes: description: Concentration of sulfate in the sample title: sulfate examples: - - value: 5 micromole per liter + - value: 5 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - sulfate + - sulfate rank: 44 is_a: core field slot_uri: MIXS:0000423 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -33857,16 +35625,16 @@ classes: description: Original sulfate concentration in the hydrocarbon resource title: sulfate in formation water examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - sulfate in formation water + - sulfate in formation water rank: 370 is_a: core field slot_uri: MIXS:0000407 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -33886,16 +35654,16 @@ classes: description: Concentration of sulfide in the sample title: sulfide examples: - - value: 2 micromole per liter + - value: 2 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - sulfide + - sulfide rank: 371 is_a: core field slot_uri: MIXS:0000424 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -33908,28 +35676,31 @@ classes: 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 + 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 + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - suspended solids + - suspended solids rank: 372 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000150 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false - 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]+)$ + 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: @@ -33942,19 +35713,22 @@ classes: 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)' + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - total acid number + - total acid number rank: 373 is_a: core field slot_uri: MIXS:0000120 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -33971,16 +35745,16 @@ classes: description: Temperature of the sample at the time of sampling. title: temperature examples: - - value: 25 degree Celsius + - value: 25 degree Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - - temperature + - temperature rank: 37 is_a: environment field slot_uri: MIXS:0000113 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -34000,16 +35774,16 @@ classes: description: Concentration of toluene in the sample title: toluene examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - toluene + - toluene rank: 375 is_a: core field slot_uri: MIXS:0000154 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -34029,16 +35803,16 @@ classes: description: Concentration of total iron in the sample title: total iron examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - total iron + - total iron rank: 376 is_a: core field slot_uri: MIXS:0000105 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -34055,19 +35829,21 @@ classes: 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' + 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 + - value: 50 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - total nitrogen concentration + - total nitrogen concentration rank: 377 is_a: core field slot_uri: MIXS:0000102 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -34084,19 +35860,20 @@ classes: occurrence: tag: occurrence value: '1' - description: 'Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus' + 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 + - value: 0.03 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - total phosphorus + - total phosphorus rank: 52 is_a: core field slot_uri: MIXS:0000117 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -34116,16 +35893,16 @@ classes: description: Concentration of total sulfur in the sample title: total sulfur examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - total sulfur + - total sulfur rank: 379 is_a: core field slot_uri: MIXS:0000419 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -34142,19 +35919,20 @@ classes: 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). + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - depth (TVDSS) of hydrocarbon resource pressure + - depth (TVDSS) of hydrocarbon resource pressure rank: 380 is_a: core field slot_uri: MIXS:0000397 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -34171,19 +35949,20 @@ classes: 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). + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - depth (TVDSS) of hydrocarbon resource temperature + - depth (TVDSS) of hydrocarbon resource temperature rank: 381 is_a: core field slot_uri: MIXS:0000394 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -34203,16 +35982,16 @@ classes: description: Concentration of Volatile Fatty Acids in the sample title: volatile fatty acids examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - volatile fatty acids + - volatile fatty acids rank: 382 is_a: core field slot_uri: MIXS:0000152 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -34229,19 +36008,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Original volatile fatty acid concentration in the hydrocarbon resource + description: Original volatile fatty acid concentration in the hydrocarbon + resource title: vfa in formation water examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - vfa in formation water + - vfa in formation water rank: 383 is_a: core field slot_uri: MIXS:0000408 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -34258,20 +36038,21 @@ classes: 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) + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - viscosity + - viscosity rank: 384 is_a: core field string_serialization: '{float} {unit};{float} {unit}' slot_uri: MIXS:0000126 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -34287,19 +36068,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Current amount of water (%) in a produced fluid stream; or the average of the combined streams + description: Current amount of water (%) in a produced fluid stream; or the + average of the combined streams title: water cut examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - water cut + - water cut rank: 386 is_a: core field slot_uri: MIXS:0000454 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -34319,16 +36101,16 @@ classes: description: Water production rates per well (e.g. 987 m3 / day) title: water production rate examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - water production rate + - water production rate rank: 387 is_a: core field slot_uri: MIXS:0000453 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -34342,20 +36124,24 @@ classes: 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)' + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - well identification number + - well identification number rank: 388 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000297 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -34374,16 +36160,16 @@ classes: description: Concentration of xylene in the sample title: xylene examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - xylene + - xylene rank: 389 is_a: core field slot_uri: MIXS:0000156 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -34402,74 +36188,74 @@ classes: from_schema: https://example.com/nmdc_submission_schema is_a: DhInterface mixins: - - DhMultiviewCommonColumnsMixin - - SampIdNewTermsMixin + - 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 - - 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_disease_stat - - 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 + - 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 + - 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_disease_stat + - 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 @@ -34477,43 +36263,48 @@ classes: 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 + 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 + - value: 100 meter from_schema: https://w3id.org/nmdc/nmdc aliases: - - altitude + - altitude rank: 26 is_a: environment field slot_uri: MIXS:0000094 owner: Biosample domain_of: - - agriculture - - air - - built environment - - core - - food-animal and animal feed - - food-farm environment - - food-food production facility - - food-human foods - - host-associated - - human-associated - - human-gut - - human-oral - - human-skin - - human-vaginal - - hydrocarbon resources-cores - - hydrocarbon resources-fluids_swabs - - microbial mat_biofilm - - miscellaneous natural or artificial environment - - plant-associated - - sediment - - soil - - symbiont-associated - - wastewater_sludge - - water - - Biosample + - agriculture + - air + - built environment + - core + - food-animal and animal feed + - food-farm environment + - food-food production facility + - food-human foods + - host-associated + - human-associated + - human-gut + - human-oral + - human-skin + - human-vaginal + - hydrocarbon resources-cores + - hydrocarbon resources-fluids_swabs + - microbial mat_biofilm + - miscellaneous natural or artificial environment + - plant-associated + - sediment + - soil + - symbiont-associated + - wastewater_sludge + - water + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -34528,20 +36319,22 @@ classes: 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) + 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 + - value: A/3*B from_schema: https://w3id.org/nmdc/nmdc aliases: - - ancestral data + - ancestral data rank: 237 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000247 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -34557,16 +36350,16 @@ classes: description: The level of genome modification. title: biological status examples: - - value: natural + - value: natural from_schema: https://w3id.org/nmdc/nmdc aliases: - - biological status + - biological status rank: 239 is_a: core field slot_uri: MIXS:0000858 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: biol_stat_enum multivalued: false @@ -34585,16 +36378,16 @@ classes: description: Resting diastolic blood pressure, measured as mm mercury title: host blood pressure diastolic examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - host blood pressure diastolic + - host blood pressure diastolic rank: 299 is_a: core field slot_uri: MIXS:0000258 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -34614,16 +36407,16 @@ classes: description: Resting systolic blood pressure, measured as mm mercury title: host blood pressure systolic examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - host blood pressure systolic + - host blood pressure systolic rank: 300 is_a: core field slot_uri: MIXS:0000259 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -34637,21 +36430,24 @@ classes: 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 + 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 + - 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 + - chemical administration rank: 17 is_a: core field string_serialization: '{termLabel} {[termID]};{timestamp}' slot_uri: MIXS:0000751 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -34666,22 +36462,23 @@ classes: 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) + - 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' + - value: '2021-04-15' + - value: 2021-04 + - value: '2021' from_schema: https://w3id.org/nmdc/nmdc aliases: - - collection date + - collection date rank: 3 is_a: environment field string_serialization: '{date, arbitrary precision}' slot_uri: MIXS:0000011 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string required: true @@ -34693,25 +36490,27 @@ classes: 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. + 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 + - Use modified term comments: - - All depths must be reported in meters. Provide the numerical portion only. + - All depths must be reported in meters. Provide the numerical portion only. examples: - - value: 0 - 0.1 - - value: '1' + - value: 0 - 0.1 + - value: '1' from_schema: https://w3id.org/nmdc/nmdc aliases: - - depth + - depth rank: 9 is_a: environment field string_serialization: '{float}|{float}-{float}' slot_uri: MIXS:0000018 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -34719,69 +36518,93 @@ classes: 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 9 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 10 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 12 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 11 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study slot_group: sample_id_section range: EcosystemTypeEnum recommended: true @@ -34791,25 +36614,31 @@ classes: 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. + 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. + - 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' + - value: '225' + - value: '0' + - value: '1250' from_schema: https://w3id.org/nmdc/nmdc aliases: - - elevation + - elevation rank: 6 is_a: environment field slot_uri: MIXS:0000093 owner: Biosample domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample slot_group: mixs_modified_section range: float required: true @@ -34819,26 +36648,44 @@ classes: 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. + 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. tooltip: tag: tooltip - value: The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context - 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' + value: The biome or major environmental system where the sample or specimen + originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] + in the Environment Ontology (ENVO). For host-associated or plant-associated + samples, use terms from the UBERON or Plant Ontology to describe the + broad anatomical or morphological context + 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) + - range changed to enumeration late in makefile, so this is modified (but + "sample ID" anyway) examples: - - value: oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean + - 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://w3id.org/nmdc/nmdc aliases: - - broad-scale environmental context + - broad-scale environmental context rank: 6 is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000012 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string required: true @@ -34849,30 +36696,45 @@ classes: annotations: expected_value: tag: expected_value - value: Environmental entities having causal influences upon the entity at time of sampling. + value: Environmental entities having causal influences upon the entity + at time of sampling. tooltip: tag: tooltip - value: The specific environmental entities or features near the sample or specimen that significantly influence its characteristics or composition. These entities are typically smaller in scale than the broad environmental context. Values for this field should be countable, material nouns and must be chosen from subclasses of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe specific anatomical structures or plant parts. - 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.' + value: The specific environmental entities or features near the sample + or specimen that significantly influence its characteristics or composition. + These entities are typically smaller in scale than the broad environmental + context. Values for this field should be countable, material nouns and + must be chosen from subclasses of BFO:0000040 (material entity) that + appear in the Environment Ontology (ENVO). For host-associated or plant-associated + samples, use terms from the UBERON or Plant Ontology to describe specific + anatomical structures or plant parts. + 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) + - 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] + - 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 aliases: - - local environmental context + - local environmental context rank: 7 is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000013 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string required: true @@ -34883,26 +36745,41 @@ classes: annotations: expected_value: tag: expected_value - value: The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]. + value: The material displaced by the entity at time of sampling. Recommend + subclasses of environmental material [ENVO:00010483]. tooltip: tag: tooltip - value: The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure - 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).' + value: The predominant environmental material or substrate that directly + surrounds or hosts the sample or specimen at the time of sampling. Choose + values from subclasses of the 'environmental material' class [ENVO:00010483] + in the Environment Ontology (ENVO). Values for this field should be + measurable or mass material nouns, representing continuous environmental + materials. For host-associated or plant-associated samples, use terms + from the UBERON or Plant Ontology to indicate a tissue, organ, or plant + structure + 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) + - range changed to enumeration late in makefile, so this is modified (but + "sample ID" anyway) examples: - - value: soil [ENVO:00001998] + - value: soil [ENVO:00001998] from_schema: https://w3id.org/nmdc/nmdc aliases: - - environmental medium + - environmental medium rank: 8 is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000014 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string required: true @@ -34914,20 +36791,25 @@ classes: 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 + 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] + - value: time series design [EFO:EFO_0001779] from_schema: https://w3id.org/nmdc/nmdc aliases: - - experimental factor + - experimental factor rank: 12 is_a: investigation field string_serialization: '{termLabel} {[termID]}|{text}' slot_uri: MIXS:0000008 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -34940,20 +36822,23 @@ classes: 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 + 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 + - value: aox1A transgenic from_schema: https://w3id.org/nmdc/nmdc aliases: - - genetic modification + - genetic modification rank: 244 is_a: core field string_serialization: '{PMID}|{DOI}|{URL}|{text}' slot_uri: MIXS:0000859 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -34962,22 +36847,24 @@ classes: 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. + 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' + - value: 'USA: Maryland, Bethesda' from_schema: https://w3id.org/nmdc/nmdc aliases: - - geographic location (country and/or sea,region) + - geographic location (country and/or sea,region) rank: 4 is_a: environment field string_serialization: '{text}: {text}, {text}' slot_uri: MIXS:0000010 owner: Biosample domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample slot_group: mixs_modified_section range: string required: true @@ -34992,20 +36879,21 @@ classes: 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 + 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 + - value: yes;due date:2018-05-11 from_schema: https://w3id.org/nmdc/nmdc aliases: - - gravidity + - gravidity rank: 312 is_a: core field string_serialization: '{boolean};{timestamp}' slot_uri: MIXS:0000875 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -35021,19 +36909,20 @@ classes: 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 + 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 + - value: 10 days from_schema: https://w3id.org/nmdc/nmdc aliases: - - host age + - host age rank: 249 is_a: core field slot_uri: MIXS:0000255 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -35050,17 +36939,17 @@ classes: description: Original body habitat where the sample was obtained from title: host body habitat examples: - - value: nasopharynx + - value: nasopharynx from_schema: https://w3id.org/nmdc/nmdc aliases: - - host body habitat + - host body habitat rank: 319 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000866 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -35073,20 +36962,23 @@ classes: 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 + 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] + - value: Portion of mucus [fma66938] from_schema: https://w3id.org/nmdc/nmdc aliases: - - host body product + - host body product rank: 320 is_a: core field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000888 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -35100,20 +36992,24 @@ classes: 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 + 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] + - value: gill [UBERON:0002535] from_schema: https://w3id.org/nmdc/nmdc aliases: - - host body site + - host body site rank: 321 is_a: core field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000867 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -35133,16 +37029,16 @@ classes: description: Core body temperature of the host when sample was collected title: host body temperature examples: - - value: 15 degree Celsius + - value: 15 degree Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - - host body temperature + - host body temperature rank: 322 is_a: core field slot_uri: MIXS:0000274 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -35159,17 +37055,17 @@ classes: description: The color of host title: host color examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - host color + - host color rank: 323 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000260 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -35185,17 +37081,17 @@ classes: description: Common name of the host. title: host common name examples: - - value: human + - value: human from_schema: https://w3id.org/nmdc/nmdc aliases: - - host common name + - host common name rank: 250 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000248 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -35208,20 +37104,22 @@ classes: 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 + 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 + - value: herbivore from_schema: https://w3id.org/nmdc/nmdc aliases: - - host diet + - host diet rank: 324 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000869 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -35231,20 +37129,23 @@ classes: expected_value: tag: expected_value value: disease name or Disease Ontology term - description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + description: List of diseases with which the host has been diagnosed; can + include multiple diagnoses. The value of the field depends on host; for + humans the terms should be chosen from the DO (Human Disease Ontology) at + https://www.disease-ontology.org, non-human host diseases are free text title: host disease status examples: - - value: rabies [DOID:11260] + - value: rabies [DOID:11260] from_schema: https://w3id.org/nmdc/nmdc aliases: - - host disease status + - host disease status rank: 390 is_a: nucleic acid sequence source field string_serialization: '{termLabel} {[termID]}|{text}' slot_uri: MIXS:0000031 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -35263,16 +37164,16 @@ classes: description: Measurement of dry mass title: host dry mass examples: - - value: 500 gram + - value: 500 gram from_schema: https://w3id.org/nmdc/nmdc aliases: - - host dry mass + - host dry mass rank: 251 is_a: core field slot_uri: MIXS:0000257 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -35286,20 +37187,21 @@ classes: occurrence: tag: occurrence value: m - description: Familial relationships to other hosts in the same study; can include multiple relationships + description: Familial relationships to other hosts in the same study; can + include multiple relationships title: host family relationship examples: - - value: offspring;Mussel25 + - value: offspring;Mussel25 from_schema: https://w3id.org/nmdc/nmdc aliases: - - host family relationship + - host family relationship rank: 325 is_a: core field string_serialization: '{text};{text}' slot_uri: MIXS:0000872 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -35315,17 +37217,17 @@ classes: description: Observed genotype title: host genotype examples: - - value: C57BL/6 + - value: C57BL/6 from_schema: https://w3id.org/nmdc/nmdc aliases: - - host genotype + - host genotype rank: 252 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000365 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -35341,17 +37243,17 @@ classes: 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 + - value: https://academic.oup.com/icesjms/article/68/2/349/617247 from_schema: https://w3id.org/nmdc/nmdc aliases: - - host growth conditions + - host growth conditions rank: 326 is_a: core field string_serialization: '{PMID}|{DOI}|{URL}|{text}' slot_uri: MIXS:0000871 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -35370,16 +37272,16 @@ classes: description: The height of subject title: host height examples: - - value: 0.1 meter + - value: 0.1 meter from_schema: https://w3id.org/nmdc/nmdc aliases: - - host height + - host height rank: 253 is_a: core field slot_uri: MIXS:0000264 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -35393,20 +37295,21 @@ classes: occurrence: tag: occurrence value: m - description: Content of last meal and time since feeding; can include multiple values + description: Content of last meal and time since feeding; can include multiple + values title: host last meal examples: - - value: corn feed;P2H + - value: corn feed;P2H from_schema: https://w3id.org/nmdc/nmdc aliases: - - host last meal + - host last meal rank: 327 is_a: core field string_serialization: '{text};{duration}' slot_uri: MIXS:0000870 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -35425,16 +37328,16 @@ classes: description: The length of subject title: host length examples: - - value: 1 meter + - value: 1 meter from_schema: https://w3id.org/nmdc/nmdc aliases: - - host length + - host length rank: 254 is_a: core field slot_uri: MIXS:0000256 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -35451,17 +37354,17 @@ classes: description: Description of life stage of host title: host life stage examples: - - value: adult + - value: adult from_schema: https://w3id.org/nmdc/nmdc aliases: - - host life stage + - host life stage rank: 255 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000251 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -35474,20 +37377,22 @@ classes: 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 + 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] + - value: elongated [PATO:0001154] from_schema: https://w3id.org/nmdc/nmdc aliases: - - host phenotype + - host phenotype rank: 256 is_a: core field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000874 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -35504,16 +37409,16 @@ classes: description: Gender or physical sex of the host. title: host sex examples: - - value: non-binary + - value: non-binary from_schema: https://w3id.org/nmdc/nmdc aliases: - - host sex + - host sex rank: 328 is_a: core field slot_uri: MIXS:0000811 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: host_sex_enum multivalued: false @@ -35529,17 +37434,17 @@ classes: description: Morphological shape of host title: host shape examples: - - value: round + - value: round from_schema: https://w3id.org/nmdc/nmdc aliases: - - host shape + - host shape rank: 329 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000261 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -35552,20 +37457,21 @@ classes: occurrence: tag: occurrence value: '1' - description: A unique identifier by which each subject can be referred to, de-identified. + description: A unique identifier by which each subject can be referred to, + de-identified. title: host subject id examples: - - value: MPI123 + - value: MPI123 from_schema: https://w3id.org/nmdc/nmdc aliases: - - host subject id + - host subject id rank: 330 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000861 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -35574,24 +37480,29 @@ classes: 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. + 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. + 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' + - value: 'serovar:Newport, variety:glabrum, cultivar: Red Delicious' from_schema: https://w3id.org/nmdc/nmdc aliases: - - host subspecific genetic lineage + - host subspecific genetic lineage rank: 257 is_a: core field string_serialization: '{rank name}:{text}' slot_uri: MIXS:0001318 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -35607,17 +37518,17 @@ classes: description: The growth substrate of the host. title: host substrate examples: - - value: rock + - value: rock from_schema: https://w3id.org/nmdc/nmdc aliases: - - host substrate + - host substrate rank: 331 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000252 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -35630,20 +37541,21 @@ classes: 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. + 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 + - value: flukeworms from_schema: https://w3id.org/nmdc/nmdc aliases: - - observed host symbionts + - observed host symbionts rank: 258 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0001298 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -35659,16 +37571,16 @@ classes: 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 + - Homo sapiens [NCBITaxon:9606] would be a reasonable has_raw_value from_schema: https://w3id.org/nmdc/nmdc aliases: - - host taxid + - host taxid rank: 259 is_a: core field slot_uri: MIXS:0000250 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -35687,16 +37599,16 @@ classes: description: Total mass of the host at collection, the unit depends on host title: host total mass examples: - - value: 2500 gram + - value: 2500 gram from_schema: https://w3id.org/nmdc/nmdc aliases: - - host total mass + - host total mass rank: 260 is_a: core field slot_uri: MIXS:0000263 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -35707,23 +37619,26 @@ classes: 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 + 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) notes: - - This is currently a required field but it's not clear if this should be required for human hosts + - This is currently a required field but it's not clear if this should be + required for human hosts examples: - - value: 50.586825 6.408977 + - value: 50.586825 6.408977 from_schema: https://w3id.org/nmdc/nmdc aliases: - - geographic location (latitude and longitude) + - geographic location (latitude and longitude) rank: 5 is_a: environment field string_serialization: '{lat lon}' slot_uri: MIXS:0000009 owner: Biosample domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample slot_group: mixs_modified_section range: string required: true @@ -35738,24 +37653,26 @@ classes: occurrence: tag: occurrence value: m - description: Any other measurement performed or parameter collected, that is not listed here + 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 + - value: Bicarbonate ion concentration;2075 micromole per kilogram from_schema: https://w3id.org/nmdc/nmdc aliases: - - miscellaneous parameter + - miscellaneous parameter rank: 23 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000752 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false - 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]+)$ + 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: @@ -35764,23 +37681,28 @@ classes: 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 + 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)' + 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 + - value: total prokaryotes;3.5e7 cells per milliliter;qPCR from_schema: https://w3id.org/nmdc/nmdc aliases: - - organism count + - organism count rank: 30 is_a: core field slot_uri: MIXS:0000103 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -35797,16 +37719,16 @@ classes: description: Oxygenation status of sample title: oxygenation status of sample examples: - - value: aerobic + - value: aerobic from_schema: https://w3id.org/nmdc/nmdc aliases: - - oxygenation status of sample + - oxygenation status of sample rank: 25 is_a: core field slot_uri: MIXS:0000753 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: OxyStatSampEnum multivalued: false @@ -35819,20 +37741,24 @@ classes: 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 + 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 + - value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - - perturbation + - perturbation rank: 33 is_a: core field string_serialization: '{text};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000754 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -35848,19 +37774,24 @@ classes: 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. + 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 + - value: 25 practical salinity unit from_schema: https://w3id.org/nmdc/nmdc aliases: - - salinity + - salinity rank: 54 is_a: core field slot_uri: MIXS:0000183 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -35877,16 +37808,16 @@ classes: description: Reason for the sample title: sample capture status examples: - - value: farm sample + - value: farm sample from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample capture status + - sample capture status rank: 282 is_a: core field slot_uri: MIXS:0000860 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: samp_capt_status_enum multivalued: false @@ -35896,22 +37827,24 @@ classes: 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). + 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 + - Report dimensions and details when applicable examples: - - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample collection device + - sample collection device rank: 14 is_a: nucleic acid sequence source field string_serialization: '{termLabel} {[termID]}|{text}' slot_uri: MIXS:0000002 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -35925,19 +37858,19 @@ classes: description: The method employed for collecting the sample. title: sample collection method comments: - - This can be a citation or description + - This can be a citation or description examples: - - value: swabbing + - value: swabbing from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample collection method + - sample collection method rank: 15 is_a: nucleic acid sequence source field string_serialization: '{PMID}|{DOI}|{URL}|{text}' slot_uri: MIXS:0001225 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -35950,19 +37883,20 @@ classes: 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. + 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 + - value: infection from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample disease stage + - sample disease stage rank: 283 is_a: core field slot_uri: MIXS:0000249 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: samp_dis_stage_enum multivalued: false @@ -35972,21 +37906,23 @@ classes: 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. + 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 + - value: filtering of seawater + - value: storing samples in ethanol from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample material processing + - sample material processing rank: 12 is_a: nucleic acid sequence source field string_serialization: '{text}' slot_uri: MIXS:0000016 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -35999,23 +37935,25 @@ classes: 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. + 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. + - 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 + - value: 5 grams + - value: 10 mL from_schema: https://w3id.org/nmdc/nmdc aliases: - - amount or size of sample collected + - amount or size of sample collected rank: 18 is_a: nucleic acid sequence source field string_serialization: '{float} {unit}' slot_uri: MIXS:0000001 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -36032,17 +37970,17 @@ classes: description: Duration for which the sample was stored title: sample storage duration examples: - - value: P1Y6M + - value: P1Y6M from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample storage duration + - sample storage duration rank: 353 is_a: core field string_serialization: '{duration}' slot_uri: MIXS:0000116 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -36055,20 +37993,21 @@ classes: occurrence: tag: occurrence value: '1' - description: Location at which sample was stored, usually name of a specific freezer/room + description: Location at which sample was stored, usually name of a specific + freezer/room title: sample storage location examples: - - value: Freezer no:5 + - value: Freezer no:5 from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample storage location + - sample storage location rank: 41 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000755 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -36087,16 +38026,16 @@ classes: description: Temperature at which the sample was stored (degrees are assumed) title: sample storage temperature examples: - - value: -80 Celsius + - value: -80 Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample storage temperature + - sample storage temperature rank: 7 is_a: core field slot_uri: MIXS:0000110 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string required: true @@ -36104,20 +38043,27 @@ classes: 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. + 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''' + - '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)' + - '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 + - value: IGSN:DSJ0284 from_schema: https://w3id.org/nmdc/nmdc rank: 5 string_serialization: '{text}:{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string recommended: true @@ -36132,34 +38078,37 @@ classes: description: Filtering pore size used in sample preparation title: size fraction selected examples: - - value: 0-0.22 micrometer + - value: 0-0.22 micrometer from_schema: https://w3id.org/nmdc/nmdc aliases: - - size fraction selected + - size fraction selected rank: 285 is_a: nucleic acid sequence source field string_serialization: '{float}-{float} {unit}' slot_uri: MIXS:0000017 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 13 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study slot_group: sample_id_section range: SpecificEcosystemEnum recommended: true @@ -36175,16 +38124,16 @@ classes: description: Temperature of the sample at the time of sampling. title: temperature examples: - - value: 25 degree Celsius + - value: 25 degree Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - - temperature + - temperature rank: 37 is_a: environment field slot_uri: MIXS:0000113 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -36203,58 +38152,58 @@ classes: from_schema: https://example.com/nmdc_submission_schema is_a: DhInterface mixins: - - DhMultiviewCommonColumnsMixin + - 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 + - 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. + - Recommended value is between 1 and 3. examples: - - value: '2.02' + - value: '2.02' from_schema: https://w3id.org/nmdc/nmdc rank: 7 is_a: biomaterial_purity owner: Biosample domain_of: - - Biosample - - ProcessedSample + - Biosample + - ProcessedSample slot_group: jgi_metagenomics_section range: float recommended: true @@ -36263,15 +38212,15 @@ classes: description: 260/230 measurement of DNA sample purity title: DNA absorbance 260/230 comments: - - Recommended value is between 1 and 3. + - Recommended value is between 1 and 3. examples: - - value: '2.02' + - value: '2.02' from_schema: https://w3id.org/nmdc/nmdc rank: 8 is_a: biomaterial_purity owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metagenomics_section range: float recommended: true @@ -36279,17 +38228,18 @@ classes: 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. + - 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' + - value: '100' from_schema: https://w3id.org/nmdc/nmdc see_also: - - nmdc:nucleic_acid_concentration + - nmdc:nucleic_acid_concentration rank: 5 owner: Biosample domain_of: - - Biosample - - ProcessedSample + - Biosample + - ProcessedSample slot_group: jgi_metagenomics_section range: float required: true @@ -36301,12 +38251,12 @@ classes: description: Tube or plate (96-well) title: DNA container type examples: - - value: plate + - value: plate from_schema: https://w3id.org/nmdc/nmdc rank: 10 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metagenomics_section range: JgiContTypeEnum required: true @@ -36315,54 +38265,56 @@ classes: 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). + - 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 + - value: B2 from_schema: https://w3id.org/nmdc/nmdc rank: 11 string_serialization: '{96 well plate pos}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metagenomics_section range: string recommended: true - pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$ multivalued: false + 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. + - 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 + - value: Pond_MT_041618 from_schema: https://w3id.org/nmdc/nmdc rank: 9 string_serialization: '{text < 20 characters}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metagenomics_section range: string required: true recommended: false - pattern: ^.{1,20}$ multivalued: false + pattern: ^.{1,20}$ dna_dnase: name: dna_dnase title: DNase treatment DNA comments: - - Note DNase treatment is required for all RNA samples. + - Note DNase treatment is required for all RNA samples. examples: - - value: 'no' + - value: 'no' from_schema: https://w3id.org/nmdc/nmdc rank: 13 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metagenomics_section range: YesNoEnum required: true @@ -36372,15 +38324,15 @@ classes: description: Describe the method/protocol/kit used to extract DNA/RNA. title: DNA isolation method examples: - - value: phenol/chloroform extraction + - value: phenol/chloroform extraction from_schema: https://w3id.org/nmdc/nmdc aliases: - - Sample Isolation Method + - Sample Isolation Method rank: 16 string_serialization: '{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metagenomics_section range: string required: true @@ -36390,15 +38342,16 @@ classes: 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. + - Do not edit these values. A template will be provided by NMDC in which these + values have been pre-filled. examples: - - value: John Jones + - value: John Jones from_schema: https://w3id.org/nmdc/nmdc rank: 18 string_serialization: '{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metagenomics_section range: string required: true @@ -36408,17 +38361,20 @@ classes: 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? + - 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. + - Do not edit these values. A template will be provided by NMDC in which these + values have been pre-filled. examples: - - value: '187654' + - value: '187654' from_schema: https://w3id.org/nmdc/nmdc rank: 3 string_serialization: '{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metagenomics_section range: string required: true @@ -36429,28 +38385,30 @@ classes: description: Solution in which the DNA sample has been suspended title: DNA sample format examples: - - value: Water + - value: Water from_schema: https://w3id.org/nmdc/nmdc rank: 12 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metagenomics_section range: DNASampleFormatEnum required: true recommended: false 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. + 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 + - value: JGI_pond_041618 from_schema: https://w3id.org/nmdc/nmdc rank: 4 string_serialization: '{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metagenomics_section range: string required: true @@ -36460,17 +38418,18 @@ classes: 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. + - Do not edit these values. A template will be provided by NMDC in which these + values have been pre-filled. examples: - - value: '1191234' + - value: '1191234' from_schema: https://w3id.org/nmdc/nmdc aliases: - - Seq Project ID + - Seq Project ID rank: 1 string_serialization: '{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metagenomics_section range: string required: true @@ -36480,15 +38439,16 @@ classes: 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. + - 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 + - value: JGI Pond metagenomics from_schema: https://w3id.org/nmdc/nmdc rank: 2 string_serialization: '{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metagenomics_section range: string required: true @@ -36498,15 +38458,16 @@ classes: 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. + - Do not edit these values. A template will be provided by NMDC in which these + values have been pre-filled. examples: - - value: Jane Johnson + - value: Jane Johnson from_schema: https://w3id.org/nmdc/nmdc rank: 17 string_serialization: '{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metagenomics_section range: string required: true @@ -36516,15 +38477,17 @@ classes: 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 + - 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' + - value: '25' from_schema: https://w3id.org/nmdc/nmdc rank: 6 string_serialization: '{float}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metagenomics_section range: float required: true @@ -36535,15 +38498,16 @@ classes: 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. + - Do not edit these values. A template will be provided by NMDC in which these + values have been pre-filled. examples: - - value: '504000' + - value: '504000' from_schema: https://w3id.org/nmdc/nmdc rank: 19 string_serialization: '{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metagenomics_section range: string required: true @@ -36553,30 +38517,33 @@ classes: name: oxy_stat_samp range: OxyStatSampEnum 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 + - 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 JgiMgLrInterface: name: JgiMgLrInterface annotations: @@ -36588,58 +38555,58 @@ classes: from_schema: https://example.com/nmdc_submission_schema is_a: DhInterface mixins: - - DhMultiviewCommonColumnsMixin + - 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 + - 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. + - Recommended value is between 1 and 3. examples: - - value: '2.02' + - value: '2.02' from_schema: https://w3id.org/nmdc/nmdc rank: 7 is_a: biomaterial_purity owner: Biosample domain_of: - - Biosample - - ProcessedSample + - Biosample + - ProcessedSample slot_group: jgi_metagenomics_section range: float required: true @@ -36649,15 +38616,15 @@ classes: description: 260/230 measurement of DNA sample purity title: DNA absorbance 260/230 comments: - - Recommended value is between 1 and 3. + - Recommended value is between 1 and 3. examples: - - value: '2.02' + - value: '2.02' from_schema: https://w3id.org/nmdc/nmdc rank: 8 is_a: biomaterial_purity owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metagenomics_section range: float required: true @@ -36666,17 +38633,18 @@ classes: 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. + - 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' + - value: '100' from_schema: https://w3id.org/nmdc/nmdc see_also: - - nmdc:nucleic_acid_concentration + - nmdc:nucleic_acid_concentration rank: 5 owner: Biosample domain_of: - - Biosample - - ProcessedSample + - Biosample + - ProcessedSample slot_group: jgi_metagenomics_section range: float required: true @@ -36688,12 +38656,12 @@ classes: description: Tube or plate (96-well) title: DNA container type examples: - - value: plate + - value: plate from_schema: https://w3id.org/nmdc/nmdc rank: 10 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metagenomics_section range: JgiContTypeEnum required: true @@ -36702,54 +38670,56 @@ classes: 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). + - 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 + - value: B2 from_schema: https://w3id.org/nmdc/nmdc rank: 11 string_serialization: '{96 well plate pos}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metagenomics_section range: string recommended: true - pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$ multivalued: false + 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. + - 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 + - value: Pond_MT_041618 from_schema: https://w3id.org/nmdc/nmdc rank: 9 string_serialization: '{text < 20 characters}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metagenomics_section range: string required: true recommended: false - pattern: ^.{1,20}$ multivalued: false + pattern: ^.{1,20}$ dna_dnase: name: dna_dnase title: DNase treatment DNA comments: - - Note DNase treatment is required for all RNA samples. + - Note DNase treatment is required for all RNA samples. examples: - - value: 'no' + - value: 'no' from_schema: https://w3id.org/nmdc/nmdc rank: 13 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metagenomics_section range: YesNoEnum required: true @@ -36759,15 +38729,15 @@ classes: description: Describe the method/protocol/kit used to extract DNA/RNA. title: DNA isolation method examples: - - value: phenol/chloroform extraction + - value: phenol/chloroform extraction from_schema: https://w3id.org/nmdc/nmdc aliases: - - Sample Isolation Method + - Sample Isolation Method rank: 16 string_serialization: '{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metagenomics_section range: string required: true @@ -36777,15 +38747,16 @@ classes: 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. + - Do not edit these values. A template will be provided by NMDC in which these + values have been pre-filled. examples: - - value: John Jones + - value: John Jones from_schema: https://w3id.org/nmdc/nmdc rank: 18 string_serialization: '{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metagenomics_section range: string required: true @@ -36795,17 +38766,20 @@ classes: 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? + - 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. + - Do not edit these values. A template will be provided by NMDC in which these + values have been pre-filled. examples: - - value: '187654' + - value: '187654' from_schema: https://w3id.org/nmdc/nmdc rank: 3 string_serialization: '{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metagenomics_section range: string required: true @@ -36816,28 +38790,30 @@ classes: description: Solution in which the DNA sample has been suspended title: DNA sample format examples: - - value: Water + - value: Water from_schema: https://w3id.org/nmdc/nmdc rank: 12 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metagenomics_section range: DNASampleFormatEnum required: true recommended: false 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. + 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 + - value: JGI_pond_041618 from_schema: https://w3id.org/nmdc/nmdc rank: 4 string_serialization: '{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metagenomics_section range: string required: true @@ -36847,17 +38823,18 @@ classes: 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. + - Do not edit these values. A template will be provided by NMDC in which these + values have been pre-filled. examples: - - value: '1191234' + - value: '1191234' from_schema: https://w3id.org/nmdc/nmdc aliases: - - Seq Project ID + - Seq Project ID rank: 1 string_serialization: '{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metagenomics_section range: string required: true @@ -36867,15 +38844,16 @@ classes: 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. + - 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 + - value: JGI Pond metagenomics from_schema: https://w3id.org/nmdc/nmdc rank: 2 string_serialization: '{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metagenomics_section range: string required: true @@ -36885,15 +38863,16 @@ classes: 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. + - Do not edit these values. A template will be provided by NMDC in which these + values have been pre-filled. examples: - - value: Jane Johnson + - value: Jane Johnson from_schema: https://w3id.org/nmdc/nmdc rank: 17 string_serialization: '{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metagenomics_section range: string required: true @@ -36903,15 +38882,17 @@ classes: 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 + - 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' + - value: '25' from_schema: https://w3id.org/nmdc/nmdc rank: 6 string_serialization: '{float}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metagenomics_section range: float required: true @@ -36922,15 +38903,16 @@ classes: 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. + - Do not edit these values. A template will be provided by NMDC in which these + values have been pre-filled. examples: - - value: '504000' + - value: '504000' from_schema: https://w3id.org/nmdc/nmdc rank: 19 string_serialization: '{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metagenomics_section range: string required: true @@ -36950,57 +38932,57 @@ classes: from_schema: https://example.com/nmdc_submission_schema is_a: DhInterface mixins: - - DhMultiviewCommonColumnsMixin + - 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 + - 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. + - Note DNase treatment is required for all RNA samples. examples: - - value: 'no' + - value: 'no' from_schema: https://w3id.org/nmdc/nmdc aliases: - - Was Sample DNAse treated? + - Was Sample DNAse treated? rank: 13 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metatranscriptomics_section range: YesNoEnum required: true @@ -37009,15 +38991,16 @@ classes: 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. + - Do not edit these values. A template will be provided by NMDC in which these + values have been pre-filled. examples: - - value: '504000' + - value: '504000' from_schema: https://w3id.org/nmdc/nmdc rank: 19 string_serialization: '{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metatranscriptomics_section range: string required: true @@ -37028,15 +39011,15 @@ classes: description: 260/280 measurement of RNA sample purity title: RNA absorbance 260/280 comments: - - Recommended value is between 1 and 3. + - Recommended value is between 1 and 3. examples: - - value: '2.02' + - value: '2.02' from_schema: https://w3id.org/nmdc/nmdc rank: 7 string_serialization: '{float}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metatranscriptomics_section range: float recommended: true @@ -37045,15 +39028,15 @@ classes: description: 260/230 measurement of RNA sample purity title: RNA absorbance 260/230 comments: - - Recommended value is between 1 and 3. + - Recommended value is between 1 and 3. examples: - - value: '2.02' + - value: '2.02' from_schema: https://w3id.org/nmdc/nmdc rank: 8 string_serialization: '{float}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metatranscriptomics_section range: float recommended: true @@ -37061,17 +39044,18 @@ classes: 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. + - 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' + - value: '100' from_schema: https://w3id.org/nmdc/nmdc see_also: - - nmdc:nucleic_acid_concentration + - nmdc:nucleic_acid_concentration rank: 5 string_serialization: '{float}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metatranscriptomics_section range: float required: true @@ -37083,12 +39067,12 @@ classes: description: Tube or plate (96-well) title: RNA container type examples: - - value: plate + - value: plate from_schema: https://w3id.org/nmdc/nmdc rank: 10 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metatranscriptomics_section range: JgiContTypeEnum required: true @@ -37097,56 +39081,58 @@ classes: 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). + - 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 + - value: B2 from_schema: https://w3id.org/nmdc/nmdc rank: 11 string_serialization: '{96 well plate pos}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metatranscriptomics_section range: string recommended: true - pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$ multivalued: false + 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. + - 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 + - value: Pond_MT_041618 from_schema: https://w3id.org/nmdc/nmdc rank: 9 string_serialization: '{text < 20 characters}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metatranscriptomics_section range: string required: true recommended: false - pattern: ^.{1,20}$ multivalued: false + 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 + - value: phenol/chloroform extraction from_schema: https://w3id.org/nmdc/nmdc aliases: - - Sample Isolation Method + - Sample Isolation Method rank: 16 string_serialization: '{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metatranscriptomics_section range: string required: true @@ -37156,15 +39142,16 @@ classes: 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. + - Do not edit these values. A template will be provided by NMDC in which these + values have been pre-filled. examples: - - value: John Jones + - value: John Jones from_schema: https://w3id.org/nmdc/nmdc rank: 18 string_serialization: '{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metatranscriptomics_section range: string required: true @@ -37174,15 +39161,16 @@ classes: 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. + - Do not edit these values. A template will be provided by NMDC in which these + values have been pre-filled. examples: - - value: '187654' + - value: '187654' from_schema: https://w3id.org/nmdc/nmdc rank: 3 string_serialization: '{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metatranscriptomics_section range: string required: true @@ -37193,50 +39181,53 @@ classes: description: Solution in which the RNA sample has been suspended title: RNA sample format examples: - - value: Water + - value: Water from_schema: https://w3id.org/nmdc/nmdc rank: 12 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metatranscriptomics_section range: RNASampleFormatEnum required: true recommended: false 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. + 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 + - value: JGI_pond_041618 from_schema: https://w3id.org/nmdc/nmdc rank: 4 string_serialization: '{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metatranscriptomics_section range: string required: true recommended: false + multivalued: false minimum_value: 0 maximum_value: 2000 - multivalued: false 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. + - Do not edit these values. A template will be provided by NMDC in which these + values have been pre-filled. examples: - - value: '1191234' + - value: '1191234' from_schema: https://w3id.org/nmdc/nmdc aliases: - - Seq Project ID + - Seq Project ID rank: 1 string_serialization: '{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metatranscriptomics_section range: string required: true @@ -37246,15 +39237,16 @@ classes: 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. + - 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 + - value: JGI Pond metatranscriptomics from_schema: https://w3id.org/nmdc/nmdc rank: 2 string_serialization: '{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metatranscriptomics_section range: string required: true @@ -37264,15 +39256,16 @@ classes: 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. + - Do not edit these values. A template will be provided by NMDC in which these + values have been pre-filled. examples: - - value: Jane Johnson + - value: Jane Johnson from_schema: https://w3id.org/nmdc/nmdc rank: 17 string_serialization: '{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metatranscriptomics_section range: string required: true @@ -37282,15 +39275,17 @@ classes: 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 + - 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' + - value: '25' from_schema: https://w3id.org/nmdc/nmdc rank: 6 string_serialization: '{float}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: jgi_metatranscriptomics_section range: float required: true @@ -37301,30 +39296,33 @@ classes: name: oxy_stat_samp range: OxyStatSampEnum 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 + - 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 annotations: @@ -37336,70 +39334,70 @@ classes: from_schema: https://example.com/nmdc_submission_schema is_a: DhInterface mixins: - - DhMultiviewCommonColumnsMixin + - 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 - - 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 + - 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 + - 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 slot_usage: alkalinity: name: alkalinity @@ -37413,19 +39411,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + 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 + - value: 50 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - alkalinity + - alkalinity rank: 1 is_a: core field slot_uri: MIXS:0000421 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -37436,43 +39435,48 @@ classes: 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 + 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 + - value: 100 meter from_schema: https://w3id.org/nmdc/nmdc aliases: - - altitude + - altitude rank: 26 is_a: environment field slot_uri: MIXS:0000094 owner: Biosample domain_of: - - agriculture - - air - - built environment - - core - - food-animal and animal feed - - food-farm environment - - food-food production facility - - food-human foods - - host-associated - - human-associated - - human-gut - - human-oral - - human-skin - - human-vaginal - - hydrocarbon resources-cores - - hydrocarbon resources-fluids_swabs - - microbial mat_biofilm - - miscellaneous natural or artificial environment - - plant-associated - - sediment - - soil - - symbiont-associated - - wastewater_sludge - - water - - Biosample + - agriculture + - air + - built environment + - core + - food-animal and animal feed + - food-farm environment + - food-food production facility + - food-human foods + - host-associated + - human-associated + - human-gut + - human-oral + - human-skin + - human-vaginal + - hydrocarbon resources-cores + - hydrocarbon resources-fluids_swabs + - microbial mat_biofilm + - miscellaneous natural or artificial environment + - plant-associated + - sediment + - soil + - symbiont-associated + - wastewater_sludge + - water + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -37493,16 +39497,16 @@ classes: description: Concentration of ammonium in the sample title: ammonium examples: - - value: 1.5 milligram per liter + - value: 1.5 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - ammonium + - ammonium rank: 4 is_a: core field slot_uri: MIXS:0000427 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -37519,24 +39523,26 @@ classes: 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 + 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 + - value: total;20 gram from_schema: https://w3id.org/nmdc/nmdc aliases: - - biomass + - biomass rank: 6 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000174 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false - 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]+)$ + 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: @@ -37552,16 +39558,16 @@ classes: description: Concentration of bromide title: bromide examples: - - value: 0.05 parts per million + - value: 0.05 parts per million from_schema: https://w3id.org/nmdc/nmdc aliases: - - bromide + - bromide rank: 8 is_a: core field slot_uri: MIXS:0000176 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -37581,16 +39587,16 @@ classes: description: Concentration of calcium in the sample title: calcium examples: - - value: 0.2 micromole per liter + - value: 0.2 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - calcium + - calcium rank: 9 is_a: core field slot_uri: MIXS:0000432 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -37604,21 +39610,24 @@ classes: 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 + 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 + - 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 + - chemical administration rank: 17 is_a: core field string_serialization: '{termLabel} {[termID]};{timestamp}' slot_uri: MIXS:0000751 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -37639,16 +39648,16 @@ classes: description: Concentration of chloride in the sample title: chloride examples: - - value: 5000 milligram per liter + - value: 5000 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - chloride + - chloride rank: 10 is_a: core field slot_uri: MIXS:0000429 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -37668,16 +39677,16 @@ classes: description: Concentration of chlorophyll title: chlorophyll examples: - - value: 5 milligram per cubic meter + - value: 5 milligram per cubic meter from_schema: https://w3id.org/nmdc/nmdc aliases: - - chlorophyll + - chlorophyll rank: 11 is_a: core field slot_uri: MIXS:0000177 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -37691,22 +39700,23 @@ classes: 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) + - 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' + - value: '2021-04-15' + - value: 2021-04 + - value: '2021' from_schema: https://w3id.org/nmdc/nmdc aliases: - - collection date + - collection date rank: 3 is_a: environment field string_serialization: '{date, arbitrary precision}' slot_uri: MIXS:0000011 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string required: true @@ -37724,19 +39734,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + 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 + - value: 1000 kilogram per cubic meter from_schema: https://w3id.org/nmdc/nmdc aliases: - - density + - density rank: 12 is_a: core field slot_uri: MIXS:0000435 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -37747,25 +39758,27 @@ classes: 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. + 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 + - Use modified term comments: - - All depths must be reported in meters. Provide the numerical portion only. + - All depths must be reported in meters. Provide the numerical portion only. examples: - - value: 0 - 0.1 - - value: '1' + - value: 0 - 0.1 + - value: '1' from_schema: https://w3id.org/nmdc/nmdc aliases: - - depth + - depth rank: 9 is_a: environment field string_serialization: '{float}|{float}-{float}' slot_uri: MIXS:0000018 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -37783,24 +39796,26 @@ classes: occurrence: tag: occurrence value: m - description: Concentration of diether lipids; can include multiple types of diether lipids + description: Concentration of diether lipids; can include multiple types of + diether lipids title: diether lipids examples: - - value: 0.2 nanogram per liter + - value: 0.2 nanogram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - diether lipids + - diether lipids rank: 13 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000178 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false - 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]+)$ + 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: @@ -37813,19 +39828,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + 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 + - value: 5 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - dissolved carbon dioxide + - dissolved carbon dioxide rank: 14 is_a: core field slot_uri: MIXS:0000436 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -37845,16 +39861,16 @@ classes: description: Concentration of dissolved hydrogen title: dissolved hydrogen examples: - - value: 0.3 micromole per liter + - value: 0.3 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - dissolved hydrogen + - dissolved hydrogen rank: 15 is_a: core field slot_uri: MIXS:0000179 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -37871,19 +39887,20 @@ classes: 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 + 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 + - value: 2059 micromole per kilogram from_schema: https://w3id.org/nmdc/nmdc aliases: - - dissolved inorganic carbon + - dissolved inorganic carbon rank: 16 is_a: core field slot_uri: MIXS:0000434 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -37900,19 +39917,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + description: Dissolved organic nitrogen concentration measured as; total dissolved + nitrogen - NH4 - NO3 - NO2 title: dissolved organic nitrogen examples: - - value: 0.05 micromole per liter + - value: 0.05 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - dissolved organic nitrogen + - dissolved organic nitrogen rank: 18 is_a: core field slot_uri: MIXS:0000162 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -37932,85 +39950,109 @@ classes: description: Concentration of dissolved oxygen title: dissolved oxygen examples: - - value: 175 micromole per kilogram + - value: 175 micromole per kilogram from_schema: https://w3id.org/nmdc/nmdc aliases: - - dissolved oxygen + - dissolved oxygen rank: 19 is_a: core field slot_uri: MIXS:0000119 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 9 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 10 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 12 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 11 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study slot_group: sample_id_section range: EcosystemTypeEnum recommended: true @@ -38020,25 +40062,31 @@ classes: 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. + 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. + - 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' + - value: '225' + - value: '0' + - value: '1250' from_schema: https://w3id.org/nmdc/nmdc aliases: - - elevation + - elevation rank: 6 is_a: environment field slot_uri: MIXS:0000093 owner: Biosample domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample slot_group: mixs_modified_section range: float required: true @@ -38048,26 +40096,44 @@ classes: 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. + 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. tooltip: tag: tooltip - value: The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context - 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' + value: The biome or major environmental system where the sample or specimen + originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] + in the Environment Ontology (ENVO). For host-associated or plant-associated + samples, use terms from the UBERON or Plant Ontology to describe the + broad anatomical or morphological context + 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) + - range changed to enumeration late in makefile, so this is modified (but + "sample ID" anyway) examples: - - value: oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean + - 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://w3id.org/nmdc/nmdc aliases: - - broad-scale environmental context + - broad-scale environmental context rank: 6 is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000012 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string required: true @@ -38078,30 +40144,45 @@ classes: annotations: expected_value: tag: expected_value - value: Environmental entities having causal influences upon the entity at time of sampling. + value: Environmental entities having causal influences upon the entity + at time of sampling. tooltip: tag: tooltip - value: The specific environmental entities or features near the sample or specimen that significantly influence its characteristics or composition. These entities are typically smaller in scale than the broad environmental context. Values for this field should be countable, material nouns and must be chosen from subclasses of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe specific anatomical structures or plant parts. - 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.' + value: The specific environmental entities or features near the sample + or specimen that significantly influence its characteristics or composition. + These entities are typically smaller in scale than the broad environmental + context. Values for this field should be countable, material nouns and + must be chosen from subclasses of BFO:0000040 (material entity) that + appear in the Environment Ontology (ENVO). For host-associated or plant-associated + samples, use terms from the UBERON or Plant Ontology to describe specific + anatomical structures or plant parts. + 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) + - 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] + - 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 aliases: - - local environmental context + - local environmental context rank: 7 is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000013 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string required: true @@ -38112,26 +40193,41 @@ classes: annotations: expected_value: tag: expected_value - value: The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]. + value: The material displaced by the entity at time of sampling. Recommend + subclasses of environmental material [ENVO:00010483]. tooltip: tag: tooltip - value: The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure - 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).' + value: The predominant environmental material or substrate that directly + surrounds or hosts the sample or specimen at the time of sampling. Choose + values from subclasses of the 'environmental material' class [ENVO:00010483] + in the Environment Ontology (ENVO). Values for this field should be + measurable or mass material nouns, representing continuous environmental + materials. For host-associated or plant-associated samples, use terms + from the UBERON or Plant Ontology to indicate a tissue, organ, or plant + structure + 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) + - range changed to enumeration late in makefile, so this is modified (but + "sample ID" anyway) examples: - - value: soil [ENVO:00001998] + - value: soil [ENVO:00001998] from_schema: https://w3id.org/nmdc/nmdc aliases: - - environmental medium + - environmental medium rank: 8 is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000014 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string required: true @@ -38143,20 +40239,25 @@ classes: 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 + 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] + - value: time series design [EFO:EFO_0001779] from_schema: https://w3id.org/nmdc/nmdc aliases: - - experimental factor + - experimental factor rank: 12 is_a: investigation field string_serialization: '{termLabel} {[termID]}|{text}' slot_uri: MIXS:0000008 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -38165,22 +40266,24 @@ classes: 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. + 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' + - value: 'USA: Maryland, Bethesda' from_schema: https://w3id.org/nmdc/nmdc aliases: - - geographic location (country and/or sea,region) + - geographic location (country and/or sea,region) rank: 4 is_a: environment field string_serialization: '{text}: {text}, {text}' slot_uri: MIXS:0000010 owner: Biosample domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample slot_group: mixs_modified_section range: string required: true @@ -38192,23 +40295,26 @@ classes: 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 + 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) notes: - - This is currently a required field but it's not clear if this should be required for human hosts + - This is currently a required field but it's not clear if this should be + required for human hosts examples: - - value: 50.586825 6.408977 + - value: 50.586825 6.408977 from_schema: https://w3id.org/nmdc/nmdc aliases: - - geographic location (latitude and longitude) + - geographic location (latitude and longitude) rank: 5 is_a: environment field string_serialization: '{lat lon}' slot_uri: MIXS:0000009 owner: Biosample domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample slot_group: mixs_modified_section range: string required: true @@ -38223,24 +40329,26 @@ classes: occurrence: tag: occurrence value: m - description: Any other measurement performed or parameter collected, that is not listed here + 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 + - value: Bicarbonate ion concentration;2075 micromole per kilogram from_schema: https://w3id.org/nmdc/nmdc aliases: - - miscellaneous parameter + - miscellaneous parameter rank: 23 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000752 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false - 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]+)$ + 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: @@ -38256,16 +40364,16 @@ classes: description: Concentration of nitrate in the sample title: nitrate examples: - - value: 65 micromole per liter + - value: 65 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - nitrate + - nitrate rank: 26 is_a: core field slot_uri: MIXS:0000425 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -38285,16 +40393,16 @@ classes: description: Concentration of nitrite in the sample title: nitrite examples: - - value: 0.5 micromole per liter + - value: 0.5 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - nitrite + - nitrite rank: 27 is_a: core field slot_uri: MIXS:0000426 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -38314,16 +40422,16 @@ classes: description: Concentration of nitrogen (total) title: nitrogen examples: - - value: 4.2 micromole per liter + - value: 4.2 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - nitrogen + - nitrogen rank: 28 is_a: core field slot_uri: MIXS:0000504 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -38343,16 +40451,16 @@ classes: description: Concentration of organic carbon title: organic carbon examples: - - value: 1.5 microgram per liter + - value: 1.5 microgram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - organic carbon + - organic carbon rank: 29 is_a: core field slot_uri: MIXS:0000508 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -38372,16 +40480,16 @@ classes: description: Concentration of organic matter title: organic matter examples: - - value: 1.75 milligram per cubic meter + - value: 1.75 milligram per cubic meter from_schema: https://w3id.org/nmdc/nmdc aliases: - - organic matter + - organic matter rank: 45 is_a: core field slot_uri: MIXS:0000204 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -38401,16 +40509,16 @@ classes: description: Concentration of organic nitrogen title: organic nitrogen examples: - - value: 4 micromole per liter + - value: 4 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - organic nitrogen + - organic nitrogen rank: 46 is_a: core field slot_uri: MIXS:0000205 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -38423,23 +40531,28 @@ classes: 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 + 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)' + 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 + - value: total prokaryotes;3.5e7 cells per milliliter;qPCR from_schema: https://w3id.org/nmdc/nmdc aliases: - - organism count + - organism count rank: 30 is_a: core field slot_uri: MIXS:0000103 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -38456,16 +40569,16 @@ classes: description: Oxygenation status of sample title: oxygenation status of sample examples: - - value: aerobic + - value: aerobic from_schema: https://w3id.org/nmdc/nmdc aliases: - - oxygenation status of sample + - oxygenation status of sample rank: 25 is_a: core field slot_uri: MIXS:0000753 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: OxyStatSampEnum multivalued: false @@ -38478,20 +40591,24 @@ classes: 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 + 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 + - value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - - perturbation + - perturbation rank: 33 is_a: core field string_serialization: '{text};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000754 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -38504,22 +40621,23 @@ classes: occurrence: tag: occurrence value: '1' - description: pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + description: pH measurement of the sample, or liquid portion of sample, or + aqueous phase of the fluid title: pH notes: - - Use modified term + - Use modified term examples: - - value: '7.2' + - value: '7.2' from_schema: https://w3id.org/nmdc/nmdc aliases: - - pH + - pH rank: 27 is_a: core field string_serialization: '{float}' slot_uri: MIXS:0001001 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: float recommended: true @@ -38538,20 +40656,20 @@ classes: 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. + - 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 + - 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 aliases: - - pH method + - pH method rank: 41 is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0001106 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -38570,16 +40688,16 @@ classes: description: Concentration of phosphate title: phosphate examples: - - value: 0.7 micromole per liter + - value: 0.7 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - phosphate + - phosphate rank: 53 is_a: core field slot_uri: MIXS:0000505 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -38596,24 +40714,26 @@ classes: occurrence: tag: occurrence value: m - description: Concentration of phospholipid fatty acids; can include multiple values + description: Concentration of phospholipid fatty acids; can include multiple + values title: phospholipid fatty acid examples: - - value: 2.98 milligram per liter + - value: 2.98 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - phospholipid fatty acid + - phospholipid fatty acid rank: 36 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000181 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false - 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]+)$ + 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: @@ -38629,16 +40749,16 @@ classes: description: Concentration of potassium in the sample title: potassium examples: - - value: 463 milligram per liter + - value: 463 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - potassium + - potassium rank: 38 is_a: core field slot_uri: MIXS:0000430 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -38658,16 +40778,16 @@ classes: description: Pressure to which the sample is subject to, in atmospheres title: pressure examples: - - value: 50 atmosphere + - value: 50 atmosphere from_schema: https://w3id.org/nmdc/nmdc aliases: - - pressure + - pressure rank: 39 is_a: core field slot_uri: MIXS:0000412 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -38684,19 +40804,24 @@ classes: 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. + 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 + - value: 25 practical salinity unit from_schema: https://w3id.org/nmdc/nmdc aliases: - - salinity + - salinity rank: 54 is_a: core field slot_uri: MIXS:0000183 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -38707,22 +40832,24 @@ classes: 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). + 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 + - Report dimensions and details when applicable examples: - - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample collection device + - sample collection device rank: 14 is_a: nucleic acid sequence source field string_serialization: '{termLabel} {[termID]}|{text}' slot_uri: MIXS:0000002 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -38736,19 +40863,19 @@ classes: description: The method employed for collecting the sample. title: sample collection method comments: - - This can be a citation or description + - This can be a citation or description examples: - - value: swabbing + - value: swabbing from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample collection method + - sample collection method rank: 15 is_a: nucleic acid sequence source field string_serialization: '{PMID}|{DOI}|{URL}|{text}' slot_uri: MIXS:0001225 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -38758,21 +40885,23 @@ classes: 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. + 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 + - value: filtering of seawater + - value: storing samples in ethanol from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample material processing + - sample material processing rank: 12 is_a: nucleic acid sequence source field string_serialization: '{text}' slot_uri: MIXS:0000016 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -38785,23 +40914,25 @@ classes: 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. + 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. + - 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 + - value: 5 grams + - value: 10 mL from_schema: https://w3id.org/nmdc/nmdc aliases: - - amount or size of sample collected + - amount or size of sample collected rank: 18 is_a: nucleic acid sequence source field string_serialization: '{float} {unit}' slot_uri: MIXS:0000001 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -38818,17 +40949,17 @@ classes: description: Duration for which the sample was stored title: sample storage duration examples: - - value: P1Y6M + - value: P1Y6M from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample storage duration + - sample storage duration rank: 353 is_a: core field string_serialization: '{duration}' slot_uri: MIXS:0000116 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -38841,20 +40972,21 @@ classes: occurrence: tag: occurrence value: '1' - description: Location at which sample was stored, usually name of a specific freezer/room + description: Location at which sample was stored, usually name of a specific + freezer/room title: sample storage location examples: - - value: Freezer no:5 + - value: Freezer no:5 from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample storage location + - sample storage location rank: 41 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000755 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -38873,16 +41005,16 @@ classes: description: Temperature at which the sample was stored (degrees are assumed) title: sample storage temperature examples: - - value: -80 Celsius + - value: -80 Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample storage temperature + - sample storage temperature rank: 7 is_a: core field slot_uri: MIXS:0000110 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string required: true @@ -38890,20 +41022,27 @@ classes: 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. + 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''' + - '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)' + - '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 + - value: IGSN:DSJ0284 from_schema: https://w3id.org/nmdc/nmdc rank: 5 string_serialization: '{text}:{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string recommended: true @@ -38924,16 +41063,16 @@ classes: description: Concentration of silicate title: silicate examples: - - value: 0.05 micromole per liter + - value: 0.05 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - silicate + - silicate rank: 43 is_a: core field slot_uri: MIXS:0000184 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -38947,17 +41086,17 @@ classes: description: Filtering pore size used in sample preparation title: size fraction selected examples: - - value: 0-0.22 micrometer + - value: 0-0.22 micrometer from_schema: https://w3id.org/nmdc/nmdc aliases: - - size fraction selected + - size fraction selected rank: 285 is_a: nucleic acid sequence source field string_serialization: '{float}-{float} {unit}' slot_uri: MIXS:0000017 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -38976,34 +41115,37 @@ classes: description: Sodium concentration in the sample title: sodium examples: - - value: 10.5 milligram per liter + - value: 10.5 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - sodium + - sodium rank: 363 is_a: core field slot_uri: MIXS:0000428 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 13 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study slot_group: sample_id_section range: SpecificEcosystemEnum recommended: true @@ -39022,16 +41164,16 @@ classes: description: Concentration of sulfate in the sample title: sulfate examples: - - value: 5 micromole per liter + - value: 5 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - sulfate + - sulfate rank: 44 is_a: core field slot_uri: MIXS:0000423 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -39051,16 +41193,16 @@ classes: description: Concentration of sulfide in the sample title: sulfide examples: - - value: 2 micromole per liter + - value: 2 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - sulfide + - sulfide rank: 371 is_a: core field slot_uri: MIXS:0000424 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -39077,16 +41219,16 @@ classes: description: Temperature of the sample at the time of sampling. title: temperature examples: - - value: 25 degree Celsius + - value: 25 degree Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - - temperature + - temperature rank: 37 is_a: environment field slot_uri: MIXS:0000113 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -39106,16 +41248,16 @@ classes: description: Measurement of magnitude and direction of flow within a fluid title: water current examples: - - value: 10 cubic meter per second + - value: 10 cubic meter per second from_schema: https://w3id.org/nmdc/nmdc aliases: - - water current + - water current rank: 236 is_a: core field slot_uri: MIXS:0000203 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -39134,105 +41276,105 @@ classes: from_schema: https://example.com/nmdc_submission_schema is_a: DhInterface mixins: - - DhMultiviewCommonColumnsMixin - - SampIdNewTermsMixin + - DhMultiviewCommonColumnsMixin + - SampIdNewTermsMixin slots: - - air_temp_regm - - ances_data - - antibiotic_regm - - biol_stat - - biotic_regm - - biotic_relationship - - chem_administration - - chem_mutagen - - climate_environment - - collection_date - - collection_date_inc - - collection_time - - cult_root_med - - depth - - ecosystem - - ecosystem_category - - ecosystem_subtype - - ecosystem_type - - elev - - env_broad_scale - - env_local_scale - - env_medium - - 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_disease_stat - - 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 - - isotope_exposure - - 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 - - salinity_meth - - 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 - - start_date_inc - - temp - - tiss_cult_growth_med - - water_temp_regm - - watering_regm + - air_temp_regm + - ances_data + - antibiotic_regm + - biol_stat + - biotic_regm + - biotic_relationship + - chem_administration + - chem_mutagen + - climate_environment + - collection_date + - collection_date_inc + - collection_time + - cult_root_med + - depth + - ecosystem + - ecosystem_category + - ecosystem_subtype + - ecosystem_type + - elev + - env_broad_scale + - env_local_scale + - env_medium + - 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_disease_stat + - 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 + - isotope_exposure + - 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 + - salinity_meth + - 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 + - start_date_inc + - temp + - tiss_cult_growth_med + - water_temp_regm + - watering_regm slot_usage: air_temp_regm: name: air_temp_regm @@ -39246,20 +41388,24 @@ classes: 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 + 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 + - 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 + - air temperature regimen rank: 16 is_a: core field string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000551 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -39273,20 +41419,22 @@ classes: 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) + 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 + - value: A/3*B from_schema: https://w3id.org/nmdc/nmdc aliases: - - ancestral data + - ancestral data rank: 237 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000247 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -39302,20 +41450,24 @@ classes: 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 + 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 + - value: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - - antibiotic regimen + - antibiotic regimen rank: 238 is_a: core field string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000553 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -39331,16 +41483,16 @@ classes: description: The level of genome modification. title: biological status examples: - - value: natural + - value: natural from_schema: https://w3id.org/nmdc/nmdc aliases: - - biological status + - biological status rank: 239 is_a: core field slot_uri: MIXS:0000858 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: biol_stat_enum multivalued: false @@ -39353,20 +41505,21 @@ classes: occurrence: tag: occurrence value: '1' - description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. + 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 + - value: sample inoculated with Rhizobium spp. Culture from_schema: https://w3id.org/nmdc/nmdc aliases: - - biotic regimen + - biotic regimen rank: 13 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0001038 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -39377,19 +41530,22 @@ classes: 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 + 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 + - value: free living from_schema: https://w3id.org/nmdc/nmdc aliases: - - observed biotic relationship + - observed biotic relationship rank: 22 is_a: nucleic acid sequence source field slot_uri: MIXS:0000028 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: biotic_relationship_enum multivalued: false @@ -39402,21 +41558,24 @@ classes: 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 + 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 + - 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 + - chemical administration rank: 17 is_a: core field string_serialization: '{termLabel} {[termID]};{timestamp}' slot_uri: MIXS:0000751 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -39434,20 +41593,23 @@ classes: 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 + 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 + - 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 + - chemical mutagen rank: 240 is_a: core field string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000555 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -39460,25 +41622,30 @@ classes: 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 + 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. + - 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. examples: - - value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + - value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - - climate environment + - climate environment rank: 19 is_a: core field string_serialization: '{text};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0001040 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -39492,22 +41659,23 @@ classes: 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) + - 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' + - value: '2021-04-15' + - value: 2021-04 + - value: '2021' from_schema: https://w3id.org/nmdc/nmdc aliases: - - collection date + - collection date rank: 3 is_a: environment field string_serialization: '{date, arbitrary precision}' slot_uri: MIXS:0000011 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string required: true @@ -39515,50 +41683,56 @@ classes: 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. + 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 + - 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. + - 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. + - value: 2021-04-15, 2021-04 and 2021 are all acceptable. from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000011 + - MIXS:0000011 rank: 2 string_serialization: '{date, arbitrary precision}' owner: Biosample domain_of: - - Biosample + - Biosample 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]))?)?$ multivalued: false + 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. + 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 + - 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' + - '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 + - value: 13:33 or 13:33:55 from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000011 + - MIXS:0000011 rank: 1 string_serialization: '{time, seconds optional}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string recommended: true - pattern: ^([01]?\d|2[0-3]|24(?=:00?:00?$)):([0-5]\d)(:([0-5]\d))?$ multivalued: false + pattern: ^([01]?\d|2[0-3]|24(?=:00?:00?$)):([0-5]\d)(:([0-5]\d))?$ cult_root_med: name: cult_root_med annotations: @@ -39568,20 +41742,23 @@ classes: 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. + 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 + - value: http://himedialabs.com/TD/PT158.pdf from_schema: https://w3id.org/nmdc/nmdc aliases: - - culture rooting medium + - culture rooting medium rank: 241 is_a: core field string_serialization: '{text}|{PMID}|{DOI}|{URL}' slot_uri: MIXS:0001041 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -39591,25 +41768,27 @@ classes: 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. + 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 + - Use modified term comments: - - All depths must be reported in meters. Provide the numerical portion only. + - All depths must be reported in meters. Provide the numerical portion only. examples: - - value: 0 - 0.1 - - value: '1' + - value: 0 - 0.1 + - value: '1' from_schema: https://w3id.org/nmdc/nmdc aliases: - - depth + - depth rank: 9 is_a: environment field string_serialization: '{float}|{float}-{float}' slot_uri: MIXS:0000018 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -39617,69 +41796,93 @@ classes: 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 9 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 10 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 12 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 11 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study slot_group: sample_id_section range: EcosystemTypeEnum recommended: true @@ -39689,25 +41892,31 @@ classes: 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. + 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. + - 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' + - value: '225' + - value: '0' + - value: '1250' from_schema: https://w3id.org/nmdc/nmdc aliases: - - elevation + - elevation rank: 6 is_a: environment field slot_uri: MIXS:0000093 owner: Biosample domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample slot_group: mixs_modified_section range: float required: true @@ -39717,26 +41926,44 @@ classes: 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. + 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. tooltip: tag: tooltip - value: The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context - 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' + value: The biome or major environmental system where the sample or specimen + originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] + in the Environment Ontology (ENVO). For host-associated or plant-associated + samples, use terms from the UBERON or Plant Ontology to describe the + broad anatomical or morphological context + 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) + - range changed to enumeration late in makefile, so this is modified (but + "sample ID" anyway) examples: - - value: oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean + - 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://w3id.org/nmdc/nmdc aliases: - - broad-scale environmental context + - broad-scale environmental context rank: 6 is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000012 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string required: true @@ -39747,30 +41974,45 @@ classes: annotations: expected_value: tag: expected_value - value: Environmental entities having causal influences upon the entity at time of sampling. + value: Environmental entities having causal influences upon the entity + at time of sampling. tooltip: tag: tooltip - value: The specific environmental entities or features near the sample or specimen that significantly influence its characteristics or composition. These entities are typically smaller in scale than the broad environmental context. Values for this field should be countable, material nouns and must be chosen from subclasses of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe specific anatomical structures or plant parts. - 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.' + value: The specific environmental entities or features near the sample + or specimen that significantly influence its characteristics or composition. + These entities are typically smaller in scale than the broad environmental + context. Values for this field should be countable, material nouns and + must be chosen from subclasses of BFO:0000040 (material entity) that + appear in the Environment Ontology (ENVO). For host-associated or plant-associated + samples, use terms from the UBERON or Plant Ontology to describe specific + anatomical structures or plant parts. + 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) + - 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] + - 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 aliases: - - local environmental context + - local environmental context rank: 7 is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000013 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string required: true @@ -39781,26 +42023,41 @@ classes: annotations: expected_value: tag: expected_value - value: The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]. + value: The material displaced by the entity at time of sampling. Recommend + subclasses of environmental material [ENVO:00010483]. tooltip: tag: tooltip - value: The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure - 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).' + value: The predominant environmental material or substrate that directly + surrounds or hosts the sample or specimen at the time of sampling. Choose + values from subclasses of the 'environmental material' class [ENVO:00010483] + in the Environment Ontology (ENVO). Values for this field should be + measurable or mass material nouns, representing continuous environmental + materials. For host-associated or plant-associated samples, use terms + from the UBERON or Plant Ontology to indicate a tissue, organ, or plant + structure + 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) + - range changed to enumeration late in makefile, so this is modified (but + "sample ID" anyway) examples: - - value: soil [ENVO:00001998] + - value: soil [ENVO:00001998] from_schema: https://w3id.org/nmdc/nmdc aliases: - - environmental medium + - environmental medium rank: 8 is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000014 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string required: true @@ -39812,20 +42069,25 @@ classes: 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 + 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] + - value: time series design [EFO:EFO_0001779] from_schema: https://w3id.org/nmdc/nmdc aliases: - - experimental factor + - experimental factor rank: 12 is_a: investigation field string_serialization: '{termLabel} {[termID]}|{text}' slot_uri: MIXS:0000008 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -39841,20 +42103,24 @@ classes: 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 + 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 + - 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 + - fertilizer regimen rank: 242 is_a: core field string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000556 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -39870,20 +42136,24 @@ classes: 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 + 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 + - 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 + - fungicide regimen rank: 243 is_a: core field string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000557 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -39892,33 +42162,41 @@ classes: annotations: expected_value: tag: expected_value - value: gaseous compound name;gaseous compound amount;treatment interval and duration + 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 + 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 + - 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 + - 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 aliases: - - gaseous environment + - gaseous environment rank: 20 is_a: core field string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000558 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -39932,20 +42210,23 @@ classes: 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 + 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 + - value: aox1A transgenic from_schema: https://w3id.org/nmdc/nmdc aliases: - - genetic modification + - genetic modification rank: 244 is_a: core field string_serialization: '{PMID}|{DOI}|{URL}|{text}' slot_uri: MIXS:0000859 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -39954,22 +42235,24 @@ classes: 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. + 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' + - value: 'USA: Maryland, Bethesda' from_schema: https://w3id.org/nmdc/nmdc aliases: - - geographic location (country and/or sea,region) + - geographic location (country and/or sea,region) rank: 4 is_a: environment field string_serialization: '{text}: {text}, {text}' slot_uri: MIXS:0000010 owner: Biosample domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample slot_group: mixs_modified_section range: string required: true @@ -39987,20 +42270,24 @@ classes: 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 + 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 + - value: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - - gravity + - gravity rank: 245 is_a: core field string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000559 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -40013,22 +42300,24 @@ classes: 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.' + 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' + - 'Removed from description: Alternatively use Crop Ontology (CO) terms' examples: - - value: Growth chamber [CO_715:0000189] + - value: Growth chamber [CO_715:0000189] from_schema: https://w3id.org/nmdc/nmdc aliases: - - growth facility + - growth facility rank: 1 is_a: core field string_serialization: '{text}|{termLabel} {[termID]}' slot_uri: MIXS:0001043 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: GrowthFacilEnum required: true @@ -40045,16 +42334,16 @@ classes: description: Characteristic shape, appearance or growth form of a plant species title: growth habit examples: - - value: spreading + - value: spreading from_schema: https://w3id.org/nmdc/nmdc aliases: - - growth habit + - growth habit rank: 246 is_a: core field slot_uri: MIXS:0001044 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: growth_habit_enum multivalued: false @@ -40063,27 +42352,32 @@ classes: annotations: expected_value: tag: expected_value - value: growth hormone name;growth hormone amount;treatment interval and duration + 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 + 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 + - 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 + - growth hormone regimen rank: 247 is_a: core field string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000560 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -40099,20 +42393,24 @@ classes: 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 + 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 + - 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 + - herbicide regimen rank: 248 is_a: core field string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000561 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -40128,19 +42426,20 @@ classes: 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 + 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 + - value: 10 days from_schema: https://w3id.org/nmdc/nmdc aliases: - - host age + - host age rank: 249 is_a: core field slot_uri: MIXS:0000255 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -40157,17 +42456,17 @@ classes: description: Common name of the host. title: host common name examples: - - value: human + - value: human from_schema: https://w3id.org/nmdc/nmdc aliases: - - host common name + - host common name rank: 250 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000248 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -40177,20 +42476,23 @@ classes: expected_value: tag: expected_value value: disease name or Disease Ontology term - description: List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text + description: List of diseases with which the host has been diagnosed; can + include multiple diagnoses. The value of the field depends on host; for + humans the terms should be chosen from the DO (Human Disease Ontology) at + https://www.disease-ontology.org, non-human host diseases are free text title: host disease status examples: - - value: rabies [DOID:11260] + - value: rabies [DOID:11260] from_schema: https://w3id.org/nmdc/nmdc aliases: - - host disease status + - host disease status rank: 390 is_a: nucleic acid sequence source field string_serialization: '{termLabel} {[termID]}|{text}' slot_uri: MIXS:0000031 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -40209,16 +42511,16 @@ classes: description: Measurement of dry mass title: host dry mass examples: - - value: 500 gram + - value: 500 gram from_schema: https://w3id.org/nmdc/nmdc aliases: - - host dry mass + - host dry mass rank: 251 is_a: core field slot_uri: MIXS:0000257 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -40235,17 +42537,17 @@ classes: description: Observed genotype title: host genotype examples: - - value: C57BL/6 + - value: C57BL/6 from_schema: https://w3id.org/nmdc/nmdc aliases: - - host genotype + - host genotype rank: 252 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000365 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -40264,16 +42566,16 @@ classes: description: The height of subject title: host height examples: - - value: 0.1 meter + - value: 0.1 meter from_schema: https://w3id.org/nmdc/nmdc aliases: - - host height + - host height rank: 253 is_a: core field slot_uri: MIXS:0000264 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -40293,16 +42595,16 @@ classes: description: The length of subject title: host length examples: - - value: 1 meter + - value: 1 meter from_schema: https://w3id.org/nmdc/nmdc aliases: - - host length + - host length rank: 254 is_a: core field slot_uri: MIXS:0000256 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -40319,17 +42621,17 @@ classes: description: Description of life stage of host title: host life stage examples: - - value: adult + - value: adult from_schema: https://w3id.org/nmdc/nmdc aliases: - - host life stage + - host life stage rank: 255 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000251 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -40342,20 +42644,22 @@ classes: 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 + 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] + - value: elongated [PATO:0001154] from_schema: https://w3id.org/nmdc/nmdc aliases: - - host phenotype + - host phenotype rank: 256 is_a: core field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000874 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -40365,24 +42669,29 @@ classes: 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. + 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. + 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' + - value: 'serovar:Newport, variety:glabrum, cultivar: Red Delicious' from_schema: https://w3id.org/nmdc/nmdc aliases: - - host subspecific genetic lineage + - host subspecific genetic lineage rank: 257 is_a: core field string_serialization: '{rank name}:{text}' slot_uri: MIXS:0001318 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -40395,20 +42704,21 @@ classes: 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. + 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 + - value: flukeworms from_schema: https://w3id.org/nmdc/nmdc aliases: - - observed host symbionts + - observed host symbionts rank: 258 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0001298 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -40424,16 +42734,16 @@ classes: 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 + - Homo sapiens [NCBITaxon:9606] would be a reasonable has_raw_value from_schema: https://w3id.org/nmdc/nmdc aliases: - - host taxid + - host taxid rank: 259 is_a: core field slot_uri: MIXS:0000250 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -40452,16 +42762,16 @@ classes: description: Total mass of the host at collection, the unit depends on host title: host total mass examples: - - value: 2500 gram + - value: 2500 gram from_schema: https://w3id.org/nmdc/nmdc aliases: - - host total mass + - host total mass rank: 260 is_a: core field slot_uri: MIXS:0000263 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -40481,16 +42791,16 @@ classes: description: Measurement of wet mass title: host wet mass examples: - - value: 1500 gram + - value: 1500 gram from_schema: https://w3id.org/nmdc/nmdc aliases: - - host wet mass + - host wet mass rank: 261 is_a: core field slot_uri: MIXS:0000567 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -40507,20 +42817,25 @@ classes: 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 + 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 + - 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 + - humidity regimen rank: 21 is_a: core field string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000568 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -40530,48 +42845,52 @@ classes: description: List isotope exposure or addition applied to your sample. title: isotope exposure/addition todos: - - Can we make the H218O correctly super and subscripted? + - Can we make the H218O correctly super and subscripted? comments: - - This is required when your experimental design includes the use of isotopically labeled compounds + - This is required when your experimental design includes the use of isotopically + labeled compounds examples: - - value: 13C glucose - - value: H218O + - value: 13C glucose + - value: H218O from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000751 + - MIXS:0000751 rank: 16 string_serialization: '{termLabel} {[termID]}; {timestamp}' owner: Biosample domain_of: - - Biosample + - Biosample 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)?)?)?)?$ multivalued: false + 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 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 + 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) notes: - - This is currently a required field but it's not clear if this should be required for human hosts + - This is currently a required field but it's not clear if this should be + required for human hosts examples: - - value: 50.586825 6.408977 + - value: 50.586825 6.408977 from_schema: https://w3id.org/nmdc/nmdc aliases: - - geographic location (latitude and longitude) + - geographic location (latitude and longitude) rank: 5 is_a: environment field string_serialization: '{lat lon}' slot_uri: MIXS:0000009 owner: Biosample domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample slot_group: mixs_modified_section range: string required: true @@ -40589,25 +42908,27 @@ classes: occurrence: tag: occurrence value: '1' - description: Information about treatment(s) involving exposure to light, including both light intensity and quality. + 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 + - value: incandescant light;10 lux;450 nanometer from_schema: https://w3id.org/nmdc/nmdc aliases: - - light regimen + - light regimen rank: 24 is_a: core field string_serialization: '{text};{float} {unit};{float} {unit}' slot_uri: MIXS:0000569 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true multivalued: false - pattern: ^\S+.*\S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ + 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: @@ -40617,20 +42938,21 @@ classes: occurrence: tag: occurrence value: m - description: Information about any mechanical damage exerted on the plant; can include multiple damages and sites + description: Information about any mechanical damage exerted on the plant; + can include multiple damages and sites title: mechanical damage examples: - - value: pruning;bark + - value: pruning;bark from_schema: https://w3id.org/nmdc/nmdc aliases: - - mechanical damage + - mechanical damage rank: 262 is_a: core field string_serialization: '{text};{text}' slot_uri: MIXS:0001052 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -40639,27 +42961,32 @@ classes: annotations: expected_value: tag: expected_value - value: mineral nutrient name;mineral nutrient amount;treatment interval and duration + 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 + 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 + - 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 + - mineral nutrient regimen rank: 263 is_a: core field string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000570 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -40672,50 +42999,58 @@ classes: occurrence: tag: occurrence value: m - description: Any other measurement performed or parameter collected, that is not listed here + 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 + - value: Bicarbonate ion concentration;2075 micromole per kilogram from_schema: https://w3id.org/nmdc/nmdc aliases: - - miscellaneous parameter + - miscellaneous parameter rank: 23 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000752 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false - 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]+)$ + 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 + 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 + 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 + - 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 + - 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 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -40727,23 +43062,28 @@ classes: 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 + 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)' + 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 + - value: total prokaryotes;3.5e7 cells per milliliter;qPCR from_schema: https://w3id.org/nmdc/nmdc aliases: - - organism count + - organism count rank: 30 is_a: core field slot_uri: MIXS:0000103 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -40760,16 +43100,16 @@ classes: description: Oxygenation status of sample title: oxygenation status of sample examples: - - value: aerobic + - value: aerobic from_schema: https://w3id.org/nmdc/nmdc aliases: - - oxygenation status of sample + - oxygenation status of sample rank: 25 is_a: core field slot_uri: MIXS:0000753 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: OxyStatSampEnum multivalued: false @@ -40782,20 +43122,24 @@ classes: 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 + 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 + - value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - - perturbation + - perturbation rank: 33 is_a: core field string_serialization: '{text};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000754 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -40811,20 +43155,24 @@ classes: 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 + 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 + - 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 + - pesticide regimen rank: 265 is_a: core field string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000573 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -40837,20 +43185,23 @@ classes: 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 + 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 + - value: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - - pH regimen + - pH regimen rank: 266 is_a: core field string_serialization: '{float};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0001056 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -40863,19 +43214,23 @@ classes: 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 + 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] + - value: hydroponic plant culture media [EO:0007067] from_schema: https://w3id.org/nmdc/nmdc aliases: - - plant growth medium + - plant growth medium rank: 267 is_a: core field slot_uri: MIXS:0001057 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -40888,20 +43243,21 @@ classes: occurrence: tag: occurrence value: '1' - description: Substance produced by the plant, where the sample was obtained from + description: Substance produced by the plant, where the sample was obtained + from title: plant product examples: - - value: xylem sap [PO:0025539] + - value: xylem sap [PO:0025539] from_schema: https://w3id.org/nmdc/nmdc aliases: - - plant product + - plant product rank: 268 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0001058 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -40914,19 +43270,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. + description: Sex of the reproductive parts on the whole plant, e.g. pistillate, + staminate, monoecieous, hermaphrodite. title: plant sex examples: - - value: Hermaphroditic + - value: Hermaphroditic from_schema: https://w3id.org/nmdc/nmdc aliases: - - plant sex + - plant sex rank: 269 is_a: core field slot_uri: MIXS:0001059 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: plant_sex_enum multivalued: false @@ -40939,20 +43296,23 @@ classes: 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. + 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] + - value: epidermis [PO:0005679] from_schema: https://w3id.org/nmdc/nmdc aliases: - - plant structure + - plant structure rank: 270 is_a: core field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0001060 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -40969,20 +43329,25 @@ classes: 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 + 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 + - 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 + - radiation regimen rank: 271 is_a: core field string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000575 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -40998,20 +43363,23 @@ classes: 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 + 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 + - value: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - - rainfall regimen + - rainfall regimen rank: 272 is_a: core field string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000576 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -41024,20 +43392,21 @@ classes: occurrence: tag: occurrence value: '1' - description: Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. + 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 + - value: http://himedialabs.com/TD/PT158.pdf from_schema: https://w3id.org/nmdc/nmdc aliases: - - rooting conditions + - rooting conditions rank: 273 is_a: core field string_serialization: '{PMID}|{DOI}|{URL}|{text}' slot_uri: MIXS:0001061 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -41053,20 +43422,21 @@ classes: occurrence: tag: occurrence value: '1' - description: Source of organic carbon in the culture rooting medium; e.g. sucrose. + description: Source of organic carbon in the culture rooting medium; e.g. + sucrose. title: rooting medium carbon examples: - - value: sucrose + - value: sucrose from_schema: https://w3id.org/nmdc/nmdc aliases: - - rooting medium carbon + - rooting medium carbon rank: 274 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000577 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -41083,20 +43453,21 @@ classes: 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). + 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 + - value: KH2PO4;170¬†milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - rooting medium macronutrients + - rooting medium macronutrients rank: 275 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000578 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -41113,20 +43484,21 @@ classes: 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). + 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 + - value: H3BO3;6.2¬†milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - rooting medium micronutrients + - rooting medium micronutrients rank: 276 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000579 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -41143,16 +43515,16 @@ classes: description: pH measurement of the culture rooting medium; e.g. 5.5. title: rooting medium pH examples: - - value: '7.5' + - value: '7.5' from_schema: https://w3id.org/nmdc/nmdc aliases: - - rooting medium pH + - rooting medium pH rank: 277 is_a: core field slot_uri: MIXS:0001062 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -41169,20 +43541,21 @@ classes: 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. + 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 + - value: abscisic acid;0.75 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - rooting medium regulators + - rooting medium regulators rank: 278 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000581 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -41196,20 +43569,21 @@ classes: occurrence: tag: occurrence value: '1' - description: Specification of the solidifying agent in the culture rooting medium; e.g. agar. + description: Specification of the solidifying agent in the culture rooting + medium; e.g. agar. title: rooting medium solidifier examples: - - value: agar + - value: agar from_schema: https://w3id.org/nmdc/nmdc aliases: - - rooting medium solidifier + - rooting medium solidifier rank: 279 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0001063 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -41225,20 +43599,22 @@ classes: 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). + 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 + - value: nicotinic acid;0.5 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - rooting medium organic supplements + - rooting medium organic supplements rank: 280 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000580 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -41255,19 +43631,24 @@ classes: 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. + 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 + - value: 25 practical salinity unit from_schema: https://w3id.org/nmdc/nmdc aliases: - - salinity + - salinity rank: 54 is_a: core field slot_uri: MIXS:0000183 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -41284,17 +43665,17 @@ classes: description: Reference or method used in determining salinity title: salinity method examples: - - value: https://doi.org/10.1007/978-1-61779-986-0_28 + - value: https://doi.org/10.1007/978-1-61779-986-0_28 from_schema: https://w3id.org/nmdc/nmdc aliases: - - salinity method + - salinity method rank: 55 is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000341 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -41310,20 +43691,24 @@ classes: 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 + 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 + - 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 + - salt regimen rank: 281 is_a: core field string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000582 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -41339,16 +43724,16 @@ classes: description: Reason for the sample title: sample capture status examples: - - value: farm sample + - value: farm sample from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample capture status + - sample capture status rank: 282 is_a: core field slot_uri: MIXS:0000860 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: samp_capt_status_enum multivalued: false @@ -41358,22 +43743,24 @@ classes: 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). + 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 + - Report dimensions and details when applicable examples: - - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample collection device + - sample collection device rank: 14 is_a: nucleic acid sequence source field string_serialization: '{termLabel} {[termID]}|{text}' slot_uri: MIXS:0000002 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -41387,19 +43774,19 @@ classes: description: The method employed for collecting the sample. title: sample collection method comments: - - This can be a citation or description + - This can be a citation or description examples: - - value: swabbing + - value: swabbing from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample collection method + - sample collection method rank: 15 is_a: nucleic acid sequence source field string_serialization: '{PMID}|{DOI}|{URL}|{text}' slot_uri: MIXS:0001225 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -41412,19 +43799,20 @@ classes: 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. + 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 + - value: infection from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample disease stage + - sample disease stage rank: 283 is_a: core field slot_uri: MIXS:0000249 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: samp_dis_stage_enum multivalued: false @@ -41434,21 +43822,23 @@ classes: 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. + 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 + - value: filtering of seawater + - value: storing samples in ethanol from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample material processing + - sample material processing rank: 12 is_a: nucleic acid sequence source field string_serialization: '{text}' slot_uri: MIXS:0000016 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -41461,23 +43851,25 @@ classes: 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. + 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. + - 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 + - value: 5 grams + - value: 10 mL from_schema: https://w3id.org/nmdc/nmdc aliases: - - amount or size of sample collected + - amount or size of sample collected rank: 18 is_a: nucleic acid sequence source field string_serialization: '{float} {unit}' slot_uri: MIXS:0000001 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -41494,17 +43886,17 @@ classes: description: Duration for which the sample was stored title: sample storage duration examples: - - value: P1Y6M + - value: P1Y6M from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample storage duration + - sample storage duration rank: 353 is_a: core field string_serialization: '{duration}' slot_uri: MIXS:0000116 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -41517,20 +43909,21 @@ classes: occurrence: tag: occurrence value: '1' - description: Location at which sample was stored, usually name of a specific freezer/room + description: Location at which sample was stored, usually name of a specific + freezer/room title: sample storage location examples: - - value: Freezer no:5 + - value: Freezer no:5 from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample storage location + - sample storage location rank: 41 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000755 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -41549,16 +43942,16 @@ classes: description: Temperature at which the sample was stored (degrees are assumed) title: sample storage temperature examples: - - value: -80 Celsius + - value: -80 Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample storage temperature + - sample storage temperature rank: 7 is_a: core field slot_uri: MIXS:0000110 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string required: true @@ -41566,20 +43959,27 @@ classes: 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. + 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''' + - '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)' + - '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 + - value: IGSN:DSJ0284 from_schema: https://w3id.org/nmdc/nmdc rank: 5 string_serialization: '{text}:{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string recommended: true @@ -41594,20 +43994,23 @@ classes: 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 + 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 + - value: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - - seasonal environment + - seasonal environment rank: 284 is_a: core field string_serialization: '{text};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0001068 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -41620,34 +44023,37 @@ classes: description: Filtering pore size used in sample preparation title: size fraction selected examples: - - value: 0-0.22 micrometer + - value: 0-0.22 micrometer from_schema: https://w3id.org/nmdc/nmdc aliases: - - size fraction selected + - size fraction selected rank: 285 is_a: nucleic acid sequence source field string_serialization: '{float}-{float} {unit}' slot_uri: MIXS:0000017 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 13 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study slot_group: sample_id_section range: SpecificEcosystemEnum recommended: true @@ -41660,46 +44066,53 @@ classes: 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 + 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 + - value: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - - standing water regimen + - standing water regimen rank: 286 is_a: core field string_serialization: '{text};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0001069 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false start_date_inc: name: start_date_inc - description: Date the incubation was started. Only relevant for incubation samples. + 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 + - 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. + - 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. + - value: 2021-04-15, 2021-04 and 2021 are all acceptable. from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000011 + - MIXS:0000011 rank: 4 string_serialization: '{date, arbitrary precision}' owner: Biosample domain_of: - - Biosample + - Biosample 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]))?)?$ multivalued: false + pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$ temp: name: temp annotations: @@ -41712,16 +44125,16 @@ classes: description: Temperature of the sample at the time of sampling. title: temperature examples: - - value: 25 degree Celsius + - value: 25 degree Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - - temperature + - temperature rank: 37 is_a: environment field slot_uri: MIXS:0000113 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -41738,17 +44151,17 @@ classes: 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 + - value: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf from_schema: https://w3id.org/nmdc/nmdc aliases: - - tissue culture growth media + - tissue culture growth media rank: 287 is_a: core field string_serialization: '{PMID}|{DOI}|{URL}|{text}' slot_uri: MIXS:0001070 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -41764,20 +44177,23 @@ classes: 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 + 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 + - 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 + - water temperature regimen rank: 288 is_a: core field string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000590 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -41793,21 +44209,24 @@ classes: 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 + 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 + - 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 aliases: - - watering regimen + - watering regimen rank: 25 is_a: core field string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000591 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -41826,123 +44245,123 @@ classes: from_schema: https://example.com/nmdc_submission_schema is_a: DhInterface mixins: - - DhMultiviewCommonColumnsMixin - - SampIdNewTermsMixin + - DhMultiviewCommonColumnsMixin + - SampIdNewTermsMixin slots: - - air_temp_regm - - alkalinity - - alkalinity_method - - alkyl_diethers - - aminopept_act - - ammonium - - bacteria_carb_prod - - biomass - - biotic_regm - - biotic_relationship - - bishomohopanol - - bromide - - calcium - - carb_nitro_ratio - - chem_administration - - chloride - - chlorophyll - - climate_environment - - collection_date - - collection_date_inc - - collection_time - - 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 - - experimental_factor - - extreme_event - - fire - - flooding - - gaseous_environment - - geo_loc_name - - glucosidase_act - - humidity_regm - - isotope_exposure - - lat_lon - - light_regm - - magnesium - - mean_frict_vel - - mean_peak_frict_vel - - methane - - micro_biomass_c_meth - - micro_biomass_meth - - micro_biomass_n_meth - - microbial_biomass - - microbial_biomass_c - - microbial_biomass_n - - misc_param - - n_alkanes - - nitrate - - nitrite - - nitro - - org_carb - - org_matter - - org_nitro - - org_nitro_method - - 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 - - salinity_meth - - samp_collec_device - - samp_collec_method - - samp_mat_process - - samp_size - - samp_store_dur - - samp_store_loc - - samp_store_temp - - sample_link - - sediment_type - - sieving - - silicate - - size_frac - - sodium - - specific_ecosystem - - start_date_inc - - sulfate - - sulfide - - temp - - tidal_stage - - tot_carb - - tot_depth_water_col - - tot_nitro_cont_meth - - tot_nitro_content - - tot_org_c_meth - - tot_org_carb - - turbidity - - water_cont_soil_meth - - water_content - - watering_regm + - air_temp_regm + - alkalinity + - alkalinity_method + - alkyl_diethers + - aminopept_act + - ammonium + - bacteria_carb_prod + - biomass + - biotic_regm + - biotic_relationship + - bishomohopanol + - bromide + - calcium + - carb_nitro_ratio + - chem_administration + - chloride + - chlorophyll + - climate_environment + - collection_date + - collection_date_inc + - collection_time + - 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 + - experimental_factor + - extreme_event + - fire + - flooding + - gaseous_environment + - geo_loc_name + - glucosidase_act + - humidity_regm + - isotope_exposure + - lat_lon + - light_regm + - magnesium + - mean_frict_vel + - mean_peak_frict_vel + - methane + - micro_biomass_c_meth + - micro_biomass_meth + - micro_biomass_n_meth + - microbial_biomass + - microbial_biomass_c + - microbial_biomass_n + - misc_param + - n_alkanes + - nitrate + - nitrite + - nitro + - org_carb + - org_matter + - org_nitro + - org_nitro_method + - 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 + - salinity_meth + - samp_collec_device + - samp_collec_method + - samp_mat_process + - samp_size + - samp_store_dur + - samp_store_loc + - samp_store_temp + - sample_link + - sediment_type + - sieving + - silicate + - size_frac + - sodium + - specific_ecosystem + - start_date_inc + - sulfate + - sulfide + - temp + - tidal_stage + - tot_carb + - tot_depth_water_col + - tot_nitro_cont_meth + - tot_nitro_content + - tot_org_c_meth + - tot_org_carb + - turbidity + - water_cont_soil_meth + - water_content + - watering_regm slot_usage: air_temp_regm: name: air_temp_regm @@ -41956,20 +44375,24 @@ classes: 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 + 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 + - 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 + - air temperature regimen rank: 16 is_a: core field string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000551 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -41985,19 +44408,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + 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 + - value: 50 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - alkalinity + - alkalinity rank: 1 is_a: core field slot_uri: MIXS:0000421 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -42014,17 +44438,17 @@ classes: description: Method used for alkalinity measurement title: alkalinity method examples: - - value: titration + - value: titration from_schema: https://w3id.org/nmdc/nmdc aliases: - - alkalinity method + - alkalinity method rank: 218 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000298 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -42043,16 +44467,16 @@ classes: description: Concentration of alkyl diethers title: alkyl diethers examples: - - value: 0.005 mole per liter + - value: 0.005 mole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - alkyl diethers + - alkyl diethers rank: 2 is_a: core field slot_uri: MIXS:0000490 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -42072,16 +44496,16 @@ classes: description: Measurement of aminopeptidase activity title: aminopeptidase activity examples: - - value: 0.269 mole per liter per hour + - value: 0.269 mole per liter per hour from_schema: https://w3id.org/nmdc/nmdc aliases: - - aminopeptidase activity + - aminopeptidase activity rank: 3 is_a: core field slot_uri: MIXS:0000172 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -42101,16 +44525,16 @@ classes: description: Concentration of ammonium in the sample title: ammonium examples: - - value: 1.5 milligram per liter + - value: 1.5 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - ammonium + - ammonium rank: 4 is_a: core field slot_uri: MIXS:0000427 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -42130,16 +44554,16 @@ classes: description: Measurement of bacterial carbon production title: bacterial carbon production examples: - - value: 2.53 microgram per liter per hour + - value: 2.53 microgram per liter per hour from_schema: https://w3id.org/nmdc/nmdc aliases: - - bacterial carbon production + - bacterial carbon production rank: 5 is_a: core field slot_uri: MIXS:0000173 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -42156,24 +44580,26 @@ classes: 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 + 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 + - value: total;20 gram from_schema: https://w3id.org/nmdc/nmdc aliases: - - biomass + - biomass rank: 6 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000174 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false - 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]+)$ + 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]+)$ biotic_regm: name: biotic_regm annotations: @@ -42183,20 +44609,21 @@ classes: occurrence: tag: occurrence value: '1' - description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. + 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 + - value: sample inoculated with Rhizobium spp. Culture from_schema: https://w3id.org/nmdc/nmdc aliases: - - biotic regimen + - biotic regimen rank: 13 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0001038 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -42206,19 +44633,22 @@ classes: 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 + 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 + - value: free living from_schema: https://w3id.org/nmdc/nmdc aliases: - - observed biotic relationship + - observed biotic relationship rank: 22 is_a: nucleic acid sequence source field slot_uri: MIXS:0000028 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: biotic_relationship_enum multivalued: false @@ -42237,16 +44667,16 @@ classes: description: Concentration of bishomohopanol title: bishomohopanol examples: - - value: 14 microgram per liter + - value: 14 microgram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - bishomohopanol + - bishomohopanol rank: 7 is_a: core field slot_uri: MIXS:0000175 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -42266,16 +44696,16 @@ classes: description: Concentration of bromide title: bromide examples: - - value: 0.05 parts per million + - value: 0.05 parts per million from_schema: https://w3id.org/nmdc/nmdc aliases: - - bromide + - bromide rank: 8 is_a: core field slot_uri: MIXS:0000176 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -42295,16 +44725,16 @@ classes: description: Concentration of calcium in the sample title: calcium examples: - - value: 0.2 micromole per liter + - value: 0.2 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - calcium + - calcium rank: 9 is_a: core field slot_uri: MIXS:0000432 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -42321,16 +44751,16 @@ classes: description: Ratio of amount or concentrations of carbon to nitrogen title: carbon/nitrogen ratio examples: - - value: '0.417361111' + - value: '0.417361111' from_schema: https://w3id.org/nmdc/nmdc aliases: - - carbon/nitrogen ratio + - carbon/nitrogen ratio rank: 44 is_a: core field slot_uri: MIXS:0000310 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: float multivalued: false @@ -42344,21 +44774,24 @@ classes: 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 + 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 + - 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 + - chemical administration rank: 17 is_a: core field string_serialization: '{termLabel} {[termID]};{timestamp}' slot_uri: MIXS:0000751 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -42379,16 +44812,16 @@ classes: description: Concentration of chloride in the sample title: chloride examples: - - value: 5000 milligram per liter + - value: 5000 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - chloride + - chloride rank: 10 is_a: core field slot_uri: MIXS:0000429 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -42408,16 +44841,16 @@ classes: description: Concentration of chlorophyll title: chlorophyll examples: - - value: 5 milligram per cubic meter + - value: 5 milligram per cubic meter from_schema: https://w3id.org/nmdc/nmdc aliases: - - chlorophyll + - chlorophyll rank: 11 is_a: core field slot_uri: MIXS:0000177 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -42431,23 +44864,27 @@ classes: 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 + 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. examples: - - value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + - value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - - climate environment + - climate environment rank: 19 is_a: core field string_serialization: '{text};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0001040 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -42460,22 +44897,23 @@ classes: 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) + - 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' + - value: '2021-04-15' + - value: 2021-04 + - value: '2021' from_schema: https://w3id.org/nmdc/nmdc aliases: - - collection date + - collection date rank: 3 is_a: environment field string_serialization: '{date, arbitrary precision}' slot_uri: MIXS:0000011 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string required: true @@ -42483,50 +44921,56 @@ classes: 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. + 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 + - 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. + - 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. + - value: 2021-04-15, 2021-04 and 2021 are all acceptable. from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000011 + - MIXS:0000011 rank: 2 string_serialization: '{date, arbitrary precision}' owner: Biosample domain_of: - - Biosample + - Biosample 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]))?)?$ multivalued: false + 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. + 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 + - 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' + - '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 + - value: 13:33 or 13:33:55 from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000011 + - MIXS:0000011 rank: 1 string_serialization: '{time, seconds optional}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string recommended: true - pattern: ^([01]?\d|2[0-3]|24(?=:00?:00?$)):([0-5]\d)(:([0-5]\d))?$ multivalued: false + pattern: ^([01]?\d|2[0-3]|24(?=:00?:00?$)):([0-5]\d)(:([0-5]\d))?$ density: name: density annotations: @@ -42539,19 +44983,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + 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 + - value: 1000 kilogram per cubic meter from_schema: https://w3id.org/nmdc/nmdc aliases: - - density + - density rank: 12 is_a: core field slot_uri: MIXS:0000435 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -42562,25 +45007,27 @@ classes: 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. + 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 + - Use modified term comments: - - All depths must be reported in meters. Provide the numerical portion only. + - All depths must be reported in meters. Provide the numerical portion only. examples: - - value: 0 - 0.1 - - value: '1' + - value: 0 - 0.1 + - value: '1' from_schema: https://w3id.org/nmdc/nmdc aliases: - - depth + - depth rank: 9 is_a: environment field string_serialization: '{float}-{float}' slot_uri: MIXS:0000018 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string required: true @@ -42598,24 +45045,26 @@ classes: occurrence: tag: occurrence value: m - description: Concentration of diether lipids; can include multiple types of diether lipids + description: Concentration of diether lipids; can include multiple types of + diether lipids title: diether lipids examples: - - value: 0.2 nanogram per liter + - value: 0.2 nanogram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - diether lipids + - diether lipids rank: 13 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000178 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false - 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]+)$ + 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: @@ -42628,19 +45077,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + 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 + - value: 5 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - dissolved carbon dioxide + - dissolved carbon dioxide rank: 14 is_a: core field slot_uri: MIXS:0000436 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -42660,16 +45110,16 @@ classes: description: Concentration of dissolved hydrogen title: dissolved hydrogen examples: - - value: 0.3 micromole per liter + - value: 0.3 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - dissolved hydrogen + - dissolved hydrogen rank: 15 is_a: core field slot_uri: MIXS:0000179 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -42686,19 +45136,20 @@ classes: 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 + 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 + - value: 2059 micromole per kilogram from_schema: https://w3id.org/nmdc/nmdc aliases: - - dissolved inorganic carbon + - dissolved inorganic carbon rank: 16 is_a: core field slot_uri: MIXS:0000434 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -42715,19 +45166,20 @@ classes: 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 + 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 + - value: 197 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - dissolved organic carbon + - dissolved organic carbon rank: 17 is_a: core field slot_uri: MIXS:0000433 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -42744,19 +45196,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + description: Dissolved organic nitrogen concentration measured as; total dissolved + nitrogen - NH4 - NO3 - NO2 title: dissolved organic nitrogen examples: - - value: 0.05 micromole per liter + - value: 0.05 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - dissolved organic nitrogen + - dissolved organic nitrogen rank: 18 is_a: core field slot_uri: MIXS:0000162 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -42776,85 +45229,109 @@ classes: description: Concentration of dissolved oxygen title: dissolved oxygen examples: - - value: 175 micromole per kilogram + - value: 175 micromole per kilogram from_schema: https://w3id.org/nmdc/nmdc aliases: - - dissolved oxygen + - dissolved oxygen rank: 19 is_a: core field slot_uri: MIXS:0000119 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 9 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 10 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 12 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 11 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study slot_group: sample_id_section range: EcosystemTypeEnum recommended: true @@ -42864,25 +45341,31 @@ classes: 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. + 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. + - 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' + - value: '225' + - value: '0' + - value: '1250' from_schema: https://w3id.org/nmdc/nmdc aliases: - - elevation + - elevation rank: 6 is_a: environment field slot_uri: MIXS:0000093 owner: Biosample domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample slot_group: mixs_modified_section range: float required: true @@ -42892,26 +45375,44 @@ classes: 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. + 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. tooltip: tag: tooltip - value: The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context - 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' + value: The biome or major environmental system where the sample or specimen + originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] + in the Environment Ontology (ENVO). For host-associated or plant-associated + samples, use terms from the UBERON or Plant Ontology to describe the + broad anatomical or morphological context + 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) + - range changed to enumeration late in makefile, so this is modified (but + "sample ID" anyway) examples: - - value: oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean + - 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://w3id.org/nmdc/nmdc aliases: - - broad-scale environmental context + - broad-scale environmental context rank: 6 is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000012 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string required: true @@ -42922,30 +45423,45 @@ classes: annotations: expected_value: tag: expected_value - value: Environmental entities having causal influences upon the entity at time of sampling. + value: Environmental entities having causal influences upon the entity + at time of sampling. tooltip: tag: tooltip - value: The specific environmental entities or features near the sample or specimen that significantly influence its characteristics or composition. These entities are typically smaller in scale than the broad environmental context. Values for this field should be countable, material nouns and must be chosen from subclasses of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe specific anatomical structures or plant parts. - 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.' + value: The specific environmental entities or features near the sample + or specimen that significantly influence its characteristics or composition. + These entities are typically smaller in scale than the broad environmental + context. Values for this field should be countable, material nouns and + must be chosen from subclasses of BFO:0000040 (material entity) that + appear in the Environment Ontology (ENVO). For host-associated or plant-associated + samples, use terms from the UBERON or Plant Ontology to describe specific + anatomical structures or plant parts. + 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) + - 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] + - 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 aliases: - - local environmental context + - local environmental context rank: 7 is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000013 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string required: true @@ -42956,26 +45472,41 @@ classes: annotations: expected_value: tag: expected_value - value: The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]. + value: The material displaced by the entity at time of sampling. Recommend + subclasses of environmental material [ENVO:00010483]. tooltip: tag: tooltip - value: The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure - 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).' + value: The predominant environmental material or substrate that directly + surrounds or hosts the sample or specimen at the time of sampling. Choose + values from subclasses of the 'environmental material' class [ENVO:00010483] + in the Environment Ontology (ENVO). Values for this field should be + measurable or mass material nouns, representing continuous environmental + materials. For host-associated or plant-associated samples, use terms + from the UBERON or Plant Ontology to indicate a tissue, organ, or plant + structure + 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) + - range changed to enumeration late in makefile, so this is modified (but + "sample ID" anyway) examples: - - value: soil [ENVO:00001998] + - value: soil [ENVO:00001998] from_schema: https://w3id.org/nmdc/nmdc aliases: - - environmental medium + - environmental medium rank: 8 is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000014 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string required: true @@ -42987,20 +45518,25 @@ classes: 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 + 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] + - value: time series design [EFO:EFO_0001779] from_schema: https://w3id.org/nmdc/nmdc aliases: - - experimental factor + - experimental factor rank: 12 is_a: investigation field string_serialization: '{termLabel} {[termID]}|{text}' slot_uri: MIXS:0000008 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -43013,16 +45549,16 @@ classes: description: Unusual physical events that may have affected microbial populations title: history/extreme events examples: - - value: 1980-05-18, volcanic eruption + - value: 1980-05-18, volcanic eruption from_schema: https://w3id.org/nmdc/nmdc aliases: - - history/extreme events + - history/extreme events rank: 13 is_a: core field slot_uri: MIXS:0000320 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -43035,21 +45571,22 @@ classes: 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? + - is "to" acceptable? Is there a better way to request that be written? comments: - - Provide the date the fire occurred. If extended burning occurred provide the date range. + - 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 + - value: '1871-10-10' + - value: 1871-10-01 to 1871-10-31 from_schema: https://w3id.org/nmdc/nmdc aliases: - - history/fire + - history/fire rank: 15 is_a: core field slot_uri: MIXS:0001086 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -43063,22 +45600,23 @@ classes: 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? + - is "to" acceptable? Is there a better way to request that be written? + - What about if the "day" isn't known? Is this ok? comments: - - Provide the date the flood occurred. If extended flooding occurred provide the date range. + - 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 + - value: '1927-04-15' + - value: 1927-04 to 1927-05 from_schema: https://w3id.org/nmdc/nmdc aliases: - - history/flooding + - history/flooding rank: 16 is_a: core field slot_uri: MIXS:0000319 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -43087,31 +45625,37 @@ classes: annotations: expected_value: tag: expected_value - value: gaseous compound name;gaseous compound amount;treatment interval and duration + 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 + 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 + - 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 aliases: - - gaseous environment + - gaseous environment rank: 20 is_a: core field string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000558 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -43120,22 +45664,24 @@ classes: 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. + 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' + - value: 'USA: Maryland, Bethesda' from_schema: https://w3id.org/nmdc/nmdc aliases: - - geographic location (country and/or sea,region) + - geographic location (country and/or sea,region) rank: 4 is_a: environment field string_serialization: '{text}: {text}, {text}' slot_uri: MIXS:0000010 owner: Biosample domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample slot_group: mixs_modified_section range: string required: true @@ -43156,16 +45702,16 @@ classes: description: Measurement of glucosidase activity title: glucosidase activity examples: - - value: 5 mol per liter per hour + - value: 5 mol per liter per hour from_schema: https://w3id.org/nmdc/nmdc aliases: - - glucosidase activity + - glucosidase activity rank: 20 is_a: core field slot_uri: MIXS:0000137 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -43182,20 +45728,25 @@ classes: 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 + 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 + - 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 + - humidity regimen rank: 21 is_a: core field string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000568 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -43204,48 +45755,52 @@ classes: description: List isotope exposure or addition applied to your sample. title: isotope exposure/addition todos: - - Can we make the H218O correctly super and subscripted? + - Can we make the H218O correctly super and subscripted? comments: - - This is required when your experimental design includes the use of isotopically labeled compounds + - This is required when your experimental design includes the use of isotopically + labeled compounds examples: - - value: 13C glucose - - value: H218O + - value: 13C glucose + - value: H218O from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000751 + - MIXS:0000751 rank: 16 string_serialization: '{termLabel} {[termID]}; {timestamp}' owner: Biosample domain_of: - - Biosample + - Biosample 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)?)?)?)?$ multivalued: false + 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 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 + 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) notes: - - This is currently a required field but it's not clear if this should be required for human hosts + - This is currently a required field but it's not clear if this should be + required for human hosts examples: - - value: 50.586825 6.408977 + - value: 50.586825 6.408977 from_schema: https://w3id.org/nmdc/nmdc aliases: - - geographic location (latitude and longitude) + - geographic location (latitude and longitude) rank: 5 is_a: environment field string_serialization: '{lat lon}' slot_uri: MIXS:0000009 owner: Biosample domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample slot_group: mixs_modified_section range: string required: true @@ -43263,24 +45818,26 @@ classes: occurrence: tag: occurrence value: '1' - description: Information about treatment(s) involving exposure to light, including both light intensity and quality. + 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 + - value: incandescant light;10 lux;450 nanometer from_schema: https://w3id.org/nmdc/nmdc aliases: - - light regimen + - light regimen rank: 24 is_a: core field string_serialization: '{text};{float} {unit};{float} {unit}' slot_uri: MIXS:0000569 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false - pattern: ^\S+.*\S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ + pattern: ^\S+.*\S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? + \S+$ magnesium: name: magnesium annotations: @@ -43289,23 +45846,24 @@ classes: value: measurement value preferred_unit: tag: preferred_unit - value: mole per liter, milligram per liter, parts per million, micromole per kilogram + 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 + - value: 52.8 micromole per kilogram from_schema: https://w3id.org/nmdc/nmdc aliases: - - magnesium + - magnesium rank: 21 is_a: core field slot_uri: MIXS:0000431 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -43325,16 +45883,16 @@ classes: description: Measurement of mean friction velocity title: mean friction velocity examples: - - value: 0.5 meter per second + - value: 0.5 meter per second from_schema: https://w3id.org/nmdc/nmdc aliases: - - mean friction velocity + - mean friction velocity rank: 22 is_a: core field slot_uri: MIXS:0000498 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -43354,16 +45912,16 @@ classes: description: Measurement of mean peak friction velocity title: mean peak friction velocity examples: - - value: 1 meter per second + - value: 1 meter per second from_schema: https://w3id.org/nmdc/nmdc aliases: - - mean peak friction velocity + - mean peak friction velocity rank: 23 is_a: core field slot_uri: MIXS:0000502 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -43383,16 +45941,16 @@ classes: description: Methane (gas) amount or concentration at the time of sampling title: methane examples: - - value: 1800 parts per billion + - value: 1800 parts per billion from_schema: https://w3id.org/nmdc/nmdc aliases: - - methane + - methane rank: 24 is_a: core field slot_uri: MIXS:0000101 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -43402,20 +45960,20 @@ classes: 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 + - How should we separate values? | or ;? lets be consistent comments: - - required if "microbial_biomass_c" is provided + - 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 + - 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:0000339 + - MIXS:0000339 rank: 1004 string_serialization: '{PMID}|{DOI}|{URL}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string recommended: true @@ -43432,17 +45990,17 @@ classes: description: Reference or method used in determining microbial biomass title: microbial biomass method examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - microbial biomass method + - microbial biomass method rank: 43 is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000339 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -43451,18 +46009,18 @@ classes: description: Reference or method used in determining microbial biomass nitrogen title: microbial biomass nitrogen method comments: - - required if "microbial_biomass_n" is provided + - 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 + - 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:0000339 + - MIXS:0000339 rank: 1004 string_serialization: '{PMID}|{DOI}|{URL}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string multivalued: false @@ -43478,63 +46036,69 @@ classes: 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 + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - microbial biomass + - microbial biomass rank: 42 is_a: core field slot_uri: MIXS:0000650 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false 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. + 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 + - 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 + - value: 0.05 ug C/g dry soil from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000650 + - MIXS:0000650 rank: 1004 string_serialization: '{float} {unit}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string - pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ multivalued: false + 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. + 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 + - 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 + - value: 0.05 ug N/g dry soil from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000650 + - MIXS:0000650 rank: 1004 string_serialization: '{float} {unit}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string - pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ multivalued: false + pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ misc_param: name: misc_param annotations: @@ -43544,24 +46108,26 @@ classes: occurrence: tag: occurrence value: m - description: Any other measurement performed or parameter collected, that is not listed here + 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 + - value: Bicarbonate ion concentration;2075 micromole per kilogram from_schema: https://w3id.org/nmdc/nmdc aliases: - - miscellaneous parameter + - miscellaneous parameter rank: 23 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000752 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false - 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]+)$ + 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: @@ -43577,21 +46143,22 @@ classes: description: Concentration of n-alkanes; can include multiple n-alkanes title: n-alkanes examples: - - value: n-hexadecane;100 milligram per liter + - value: n-hexadecane;100 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - n-alkanes + - n-alkanes rank: 25 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000503 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false - 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]+)$ + 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: @@ -43607,16 +46174,16 @@ classes: description: Concentration of nitrate in the sample title: nitrate examples: - - value: 65 micromole per liter + - value: 65 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - nitrate + - nitrate rank: 26 is_a: core field slot_uri: MIXS:0000425 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -43636,16 +46203,16 @@ classes: description: Concentration of nitrite in the sample title: nitrite examples: - - value: 0.5 micromole per liter + - value: 0.5 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - nitrite + - nitrite rank: 27 is_a: core field slot_uri: MIXS:0000426 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -43665,16 +46232,16 @@ classes: description: Concentration of nitrogen (total) title: nitrogen examples: - - value: 4.2 micromole per liter + - value: 4.2 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - nitrogen + - nitrogen rank: 28 is_a: core field slot_uri: MIXS:0000504 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -43694,16 +46261,16 @@ classes: description: Concentration of organic carbon title: organic carbon examples: - - value: 1.5 microgram per liter + - value: 1.5 microgram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - organic carbon + - organic carbon rank: 29 is_a: core field slot_uri: MIXS:0000508 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -43723,16 +46290,16 @@ classes: description: Concentration of organic matter title: organic matter examples: - - value: 1.75 milligram per cubic meter + - value: 1.75 milligram per cubic meter from_schema: https://w3id.org/nmdc/nmdc aliases: - - organic matter + - organic matter rank: 45 is_a: core field slot_uri: MIXS:0000204 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -43752,16 +46319,16 @@ classes: description: Concentration of organic nitrogen title: organic nitrogen examples: - - value: 4 micromole per liter + - value: 4 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - organic nitrogen + - organic nitrogen rank: 46 is_a: core field slot_uri: MIXS:0000205 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -43771,18 +46338,18 @@ classes: description: Method used for obtaining organic nitrogen title: organic nitrogen method comments: - - required if "org_nitro" is provided + - required if "org_nitro" is provided examples: - - value: https://doi.org/10.1016/0038-0717(85)90144-0 + - value: https://doi.org/10.1016/0038-0717(85)90144-0 from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000338 - - MIXS:0000205 + - MIXS:0000338 + - MIXS:0000205 rank: 14 string_serialization: '{PMID}|{DOI}|{URL}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string multivalued: false @@ -43794,23 +46361,28 @@ classes: 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 + 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)' + 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 + - value: total prokaryotes;3.5e7 cells per milliliter;qPCR from_schema: https://w3id.org/nmdc/nmdc aliases: - - organism count + - organism count rank: 30 is_a: core field slot_uri: MIXS:0000103 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -43827,16 +46399,16 @@ classes: description: Oxygenation status of sample title: oxygenation status of sample examples: - - value: aerobic + - value: aerobic from_schema: https://w3id.org/nmdc/nmdc aliases: - - oxygenation status of sample + - oxygenation status of sample rank: 25 is_a: core field slot_uri: MIXS:0000753 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: OxyStatSampEnum multivalued: false @@ -43855,16 +46427,16 @@ classes: description: Concentration of particulate organic carbon title: particulate organic carbon examples: - - value: 1.92 micromole per liter + - value: 1.92 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - particulate organic carbon + - particulate organic carbon rank: 31 is_a: core field slot_uri: MIXS:0000515 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -43881,24 +46453,28 @@ classes: 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 + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - particle classification + - particle classification rank: 32 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000206 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false - 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]+)$ + 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]+)$ perturbation: name: perturbation annotations: @@ -43908,20 +46484,24 @@ classes: 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 + 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 + - value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - - perturbation + - perturbation rank: 33 is_a: core field string_serialization: '{text};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000754 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -43940,16 +46520,16 @@ classes: description: Concentration of petroleum hydrocarbon title: petroleum hydrocarbon examples: - - value: 0.05 micromole per liter + - value: 0.05 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - petroleum hydrocarbon + - petroleum hydrocarbon rank: 34 is_a: core field slot_uri: MIXS:0000516 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -43963,22 +46543,23 @@ classes: occurrence: tag: occurrence value: '1' - description: pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + description: pH measurement of the sample, or liquid portion of sample, or + aqueous phase of the fluid title: pH notes: - - Use modified term + - Use modified term examples: - - value: '7.2' + - value: '7.2' from_schema: https://w3id.org/nmdc/nmdc aliases: - - pH + - pH rank: 27 is_a: core field string_serialization: '{float}' slot_uri: MIXS:0001001 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: float recommended: true @@ -43997,20 +46578,20 @@ classes: 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. + - 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 + - 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 aliases: - - pH method + - pH method rank: 41 is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0001106 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -44029,21 +46610,22 @@ classes: description: Concentration of phaeopigments; can include multiple phaeopigments title: phaeopigments examples: - - value: 2.5 milligram per cubic meter + - value: 2.5 milligram per cubic meter from_schema: https://w3id.org/nmdc/nmdc aliases: - - phaeopigments + - phaeopigments rank: 35 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000180 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false - 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]+)$ + 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: @@ -44059,16 +46641,16 @@ classes: description: Concentration of phosphate title: phosphate examples: - - value: 0.7 micromole per liter + - value: 0.7 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - phosphate + - phosphate rank: 53 is_a: core field slot_uri: MIXS:0000505 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -44085,24 +46667,26 @@ classes: occurrence: tag: occurrence value: m - description: Concentration of phospholipid fatty acids; can include multiple values + description: Concentration of phospholipid fatty acids; can include multiple + values title: phospholipid fatty acid examples: - - value: 2.98 milligram per liter + - value: 2.98 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - phospholipid fatty acid + - phospholipid fatty acid rank: 36 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000181 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false - 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]+)$ + 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]+)$ porosity: name: porosity annotations: @@ -44115,20 +46699,21 @@ classes: occurrence: tag: occurrence value: '1' - description: Porosity of deposited sediment is volume of voids divided by the total volume of sample + description: Porosity of deposited sediment is volume of voids divided by + the total volume of sample title: porosity examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - porosity + - porosity rank: 37 is_a: core field string_serialization: '{float} - {float} {unit}' slot_uri: MIXS:0000211 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -44147,16 +46732,16 @@ classes: description: Concentration of potassium in the sample title: potassium examples: - - value: 463 milligram per liter + - value: 463 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - potassium + - potassium rank: 38 is_a: core field slot_uri: MIXS:0000430 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -44176,16 +46761,16 @@ classes: description: Pressure to which the sample is subject to, in atmospheres title: pressure examples: - - value: 50 atmosphere + - value: 50 atmosphere from_schema: https://w3id.org/nmdc/nmdc aliases: - - pressure + - pressure rank: 39 is_a: core field slot_uri: MIXS:0000412 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -44202,19 +46787,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + description: Redox potential, measured relative to a hydrogen cell, indicating + oxidation or reduction potential title: redox potential examples: - - value: 300 millivolt + - value: 300 millivolt from_schema: https://w3id.org/nmdc/nmdc aliases: - - redox potential + - redox potential rank: 40 is_a: core field slot_uri: MIXS:0000182 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -44231,19 +46817,24 @@ classes: 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. + 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 + - value: 25 practical salinity unit from_schema: https://w3id.org/nmdc/nmdc aliases: - - salinity + - salinity rank: 54 is_a: core field slot_uri: MIXS:0000183 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -44260,17 +46851,17 @@ classes: description: Reference or method used in determining salinity title: salinity method examples: - - value: https://doi.org/10.1007/978-1-61779-986-0_28 + - value: https://doi.org/10.1007/978-1-61779-986-0_28 from_schema: https://w3id.org/nmdc/nmdc aliases: - - salinity method + - salinity method rank: 55 is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000341 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -44280,22 +46871,24 @@ classes: 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). + 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 + - Report dimensions and details when applicable examples: - - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample collection device + - sample collection device rank: 14 is_a: nucleic acid sequence source field string_serialization: '{termLabel} {[termID]}|{text}' slot_uri: MIXS:0000002 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -44309,19 +46902,19 @@ classes: description: The method employed for collecting the sample. title: sample collection method comments: - - This can be a citation or description + - This can be a citation or description examples: - - value: swabbing + - value: swabbing from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample collection method + - sample collection method rank: 15 is_a: nucleic acid sequence source field string_serialization: '{PMID}|{DOI}|{URL}|{text}' slot_uri: MIXS:0001225 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -44331,21 +46924,23 @@ classes: 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. + 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 + - value: filtering of seawater + - value: storing samples in ethanol from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample material processing + - sample material processing rank: 12 is_a: nucleic acid sequence source field string_serialization: '{text}' slot_uri: MIXS:0000016 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -44358,23 +46953,25 @@ classes: 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. + 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. + - 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 + - value: 5 grams + - value: 10 mL from_schema: https://w3id.org/nmdc/nmdc aliases: - - amount or size of sample collected + - amount or size of sample collected rank: 18 is_a: nucleic acid sequence source field string_serialization: '{float} {unit}' slot_uri: MIXS:0000001 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -44391,17 +46988,17 @@ classes: description: Duration for which the sample was stored title: sample storage duration examples: - - value: P1Y6M + - value: P1Y6M from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample storage duration + - sample storage duration rank: 353 is_a: core field string_serialization: '{duration}' slot_uri: MIXS:0000116 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -44414,20 +47011,21 @@ classes: occurrence: tag: occurrence value: '1' - description: Location at which sample was stored, usually name of a specific freezer/room + description: Location at which sample was stored, usually name of a specific + freezer/room title: sample storage location examples: - - value: Freezer no:5 + - value: Freezer no:5 from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample storage location + - sample storage location rank: 41 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000755 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -44446,16 +47044,16 @@ classes: description: Temperature at which the sample was stored (degrees are assumed) title: sample storage temperature examples: - - value: -80 Celsius + - value: -80 Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample storage temperature + - sample storage temperature rank: 7 is_a: core field slot_uri: MIXS:0000110 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string required: true @@ -44463,20 +47061,27 @@ classes: 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. + 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''' + - '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)' + - '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 + - value: IGSN:DSJ0284 from_schema: https://w3id.org/nmdc/nmdc rank: 5 string_serialization: '{text}:{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string recommended: true @@ -44494,16 +47099,16 @@ classes: description: Information about the sediment type based on major constituents title: sediment type examples: - - value: biogenous + - value: biogenous from_schema: https://w3id.org/nmdc/nmdc aliases: - - sediment type + - sediment type rank: 42 is_a: core field slot_uri: MIXS:0001078 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: sediment_type_enum multivalued: false @@ -44516,27 +47121,28 @@ classes: occurrence: tag: occurrence value: '1' - description: Collection design of pooled samples and/or sieve size and amount of sample sieved + 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. + - Describe how samples were composited or sieved. + - Use 'sample link' to indicate which samples were combined. examples: - - value: combined 2 cores | 4mm sieved - - value: 4 mm sieved and homogenized - - value: 50 g | 5 cores | 2 mm sieved + - value: combined 2 cores | 4mm sieved + - value: 4 mm sieved and homogenized + - value: 50 g | 5 cores | 2 mm sieved from_schema: https://w3id.org/nmdc/nmdc aliases: - - composite design/sieving + - composite design/sieving rank: 8 is_a: core field string_serialization: '{{text}|{float} {unit}};{float} {unit}' slot_uri: MIXS:0000322 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -44555,16 +47161,16 @@ classes: description: Concentration of silicate title: silicate examples: - - value: 0.05 micromole per liter + - value: 0.05 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - silicate + - silicate rank: 43 is_a: core field slot_uri: MIXS:0000184 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -44578,17 +47184,17 @@ classes: description: Filtering pore size used in sample preparation title: size fraction selected examples: - - value: 0-0.22 micrometer + - value: 0-0.22 micrometer from_schema: https://w3id.org/nmdc/nmdc aliases: - - size fraction selected + - size fraction selected rank: 285 is_a: nucleic acid sequence source field string_serialization: '{float}-{float} {unit}' slot_uri: MIXS:0000017 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -44607,60 +47213,66 @@ classes: description: Sodium concentration in the sample title: sodium examples: - - value: 10.5 milligram per liter + - value: 10.5 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - sodium + - sodium rank: 363 is_a: core field slot_uri: MIXS:0000428 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 13 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study 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. + 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 + - 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. + - 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. + - value: 2021-04-15, 2021-04 and 2021 are all acceptable. from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000011 + - MIXS:0000011 rank: 4 string_serialization: '{date, arbitrary precision}' owner: Biosample domain_of: - - Biosample + - Biosample 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]))?)?$ multivalued: false + pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$ sulfate: name: sulfate annotations: @@ -44676,16 +47288,16 @@ classes: description: Concentration of sulfate in the sample title: sulfate examples: - - value: 5 micromole per liter + - value: 5 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - sulfate + - sulfate rank: 44 is_a: core field slot_uri: MIXS:0000423 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -44705,16 +47317,16 @@ classes: description: Concentration of sulfide in the sample title: sulfide examples: - - value: 2 micromole per liter + - value: 2 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - sulfide + - sulfide rank: 371 is_a: core field slot_uri: MIXS:0000424 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -44731,16 +47343,16 @@ classes: description: Temperature of the sample at the time of sampling. title: temperature examples: - - value: 25 degree Celsius + - value: 25 degree Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - - temperature + - temperature rank: 37 is_a: environment field slot_uri: MIXS:0000113 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -44757,16 +47369,16 @@ classes: description: Stage of tide title: tidal stage examples: - - value: high tide + - value: high tide from_schema: https://w3id.org/nmdc/nmdc aliases: - - tidal stage + - tidal stage rank: 45 is_a: core field slot_uri: MIXS:0000750 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: tidal_stage_enum multivalued: false @@ -44785,21 +47397,25 @@ classes: 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 + - 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 + - value: 1 ug/L from_schema: https://w3id.org/nmdc/nmdc aliases: - - total carbon + - total carbon rank: 47 is_a: core field slot_uri: MIXS:0000525 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -44819,16 +47435,16 @@ classes: description: Measurement of total depth of water column title: total depth of water column examples: - - value: 500 meter + - value: 500 meter from_schema: https://w3id.org/nmdc/nmdc aliases: - - total depth of water column + - total depth of water column rank: 46 is_a: core field slot_uri: MIXS:0000634 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -44845,18 +47461,18 @@ classes: 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 + - 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 aliases: - - total nitrogen content method + - total nitrogen content method rank: 49 is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000338 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -44875,16 +47491,16 @@ classes: description: Total nitrogen content of the sample title: total nitrogen content examples: - - value: 5 mg N/ L + - value: 5 mg N/ L from_schema: https://w3id.org/nmdc/nmdc aliases: - - total nitrogen content + - total nitrogen content rank: 48 is_a: core field slot_uri: MIXS:0000530 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -44901,17 +47517,17 @@ classes: description: Reference or method used in determining total organic carbon title: total organic carbon method examples: - - value: https://doi.org/10.1080/07352680902776556 + - value: https://doi.org/10.1080/07352680902776556 from_schema: https://w3id.org/nmdc/nmdc aliases: - - total organic carbon method + - total organic carbon method rank: 51 is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000337 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -44927,22 +47543,23 @@ classes: occurrence: tag: occurrence value: '1' - description: 'Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content' + 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? + - check description. How are they different? + - check description. How are they different? examples: - - value: 5 mg N/ L + - value: 5 mg N/ L from_schema: https://w3id.org/nmdc/nmdc aliases: - - total organic carbon + - total organic carbon rank: 50 is_a: core field slot_uri: MIXS:0000533 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -44959,19 +47576,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Measure of the amount of cloudiness or haziness in water caused by individual particles + description: Measure of the amount of cloudiness or haziness in water caused + by individual particles title: turbidity examples: - - value: 0.3 nephelometric turbidity units + - value: 0.3 nephelometric turbidity units from_schema: https://w3id.org/nmdc/nmdc aliases: - - turbidity + - turbidity rank: 47 is_a: core field slot_uri: MIXS:0000191 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -44985,27 +47603,31 @@ classes: occurrence: tag: occurrence value: '1' - description: Reference or method used in determining the water content of soil + 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 + - 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 + - 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 aliases: - - water content method + - water content method rank: 40 is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000323 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -45021,24 +47643,24 @@ classes: 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 - - 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 + - how to manage multiple water content methods? examples: - - 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 + - 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 aliases: - - water content + - water content rank: 39 is_a: core field string_serialization: '{float or pct} {unit}' slot_uri: MIXS:0000185 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -45055,21 +47677,24 @@ classes: 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 + 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 + - 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 aliases: - - watering regimen + - watering regimen rank: 25 is_a: core field string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000591 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -45087,129 +47712,129 @@ classes: from_schema: https://example.com/nmdc_submission_schema is_a: DhInterface mixins: - - DhMultiviewCommonColumnsMixin - - SampIdNewTermsMixin - - SoilMixsInspiredMixin + - DhMultiviewCommonColumnsMixin + - SampIdNewTermsMixin + - SoilMixsInspiredMixin slots: - - agrochem_addition - - air_temp_regm - - al_sat - - al_sat_meth - - ammonium_nitrogen - - annual_precpt - - annual_temp - - biotic_regm - - biotic_relationship - - bulk_elect_conductivity - - 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 - - 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 - - infiltrations - - isotope_exposure - - lat_lon - - lbc_thirty - - lbceq - - light_regm - - link_addit_analys - - 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 + - agrochem_addition + - air_temp_regm + - al_sat + - al_sat_meth + - ammonium_nitrogen + - annual_precpt + - annual_temp + - biotic_regm + - biotic_relationship + - bulk_elect_conductivity + - 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 + - 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 + - infiltrations + - isotope_exposure + - lat_lon + - lbc_thirty + - lbceq + - light_regm + - link_addit_analys + - 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 @@ -45223,20 +47848,21 @@ classes: occurrence: tag: occurrence value: m - description: Addition of fertilizers, pesticides, etc. - amount and time of applications + 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 + - value: roundup;5 milligram per liter;2018-06-21 from_schema: https://w3id.org/nmdc/nmdc aliases: - - history/agrochemical additions + - history/agrochemical additions rank: 2 is_a: core field string_serialization: '{text};{float} {unit};{timestamp}' slot_uri: MIXS:0000639 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -45253,20 +47879,24 @@ classes: 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 + 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 + - 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 + - air temperature regimen rank: 16 is_a: core field string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000551 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -45286,24 +47916,32 @@ classes: description: The relative abundance of aluminum in the sample title: aluminum saturation/ extreme unusual properties todos: - - Example & validation. Can we configure things so 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. + - Example & validation. Can we configure things so 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: - - 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. + - 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' + - value: '0.27' from_schema: https://w3id.org/nmdc/nmdc aliases: - - extreme_unusual_properties/Al saturation + - extreme_unusual_properties/Al saturation rank: 3 is_a: core field slot_uri: MIXS:0000607 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -45320,23 +47958,26 @@ classes: description: Reference or method used in determining Aluminum saturation title: aluminum saturation method/ extreme unusual properties todos: - - 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? + - 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. + - Required when aluminum saturation is provided. examples: - - value: https://doi.org/10.1371/journal.pone.0176357 + - value: https://doi.org/10.1371/journal.pone.0176357 from_schema: https://w3id.org/nmdc/nmdc aliases: - - extreme_unusual_properties/Al saturation method + - extreme_unusual_properties/Al saturation method rank: 4 is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000324 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -45355,21 +47996,21 @@ classes: description: Concentration of ammonium nitrogen in the sample title: ammonium nitrogen examples: - - value: 2.3 mg/kg + - value: 2.3 mg/kg from_schema: https://w3id.org/nmdc/nmdc see_also: - - https://www.ornl.gov/content/bio-scales-0 + - https://www.ornl.gov/content/bio-scales-0 aliases: - - ammonium_nitrogen - - NH4-N + - ammonium_nitrogen + - NH4-N rank: 1005 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string - pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ multivalued: false + pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ annual_precpt: name: annual_precpt annotations: @@ -45382,21 +48023,24 @@ classes: 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. + 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 + - value: 8.94 inch from_schema: https://w3id.org/nmdc/nmdc aliases: - - mean annual precipitation + - mean annual precipitation rank: 5 is_a: core field slot_uri: MIXS:0000644 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -45416,16 +48060,16 @@ classes: description: Mean annual temperature title: mean annual temperature examples: - - value: 12.5 degree Celsius + - value: 12.5 degree Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - - mean annual temperature + - mean annual temperature rank: 6 is_a: core field slot_uri: MIXS:0000642 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -45439,20 +48083,21 @@ classes: occurrence: tag: occurrence value: '1' - description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. + 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 + - value: sample inoculated with Rhizobium spp. Culture from_schema: https://w3id.org/nmdc/nmdc aliases: - - biotic regimen + - biotic regimen rank: 13 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0001038 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -45463,39 +48108,44 @@ classes: 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 + 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 + - value: free living from_schema: https://w3id.org/nmdc/nmdc aliases: - - observed biotic relationship + - observed biotic relationship rank: 22 is_a: nucleic acid sequence source field slot_uri: MIXS:0000028 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: biotic_relationship_enum multivalued: false bulk_elect_conductivity: name: bulk_elect_conductivity - description: Electrical conductivity is a measure of the ability to carry electric current, which is mostly dictated by the chemistry of and amount of water. + description: Electrical conductivity is a measure of the ability to carry + electric current, which is mostly dictated by the chemistry of and amount + of water. title: bulk electrical conductivity comments: - - Provide the value output of the field instrument. + - Provide the value output of the field instrument. examples: - - value: 0.017 mS/cm + - value: 0.017 mS/cm from_schema: https://w3id.org/nmdc/nmdc rank: 1008 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string - pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ multivalued: false + pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ carb_nitro_ratio: name: carb_nitro_ratio annotations: @@ -45508,16 +48158,16 @@ classes: description: Ratio of amount or concentrations of carbon to nitrogen title: carbon/nitrogen ratio examples: - - value: '0.417361111' + - value: '0.417361111' from_schema: https://w3id.org/nmdc/nmdc aliases: - - carbon/nitrogen ratio + - carbon/nitrogen ratio rank: 44 is_a: core field slot_uri: MIXS:0000310 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: float multivalued: false @@ -45531,21 +48181,24 @@ classes: 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 + 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 + - 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 + - chemical administration rank: 17 is_a: core field string_serialization: '{termLabel} {[termID]};{timestamp}' slot_uri: MIXS:0000751 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -45560,25 +48213,30 @@ classes: 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 + 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. + - 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. examples: - - value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + - value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - - climate environment + - climate environment rank: 19 is_a: core field string_serialization: '{text};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0001040 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -45592,22 +48250,23 @@ classes: 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) + - 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' + - value: '2021-04-15' + - value: 2021-04 + - value: '2021' from_schema: https://w3id.org/nmdc/nmdc aliases: - - collection date + - collection date rank: 3 is_a: environment field string_serialization: '{date, arbitrary precision}' slot_uri: MIXS:0000011 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string required: true @@ -45615,73 +48274,82 @@ classes: 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. + 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 + - 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. + - 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. + - value: 2021-04-15, 2021-04 and 2021 are all acceptable. from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000011 + - MIXS:0000011 rank: 2 string_serialization: '{date, arbitrary precision}' owner: Biosample domain_of: - - Biosample + - Biosample 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]))?)?$ multivalued: false + 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. + 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 + - 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' + - '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 + - value: 13:33 or 13:33:55 from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000011 + - MIXS:0000011 rank: 1 string_serialization: '{time, seconds optional}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string recommended: true - pattern: ^([01]?\d|2[0-3]|24(?=:00?:00?$)):([0-5]\d)(:([0-5]\d))?$ multivalued: false + 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. + 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 + - 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' + - '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 + - value: 13:33 or 13:33:55 from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000011 + - MIXS:0000011 rank: 3 string_serialization: '{time, seconds optional}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string recommended: true - pattern: ^([01]?\d|2[0-3]|24(?=:00?:00?$)):([0-5]\d)(:([0-5]\d))?$ multivalued: false + pattern: ^([01]?\d|2[0-3]|24(?=:00?:00?$)):([0-5]\d)(:([0-5]\d))?$ crop_rotation: name: crop_rotation annotations: @@ -45694,17 +48362,17 @@ classes: 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 + - value: yes;R2/2017-01-01/2018-12-31/P6M from_schema: https://w3id.org/nmdc/nmdc aliases: - - history/crop rotation + - history/crop rotation rank: 7 is_a: core field string_serialization: '{boolean};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000318 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -45720,16 +48388,16 @@ classes: description: Present state of sample site title: current land use examples: - - value: conifers + - value: conifers from_schema: https://w3id.org/nmdc/nmdc aliases: - - current land use + - current land use rank: 8 is_a: core field slot_uri: MIXS:0001080 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: cur_land_use_enum multivalued: false @@ -45742,30 +48410,33 @@ classes: occurrence: tag: occurrence value: '1' - description: Vegetation classification from one or more standard classification systems, or agricultural crop + description: Vegetation classification from one or more standard classification + systems, or agricultural crop title: current vegetation todos: - - 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? + - 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 + - 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 + - value: deciduous forest + - value: forest + - value: Bauhinia variegata from_schema: https://w3id.org/nmdc/nmdc aliases: - - current vegetation + - current vegetation rank: 9 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000312 owner: Biosample domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample slot_group: mixs_section range: string multivalued: false @@ -45781,23 +48452,26 @@ classes: description: Reference or method used in vegetation classification title: current vegetation method todos: - - 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. + - 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. + - Required when current vegetation is provided. examples: - - value: https://doi.org/10.1111/j.1654-109X.2011.01154.x + - value: https://doi.org/10.1111/j.1654-109X.2011.01154.x from_schema: https://w3id.org/nmdc/nmdc aliases: - - current vegetation method + - current vegetation method rank: 10 is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000314 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -45807,25 +48481,27 @@ classes: 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. + 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 + - Use modified term comments: - - All depths must be reported in meters. Provide the numerical portion only. + - All depths must be reported in meters. Provide the numerical portion only. examples: - - value: 0 - 0.1 - - value: '1' + - value: 0 - 0.1 + - value: '1' from_schema: https://w3id.org/nmdc/nmdc aliases: - - depth + - depth rank: 9 is_a: environment field string_serialization: '{float}-{float}' slot_uri: MIXS:0000018 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string required: true @@ -45840,87 +48516,112 @@ classes: occurrence: tag: occurrence value: '1' - description: Drainage classification from a standard system such as the USDA system + description: Drainage classification from a standard system such as the USDA + system title: drainage classification examples: - - value: well + - value: well from_schema: https://w3id.org/nmdc/nmdc aliases: - - drainage classification + - drainage classification rank: 11 is_a: core field slot_uri: MIXS:0001085 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: drainage_class_enum multivalued: false 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 9 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study slot_group: sample_id_section range: EcosystemForSoilEnum 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 10 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study slot_group: sample_id_section range: EcosystemCategoryForSoilEnum 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 12 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study slot_group: sample_id_section range: EcosystemSubtypeForSoilEnum 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 11 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study slot_group: sample_id_section range: EcosystemTypeForSoilEnum recommended: true @@ -45930,25 +48631,31 @@ classes: 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. + 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. + - 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' + - value: '225' + - value: '0' + - value: '1250' from_schema: https://w3id.org/nmdc/nmdc aliases: - - elevation + - elevation rank: 6 is_a: environment field slot_uri: MIXS:0000093 owner: Biosample domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample slot_group: mixs_modified_section range: float required: true @@ -45958,143 +48665,198 @@ classes: 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. + 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. tooltip: tag: tooltip - value: The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context - 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' + value: The biome or major environmental system where the sample or specimen + originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] + in the Environment Ontology (ENVO). For host-associated or plant-associated + samples, use terms from the UBERON or Plant Ontology to describe the + broad anatomical or morphological context + 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) + - range changed to enumeration late in makefile, so this is modified (but + "sample ID" anyway) examples: - - value: oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean + - 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://w3id.org/nmdc/nmdc aliases: - - broad-scale environmental context + - broad-scale environmental context rank: 6 is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000012 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section required: true multivalued: false pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ any_of: - - range: EnvBroadScaleSoilEnum - - range: string + - range: EnvBroadScaleSoilEnum + - 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. + value: Environmental entities having causal influences upon the entity + at time of sampling. tooltip: tag: tooltip - value: The specific environmental entities or features near the sample or specimen that significantly influence its characteristics or composition. These entities are typically smaller in scale than the broad environmental context. Values for this field should be countable, material nouns and must be chosen from subclasses of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe specific anatomical structures or plant parts. - 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.' + value: The specific environmental entities or features near the sample + or specimen that significantly influence its characteristics or composition. + These entities are typically smaller in scale than the broad environmental + context. Values for this field should be countable, material nouns and + must be chosen from subclasses of BFO:0000040 (material entity) that + appear in the Environment Ontology (ENVO). For host-associated or plant-associated + samples, use terms from the UBERON or Plant Ontology to describe specific + anatomical structures or plant parts. + 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) + - 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] + - 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 aliases: - - local environmental context + - local environmental context rank: 7 is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000013 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section required: true multivalued: false pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ any_of: - - range: EnvLocalScaleSoilEnum - - range: string + - range: EnvLocalScaleSoilEnum + - 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]. + value: The material displaced by the entity at time of sampling. Recommend + subclasses of environmental material [ENVO:00010483]. tooltip: tag: tooltip - value: The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure - 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).' + value: The predominant environmental material or substrate that directly + surrounds or hosts the sample or specimen at the time of sampling. Choose + values from subclasses of the 'environmental material' class [ENVO:00010483] + in the Environment Ontology (ENVO). Values for this field should be + measurable or mass material nouns, representing continuous environmental + materials. For host-associated or plant-associated samples, use terms + from the UBERON or Plant Ontology to indicate a tissue, organ, or plant + structure + 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) + - range changed to enumeration late in makefile, so this is modified (but + "sample ID" anyway) examples: - - value: soil [ENVO:00001998] + - value: soil [ENVO:00001998] from_schema: https://w3id.org/nmdc/nmdc aliases: - - environmental medium + - environmental medium rank: 8 is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000014 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section required: true multivalued: false pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ any_of: - - range: EnvMediumSoilEnum - - range: string + - range: EnvMediumSoilEnum + - 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 + 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] + - value: time series design [EFO:0001779] from_schema: https://w3id.org/nmdc/nmdc aliases: - - experimental factor + - experimental factor rank: 12 is_a: investigation field string_serialization: '{termLabel} {[termID]}|{text}' slot_uri: MIXS:0000008 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false 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. + 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. + - 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' + - value: 'experimental treatment: value' from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000008 - - MIXS:0000300 + - MIXS:0000008 + - MIXS:0000300 rank: 7 string_serialization: '{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string recommended: true @@ -46108,18 +48870,19 @@ classes: 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 + - value: 1980-05-18, volcanic eruption from_schema: https://w3id.org/nmdc/nmdc aliases: - - history/extreme events + - history/extreme events rank: 13 is_a: core field slot_uri: MIXS:0000320 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -46132,19 +48895,20 @@ classes: 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 + 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 + - value: Luvisols from_schema: https://w3id.org/nmdc/nmdc aliases: - - soil_taxonomic/FAO classification + - soil_taxonomic/FAO classification rank: 14 is_a: core field slot_uri: MIXS:0001083 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: fao_class_enum multivalued: false @@ -46153,18 +48917,18 @@ classes: 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 + - describe the filter or provide a catalog number and manufacturer examples: - - value: C18 - - value: Basix PES, 13-100-106 FisherSci + - value: C18 + - value: Basix PES, 13-100-106 FisherSci from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000765 + - MIXS:0000765 rank: 6 string_serialization: '{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string recommended: true @@ -46178,23 +48942,25 @@ classes: 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? - - 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? + - 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. + - 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 + - value: '1871-10-10' + - value: 1871-10-01 to 1871-10-31 from_schema: https://w3id.org/nmdc/nmdc aliases: - - history/fire + - history/fire rank: 15 is_a: core field slot_uri: MIXS:0001086 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -46208,25 +48974,27 @@ classes: 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? - - 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? + - 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. + - 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 + - value: '1927-04-15' + - value: 1927-04 to 1927-05 from_schema: https://w3id.org/nmdc/nmdc aliases: - - history/flooding + - history/flooding rank: 16 is_a: core field slot_uri: MIXS:0000319 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -46235,33 +49003,41 @@ classes: annotations: expected_value: tag: expected_value - value: gaseous compound name;gaseous compound amount;treatment interval and duration + 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 + 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 + - 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 + - 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 aliases: - - gaseous environment + - gaseous environment rank: 20 is_a: core field string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000558 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -46271,22 +49047,24 @@ classes: 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. + 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' + - value: 'USA: Maryland, Bethesda' from_schema: https://w3id.org/nmdc/nmdc aliases: - - geographic location (country and/or sea,region) + - geographic location (country and/or sea,region) rank: 4 is_a: environment field string_serialization: '{text}: {text}, {text}' slot_uri: MIXS:0000010 owner: Biosample domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample slot_group: mixs_modified_section range: string required: true @@ -46301,22 +49079,24 @@ classes: 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.' + 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' + - 'Removed from description: Alternatively use Crop Ontology (CO) terms' examples: - - value: Growth chamber [CO_715:0000189] + - value: Growth chamber [CO_715:0000189] from_schema: https://w3id.org/nmdc/nmdc aliases: - - growth facility + - growth facility rank: 1 is_a: core field string_serialization: '{text}|{termLabel} {[termID]}' slot_uri: MIXS:0001043 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: GrowthFacilEnum required: true @@ -46336,32 +49116,40 @@ classes: description: Heavy metals present in the sample and their concentrations. title: heavy metals/ extreme unusual properties todos: - - Example & validation. Can we configure things so 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. + - Example & validation. Can we configure things so 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 ; + - 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 + - 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 aliases: - - extreme_unusual_properties/heavy metals + - extreme_unusual_properties/heavy metals rank: 17 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000652 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false - 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]+)$ + 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 annotations: @@ -46374,23 +49162,25 @@ classes: 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 ; + - 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 + - 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 aliases: - - extreme_unusual_properties/heavy metals method + - extreme_unusual_properties/heavy metals method rank: 18 is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000343 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -46406,17 +49196,17 @@ classes: description: Reference or method used in determining the horizon title: soil horizon method examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - soil horizon method + - soil horizon method rank: 19 is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000321 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -46432,20 +49222,25 @@ classes: 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 + 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 + - 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 + - humidity regimen rank: 21 is_a: core field string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000568 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -46454,18 +49249,18 @@ classes: name: infiltrations description: The amount of time it takes to complete each infiltration activity examples: - - value: 00:01:32;00:00:53 + - value: 00:01:32;00:00:53 from_schema: https://w3id.org/nmdc/nmdc see_also: - - https://www.protocols.io/view/field-sampling-protocol-kqdg3962pg25/v1 + - https://www.protocols.io/view/field-sampling-protocol-kqdg3962pg25/v1 aliases: - - infiltration_1 - - infiltration_2 + - infiltration_1 + - infiltration_2 rank: 1009 list_elements_ordered: true owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string multivalued: false @@ -46475,48 +49270,52 @@ classes: description: List isotope exposure or addition applied to your sample. title: isotope exposure/addition todos: - - Can we make the H218O correctly super and subscripted? + - Can we make the H218O correctly super and subscripted? comments: - - This is required when your experimental design includes the use of isotopically labeled compounds + - This is required when your experimental design includes the use of isotopically + labeled compounds examples: - - value: 13C glucose - - value: H218O + - value: 13C glucose + - value: H218O from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000751 + - MIXS:0000751 rank: 16 string_serialization: '{termLabel} {[termID]}; {timestamp}' owner: Biosample domain_of: - - Biosample + - Biosample 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)?)?)?)?$ multivalued: false + 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 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 + 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) notes: - - This is currently a required field but it's not clear if this should be required for human hosts + - This is currently a required field but it's not clear if this should be + required for human hosts examples: - - value: 50.586825 6.408977 + - value: 50.586825 6.408977 from_schema: https://w3id.org/nmdc/nmdc aliases: - - geographic location (latitude and longitude) + - geographic location (latitude and longitude) rank: 5 is_a: environment field string_serialization: '{lat lon}' slot_uri: MIXS:0000009 owner: Biosample domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample slot_group: mixs_modified_section range: string required: true @@ -46537,25 +49336,26 @@ classes: 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 + - 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 + - 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 + - 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) + - lbc_thirty + - lbc30 + - lime buffer capacity (at 30 minutes) rank: 1001 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string - pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ multivalued: false + pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ lbceq: name: lbceq annotations: @@ -46571,23 +49371,24 @@ classes: 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 + - 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 + - value: 1575 mg/kg from_schema: https://w3id.org/nmdc/nmdc see_also: - - https://www.ornl.gov/content/bio-scales-0 + - https://www.ornl.gov/content/bio-scales-0 aliases: - - lbceq - - lime buffer capacity (at 5-day equilibrium) + - lbceq + - lime buffer capacity (at 5-day equilibrium) rank: 1002 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string - pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ multivalued: false + pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ light_regm: name: light_regm annotations: @@ -46600,25 +49401,27 @@ classes: occurrence: tag: occurrence value: '1' - description: Information about treatment(s) involving exposure to light, including both light intensity and quality. + 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 + - value: incandescant light;10 lux;450 nanometer from_schema: https://w3id.org/nmdc/nmdc aliases: - - light regimen + - light regimen rank: 24 is_a: core field string_serialization: '{text};{float} {unit};{float} {unit}' slot_uri: MIXS:0000569 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true multivalued: false - pattern: ^\S+.*\S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ + pattern: ^\S+.*\S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? + \S+$ link_addit_analys: name: link_addit_analys annotations: @@ -46631,17 +49434,17 @@ classes: description: Link to additional analysis results performed on the sample title: links to additional analysis examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - links to additional analysis + - links to additional analysis rank: 56 is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000340 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -46657,17 +49460,17 @@ classes: description: Link to digitized soil maps or other soil classification information title: link to classification information examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - link to classification information + - link to classification information rank: 20 is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000329 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -46683,17 +49486,17 @@ classes: description: Link to climate resource title: link to climate information examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - link to climate information + - link to climate information rank: 21 is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000328 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -46709,18 +49512,18 @@ classes: description: Soil classification based on local soil classification system title: soil_taxonomic/local classification examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - soil_taxonomic/local classification + - soil_taxonomic/local classification rank: 22 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000330 owner: Biosample domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample slot_group: mixs_section range: string multivalued: false @@ -46736,17 +49539,17 @@ classes: description: Reference or method used in determining the local soil classification title: soil_taxonomic/local classification method examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - soil_taxonomic/local classification method + - soil_taxonomic/local classification method rank: 24 is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000331 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -46765,39 +49568,39 @@ classes: description: Concentration of manganese in the sample title: manganese examples: - - value: 24.7 mg/kg + - value: 24.7 mg/kg from_schema: https://w3id.org/nmdc/nmdc see_also: - - https://www.ornl.gov/content/bio-scales-0 + - https://www.ornl.gov/content/bio-scales-0 aliases: - - manganese + - manganese rank: 1003 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string - pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ multivalued: false + 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 + - How should we separate values? | or ;? lets be consistent comments: - - required if "microbial_biomass_c" is provided + - 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 + - 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:0000339 + - MIXS:0000339 rank: 1004 string_serialization: '{PMID}|{DOI}|{URL}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string recommended: true @@ -46814,17 +49617,17 @@ classes: description: Reference or method used in determining microbial biomass title: microbial biomass method examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - microbial biomass method + - microbial biomass method rank: 43 is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000339 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -46833,18 +49636,18 @@ classes: description: Reference or method used in determining microbial biomass nitrogen title: microbial biomass nitrogen method comments: - - required if "microbial_biomass_n" is provided + - 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 + - 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:0000339 + - MIXS:0000339 rank: 1004 string_serialization: '{PMID}|{DOI}|{URL}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string multivalued: false @@ -46860,63 +49663,69 @@ classes: 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 + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - microbial biomass + - microbial biomass rank: 42 is_a: core field slot_uri: MIXS:0000650 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false 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. + 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 + - 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 + - value: 0.05 ug C/g dry soil from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000650 + - MIXS:0000650 rank: 1004 string_serialization: '{float} {unit}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string - pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ multivalued: false + 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. + 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 + - 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 + - value: 0.05 ug N/g dry soil from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000650 + - MIXS:0000650 rank: 1004 string_serialization: '{float} {unit}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string - pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ multivalued: false + pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ misc_param: name: misc_param annotations: @@ -46926,24 +49735,26 @@ classes: occurrence: tag: occurrence value: m - description: Any other measurement performed or parameter collected, that is not listed here + 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 + - value: Bicarbonate ion concentration;2075 micromole per kilogram from_schema: https://w3id.org/nmdc/nmdc aliases: - - miscellaneous parameter + - miscellaneous parameter rank: 23 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000752 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false - 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]+)$ + 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: @@ -46959,23 +49770,23 @@ classes: description: Concentration of nitrate nitrogen in the sample title: nitrate_nitrogen comments: - - often below some specified limit of detection + - often below some specified limit of detection examples: - - value: 0.29 mg/kg + - value: 0.29 mg/kg from_schema: https://w3id.org/nmdc/nmdc see_also: - - https://www.ornl.gov/content/bio-scales-0 + - https://www.ornl.gov/content/bio-scales-0 aliases: - - nitrate_nitrogen - - NO3-N + - nitrate_nitrogen + - NO3-N rank: 1006 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string - pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ multivalued: false + pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ nitrite_nitrogen: name: nitrite_nitrogen annotations: @@ -46991,56 +49802,58 @@ classes: description: Concentration of nitrite nitrogen in the sample title: nitrite_nitrogen examples: - - value: 1.2 mg/kg + - value: 1.2 mg/kg from_schema: https://w3id.org/nmdc/nmdc see_also: - - https://www.ornl.gov/content/bio-scales-0 + - https://www.ornl.gov/content/bio-scales-0 aliases: - - nitrite_nitrogen - - NO2-N + - nitrite_nitrogen + - NO2-N rank: 1007 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string - pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ multivalued: false + 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 ; + 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 + - value: insect 0.23 ug; plant 1g from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000174 - - MIXS:0000650 + - MIXS:0000174 + - MIXS:0000650 rank: 8 string_serialization: '{text};{float} {unit}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string - pattern: ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$ multivalued: false + 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 + - required if "non-microbial biomass" is provided examples: - - value: https://doi.org/10.1038/s41467-021-26181-3 + - value: https://doi.org/10.1038/s41467-021-26181-3 from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000650 + - MIXS:0000650 rank: 9 string_serialization: '{PMID}|{DOI}|{URL}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string multivalued: false @@ -47059,16 +49872,16 @@ classes: description: Concentration of organic matter title: organic matter examples: - - value: 1.75 milligram per cubic meter + - value: 1.75 milligram per cubic meter from_schema: https://w3id.org/nmdc/nmdc aliases: - - organic matter + - organic matter rank: 45 is_a: core field slot_uri: MIXS:0000204 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -47088,16 +49901,16 @@ classes: description: Concentration of organic nitrogen title: organic nitrogen examples: - - value: 4 micromole per liter + - value: 4 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - organic nitrogen + - organic nitrogen rank: 46 is_a: core field slot_uri: MIXS:0000205 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -47107,37 +49920,39 @@ classes: description: Method used for obtaining organic nitrogen title: organic nitrogen method comments: - - required if "org_nitro" is provided + - required if "org_nitro" is provided examples: - - value: https://doi.org/10.1016/0038-0717(85)90144-0 + - value: https://doi.org/10.1016/0038-0717(85)90144-0 from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000338 - - MIXS:0000205 + - MIXS:0000338 + - MIXS:0000205 rank: 14 string_serialization: '{PMID}|{DOI}|{URL}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string multivalued: false other_treatment: name: other_treatment - description: Other treatments applied to your samples that are not applicable to the provided fields + description: Other treatments applied to your samples that are not applicable + to the provided fields title: other treatments notes: - - Values entered here will be used to determine potential new slots. + - Values entered here will be used to determine potential new slots. comments: - - This is an open text field to provide any treatments that cannot be captured in the provided slots. + - 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:0000300 + - MIXS:0000300 rank: 15 string_serialization: '{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string recommended: true @@ -47154,16 +49969,16 @@ classes: description: Oxygenation status of sample title: oxygenation status of sample examples: - - value: aerobic + - value: aerobic from_schema: https://w3id.org/nmdc/nmdc aliases: - - oxygenation status of sample + - oxygenation status of sample rank: 25 is_a: core field slot_uri: MIXS:0000753 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: OxyStatSampEnum multivalued: false @@ -47176,22 +49991,23 @@ classes: occurrence: tag: occurrence value: '1' - description: pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + description: pH measurement of the sample, or liquid portion of sample, or + aqueous phase of the fluid title: pH notes: - - Use modified term + - Use modified term examples: - - value: '7.2' + - value: '7.2' from_schema: https://w3id.org/nmdc/nmdc aliases: - - pH + - pH rank: 27 is_a: core field string_serialization: '{float}' slot_uri: MIXS:0001001 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: float recommended: true @@ -47210,20 +50026,20 @@ classes: 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. + - 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 + - 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 aliases: - - pH method + - pH method rank: 41 is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0001106 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -47242,16 +50058,16 @@ classes: description: Concentration of phosphate title: phosphate examples: - - value: 0.7 micromole per liter + - value: 0.7 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - phosphate + - phosphate rank: 53 is_a: core field slot_uri: MIXS:0000505 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -47265,20 +50081,21 @@ classes: occurrence: tag: occurrence value: '1' - description: Reference or method used in determining previous land use and dates + description: Reference or method used in determining previous land use and + dates title: history/previous land use method examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - history/previous land use method + - history/previous land use method rank: 26 is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000316 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -47294,17 +50111,17 @@ classes: description: Previous land use and dates title: history/previous land use examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - history/previous land use + - history/previous land use rank: 27 is_a: core field string_serialization: '{text};{timestamp}' slot_uri: MIXS:0000315 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -47318,19 +50135,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas + 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 + - value: summit from_schema: https://w3id.org/nmdc/nmdc aliases: - - profile position + - profile position rank: 28 is_a: core field slot_uri: MIXS:0001084 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: profile_position_enum multivalued: false @@ -47346,19 +50164,24 @@ classes: 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. + 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 + - value: 25 practical salinity unit from_schema: https://w3id.org/nmdc/nmdc aliases: - - salinity + - salinity rank: 54 is_a: core field slot_uri: MIXS:0000183 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -47375,17 +50198,17 @@ classes: description: Reference or method used in determining salinity title: salinity method examples: - - value: https://doi.org/10.1007/978-1-61779-986-0_28 + - value: https://doi.org/10.1007/978-1-61779-986-0_28 from_schema: https://w3id.org/nmdc/nmdc aliases: - - salinity method + - salinity method rank: 55 is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000341 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -47395,22 +50218,24 @@ classes: 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). + 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 + - Report dimensions and details when applicable examples: - - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample collection device + - sample collection device rank: 14 is_a: nucleic acid sequence source field string_serialization: '{termLabel} {[termID]}|{text}' slot_uri: MIXS:0000002 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -47424,19 +50249,19 @@ classes: description: The method employed for collecting the sample. title: sample collection method comments: - - This can be a citation or description + - This can be a citation or description examples: - - value: swabbing + - value: swabbing from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample collection method + - sample collection method rank: 15 is_a: nucleic acid sequence source field string_serialization: '{PMID}|{DOI}|{URL}|{text}' slot_uri: MIXS:0001225 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -47446,21 +50271,23 @@ classes: 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. + 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 + - value: filtering of seawater + - value: storing samples in ethanol from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample material processing + - sample material processing rank: 12 is_a: nucleic acid sequence source field string_serialization: '{text}' slot_uri: MIXS:0000016 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -47473,23 +50300,25 @@ classes: 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. + 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. + - 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 + - value: 5 grams + - value: 10 mL from_schema: https://w3id.org/nmdc/nmdc aliases: - - amount or size of sample collected + - amount or size of sample collected rank: 18 is_a: nucleic acid sequence source field string_serialization: '{float} {unit}' slot_uri: MIXS:0000001 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -47509,16 +50338,16 @@ classes: description: Temperature at which the sample was stored (degrees are assumed) title: sample storage temperature examples: - - value: -80 Celsius + - value: -80 Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample storage temperature + - sample storage temperature rank: 7 is_a: core field slot_uri: MIXS:0000110 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string required: true @@ -47526,20 +50355,27 @@ classes: 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. + 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''' + - '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)' + - '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 + - value: IGSN:DSJ0284 from_schema: https://w3id.org/nmdc/nmdc rank: 5 string_serialization: '{text}:{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string recommended: true @@ -47557,29 +50393,35 @@ classes: 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. + 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: - - 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 + - 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 + - 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). + - 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 + - value: 0.4 inch + - value: 10.16 mm from_schema: https://w3id.org/nmdc/nmdc aliases: - - mean seasonal precipitation + - mean seasonal precipitation rank: 29 is_a: core field slot_uri: MIXS:0000645 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -47599,16 +50441,16 @@ classes: description: Mean seasonal temperature title: mean seasonal temperature examples: - - value: 18 degree Celsius + - value: 18 degree Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - - mean seasonal temperature + - mean seasonal temperature rank: 30 is_a: core field slot_uri: MIXS:0000643 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -47622,31 +50464,32 @@ classes: occurrence: tag: occurrence value: '1' - description: Collection design of pooled samples and/or sieve size and amount of sample sieved + 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 + - 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. + - 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 + - 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 aliases: - - composite design/sieving + - composite design/sieving rank: 8 is_a: core field string_serialization: '{{text}|{float} {unit}};{float} {unit}' slot_uri: MIXS:0000322 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -47663,19 +50506,20 @@ classes: 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 + 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 + - value: 0.2 micrometer from_schema: https://w3id.org/nmdc/nmdc aliases: - - size-fraction lower threshold + - size-fraction lower threshold rank: 10 is_a: core field slot_uri: MIXS:0000735 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: false @@ -47693,19 +50537,20 @@ classes: 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 + 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 + - value: 20 micrometer from_schema: https://w3id.org/nmdc/nmdc aliases: - - size-fraction upper threshold + - size-fraction upper threshold rank: 11 is_a: core field slot_uri: MIXS:0000736 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: false @@ -47723,23 +50568,29 @@ classes: 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). - This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. + 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. + - 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' + - value: '35' from_schema: https://w3id.org/nmdc/nmdc aliases: - - slope aspect + - slope aspect rank: 1 is_a: core field slot_uri: MIXS:0000647 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -47756,24 +50607,26 @@ classes: 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 + 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 + - 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' + - value: 10% + - value: 10 % + - value: '0.1' from_schema: https://w3id.org/nmdc/nmdc aliases: - - slope gradient + - slope gradient rank: 31 is_a: core field slot_uri: MIXS:0000646 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -47787,19 +50640,21 @@ classes: 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 + 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 + - value: A horizon from_schema: https://w3id.org/nmdc/nmdc aliases: - - soil horizon + - soil horizon rank: 32 is_a: core field slot_uri: MIXS:0001082 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: soil_horizon_enum multivalued: false @@ -47812,19 +50667,22 @@ classes: 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. + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - soil texture measurement + - soil texture measurement rank: 33 is_a: core field slot_uri: MIXS:0000335 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -47841,17 +50699,17 @@ classes: description: Reference or method used in determining soil texture title: soil texture method examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - soil texture method + - soil texture method rank: 34 is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000336 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -47864,21 +50722,23 @@ classes: 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. + 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] + - value: plinthosol [ENVO:00002250] from_schema: https://w3id.org/nmdc/nmdc aliases: - - soil type + - soil type rank: 35 is_a: core field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000332 owner: Biosample domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample slot_group: mixs_section range: string multivalued: false @@ -47892,86 +50752,96 @@ classes: occurrence: tag: occurrence value: '1' - description: Reference or method used in determining soil series name or other lower-level classification + description: Reference or method used in determining soil series name or other + lower-level classification title: soil type method examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - soil type method + - soil type method rank: 36 is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000334 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 13 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study slot_group: sample_id_section range: SpecificEcosystemForSoilEnum recommended: true start_date_inc: name: start_date_inc - description: Date the incubation was started. Only relevant for incubation samples. + 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 + - 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. + - 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. + - value: 2021-04-15, 2021-04 and 2021 are all acceptable. from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000011 + - MIXS:0000011 rank: 4 string_serialization: '{date, arbitrary precision}' owner: Biosample domain_of: - - Biosample + - Biosample 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]))?)?$ multivalued: false + 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. + 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 + - 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' + - '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 + - value: 13:33 or 13:33:55 from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000011 + - MIXS:0000011 rank: 5 string_serialization: '{time, seconds optional}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string recommended: true - pattern: ^([01]?\d|2[0-3]|24(?=:00?:00?$)):([0-5]\d)(:([0-5]\d))?$ multivalued: false + pattern: ^([01]?\d|2[0-3]|24(?=:00?:00?$)):([0-5]\d)(:([0-5]\d))?$ store_cond: name: store_cond annotations: @@ -47984,17 +50854,17 @@ classes: description: Explain how the soil sample is stored (fresh/frozen/other). title: storage conditions examples: - - value: -20 degree Celsius freezer;P2Y10D + - value: -20 degree Celsius freezer;P2Y10D from_schema: https://w3id.org/nmdc/nmdc aliases: - - storage conditions + - storage conditions rank: 2 is_a: core field string_serialization: '{text};{duration}' slot_uri: MIXS:0000327 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: StoreCondEnum required: true @@ -48011,16 +50881,16 @@ classes: description: Temperature of the sample at the time of sampling. title: temperature examples: - - value: 25 degree Celsius + - value: 25 degree Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - - temperature + - temperature rank: 37 is_a: environment field slot_uri: MIXS:0000113 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -48037,16 +50907,16 @@ classes: description: Note method(s) used for tilling title: history/tillage examples: - - value: chisel + - value: chisel from_schema: https://w3id.org/nmdc/nmdc aliases: - - history/tillage + - history/tillage rank: 38 is_a: core field slot_uri: MIXS:0001081 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: tillage_enum multivalued: true @@ -48065,21 +50935,25 @@ classes: 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 + - 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 + - value: 1 ug/L from_schema: https://w3id.org/nmdc/nmdc aliases: - - total carbon + - total carbon rank: 47 is_a: core field slot_uri: MIXS:0000525 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -48096,18 +50970,18 @@ classes: 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 + - 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 aliases: - - total nitrogen content method + - total nitrogen content method rank: 49 is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000338 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -48126,16 +51000,16 @@ classes: description: Total nitrogen content of the sample title: total nitrogen content examples: - - value: 5 mg N/ L + - value: 5 mg N/ L from_schema: https://w3id.org/nmdc/nmdc aliases: - - total nitrogen content + - total nitrogen content rank: 48 is_a: core field slot_uri: MIXS:0000530 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -48152,17 +51026,17 @@ classes: description: Reference or method used in determining total organic carbon title: total organic carbon method examples: - - value: https://doi.org/10.1080/07352680902776556 + - value: https://doi.org/10.1080/07352680902776556 from_schema: https://w3id.org/nmdc/nmdc aliases: - - total organic carbon method + - total organic carbon method rank: 51 is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000337 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -48178,22 +51052,23 @@ classes: occurrence: tag: occurrence value: '1' - description: 'Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content' + 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? + - check description. How are they different? + - check description. How are they different? examples: - - value: 5 mg N/ L + - value: 5 mg N/ L from_schema: https://w3id.org/nmdc/nmdc aliases: - - total organic carbon + - total organic carbon rank: 50 is_a: core field slot_uri: MIXS:0000533 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -48210,19 +51085,20 @@ classes: occurrence: tag: occurrence value: '1' - description: 'Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus' + 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 + - value: 0.03 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - total phosphorus + - total phosphorus rank: 52 is_a: core field slot_uri: MIXS:0000117 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -48236,30 +51112,37 @@ classes: occurrence: tag: occurrence value: '1' - description: Reference or method used in determining the water content of soil + 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? + - 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 + - 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 + - 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 aliases: - - water content method + - water content method rank: 40 is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000323 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -48275,24 +51158,24 @@ classes: 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 - - 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 + - how to manage multiple water content methods? examples: - - 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 + - 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 aliases: - - water content + - water content rank: 39 is_a: core field string_serialization: '{float or pct} {unit}' slot_uri: MIXS:0000185 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -48309,21 +51192,24 @@ classes: 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 + 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 + - 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 aliases: - - watering regimen + - watering regimen rank: 25 is_a: core field string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000591 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -48343,25 +51229,26 @@ classes: description: Concentration of zinc in the sample title: zinc examples: - - value: 2.5 mg/kg + - value: 2.5 mg/kg from_schema: https://w3id.org/nmdc/nmdc see_also: - - https://www.ornl.gov/content/bio-scales-0 + - https://www.ornl.gov/content/bio-scales-0 aliases: - - zinc + - zinc rank: 1004 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string - pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ multivalued: false + pattern: ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ organism_count: name: organism_count 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))$ multivalued: false + 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))$ WastewaterSludgeInterface: name: WastewaterSludgeInterface annotations: @@ -48373,66 +51260,66 @@ classes: from_schema: https://example.com/nmdc_submission_schema is_a: DhInterface mixins: - - DhMultiviewCommonColumnsMixin - - SampIdNewTermsMixin + - 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 - - 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 + - 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 + - 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 slot_usage: alkalinity: name: alkalinity @@ -48446,19 +51333,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + 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 + - value: 50 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - alkalinity + - alkalinity rank: 1 is_a: core field slot_uri: MIXS:0000421 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -48475,19 +51363,21 @@ classes: 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 + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - biochemical oxygen demand + - biochemical oxygen demand rank: 296 is_a: core field slot_uri: MIXS:0000653 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -48501,21 +51391,24 @@ classes: 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 + 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 + - 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 + - chemical administration rank: 17 is_a: core field string_serialization: '{termLabel} {[termID]};{timestamp}' slot_uri: MIXS:0000751 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -48533,19 +51426,21 @@ classes: 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 + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - chemical oxygen demand + - chemical oxygen demand rank: 301 is_a: core field slot_uri: MIXS:0000656 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -48559,22 +51454,23 @@ classes: 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) + - 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' + - value: '2021-04-15' + - value: 2021-04 + - value: '2021' from_schema: https://w3id.org/nmdc/nmdc aliases: - - collection date + - collection date rank: 3 is_a: environment field string_serialization: '{date, arbitrary precision}' slot_uri: MIXS:0000011 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string required: true @@ -48586,25 +51482,27 @@ classes: 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. + 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 + - Use modified term comments: - - All depths must be reported in meters. Provide the numerical portion only. + - All depths must be reported in meters. Provide the numerical portion only. examples: - - value: 0 - 0.1 - - value: '1' + - value: 0 - 0.1 + - value: '1' from_schema: https://w3id.org/nmdc/nmdc aliases: - - depth + - depth rank: 9 is_a: environment field string_serialization: '{float}|{float}-{float}' slot_uri: MIXS:0000018 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -48612,69 +51510,93 @@ classes: 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 9 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 10 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 12 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 11 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study slot_group: sample_id_section range: EcosystemTypeEnum recommended: true @@ -48693,16 +51615,16 @@ classes: description: Percentage of volatile solids removed from the anaerobic digestor title: efficiency percent examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - efficiency percent + - efficiency percent rank: 307 is_a: core field slot_uri: MIXS:0000657 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -48713,25 +51635,31 @@ classes: 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. + 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. + - 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' + - value: '225' + - value: '0' + - value: '1250' from_schema: https://w3id.org/nmdc/nmdc aliases: - - elevation + - elevation rank: 6 is_a: environment field slot_uri: MIXS:0000093 owner: Biosample domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample slot_group: mixs_modified_section range: float required: true @@ -48748,49 +51676,70 @@ classes: 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 + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - emulsions + - emulsions rank: 308 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000660 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false - 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]+)$ + 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 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. + 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. tooltip: tag: tooltip - value: The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context - 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' + value: The biome or major environmental system where the sample or specimen + originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] + in the Environment Ontology (ENVO). For host-associated or plant-associated + samples, use terms from the UBERON or Plant Ontology to describe the + broad anatomical or morphological context + 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) + - range changed to enumeration late in makefile, so this is modified (but + "sample ID" anyway) examples: - - value: oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean + - 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://w3id.org/nmdc/nmdc aliases: - - broad-scale environmental context + - broad-scale environmental context rank: 6 is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000012 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string required: true @@ -48801,30 +51750,45 @@ classes: annotations: expected_value: tag: expected_value - value: Environmental entities having causal influences upon the entity at time of sampling. + value: Environmental entities having causal influences upon the entity + at time of sampling. tooltip: tag: tooltip - value: The specific environmental entities or features near the sample or specimen that significantly influence its characteristics or composition. These entities are typically smaller in scale than the broad environmental context. Values for this field should be countable, material nouns and must be chosen from subclasses of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe specific anatomical structures or plant parts. - 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.' + value: The specific environmental entities or features near the sample + or specimen that significantly influence its characteristics or composition. + These entities are typically smaller in scale than the broad environmental + context. Values for this field should be countable, material nouns and + must be chosen from subclasses of BFO:0000040 (material entity) that + appear in the Environment Ontology (ENVO). For host-associated or plant-associated + samples, use terms from the UBERON or Plant Ontology to describe specific + anatomical structures or plant parts. + 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) + - 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] + - 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 aliases: - - local environmental context + - local environmental context rank: 7 is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000013 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string required: true @@ -48835,26 +51799,41 @@ classes: annotations: expected_value: tag: expected_value - value: The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]. + value: The material displaced by the entity at time of sampling. Recommend + subclasses of environmental material [ENVO:00010483]. tooltip: tag: tooltip - value: The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure - 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).' + value: The predominant environmental material or substrate that directly + surrounds or hosts the sample or specimen at the time of sampling. Choose + values from subclasses of the 'environmental material' class [ENVO:00010483] + in the Environment Ontology (ENVO). Values for this field should be + measurable or mass material nouns, representing continuous environmental + materials. For host-associated or plant-associated samples, use terms + from the UBERON or Plant Ontology to indicate a tissue, organ, or plant + structure + 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) + - range changed to enumeration late in makefile, so this is modified (but + "sample ID" anyway) examples: - - value: soil [ENVO:00001998] + - value: soil [ENVO:00001998] from_schema: https://w3id.org/nmdc/nmdc aliases: - - environmental medium + - environmental medium rank: 8 is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000014 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string required: true @@ -48866,20 +51845,25 @@ classes: 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 + 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] + - value: time series design [EFO:EFO_0001779] from_schema: https://w3id.org/nmdc/nmdc aliases: - - experimental factor + - experimental factor rank: 12 is_a: investigation field string_serialization: '{termLabel} {[termID]}|{text}' slot_uri: MIXS:0000008 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -48895,45 +51879,49 @@ classes: occurrence: tag: occurrence value: m - description: Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances + description: Amount or concentration of substances such as hydrogen sulfide, + carbon dioxide, methane, etc.; can include multiple substances title: gaseous substances examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - gaseous substances + - gaseous substances rank: 311 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000661 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false - 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]+)$ + 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. + 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' + - value: 'USA: Maryland, Bethesda' from_schema: https://w3id.org/nmdc/nmdc aliases: - - geographic location (country and/or sea,region) + - geographic location (country and/or sea,region) rank: 4 is_a: environment field string_serialization: '{text}: {text}, {text}' slot_uri: MIXS:0000010 owner: Biosample domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample slot_group: mixs_modified_section range: string required: true @@ -48951,19 +51939,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Percentage of industrial effluents received by wastewater treatment plant + description: Percentage of industrial effluents received by wastewater treatment + plant title: industrial effluent percent examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - industrial effluent percent + - industrial effluent percent rank: 332 is_a: core field slot_uri: MIXS:0000662 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -48980,47 +51969,52 @@ classes: occurrence: tag: occurrence value: m - description: Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles + description: Concentration of particles such as sand, grit, metal particles, + ceramics, etc.; can include multiple particles title: inorganic particles examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - inorganic particles + - inorganic particles rank: 333 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000664 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false - 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]+)$ + 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 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 + 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) notes: - - This is currently a required field but it's not clear if this should be required for human hosts + - This is currently a required field but it's not clear if this should be + required for human hosts examples: - - value: 50.586825 6.408977 + - value: 50.586825 6.408977 from_schema: https://w3id.org/nmdc/nmdc aliases: - - geographic location (latitude and longitude) + - geographic location (latitude and longitude) rank: 5 is_a: environment field string_serialization: '{lat lon}' slot_uri: MIXS:0000009 owner: Biosample domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample slot_group: mixs_modified_section range: string required: true @@ -49035,24 +52029,26 @@ classes: occurrence: tag: occurrence value: m - description: Any other measurement performed or parameter collected, that is not listed here + 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 + - value: Bicarbonate ion concentration;2075 micromole per kilogram from_schema: https://w3id.org/nmdc/nmdc aliases: - - miscellaneous parameter + - miscellaneous parameter rank: 23 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000752 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false - 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]+)$ + 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: @@ -49068,16 +52064,16 @@ classes: description: Concentration of nitrate in the sample title: nitrate examples: - - value: 65 micromole per liter + - value: 65 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - nitrate + - nitrate rank: 26 is_a: core field slot_uri: MIXS:0000425 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -49094,24 +52090,26 @@ classes: occurrence: tag: occurrence value: m - description: Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. + description: Concentration of particles such as faeces, hairs, food, vomit, + paper fibers, plant material, humus, etc. title: organic particles examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - organic particles + - organic particles rank: 338 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000665 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false - 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]+)$ + 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: @@ -49120,23 +52118,28 @@ classes: 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 + 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)' + 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 + - value: total prokaryotes;3.5e7 cells per milliliter;qPCR from_schema: https://w3id.org/nmdc/nmdc aliases: - - organism count + - organism count rank: 30 is_a: core field slot_uri: MIXS:0000103 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -49153,16 +52156,16 @@ classes: description: Oxygenation status of sample title: oxygenation status of sample examples: - - value: aerobic + - value: aerobic from_schema: https://w3id.org/nmdc/nmdc aliases: - - oxygenation status of sample + - oxygenation status of sample rank: 25 is_a: core field slot_uri: MIXS:0000753 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: OxyStatSampEnum multivalued: false @@ -49175,20 +52178,24 @@ classes: 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 + 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 + - value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - - perturbation + - perturbation rank: 33 is_a: core field string_serialization: '{text};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000754 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -49201,22 +52208,23 @@ classes: occurrence: tag: occurrence value: '1' - description: pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + description: pH measurement of the sample, or liquid portion of sample, or + aqueous phase of the fluid title: pH notes: - - Use modified term + - Use modified term examples: - - value: '7.2' + - value: '7.2' from_schema: https://w3id.org/nmdc/nmdc aliases: - - pH + - pH rank: 27 is_a: core field string_serialization: '{float}' slot_uri: MIXS:0001001 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: float recommended: true @@ -49235,20 +52243,20 @@ classes: 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. + - 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 + - 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 aliases: - - pH method + - pH method rank: 41 is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0001106 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -49267,16 +52275,16 @@ classes: description: Concentration of phosphate title: phosphate examples: - - value: 0.7 micromole per liter + - value: 0.7 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - phosphate + - phosphate rank: 53 is_a: core field slot_uri: MIXS:0000505 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -49290,20 +52298,21 @@ classes: occurrence: tag: occurrence value: '1' - description: The process of pre-treatment removes materials that can be easily collected from the raw wastewater + description: The process of pre-treatment removes materials that can be easily + collected from the raw wastewater title: pre-treatment examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - pre-treatment + - pre-treatment rank: 342 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000348 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -49316,20 +52325,22 @@ classes: 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 + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - primary treatment + - primary treatment rank: 343 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000349 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -49342,20 +52353,22 @@ classes: 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 + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - reactor type + - reactor type rank: 346 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000350 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -49371,19 +52384,24 @@ classes: 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. + 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 + - value: 25 practical salinity unit from_schema: https://w3id.org/nmdc/nmdc aliases: - - salinity + - salinity rank: 54 is_a: core field slot_uri: MIXS:0000183 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -49394,22 +52412,24 @@ classes: 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). + 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 + - Report dimensions and details when applicable examples: - - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample collection device + - sample collection device rank: 14 is_a: nucleic acid sequence source field string_serialization: '{termLabel} {[termID]}|{text}' slot_uri: MIXS:0000002 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -49423,19 +52443,19 @@ classes: description: The method employed for collecting the sample. title: sample collection method comments: - - This can be a citation or description + - This can be a citation or description examples: - - value: swabbing + - value: swabbing from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample collection method + - sample collection method rank: 15 is_a: nucleic acid sequence source field string_serialization: '{PMID}|{DOI}|{URL}|{text}' slot_uri: MIXS:0001225 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -49445,21 +52465,23 @@ classes: 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. + 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 + - value: filtering of seawater + - value: storing samples in ethanol from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample material processing + - sample material processing rank: 12 is_a: nucleic acid sequence source field string_serialization: '{text}' slot_uri: MIXS:0000016 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -49472,23 +52494,25 @@ classes: 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. + 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. + - 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 + - value: 5 grams + - value: 10 mL from_schema: https://w3id.org/nmdc/nmdc aliases: - - amount or size of sample collected + - amount or size of sample collected rank: 18 is_a: nucleic acid sequence source field string_serialization: '{float} {unit}' slot_uri: MIXS:0000001 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -49505,17 +52529,17 @@ classes: description: Duration for which the sample was stored title: sample storage duration examples: - - value: P1Y6M + - value: P1Y6M from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample storage duration + - sample storage duration rank: 353 is_a: core field string_serialization: '{duration}' slot_uri: MIXS:0000116 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -49528,20 +52552,21 @@ classes: occurrence: tag: occurrence value: '1' - description: Location at which sample was stored, usually name of a specific freezer/room + description: Location at which sample was stored, usually name of a specific + freezer/room title: sample storage location examples: - - value: Freezer no:5 + - value: Freezer no:5 from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample storage location + - sample storage location rank: 41 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000755 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -49560,16 +52585,16 @@ classes: description: Temperature at which the sample was stored (degrees are assumed) title: sample storage temperature examples: - - value: -80 Celsius + - value: -80 Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample storage temperature + - sample storage temperature rank: 7 is_a: core field slot_uri: MIXS:0000110 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string required: true @@ -49577,20 +52602,27 @@ classes: 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. + 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''' + - '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)' + - '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 + - value: IGSN:DSJ0284 from_schema: https://w3id.org/nmdc/nmdc rank: 5 string_serialization: '{text}:{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string recommended: true @@ -49605,20 +52637,21 @@ classes: occurrence: tag: occurrence value: '1' - description: The process for substantially degrading the biological content of the sewage + description: The process for substantially degrading the biological content + of the sewage title: secondary treatment examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - secondary treatment + - secondary treatment rank: 360 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000351 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -49634,17 +52667,17 @@ classes: description: Type of wastewater treatment plant as municipial or industrial title: sewage type examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - sewage type + - sewage type rank: 361 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000215 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -49657,17 +52690,17 @@ classes: description: Filtering pore size used in sample preparation title: size fraction selected examples: - - value: 0-0.22 micrometer + - value: 0-0.22 micrometer from_schema: https://w3id.org/nmdc/nmdc aliases: - - size fraction selected + - size fraction selected rank: 285 is_a: nucleic acid sequence source field string_serialization: '{float}-{float} {unit}' slot_uri: MIXS:0000017 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -49686,16 +52719,16 @@ classes: description: The time activated sludge remains in reactor title: sludge retention time examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - sludge retention time + - sludge retention time rank: 362 is_a: core field slot_uri: MIXS:0000669 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -49715,16 +52748,16 @@ classes: description: Sodium concentration in the sample title: sodium examples: - - value: 10.5 milligram per liter + - value: 10.5 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - sodium + - sodium rank: 363 is_a: core field slot_uri: MIXS:0000428 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -49741,24 +52774,26 @@ classes: occurrence: tag: occurrence value: m - description: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. + description: Concentration of substances such as ammonia, road-salt, sea-salt, + cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. title: soluble inorganic material examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - soluble inorganic material + - soluble inorganic material rank: 364 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000672 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false - 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]+)$ + 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: @@ -49771,38 +52806,43 @@ classes: occurrence: tag: occurrence value: m - description: Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. + description: Concentration of substances such as urea, fruit sugars, soluble + proteins, drugs, pharmaceuticals, etc. title: soluble organic material examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - soluble organic material + - soluble organic material rank: 365 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000673 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false - 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]+)$ + 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 13 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study slot_group: sample_id_section range: SpecificEcosystemEnum recommended: true @@ -49814,28 +52854,31 @@ classes: 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 + 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 + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - suspended solids + - suspended solids rank: 372 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000150 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false - 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]+)$ + 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: @@ -49848,16 +52891,16 @@ classes: description: Temperature of the sample at the time of sampling. title: temperature examples: - - value: 25 degree Celsius + - value: 25 degree Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - - temperature + - temperature rank: 37 is_a: environment field slot_uri: MIXS:0000113 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -49871,20 +52914,21 @@ classes: 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 + 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: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - tertiary treatment + - tertiary treatment rank: 374 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000352 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -49900,19 +52944,21 @@ classes: 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' + 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 + - value: 50 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - total nitrogen concentration + - total nitrogen concentration rank: 377 is_a: core field slot_uri: MIXS:0000102 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -49932,16 +52978,16 @@ classes: description: Total amount or concentration of phosphate title: total phosphate examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - total phosphate + - total phosphate rank: 378 is_a: core field slot_uri: MIXS:0000689 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -49955,20 +53001,21 @@ classes: occurrence: tag: occurrence value: '1' - description: The origin of wastewater such as human waste, rainfall, storm drains, etc. + description: The origin of wastewater such as human waste, rainfall, storm + drains, etc. title: wastewater type examples: - - value: '' + - value: '' from_schema: https://w3id.org/nmdc/nmdc aliases: - - wastewater type + - wastewater type rank: 385 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000353 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -49986,123 +53033,123 @@ classes: from_schema: https://example.com/nmdc_submission_schema is_a: DhInterface mixins: - - DhMultiviewCommonColumnsMixin - - SampIdNewTermsMixin + - DhMultiviewCommonColumnsMixin + - SampIdNewTermsMixin slots: - - air_temp_regm - - alkalinity - - alkalinity_method - - alkyl_diethers - - aminopept_act - - ammonium - - atmospheric_data - - bac_prod - - bac_resp - - bacteria_carb_prod - - biomass - - biotic_regm - - bishomohopanol - - bromide - - calcium - - carb_nitro_ratio - - chem_administration - - chloride - - chlorophyll - - climate_environment - - collection_date - - collection_date_inc - - collection_time - - 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 - - experimental_factor - - filter_method - - fluor - - gaseous_environment - - geo_loc_name - - glucosidase_act - - humidity_regm - - isotope_exposure - - lat_lon - - light_intensity - - light_regm - - magnesium - - 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 - - salinity_meth - - 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 - - start_date_inc - - sulfate - - sulfide - - suspend_part_matter - - temp - - tidal_stage - - tot_depth_water_col - - tot_diss_nitro - - tot_inorg_nitro - - tot_nitro - - tot_part_carb - - tot_phosp - - turbidity - - water_current - - watering_regm + - air_temp_regm + - alkalinity + - alkalinity_method + - alkyl_diethers + - aminopept_act + - ammonium + - atmospheric_data + - bac_prod + - bac_resp + - bacteria_carb_prod + - biomass + - biotic_regm + - bishomohopanol + - bromide + - calcium + - carb_nitro_ratio + - chem_administration + - chloride + - chlorophyll + - climate_environment + - collection_date + - collection_date_inc + - collection_time + - 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 + - experimental_factor + - filter_method + - fluor + - gaseous_environment + - geo_loc_name + - glucosidase_act + - humidity_regm + - isotope_exposure + - lat_lon + - light_intensity + - light_regm + - magnesium + - 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 + - salinity_meth + - 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 + - start_date_inc + - sulfate + - sulfide + - suspend_part_matter + - temp + - tidal_stage + - tot_depth_water_col + - tot_diss_nitro + - tot_inorg_nitro + - tot_nitro + - tot_part_carb + - tot_phosp + - turbidity + - water_current + - watering_regm slot_usage: air_temp_regm: name: air_temp_regm @@ -50116,20 +53163,24 @@ classes: 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 + 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 + - 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 + - air temperature regimen rank: 16 is_a: core field string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000551 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -50145,19 +53196,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate + 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 + - value: 50 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - alkalinity + - alkalinity rank: 1 is_a: core field slot_uri: MIXS:0000421 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -50174,17 +53226,17 @@ classes: description: Method used for alkalinity measurement title: alkalinity method examples: - - value: titration + - value: titration from_schema: https://w3id.org/nmdc/nmdc aliases: - - alkalinity method + - alkalinity method rank: 218 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000298 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -50203,16 +53255,16 @@ classes: description: Concentration of alkyl diethers title: alkyl diethers examples: - - value: 0.005 mole per liter + - value: 0.005 mole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - alkyl diethers + - alkyl diethers rank: 2 is_a: core field slot_uri: MIXS:0000490 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -50232,16 +53284,16 @@ classes: description: Measurement of aminopeptidase activity title: aminopeptidase activity examples: - - value: 0.269 mole per liter per hour + - value: 0.269 mole per liter per hour from_schema: https://w3id.org/nmdc/nmdc aliases: - - aminopeptidase activity + - aminopeptidase activity rank: 3 is_a: core field slot_uri: MIXS:0000172 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -50261,16 +53313,16 @@ classes: description: Concentration of ammonium in the sample title: ammonium examples: - - value: 1.5 milligram per liter + - value: 1.5 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - ammonium + - ammonium rank: 4 is_a: core field slot_uri: MIXS:0000427 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -50287,21 +53339,22 @@ classes: description: Measurement of atmospheric data; can include multiple data title: atmospheric data examples: - - value: wind speed;9 knots + - value: wind speed;9 knots from_schema: https://w3id.org/nmdc/nmdc aliases: - - atmospheric data + - atmospheric data rank: 219 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0001097 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false - 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]+)$ + 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]+)$ bac_prod: name: bac_prod annotations: @@ -50314,19 +53367,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Bacterial production in the water column measured by isotope uptake + description: Bacterial production in the water column measured by isotope + uptake title: bacterial production examples: - - value: 5 milligram per cubic meter per day + - value: 5 milligram per cubic meter per day from_schema: https://w3id.org/nmdc/nmdc aliases: - - bacterial production + - bacterial production rank: 220 is_a: core field slot_uri: MIXS:0000683 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -50339,23 +53393,24 @@ classes: value: measurement value preferred_unit: tag: preferred_unit - value: milligram per cubic meter per day, micromole oxygen per liter per hour + 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 + - value: 300 micromole oxygen per liter per hour from_schema: https://w3id.org/nmdc/nmdc aliases: - - bacterial respiration + - bacterial respiration rank: 221 is_a: core field slot_uri: MIXS:0000684 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -50375,16 +53430,16 @@ classes: description: Measurement of bacterial carbon production title: bacterial carbon production examples: - - value: 2.53 microgram per liter per hour + - value: 2.53 microgram per liter per hour from_schema: https://w3id.org/nmdc/nmdc aliases: - - bacterial carbon production + - bacterial carbon production rank: 5 is_a: core field slot_uri: MIXS:0000173 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -50401,24 +53456,26 @@ classes: 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 + 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 + - value: total;20 gram from_schema: https://w3id.org/nmdc/nmdc aliases: - - biomass + - biomass rank: 6 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000174 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false - 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]+)$ + 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]+)$ biotic_regm: name: biotic_regm annotations: @@ -50428,20 +53485,21 @@ classes: occurrence: tag: occurrence value: '1' - description: Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. + 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 + - value: sample inoculated with Rhizobium spp. Culture from_schema: https://w3id.org/nmdc/nmdc aliases: - - biotic regimen + - biotic regimen rank: 13 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0001038 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -50460,16 +53518,16 @@ classes: description: Concentration of bishomohopanol title: bishomohopanol examples: - - value: 14 microgram per liter + - value: 14 microgram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - bishomohopanol + - bishomohopanol rank: 7 is_a: core field slot_uri: MIXS:0000175 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -50489,16 +53547,16 @@ classes: description: Concentration of bromide title: bromide examples: - - value: 0.05 parts per million + - value: 0.05 parts per million from_schema: https://w3id.org/nmdc/nmdc aliases: - - bromide + - bromide rank: 8 is_a: core field slot_uri: MIXS:0000176 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -50518,16 +53576,16 @@ classes: description: Concentration of calcium in the sample title: calcium examples: - - value: 0.2 micromole per liter + - value: 0.2 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - calcium + - calcium rank: 9 is_a: core field slot_uri: MIXS:0000432 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -50544,16 +53602,16 @@ classes: description: Ratio of amount or concentrations of carbon to nitrogen title: carbon/nitrogen ratio examples: - - value: '0.417361111' + - value: '0.417361111' from_schema: https://w3id.org/nmdc/nmdc aliases: - - carbon/nitrogen ratio + - carbon/nitrogen ratio rank: 44 is_a: core field slot_uri: MIXS:0000310 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: float multivalued: false @@ -50567,21 +53625,24 @@ classes: 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 + 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 + - 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 + - chemical administration rank: 17 is_a: core field string_serialization: '{termLabel} {[termID]};{timestamp}' slot_uri: MIXS:0000751 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string recommended: true @@ -50602,16 +53663,16 @@ classes: description: Concentration of chloride in the sample title: chloride examples: - - value: 5000 milligram per liter + - value: 5000 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - chloride + - chloride rank: 10 is_a: core field slot_uri: MIXS:0000429 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -50631,16 +53692,16 @@ classes: description: Concentration of chlorophyll title: chlorophyll examples: - - value: 5 milligram per cubic meter + - value: 5 milligram per cubic meter from_schema: https://w3id.org/nmdc/nmdc aliases: - - chlorophyll + - chlorophyll rank: 11 is_a: core field slot_uri: MIXS:0000177 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -50654,23 +53715,27 @@ classes: 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 + 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. examples: - - value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + - value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - - climate environment + - climate environment rank: 19 is_a: core field string_serialization: '{text};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0001040 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -50683,22 +53748,23 @@ classes: 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) + - 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' + - value: '2021-04-15' + - value: 2021-04 + - value: '2021' from_schema: https://w3id.org/nmdc/nmdc aliases: - - collection date + - collection date rank: 3 is_a: environment field string_serialization: '{date, arbitrary precision}' slot_uri: MIXS:0000011 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string required: true @@ -50706,50 +53772,56 @@ classes: 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. + 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 + - 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. + - 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. + - value: 2021-04-15, 2021-04 and 2021 are all acceptable. from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000011 + - MIXS:0000011 rank: 2 string_serialization: '{date, arbitrary precision}' owner: Biosample domain_of: - - Biosample + - Biosample 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]))?)?$ multivalued: false + 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. + 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 + - 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' + - '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 + - value: 13:33 or 13:33:55 from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000011 + - MIXS:0000011 rank: 1 string_serialization: '{time, seconds optional}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string recommended: true - pattern: ^([01]?\d|2[0-3]|24(?=:00?:00?$)):([0-5]\d)(:([0-5]\d))?$ multivalued: false + pattern: ^([01]?\d|2[0-3]|24(?=:00?:00?$)):([0-5]\d)(:([0-5]\d))?$ conduc: name: conduc annotations: @@ -50765,16 +53837,16 @@ classes: description: Electrical conductivity of water title: conductivity examples: - - value: 10 milliSiemens per centimeter + - value: 10 milliSiemens per centimeter from_schema: https://w3id.org/nmdc/nmdc aliases: - - conductivity + - conductivity rank: 222 is_a: core field slot_uri: MIXS:0000692 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -50791,19 +53863,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Density of the sample, which is its mass per unit volume (aka volumetric mass density) + 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 + - value: 1000 kilogram per cubic meter from_schema: https://w3id.org/nmdc/nmdc aliases: - - density + - density rank: 12 is_a: core field slot_uri: MIXS:0000435 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -50814,25 +53887,27 @@ classes: 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. + 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 + - Use modified term comments: - - All depths must be reported in meters. Provide the numerical portion only. + - All depths must be reported in meters. Provide the numerical portion only. examples: - - value: 0 - 0.1 - - value: '1' + - value: 0 - 0.1 + - value: '1' from_schema: https://w3id.org/nmdc/nmdc aliases: - - depth + - depth rank: 9 is_a: environment field string_serialization: '{float}|{float}-{float}' slot_uri: MIXS:0000018 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string required: true @@ -50850,24 +53925,26 @@ classes: occurrence: tag: occurrence value: m - description: Concentration of diether lipids; can include multiple types of diether lipids + description: Concentration of diether lipids; can include multiple types of + diether lipids title: diether lipids examples: - - value: 0.2 nanogram per liter + - value: 0.2 nanogram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - diether lipids + - diether lipids rank: 13 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000178 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false - 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]+)$ + 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: @@ -50880,19 +53957,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample + 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 + - value: 5 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - dissolved carbon dioxide + - dissolved carbon dioxide rank: 14 is_a: core field slot_uri: MIXS:0000436 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -50912,16 +53990,16 @@ classes: description: Concentration of dissolved hydrogen title: dissolved hydrogen examples: - - value: 0.3 micromole per liter + - value: 0.3 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - dissolved hydrogen + - dissolved hydrogen rank: 15 is_a: core field slot_uri: MIXS:0000179 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -50938,19 +54016,20 @@ classes: 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 + 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 + - value: 2059 micromole per kilogram from_schema: https://w3id.org/nmdc/nmdc aliases: - - dissolved inorganic carbon + - dissolved inorganic carbon rank: 16 is_a: core field slot_uri: MIXS:0000434 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -50970,16 +54049,16 @@ classes: description: Concentration of dissolved inorganic nitrogen title: dissolved inorganic nitrogen examples: - - value: 761 micromole per liter + - value: 761 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - dissolved inorganic nitrogen + - dissolved inorganic nitrogen rank: 223 is_a: core field slot_uri: MIXS:0000698 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -50999,16 +54078,16 @@ classes: description: Concentration of dissolved inorganic phosphorus in the sample title: dissolved inorganic phosphorus examples: - - value: 56.5 micromole per liter + - value: 56.5 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - dissolved inorganic phosphorus + - dissolved inorganic phosphorus rank: 224 is_a: core field slot_uri: MIXS:0000106 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -51025,19 +54104,20 @@ classes: 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 + 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 + - value: 197 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - dissolved organic carbon + - dissolved organic carbon rank: 17 is_a: core field slot_uri: MIXS:0000433 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -51054,19 +54134,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 + description: Dissolved organic nitrogen concentration measured as; total dissolved + nitrogen - NH4 - NO3 - NO2 title: dissolved organic nitrogen examples: - - value: 0.05 micromole per liter + - value: 0.05 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - dissolved organic nitrogen + - dissolved organic nitrogen rank: 18 is_a: core field slot_uri: MIXS:0000162 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -51086,16 +54167,16 @@ classes: description: Concentration of dissolved oxygen title: dissolved oxygen examples: - - value: 175 micromole per kilogram + - value: 175 micromole per kilogram from_schema: https://w3id.org/nmdc/nmdc aliases: - - dissolved oxygen + - dissolved oxygen rank: 19 is_a: core field slot_uri: MIXS:0000119 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -51108,95 +54189,121 @@ classes: value: measurement value preferred_unit: tag: preferred_unit - value: microEinstein per square meter per second, microEinstein per square centimeter per second + 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 + description: Visible waveband radiance and irradiance measurements in the + water column title: downward PAR examples: - - value: 28.71 microEinstein per square meter per second + - value: 28.71 microEinstein per square meter per second from_schema: https://w3id.org/nmdc/nmdc aliases: - - downward PAR + - downward PAR rank: 225 is_a: core field slot_uri: MIXS:0000703 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 9 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study slot_group: sample_id_section range: string recommended: true multivalued: false 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 10 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study slot_group: sample_id_section range: string recommended: true multivalued: false 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 12 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study slot_group: sample_id_section range: string recommended: true multivalued: false 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 11 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study slot_group: sample_id_section range: string recommended: true @@ -51207,23 +54314,29 @@ classes: 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. + 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. + - 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' + - value: '100' from_schema: https://w3id.org/nmdc/nmdc aliases: - - elevation + - elevation rank: 6 is_a: environment field slot_uri: MIXS:0000093 owner: Biosample domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample slot_group: mixs_modified_section range: float multivalued: false @@ -51232,24 +54345,36 @@ classes: 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. + 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. tooltip: tag: tooltip - value: The biome or major environmental system where the sample or specimen originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe the broad anatomical or morphological context - 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' + value: The biome or major environmental system where the sample or specimen + originated. Choose values from subclasses of the 'biome' class [ENVO:00000428] + in the Environment Ontology (ENVO). For host-associated or plant-associated + samples, use terms from the UBERON or Plant Ontology to describe the + broad anatomical or morphological context + 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 + - 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://w3id.org/nmdc/nmdc aliases: - - broad-scale environmental context + - broad-scale environmental context rank: 6 is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000012 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string required: true @@ -51260,24 +54385,41 @@ classes: annotations: expected_value: tag: expected_value - value: Environmental entities having causal influences upon the entity at time of sampling. + value: Environmental entities having causal influences upon the entity + at time of sampling. tooltip: tag: tooltip - value: The specific environmental entities or features near the sample or specimen that significantly influence its characteristics or composition. These entities are typically smaller in scale than the broad environmental context. Values for this field should be countable, material nouns and must be chosen from subclasses of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO). For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to describe specific anatomical structures or plant parts. - 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.' + value: The specific environmental entities or features near the sample + or specimen that significantly influence its characteristics or composition. + These entities are typically smaller in scale than the broad environmental + context. Values for this field should be countable, material nouns and + must be chosen from subclasses of BFO:0000040 (material entity) that + appear in the Environment Ontology (ENVO). For host-associated or plant-associated + samples, use terms from the UBERON or Plant Ontology to describe specific + anatomical structures or plant parts. + 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].' + - 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://w3id.org/nmdc/nmdc aliases: - - local environmental context + - local environmental context rank: 7 is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000013 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string required: true @@ -51288,24 +54430,40 @@ classes: annotations: expected_value: tag: expected_value - value: The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]. + value: The material displaced by the entity at time of sampling. Recommend + subclasses of environmental material [ENVO:00010483]. tooltip: tag: tooltip - value: The predominant environmental material or substrate that directly surrounds or hosts the sample or specimen at the time of sampling. Choose values from subclasses of the 'environmental material' class [ENVO:00010483] in the Environment Ontology (ENVO). Values for this field should be measurable or mass material nouns, representing continuous environmental materials. For host-associated or plant-associated samples, use terms from the UBERON or Plant Ontology to indicate a tissue, organ, or plant structure - 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).' + value: The predominant environmental material or substrate that directly + surrounds or hosts the sample or specimen at the time of sampling. Choose + values from subclasses of the 'environmental material' class [ENVO:00010483] + in the Environment Ontology (ENVO). Values for this field should be + measurable or mass material nouns, representing continuous environmental + materials. For host-associated or plant-associated samples, use terms + from the UBERON or Plant Ontology to indicate a tissue, organ, or plant + structure + 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]' + - 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://w3id.org/nmdc/nmdc aliases: - - environmental medium + - environmental medium rank: 8 is_a: environment field string_serialization: '{termLabel} {[termID]}' slot_uri: MIXS:0000014 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string required: true @@ -51317,20 +54475,25 @@ classes: 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 + 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] + - value: time series design [EFO:0001779] from_schema: https://w3id.org/nmdc/nmdc aliases: - - experimental factor + - experimental factor rank: 12 is_a: investigation field string_serialization: '{termLabel} {[termID]}|{text}' slot_uri: MIXS:0000008 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -51339,18 +54502,18 @@ classes: 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 + - describe the filter or provide a catalog number and manufacturer examples: - - value: C18 - - value: Basix PES, 13-100-106 FisherSci + - value: C18 + - value: Basix PES, 13-100-106 FisherSci from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000765 + - MIXS:0000765 rank: 6 string_serialization: '{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string recommended: true @@ -51370,16 +54533,16 @@ classes: description: Raw or converted fluorescence of water title: fluorescence examples: - - value: 2.5 volts + - value: 2.5 volts from_schema: https://w3id.org/nmdc/nmdc aliases: - - fluorescence + - fluorescence rank: 226 is_a: core field slot_uri: MIXS:0000704 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -51389,31 +54552,37 @@ classes: annotations: expected_value: tag: expected_value - value: gaseous compound name;gaseous compound amount;treatment interval and duration + 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 + 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 + - 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 aliases: - - gaseous environment + - gaseous environment rank: 20 is_a: core field string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000558 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -51422,22 +54591,24 @@ classes: 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. + 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' + - value: 'USA: Maryland, Bethesda' from_schema: https://w3id.org/nmdc/nmdc aliases: - - geographic location (country and/or sea,region) + - geographic location (country and/or sea,region) rank: 4 is_a: environment field string_serialization: '{term}: {term}, {text}' slot_uri: MIXS:0000010 owner: Biosample domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample slot_group: mixs_modified_section range: string required: true @@ -51457,16 +54628,16 @@ classes: description: Measurement of glucosidase activity title: glucosidase activity examples: - - value: 5 mol per liter per hour + - value: 5 mol per liter per hour from_schema: https://w3id.org/nmdc/nmdc aliases: - - glucosidase activity + - glucosidase activity rank: 20 is_a: core field slot_uri: MIXS:0000137 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -51483,20 +54654,25 @@ classes: 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 + 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 + - 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 + - humidity regimen rank: 21 is_a: core field string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000568 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -51505,48 +54681,52 @@ classes: description: List isotope exposure or addition applied to your sample. title: isotope exposure/addition todos: - - Can we make the H218O correctly super and subscripted? + - Can we make the H218O correctly super and subscripted? comments: - - This is required when your experimental design includes the use of isotopically labeled compounds + - This is required when your experimental design includes the use of isotopically + labeled compounds examples: - - value: 13C glucose - - value: H218O + - value: 13C glucose + - value: H218O from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000751 + - MIXS:0000751 rank: 16 string_serialization: '{termLabel} {[termID]}; {timestamp}' owner: Biosample domain_of: - - Biosample + - Biosample 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)?)?)?)?$ multivalued: false + 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 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 + 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) notes: - - This is currently a required field but it's not clear if this should be required for human hosts + - This is currently a required field but it's not clear if this should be + required for human hosts examples: - - value: 50.586825 6.408977 + - value: 50.586825 6.408977 from_schema: https://w3id.org/nmdc/nmdc aliases: - - geographic location (latitude and longitude) + - geographic location (latitude and longitude) rank: 5 is_a: environment field string_serialization: '{float} {float}' slot_uri: MIXS:0000009 owner: Biosample domain_of: - - FieldResearchSite - - Biosample + - FieldResearchSite + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -51566,16 +54746,16 @@ classes: description: Measurement of light intensity title: light intensity examples: - - value: 0.3 lux + - value: 0.3 lux from_schema: https://w3id.org/nmdc/nmdc aliases: - - light intensity + - light intensity rank: 227 is_a: core field slot_uri: MIXS:0000706 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -51592,24 +54772,26 @@ classes: occurrence: tag: occurrence value: '1' - description: Information about treatment(s) involving exposure to light, including both light intensity and quality. + 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 + - value: incandescant light;10 lux;450 nanometer from_schema: https://w3id.org/nmdc/nmdc aliases: - - light regimen + - light regimen rank: 24 is_a: core field string_serialization: '{text};{float} {unit};{float} {unit}' slot_uri: MIXS:0000569 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false - pattern: ^\S+.*\S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ + pattern: ^\S+.*\S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? + \S+$ magnesium: name: magnesium annotations: @@ -51618,23 +54800,24 @@ classes: value: measurement value preferred_unit: tag: preferred_unit - value: mole per liter, milligram per liter, parts per million, micromole per kilogram + 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 + - value: 52.8 micromole per kilogram from_schema: https://w3id.org/nmdc/nmdc aliases: - - magnesium + - magnesium rank: 21 is_a: core field slot_uri: MIXS:0000431 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -51654,16 +54837,16 @@ classes: description: Measurement of mean friction velocity title: mean friction velocity examples: - - value: 0.5 meter per second + - value: 0.5 meter per second from_schema: https://w3id.org/nmdc/nmdc aliases: - - mean friction velocity + - mean friction velocity rank: 22 is_a: core field slot_uri: MIXS:0000498 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -51683,16 +54866,16 @@ classes: description: Measurement of mean peak friction velocity title: mean peak friction velocity examples: - - value: 1 meter per second + - value: 1 meter per second from_schema: https://w3id.org/nmdc/nmdc aliases: - - mean peak friction velocity + - mean peak friction velocity rank: 23 is_a: core field slot_uri: MIXS:0000502 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -51706,24 +54889,26 @@ classes: occurrence: tag: occurrence value: m - description: Any other measurement performed or parameter collected, that is not listed here + 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 + - value: Bicarbonate ion concentration;2075 micromole per kilogram from_schema: https://w3id.org/nmdc/nmdc aliases: - - miscellaneous parameter + - miscellaneous parameter rank: 23 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000752 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false - 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]+)$ + 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: @@ -51739,21 +54924,22 @@ classes: description: Concentration of n-alkanes; can include multiple n-alkanes title: n-alkanes examples: - - value: n-hexadecane;100 milligram per liter + - value: n-hexadecane;100 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - n-alkanes + - n-alkanes rank: 25 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000503 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false - 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]+)$ + 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: @@ -51769,16 +54955,16 @@ classes: description: Concentration of nitrate in the sample title: nitrate examples: - - value: 65 micromole per liter + - value: 65 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - nitrate + - nitrate rank: 26 is_a: core field slot_uri: MIXS:0000425 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -51798,16 +54984,16 @@ classes: description: Concentration of nitrite in the sample title: nitrite examples: - - value: 0.5 micromole per liter + - value: 0.5 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - nitrite + - nitrite rank: 27 is_a: core field slot_uri: MIXS:0000426 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -51827,16 +55013,16 @@ classes: description: Concentration of nitrogen (total) title: nitrogen examples: - - value: 4.2 micromole per liter + - value: 4.2 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - nitrogen + - nitrogen rank: 28 is_a: core field slot_uri: MIXS:0000504 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -51856,16 +55042,16 @@ classes: description: Concentration of organic carbon title: organic carbon examples: - - value: 1.5 microgram per liter + - value: 1.5 microgram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - organic carbon + - organic carbon rank: 29 is_a: core field slot_uri: MIXS:0000508 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -51885,16 +55071,16 @@ classes: description: Concentration of organic matter title: organic matter examples: - - value: 1.75 milligram per cubic meter + - value: 1.75 milligram per cubic meter from_schema: https://w3id.org/nmdc/nmdc aliases: - - organic matter + - organic matter rank: 45 is_a: core field slot_uri: MIXS:0000204 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -51914,16 +55100,16 @@ classes: description: Concentration of organic nitrogen title: organic nitrogen examples: - - value: 4 micromole per liter + - value: 4 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - organic nitrogen + - organic nitrogen rank: 46 is_a: core field slot_uri: MIXS:0000205 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -51936,27 +55122,33 @@ classes: 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 + 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)' + 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 + - value: total prokaryotes;3.5e7 cells per milliliter;qPCR from_schema: https://w3id.org/nmdc/nmdc aliases: - - organism count + - organism count rank: 30 is_a: core field slot_uri: MIXS:0000103 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false - 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))$ + 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))$ oxy_stat_samp: name: oxy_stat_samp annotations: @@ -51969,16 +55161,16 @@ classes: description: Oxygenation status of sample title: oxygenation status of sample examples: - - value: aerobic + - value: aerobic from_schema: https://w3id.org/nmdc/nmdc aliases: - - oxygenation status of sample + - oxygenation status of sample rank: 25 is_a: core field slot_uri: MIXS:0000753 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: OxyStatSampEnum multivalued: false @@ -51997,16 +55189,16 @@ classes: description: Concentration of particulate organic carbon title: particulate organic carbon examples: - - value: 1.92 micromole per liter + - value: 1.92 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - particulate organic carbon + - particulate organic carbon rank: 31 is_a: core field slot_uri: MIXS:0000515 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -52026,16 +55218,16 @@ classes: description: Concentration of particulate organic nitrogen title: particulate organic nitrogen examples: - - value: 0.3 micromole per liter + - value: 0.3 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - particulate organic nitrogen + - particulate organic nitrogen rank: 228 is_a: core field slot_uri: MIXS:0000719 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -52049,20 +55241,24 @@ classes: 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 + 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 + - value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M from_schema: https://w3id.org/nmdc/nmdc aliases: - - perturbation + - perturbation rank: 33 is_a: core field string_serialization: '{text};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000754 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -52081,16 +55277,16 @@ classes: description: Concentration of petroleum hydrocarbon title: petroleum hydrocarbon examples: - - value: 0.05 micromole per liter + - value: 0.05 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - petroleum hydrocarbon + - petroleum hydrocarbon rank: 34 is_a: core field slot_uri: MIXS:0000516 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -52104,19 +55300,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid + description: Ph measurement of the sample, or liquid portion of sample, or + aqueous phase of the fluid title: pH examples: - - value: '7.2' + - value: '7.2' from_schema: https://w3id.org/nmdc/nmdc aliases: - - pH + - pH rank: 27 is_a: core field slot_uri: MIXS:0001001 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: double multivalued: false @@ -52132,20 +55329,20 @@ classes: 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. + - 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 + - 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 aliases: - - pH method + - pH method rank: 41 is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0001106 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -52164,21 +55361,22 @@ classes: description: Concentration of phaeopigments; can include multiple phaeopigments title: phaeopigments examples: - - value: 2.5 milligram per cubic meter + - value: 2.5 milligram per cubic meter from_schema: https://w3id.org/nmdc/nmdc aliases: - - phaeopigments + - phaeopigments rank: 35 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000180 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false - 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]+)$ + 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: @@ -52194,16 +55392,16 @@ classes: description: Concentration of phosphate title: phosphate examples: - - value: 0.7 micromole per liter + - value: 0.7 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - phosphate + - phosphate rank: 53 is_a: core field slot_uri: MIXS:0000505 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -52220,24 +55418,26 @@ classes: occurrence: tag: occurrence value: m - description: Concentration of phospholipid fatty acids; can include multiple values + description: Concentration of phospholipid fatty acids; can include multiple + values title: phospholipid fatty acid examples: - - value: 2.98 milligram per liter + - value: 2.98 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - phospholipid fatty acid + - phospholipid fatty acid rank: 36 is_a: core field string_serialization: '{text};{float} {unit}' slot_uri: MIXS:0000181 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false - 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]+)$ + 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: @@ -52253,16 +55453,16 @@ classes: description: Measurement of photon flux title: photon flux examples: - - value: 3.926 micromole photons per second per square meter + - value: 3.926 micromole photons per second per square meter from_schema: https://w3id.org/nmdc/nmdc aliases: - - photon flux + - photon flux rank: 229 is_a: core field slot_uri: MIXS:0000725 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -52282,16 +55482,16 @@ classes: description: Concentration of potassium in the sample title: potassium examples: - - value: 463 milligram per liter + - value: 463 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - potassium + - potassium rank: 38 is_a: core field slot_uri: MIXS:0000430 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -52311,16 +55511,16 @@ classes: description: Pressure to which the sample is subject to, in atmospheres title: pressure examples: - - value: 50 atmosphere + - value: 50 atmosphere from_schema: https://w3id.org/nmdc/nmdc aliases: - - pressure + - pressure rank: 39 is_a: core field slot_uri: MIXS:0000412 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -52337,19 +55537,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Measurement of primary production, generally measured as isotope uptake + description: Measurement of primary production, generally measured as isotope + uptake title: primary production examples: - - value: 100 milligram per cubic meter per day + - value: 100 milligram per cubic meter per day from_schema: https://w3id.org/nmdc/nmdc aliases: - - primary production + - primary production rank: 230 is_a: core field slot_uri: MIXS:0000728 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -52366,19 +55567,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential + description: Redox potential, measured relative to a hydrogen cell, indicating + oxidation or reduction potential title: redox potential examples: - - value: 300 millivolt + - value: 300 millivolt from_schema: https://w3id.org/nmdc/nmdc aliases: - - redox potential + - redox potential rank: 40 is_a: core field slot_uri: MIXS:0000182 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -52395,19 +55597,24 @@ classes: 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. + 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 + - value: 25 practical salinity unit from_schema: https://w3id.org/nmdc/nmdc aliases: - - salinity + - salinity rank: 54 is_a: core field slot_uri: MIXS:0000183 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -52424,17 +55631,17 @@ classes: description: Reference or method used in determining salinity title: salinity method examples: - - value: https://doi.org/10.1007/978-1-61779-986-0_28 + - value: https://doi.org/10.1007/978-1-61779-986-0_28 from_schema: https://w3id.org/nmdc/nmdc aliases: - - salinity method + - salinity method rank: 55 is_a: core field string_serialization: '{PMID}|{DOI}|{URL}' slot_uri: MIXS:0000341 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -52444,20 +55651,22 @@ classes: 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). + 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] + - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample collection device + - sample collection device rank: 14 is_a: nucleic acid sequence source field string_serialization: '{termLabel} {[termID]}|{text}' slot_uri: MIXS:0000002 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -52470,17 +55679,17 @@ classes: description: The method employed for collecting the sample. title: sample collection method examples: - - value: swabbing + - value: swabbing from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample collection method + - sample collection method rank: 15 is_a: nucleic acid sequence source field string_serialization: '{PMID}|{DOI}|{URL}|{text}' slot_uri: MIXS:0001225 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -52490,21 +55699,23 @@ classes: 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. + 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 + - value: filtering of seawater + - value: storing samples in ethanol from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample material processing + - sample material processing rank: 12 is_a: nucleic acid sequence source field string_serialization: '{text}' slot_uri: MIXS:0000016 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -52517,19 +55728,20 @@ classes: 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. + 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 + - value: 5 liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - amount or size of sample collected + - amount or size of sample collected rank: 18 is_a: nucleic acid sequence source field slot_uri: MIXS:0000001 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -52546,17 +55758,17 @@ classes: description: Duration for which the sample was stored title: sample storage duration examples: - - value: P1Y6M + - value: P1Y6M from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample storage duration + - sample storage duration rank: 353 is_a: core field string_serialization: '{duration}' slot_uri: MIXS:0000116 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -52569,20 +55781,21 @@ classes: occurrence: tag: occurrence value: '1' - description: Location at which sample was stored, usually name of a specific freezer/room + description: Location at which sample was stored, usually name of a specific + freezer/room title: sample storage location examples: - - value: Freezer no:5 + - value: Freezer no:5 from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample storage location + - sample storage location rank: 41 is_a: core field string_serialization: '{text}' slot_uri: MIXS:0000755 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -52601,36 +55814,43 @@ classes: description: Temperature at which sample was stored, e.g. -80 degree Celsius title: sample storage temperature examples: - - value: -80 degree Celsius + - value: -80 degree Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample storage temperature + - sample storage temperature rank: 7 is_a: core field slot_uri: MIXS:0000110 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false 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. + 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''' + - '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)' + - '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 + - value: IGSN:DSJ0284 from_schema: https://w3id.org/nmdc/nmdc rank: 5 string_serialization: '{text}:{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string recommended: true @@ -52651,16 +55871,16 @@ classes: description: Concentration of silicate title: silicate examples: - - value: 0.05 micromole per liter + - value: 0.05 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - silicate + - silicate rank: 43 is_a: core field slot_uri: MIXS:0000184 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -52674,17 +55894,17 @@ classes: description: Filtering pore size used in sample preparation title: size fraction selected examples: - - value: 0-0.22 micrometer + - value: 0-0.22 micrometer from_schema: https://w3id.org/nmdc/nmdc aliases: - - size fraction selected + - size fraction selected rank: 285 is_a: nucleic acid sequence source field string_serialization: '{float}-{float} {unit}' slot_uri: MIXS:0000017 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -52700,19 +55920,20 @@ classes: 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 + 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 + - value: 0.2 micrometer from_schema: https://w3id.org/nmdc/nmdc aliases: - - size-fraction lower threshold + - size-fraction lower threshold rank: 10 is_a: core field slot_uri: MIXS:0000735 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -52729,19 +55950,20 @@ classes: 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 + 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 + - value: 20 micrometer from_schema: https://w3id.org/nmdc/nmdc aliases: - - size-fraction upper threshold + - size-fraction upper threshold rank: 11 is_a: core field slot_uri: MIXS:0000736 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -52761,16 +55983,16 @@ classes: description: Sodium concentration in the sample title: sodium examples: - - value: 10.5 milligram per liter + - value: 10.5 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - sodium + - sodium rank: 363 is_a: core field slot_uri: MIXS:0000428 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -52790,61 +56012,67 @@ classes: description: Concentration of soluble reactive phosphorus title: soluble reactive phosphorus examples: - - value: 0.1 milligram per liter + - value: 0.1 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - soluble reactive phosphorus + - soluble reactive phosphorus rank: 231 is_a: core field slot_uri: MIXS:0000738 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false 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. + 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. + - 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 + - https://gold.jgi.doe.gov/help rank: 13 is_a: gold_path_field owner: Biosample domain_of: - - Biosample - - Study + - Biosample + - Study slot_group: sample_id_section range: string recommended: true multivalued: false start_date_inc: name: start_date_inc - description: Date the incubation was started. Only relevant for incubation samples. + 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 + - 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. + - 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. + - value: 2021-04-15, 2021-04 and 2021 are all acceptable. from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000011 + - MIXS:0000011 rank: 4 string_serialization: '{date, arbitrary precision}' owner: Biosample domain_of: - - Biosample + - Biosample 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]))?)?$ multivalued: false + pattern: ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$ sulfate: name: sulfate annotations: @@ -52860,16 +56088,16 @@ classes: description: Concentration of sulfate in the sample title: sulfate examples: - - value: 5 micromole per liter + - value: 5 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - sulfate + - sulfate rank: 44 is_a: core field slot_uri: MIXS:0000423 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -52889,16 +56117,16 @@ classes: description: Concentration of sulfide in the sample title: sulfide examples: - - value: 2 micromole per liter + - value: 2 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - sulfide + - sulfide rank: 371 is_a: core field slot_uri: MIXS:0000424 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -52918,16 +56146,16 @@ classes: description: Concentration of suspended particulate matter title: suspended particulate matter examples: - - value: 0.5 milligram per liter + - value: 0.5 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - suspended particulate matter + - suspended particulate matter rank: 232 is_a: core field slot_uri: MIXS:0000741 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -52944,16 +56172,16 @@ classes: description: Temperature of the sample at the time of sampling. title: temperature examples: - - value: 25 degree Celsius + - value: 25 degree Celsius from_schema: https://w3id.org/nmdc/nmdc aliases: - - temperature + - temperature rank: 37 is_a: environment field slot_uri: MIXS:0000113 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -52970,16 +56198,16 @@ classes: description: Stage of tide title: tidal stage examples: - - value: high tide + - value: high tide from_schema: https://w3id.org/nmdc/nmdc aliases: - - tidal stage + - tidal stage rank: 45 is_a: core field slot_uri: MIXS:0000750 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: tidal_stage_enum multivalued: false @@ -52998,16 +56226,16 @@ classes: description: Measurement of total depth of water column title: total depth of water column examples: - - value: 500 meter + - value: 500 meter from_schema: https://w3id.org/nmdc/nmdc aliases: - - total depth of water column + - total depth of water column rank: 46 is_a: core field slot_uri: MIXS:0000634 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -53024,19 +56252,21 @@ classes: occurrence: tag: occurrence value: '1' - description: 'Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen' + 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 + - value: 40 microgram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - total dissolved nitrogen + - total dissolved nitrogen rank: 233 is_a: core field slot_uri: MIXS:0000744 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -53056,16 +56286,16 @@ classes: description: Total inorganic nitrogen content title: total inorganic nitrogen examples: - - value: 40 microgram per liter + - value: 40 microgram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - total inorganic nitrogen + - total inorganic nitrogen rank: 234 is_a: core field slot_uri: MIXS:0000745 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -53082,19 +56312,21 @@ classes: 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' + 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 + - value: 50 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - total nitrogen concentration + - total nitrogen concentration rank: 377 is_a: core field slot_uri: MIXS:0000102 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -53114,16 +56346,16 @@ classes: description: Total particulate carbon content title: total particulate carbon examples: - - value: 35 micromole per liter + - value: 35 micromole per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - total particulate carbon + - total particulate carbon rank: 235 is_a: core field slot_uri: MIXS:0000747 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -53140,19 +56372,20 @@ classes: occurrence: tag: occurrence value: '1' - description: 'Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus' + 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 + - value: 0.03 milligram per liter from_schema: https://w3id.org/nmdc/nmdc aliases: - - total phosphorus + - total phosphorus rank: 52 is_a: core field slot_uri: MIXS:0000117 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_section range: string multivalued: false @@ -53169,19 +56402,20 @@ classes: occurrence: tag: occurrence value: '1' - description: Measure of the amount of cloudiness or haziness in water caused by individual particles + description: Measure of the amount of cloudiness or haziness in water caused + by individual particles title: turbidity examples: - - value: 0.3 nephelometric turbidity units + - value: 0.3 nephelometric turbidity units from_schema: https://w3id.org/nmdc/nmdc aliases: - - turbidity + - turbidity rank: 47 is_a: core field slot_uri: MIXS:0000191 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -53201,16 +56435,16 @@ classes: description: Measurement of magnitude and direction of flow within a fluid title: water current examples: - - value: 10 cubic meter per second + - value: 10 cubic meter per second from_schema: https://w3id.org/nmdc/nmdc aliases: - - water current + - water current rank: 236 is_a: core field slot_uri: MIXS:0000203 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_core_section range: string multivalued: false @@ -53227,21 +56461,24 @@ classes: 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 + 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 + - 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 aliases: - - watering regimen + - watering regimen rank: 25 is_a: core field string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}' slot_uri: MIXS:0000591 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_modified_section range: string multivalued: false @@ -53252,23 +56489,23 @@ classes: from_schema: https://example.com/nmdc_submission_schema mixin: true slots: - - analysis_type - - samp_name - - source_mat_id + - 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 + - value: metagenomics; metabolomics; proteomics from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIxS:investigation_type + - MIxS:investigation_type rank: 3 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: AnalysisTypeEnum required: true @@ -53280,15 +56517,17 @@ classes: 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. + 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. + - 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 + - value: Rock core CB1178(5-6) from NSW from_schema: https://w3id.org/nmdc/nmdc aliases: - - sample name + - sample name rank: 1 is_a: investigation field string_serialization: '{text}' @@ -53296,7 +56535,7 @@ classes: identifier: true owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string required: true @@ -53306,30 +56545,43 @@ classes: annotations: expected_value: tag: expected_value - value: 'for cultures of microorganisms: identifiers for two culture collections; for other material a unique arbitrary identifer' + value: 'for cultures of microorganisms: identifiers for two culture collections; + for other material a unique arbitrary identifer' 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. + - 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 + - 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/). + - 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 + - value: IGSN:AU1243 + - value: UUID:24f1467a-40f4-11ed-b878-0242ac120002 from_schema: https://w3id.org/nmdc/nmdc aliases: - - source material identifiers + - source material identifiers rank: 2 is_a: nucleic acid sequence source field string_serialization: '{text}:{text}' slot_uri: MIXS:0000026 owner: Biosample domain_of: - - Biosample + - Biosample slot_group: sample_id_section range: string multivalued: false @@ -53344,8 +56596,7 @@ classes: from_schema: https://example.com/nmdc_submission_schema mixin: true slots: - - sample_link - slot_usage: [] + - sample_link SoilMixsInspiredMixin: name: SoilMixsInspiredMixin description: Mixin with SoilMixsInspired Terms @@ -53353,127 +56604,138 @@ classes: 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 + - 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. + 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 + - 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. + - 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. + - value: 2021-04-15, 2021-04 and 2021 are all acceptable. from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000011 + - MIXS:0000011 rank: 2 string_serialization: '{date, arbitrary precision}' owner: Biosample domain_of: - - Biosample + - Biosample 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]))?)?$ multivalued: false + 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. + 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 + - 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' + - '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 + - value: 13:33 or 13:33:55 from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000011 + - MIXS:0000011 rank: 1 string_serialization: '{time, seconds optional}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string recommended: true - pattern: ^([01]?\d|2[0-3]|24(?=:00?:00?$)):([0-5]\d)(:([0-5]\d))?$ multivalued: false + 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. + 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 + - 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' + - '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 + - value: 13:33 or 13:33:55 from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000011 + - MIXS:0000011 rank: 3 string_serialization: '{time, seconds optional}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string recommended: true - pattern: ^([01]?\d|2[0-3]|24(?=:00?:00?$)):([0-5]\d)(:([0-5]\d))?$ multivalued: false + 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. + 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. + - 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' + - value: 'experimental treatment: value' from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000008 - - MIXS:0000300 + - MIXS:0000008 + - MIXS:0000300 rank: 7 string_serialization: '{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string recommended: true @@ -53483,18 +56745,18 @@ classes: 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 + - describe the filter or provide a catalog number and manufacturer examples: - - value: C18 - - value: Basix PES, 13-100-106 FisherSci + - value: C18 + - value: Basix PES, 13-100-106 FisherSci from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000765 + - MIXS:0000765 rank: 6 string_serialization: '{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string recommended: true @@ -53504,44 +56766,45 @@ classes: description: List isotope exposure or addition applied to your sample. title: isotope exposure/addition todos: - - Can we make the H218O correctly super and subscripted? + - Can we make the H218O correctly super and subscripted? comments: - - This is required when your experimental design includes the use of isotopically labeled compounds + - This is required when your experimental design includes the use of isotopically + labeled compounds examples: - - value: 13C glucose - - value: H218O + - value: 13C glucose + - value: H218O from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000751 + - MIXS:0000751 rank: 16 string_serialization: '{termLabel} {[termID]}; {timestamp}' owner: Biosample domain_of: - - Biosample + - Biosample 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)?)?)?)?$ multivalued: false + 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 + - How should we separate values? | or ;? lets be consistent comments: - - required if "microbial_biomass_c" is provided + - 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 + - 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:0000339 + - MIXS:0000339 rank: 1004 string_serialization: '{PMID}|{DOI}|{URL}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string recommended: true @@ -53551,96 +56814,102 @@ classes: description: Reference or method used in determining microbial biomass nitrogen title: microbial biomass nitrogen method comments: - - required if "microbial_biomass_n" is provided + - 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 + - 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:0000339 + - MIXS:0000339 rank: 1004 string_serialization: '{PMID}|{DOI}|{URL}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string multivalued: false 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. + 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 + - 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 + - value: 0.05 ug C/g dry soil from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000650 + - MIXS:0000650 rank: 1004 string_serialization: '{float} {unit}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string - pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ multivalued: false + 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. + 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 + - 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 + - value: 0.05 ug N/g dry soil from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000650 + - MIXS:0000650 rank: 1004 string_serialization: '{float} {unit}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string - pattern: ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ multivalued: false + 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 ; + 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 + - value: insect 0.23 ug; plant 1g from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000174 - - MIXS:0000650 + - MIXS:0000174 + - MIXS:0000650 rank: 8 string_serialization: '{text};{float} {unit}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string - pattern: ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$ multivalued: false + 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 + - required if "non-microbial biomass" is provided examples: - - value: https://doi.org/10.1038/s41467-021-26181-3 + - value: https://doi.org/10.1038/s41467-021-26181-3 from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000650 + - MIXS:0000650 rank: 9 string_serialization: '{PMID}|{DOI}|{URL}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string multivalued: false @@ -53649,125 +56918,133 @@ classes: description: Method used for obtaining organic nitrogen title: organic nitrogen method comments: - - required if "org_nitro" is provided + - required if "org_nitro" is provided examples: - - value: https://doi.org/10.1016/0038-0717(85)90144-0 + - value: https://doi.org/10.1016/0038-0717(85)90144-0 from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000338 - - MIXS:0000205 + - MIXS:0000338 + - MIXS:0000205 rank: 14 string_serialization: '{PMID}|{DOI}|{URL}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string multivalued: false other_treatment: name: other_treatment - description: Other treatments applied to your samples that are not applicable to the provided fields + description: Other treatments applied to your samples that are not applicable + to the provided fields title: other treatments notes: - - Values entered here will be used to determine potential new slots. + - Values entered here will be used to determine potential new slots. comments: - - This is an open text field to provide any treatments that cannot be captured in the provided slots. + - 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:0000300 + - MIXS:0000300 rank: 15 string_serialization: '{text}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string recommended: true multivalued: false start_date_inc: name: start_date_inc - description: Date the incubation was started. Only relevant for incubation samples. + 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 + - 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. + - 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. + - value: 2021-04-15, 2021-04 and 2021 are all acceptable. from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000011 + - MIXS:0000011 rank: 4 string_serialization: '{date, arbitrary precision}' owner: Biosample domain_of: - - Biosample + - Biosample 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]))?)?$ multivalued: false + 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. + 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 + - 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' + - '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 + - value: 13:33 or 13:33:55 from_schema: https://w3id.org/nmdc/nmdc see_also: - - MIXS:0000011 + - MIXS:0000011 rank: 5 string_serialization: '{time, seconds optional}' owner: Biosample domain_of: - - Biosample + - Biosample slot_group: mixs_inspired_section range: string recommended: true - pattern: ^([01]?\d|2[0-3]|24(?=:00?:00?$)):([0-5]\d)(:([0-5]\d))?$ multivalued: false + 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 + 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 - slot_usage: [] SampleData: name: SampleData - description: represents data produced by the DataHarmonizer tabs of the submission portal + 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_lr_data - - jgi_mg_data - - jgi_mt_data + - 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_lr_data + - jgi_mg_data + - jgi_mt_data tree_root: true - slot_usage: [] 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 - - type + - id + - name + - description + - alternative_identifiers + - type class_uri: nmdc:NamedThing - slot_usage: [] -source_file: local/with_modifications.yaml.raw +source_file: /Users/SMoxon/Documents/src/submission-schema/src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml diff --git a/src/nmdc_submission_schema/scripts/generate_env_triad_enums.py b/src/nmdc_submission_schema/scripts/generate_env_triad_enums.py index 55288dba..4085283d 100644 --- a/src/nmdc_submission_schema/scripts/generate_env_triad_enums.py +++ b/src/nmdc_submission_schema/scripts/generate_env_triad_enums.py @@ -1,59 +1,88 @@ -import json -from collections import defaultdict -from enum import Enum from pathlib import Path -from typing import Dict, Set, Iterable, Optional - -import click from linkml_runtime import SchemaView from linkml_runtime.dumpers import yaml_dumper -from linkml_runtime.linkml_model import EnumDefinition, PermissibleValue, SchemaDefinition -from linkml_runtime.loaders import yaml_loader +from linkml_runtime.linkml_model import EnumDefinition, EnumDefinitionName, PermissibleValue, SchemaDefinition import csv +repo_root = Path(__file__).resolve().parent.parent.parent.parent + +# Paths to the source and target schema files +SOURCE_SCHEMA_YAML_PATH = repo_root / "src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml" +TARGET_SCHEMA_YAML_PATH = repo_root / "src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml" + +# Paths to the TSV files +SOIL_ENV_LOCAL_PATH = repo_root / "notebooks/post_google_sheets_soil_env_local_scale.tsv" +SOIL_ENV_MEDIUM_PATH = repo_root / "notebooks/post_google_sheets_soil_env_medium_scale.tsv" +SOIL_ENV_BROAD_PATH = repo_root / "notebooks/post_google_sheets_soil_env_broad_scale.tsv" + def parse_tsv_to_dict(file_path): """ - Parse a TSV file into a dictionary. - Assumes the first column is the key, and the rest are values. + Parse a TSV file into a list of dictionaries representing each row in the file. - :param file_path: Path to the TSV file. - :return: Dictionary with the first column as keys and rows as values. + :param file_path: Path to the TSV file to parse. + :return: A list of dictionaries representing each row in the file. """ - data_dict = {} + data_dict = [] with open(file_path, mode='r', newline='', encoding='utf-8') as file: reader = csv.reader(file, delimiter='\t') + next(reader, None) # Skip the header for row in reader: if row: - # Use the first column as the key and the rest as values - key = row[0] - values = row[1:] if len(row) > 1 else [] - data_dict[key] = values + data_dict.append({"term_id": row[0], "term_name": row[1]}) return data_dict -def inject_env_local_scale_terms (env_local_path: Path, input_schema_path: SchemaDefinition) -> SchemaDefinition: - """Inject gold pathway terms into the schema.""" - data = parse_tsv_to_dict(env_local_path) - print(data) - schemaview = SchemaView(input_schema_path) - - for term in data: - pvs = [PermissibleValue(text=term_id) for term in data] - schemaview.add_enum(EnumDefinition( - name='EnvironmentalTriadLocalEnum', - permissible_values=pvs - )) - - return schemaview.schema - -@click.command() -@click.option('--env-local-file', '-g', type=click.Path(exists=True)) -@click.option('--schema-input-file', '-i', type=click.File('r'), default="-") -@click.option('--schema-output-file', '-o', type=click.File('w'), default="-") -def main(env_local_file, input_file, output_file): - schema = yaml_loader.loads(input_file.read(), SchemaDefinition) - output = inject_env_local_scale_terms(Path(env_local_file), schema) - print(yaml_dumper.dumps(output), file=output_file) +def inject_terms_into_schema(env_path: Path, enum_name: str, sv: SchemaView) -> SchemaDefinition: + """ + Inject terms from a TSV file into the schema under a specified enumeration name. + + :param env_path: Path to the TSV file containing the terms to inject. + :param schema_yaml_path: Path to the schema YAML file to inject the terms into. + :param enum_name: Name of the enumeration to add or update in the schema. + :param sv: SchemaView object representing the schema. + :return: The updated schema. + """ + data = parse_tsv_to_dict(env_path) + sorted_data = sorted(data, key=lambda x: x["term_name"]) + + pvs = [PermissibleValue(text=f"{term['term_name']} [{term['term_id']}]") for term in sorted_data] + + enum_def = EnumDefinition( + name=enum_name, + permissible_values=pvs + ) + + # Check if the enum already exists; if so, delete it before adding the new one + if sv.schema.enums.get(enum_name): + sv.delete_enum(EnumDefinitionName(enum_name)) + + sv.add_enum(enum_def) + return sv.schema + + +def main(): + """ + Inject terms from multiple TSV files into the schema, each under a specified enumeration name. + """ + # Define files and corresponding enumeration names + file_enum_mappings = [ + (SOIL_ENV_LOCAL_PATH, "EnvLocalScaleSoilEnum"), + (SOIL_ENV_MEDIUM_PATH, "EnvMediumScaleSoilEnum"), + (SOIL_ENV_BROAD_PATH, "EnvBroadScaleSoilEnum") + ] + schemaview = SchemaView(SOURCE_SCHEMA_YAML_PATH) + # Load, inject terms, and save the updated schema for each file + schema = None + for env_path, enum_name in file_enum_mappings: + schema = inject_terms_into_schema(env_path, enum_name, schemaview) + + # Dump the updated schema to the specified output file + with TARGET_SCHEMA_YAML_PATH.open("w", encoding="utf-8") as file: + file.write(yaml_dumper.dumps(schema)) + + +if __name__ == "__main__": + main() diff --git a/tests/test_env_triad.py b/tests/test_env_triad.py index 819dfdef..4e1fa7d3 100644 --- a/tests/test_env_triad.py +++ b/tests/test_env_triad.py @@ -4,6 +4,8 @@ from src.nmdc_submission_schema.scripts.generate_env_triad_enums import main from linkml_runtime.loaders import yaml_loader +SCHEMA_YAML_PATH = Path(__file__).parent / "../src/nmdc_submission_schema/schema/nmdc_submission_schema_base.yaml" + def test_inject_env_local_scale_terms_cli(): runner = CliRunner() From 8e2578caf532fc96fac34b73b6e0c53e6f8f8e39 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Wed, 6 Nov 2024 15:07:02 -0800 Subject: [PATCH 3/9] add tests and test files --- .../scripts/generate_env_triad_enums.py | 41 ++++---- tests/inputs/base_schema.yaml | 34 +++++++ tests/inputs/soil_env_broad_test.tsv | 4 + ...ut_example.tsv => soil_env_local_test.tsv} | 2 +- tests/inputs/soil_env_medium_test.tsv | 4 + tests/test_env_triad.py | 94 ++++++++++++++----- 6 files changed, 131 insertions(+), 48 deletions(-) create mode 100644 tests/inputs/base_schema.yaml create mode 100644 tests/inputs/soil_env_broad_test.tsv rename tests/inputs/{env_local_input_example.tsv => soil_env_local_test.tsv} (82%) create mode 100644 tests/inputs/soil_env_medium_test.tsv diff --git a/src/nmdc_submission_schema/scripts/generate_env_triad_enums.py b/src/nmdc_submission_schema/scripts/generate_env_triad_enums.py index 4085283d..2d789b27 100644 --- a/src/nmdc_submission_schema/scripts/generate_env_triad_enums.py +++ b/src/nmdc_submission_schema/scripts/generate_env_triad_enums.py @@ -10,11 +10,6 @@ SOURCE_SCHEMA_YAML_PATH = repo_root / "src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml" TARGET_SCHEMA_YAML_PATH = repo_root / "src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml" -# Paths to the TSV files -SOIL_ENV_LOCAL_PATH = repo_root / "notebooks/post_google_sheets_soil_env_local_scale.tsv" -SOIL_ENV_MEDIUM_PATH = repo_root / "notebooks/post_google_sheets_soil_env_medium_scale.tsv" -SOIL_ENV_BROAD_PATH = repo_root / "notebooks/post_google_sheets_soil_env_broad_scale.tsv" - def parse_tsv_to_dict(file_path): """ @@ -34,18 +29,18 @@ def parse_tsv_to_dict(file_path): return data_dict - -def inject_terms_into_schema(env_path: Path, enum_name: str, sv: SchemaView) -> SchemaDefinition: +def inject_terms_into_schema(values_file_path: Path, + enum_name: str, + sv: SchemaView) -> SchemaDefinition: """ Inject terms from a TSV file into the schema under a specified enumeration name. - :param env_path: Path to the TSV file containing the terms to inject. - :param schema_yaml_path: Path to the schema YAML file to inject the terms into. + :param values_file_path: Path to the TSV file containing the terms to inject. :param enum_name: Name of the enumeration to add or update in the schema. :param sv: SchemaView object representing the schema. :return: The updated schema. """ - data = parse_tsv_to_dict(env_path) + data = parse_tsv_to_dict(values_file_path) sorted_data = sorted(data, key=lambda x: x["term_name"]) pvs = [PermissibleValue(text=f"{term['term_name']} [{term['term_id']}]") for term in sorted_data] @@ -63,26 +58,30 @@ def inject_terms_into_schema(env_path: Path, enum_name: str, sv: SchemaView) -> return sv.schema -def main(): +def main(enum_name: str, + values_file_path: Path, + source_schema_yaml_path: Path = SOURCE_SCHEMA_YAML_PATH, + target_schema_yaml_path: Path = TARGET_SCHEMA_YAML_PATH) -> None: """ Inject terms from multiple TSV files into the schema, each under a specified enumeration name. + + :param enum_name : Name of the enumeration to add or update in the schema. + :param values_file_path: Path to the TSV file containing the terms to replace the Enum PVs with + :param source_schema_yaml_path: Path to the source schema YAML file. + :param target_schema_yaml_path: Path to the target schema YAML file. """ # Define files and corresponding enumeration names - file_enum_mappings = [ - (SOIL_ENV_LOCAL_PATH, "EnvLocalScaleSoilEnum"), - (SOIL_ENV_MEDIUM_PATH, "EnvMediumScaleSoilEnum"), - (SOIL_ENV_BROAD_PATH, "EnvBroadScaleSoilEnum") - ] - schemaview = SchemaView(SOURCE_SCHEMA_YAML_PATH) + schemaview = SchemaView(source_schema_yaml_path) # Load, inject terms, and save the updated schema for each file - schema = None - for env_path, enum_name in file_enum_mappings: - schema = inject_terms_into_schema(env_path, enum_name, schemaview) + schema = inject_terms_into_schema(values_file_path, + enum_name, + schemaview) # Dump the updated schema to the specified output file - with TARGET_SCHEMA_YAML_PATH.open("w", encoding="utf-8") as file: + with target_schema_yaml_path.open("w", encoding="utf-8") as file: file.write(yaml_dumper.dumps(schema)) if __name__ == "__main__": main() + diff --git a/tests/inputs/base_schema.yaml b/tests/inputs/base_schema.yaml new file mode 100644 index 00000000..cdee70ac --- /dev/null +++ b/tests/inputs/base_schema.yaml @@ -0,0 +1,34 @@ +name: nmdc_submission_schema_test +description: nmdc_submission_schema_test +id: https://example.com/nmdc_submission_schema_test +version: 0.0.0 +default_prefix: https://example.com/nmdc_submission_schema_test/ +enums: + EnvLocalScaleSoilEnum: + name: EnvLocalScaleSoilEnum + permissible_values: + agricultural soil [ENVO:00000077]: + text: agricultural soil [ENVO:00000077] + dune soil [ENVO:00000170]: + text: dune soil [ENVO:00000170] + forest soil [ENVO:00000111]: + text: forest soil [ENVO:00000111] + EnvMediumScaleSoilEnum: + name: EnvMediumScaleSoilEnum + permissible_values: + alluvial paddy field soil [ENVO:00005759]: + text: alluvial paddy field soil [ENVO:00005759] + fertilized soil [ENVO:00005754]: + text: fertilized soil [ENVO:00005754] + gypsisol [ENVO:00002245]: + text: gypsisol [ENVO:00002245] + EnvBroadScaleSoilEnum: + name: EnvBroadScaleSoilEnum + permissible_values: + savanna biome [ENVO:01000178]: + text: savanna biome [ENVO:01000178] + subtropical coniferous forest biome [ENVO:01000209]: + text: subtropical coniferous forest biome [ENVO:01000209] + tidal mangrove shrubland [ENVO:01001369]: + text: tidal mangrove shrubland [ENVO:01001369] +source_file: /Users/SMoxon/Documents/src/submission-schema/tests/inputs/base_schema.yaml diff --git a/tests/inputs/soil_env_broad_test.tsv b/tests/inputs/soil_env_broad_test.tsv new file mode 100644 index 00000000..25e3c9cb --- /dev/null +++ b/tests/inputs/soil_env_broad_test.tsv @@ -0,0 +1,4 @@ +id label +ENVO:01000209 subtropical coniferous forest biome +ENVO:01000178 savanna biome +ENVO:01001369 tidal mangrove shrubland \ No newline at end of file diff --git a/tests/inputs/env_local_input_example.tsv b/tests/inputs/soil_env_local_test.tsv similarity index 82% rename from tests/inputs/env_local_input_example.tsv rename to tests/inputs/soil_env_local_test.tsv index 1c36a292..fc3682e5 100644 --- a/tests/inputs/env_local_input_example.tsv +++ b/tests/inputs/soil_env_local_test.tsv @@ -1,4 +1,4 @@ -term_id term_name +id label ENVO:00000077 agricultural soil ENVO:00000170 dune soil ENVO:00000111 forest soil diff --git a/tests/inputs/soil_env_medium_test.tsv b/tests/inputs/soil_env_medium_test.tsv new file mode 100644 index 00000000..db429513 --- /dev/null +++ b/tests/inputs/soil_env_medium_test.tsv @@ -0,0 +1,4 @@ +id label +ENVO:00005759 alluvial paddy field soil +ENVO:00005754 fertilized soil +ENVO:00002245 gypsisol \ No newline at end of file diff --git a/tests/test_env_triad.py b/tests/test_env_triad.py index 4e1fa7d3..23beee40 100644 --- a/tests/test_env_triad.py +++ b/tests/test_env_triad.py @@ -1,37 +1,79 @@ +from pprint import pprint + import pytest from pathlib import Path -from click.testing import CliRunner -from src.nmdc_submission_schema.scripts.generate_env_triad_enums import main -from linkml_runtime.loaders import yaml_loader +from linkml_runtime import SchemaView +from linkml_runtime.linkml_model import PermissibleValue +from src.nmdc_submission_schema.scripts.generate_env_triad_enums import parse_tsv_to_dict, inject_terms_into_schema, main # Replace 'your_module' with your script filename + + +repo_root = Path(__file__).resolve().parent.parent + +# Define the paths to the test input files +SOIL_ENV_LOCAL_PATH = repo_root / "tests/inputs/soil_env_local_test.tsv" +SOIL_ENV_MEDIUM_PATH = repo_root / "tests/inputs/soil_env_medium_test.tsv" +SOIL_ENV_BROAD_PATH = repo_root / "tests/inputs/soil_env_broad_test.tsv" +BASE_SCHEMA_PATH = repo_root / "tests/inputs/base_schema.yaml" +OUTPUT_SCHEMA_PATH = repo_root / "tests/inputs/output_schema.yaml" # Location for output schema + + +@pytest.fixture +def sample_schema_view(): + # Create a SchemaView instance from the base schema file + return SchemaView(str(BASE_SCHEMA_PATH)) + + +def test_parse_tsv_to_dict(): + # Test parsing of a sample TSV file + parsed_data = parse_tsv_to_dict(SOIL_ENV_LOCAL_PATH) + expected_data = [ + {"term_id": "ENVO:00000077", "term_name": "agricultural soil"}, + {"term_id": "ENVO:00000170", "term_name": "dune soil"}, + {"term_id": "ENVO:00000111", "term_name": "forest soil"} + # Add more expected terms if they are present in the actual file + ] + assert parsed_data == expected_data, "Parsed data does not match expected data" + + +def test_inject_terms_into_schema(sample_schema_view): + # Inject terms into the schema with a specific enum name + enum_name = "TestEnum" + updated_schema = inject_terms_into_schema(SOIL_ENV_LOCAL_PATH, enum_name, sample_schema_view) + + # Check if the enumeration was added + assert enum_name in updated_schema.enums, f"Enum '{enum_name}' not found in schema" -SCHEMA_YAML_PATH = Path(__file__).parent / "../src/nmdc_submission_schema/schema/nmdc_submission_schema_base.yaml" + # Verify the permissible values + enum_def = updated_schema.enums[enum_name] + expected_pvs = ["agricultural soil [ENVO:00000077]", "dune soil [ENVO:00000170]", "forest soil [ENVO:00000111]"] + for pv in expected_pvs: + assert pv in enum_def.permissible_values.keys() -def test_inject_env_local_scale_terms_cli(): - runner = CliRunner() - # Run the CLI command with the --env-local-file, --schema-input-file, and --schema-output-file options - result = runner.invoke( - main, - [ - "--env-local-file", str("/Users/SMoxon/Documents/src/submission-schema/tests/input/env_local_input_examlpe.tsv"), - "--schema-input-file", str("/Users/SMoxon/Documents/src/submission-schema/src/nmdc_submission_schema/schema/nmdc_submission_schema_base.yaml"), - "--schema-output-file", str("/Users/SMoxon/Documents/src/submission-schema/src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml") - ] - ) +def test_main(tmp_path): + # Define paths to the TSV files and expected enums - output_file = tmp_path / "output_schema.yaml" + file_enum_mappings = [ + (SOIL_ENV_LOCAL_PATH, "EnvLocalScaleSoilEnum"), + (SOIL_ENV_MEDIUM_PATH, "EnvMediumScaleSoilEnum"), + (SOIL_ENV_BROAD_PATH, "EnvBroadScaleSoilEnum") + ] - # Check that the command completed successfully - assert result.exit_code == 0, f"CLI command failed with error: {result.output}" + # Run `main` with real file paths + for tsv_path, enum_name in file_enum_mappings: + main(enum_name, tsv_path, BASE_SCHEMA_PATH, BASE_SCHEMA_PATH) - output_schema = yaml_loader.load(output_file, SchemaDefinition) + # Verify that the output schema file contains the injected enums with the correct permissible values + output_schema_view = SchemaView(str(BASE_SCHEMA_PATH)) - # Verify the enum was added to the schema - assert 'EnvironmentalTriadLocalEnum' in output_schema.enums - enum_def = output_schema.enums['EnvironmentalTriadLocalEnum'] + # Check that each enum exists with expected permissible values + for tsv_path, enum_name in file_enum_mappings: + assert enum_name in output_schema_view.schema.enums, f"Enum '{enum_name}' not found in output schema" - # Check permissible values - expected_terms = ["TERM1", "TERM2", "TERM3"] - actual_terms = [pv.text for pv in enum_def.permissible_values] + # Load and check permissible values + expected_data = parse_tsv_to_dict(tsv_path) + sorted_data = sorted(expected_data, key=lambda x: x["term_name"]) + expected_pvs = [PermissibleValue(text=f"{term['term_name']} [{term['term_id']}]") for term in sorted_data] - assert set(expected_terms) == set(actual_terms), "Permissible values do not match expected terms" + enum_def = output_schema_view.schema.enums[enum_name] + assert list(enum_def.permissible_values.values()) == expected_pvs, f"Permissible values for '{enum_name}' do not match expected data" From 39927421a26d816becfce24826cf3b8555f8e84f Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Wed, 6 Nov 2024 15:24:07 -0800 Subject: [PATCH 4/9] add tests and test files --- .../scripts/generate_env_triad_enums.py | 17 +++++++---------- tests/test_env_triad.py | 9 ++++++--- 2 files changed, 13 insertions(+), 13 deletions(-) diff --git a/src/nmdc_submission_schema/scripts/generate_env_triad_enums.py b/src/nmdc_submission_schema/scripts/generate_env_triad_enums.py index 2d789b27..45eb07d9 100644 --- a/src/nmdc_submission_schema/scripts/generate_env_triad_enums.py +++ b/src/nmdc_submission_schema/scripts/generate_env_triad_enums.py @@ -58,10 +58,10 @@ def inject_terms_into_schema(values_file_path: Path, return sv.schema -def main(enum_name: str, - values_file_path: Path, - source_schema_yaml_path: Path = SOURCE_SCHEMA_YAML_PATH, - target_schema_yaml_path: Path = TARGET_SCHEMA_YAML_PATH) -> None: +def ingest(enum_name: str, + values_file_path: Path, + source_schema_yaml_path: Path = SOURCE_SCHEMA_YAML_PATH, + target_schema_yaml_path: Path = TARGET_SCHEMA_YAML_PATH) -> None: """ Inject terms from multiple TSV files into the schema, each under a specified enumeration name. @@ -71,17 +71,14 @@ def main(enum_name: str, :param target_schema_yaml_path: Path to the target schema YAML file. """ # Define files and corresponding enumeration names - schemaview = SchemaView(source_schema_yaml_path) + + sv = SchemaView(source_schema_yaml_path) # Load, inject terms, and save the updated schema for each file schema = inject_terms_into_schema(values_file_path, enum_name, - schemaview) + sv) # Dump the updated schema to the specified output file with target_schema_yaml_path.open("w", encoding="utf-8") as file: file.write(yaml_dumper.dumps(schema)) - -if __name__ == "__main__": - main() - diff --git a/tests/test_env_triad.py b/tests/test_env_triad.py index 23beee40..d77a7bcf 100644 --- a/tests/test_env_triad.py +++ b/tests/test_env_triad.py @@ -4,7 +4,7 @@ from pathlib import Path from linkml_runtime import SchemaView from linkml_runtime.linkml_model import PermissibleValue -from src.nmdc_submission_schema.scripts.generate_env_triad_enums import parse_tsv_to_dict, inject_terms_into_schema, main # Replace 'your_module' with your script filename +from src.nmdc_submission_schema.scripts.generate_env_triad_enums import parse_tsv_to_dict, inject_terms_into_schema, ingest # Replace 'your_module' with your script filename repo_root = Path(__file__).resolve().parent.parent @@ -50,7 +50,7 @@ def test_inject_terms_into_schema(sample_schema_view): assert pv in enum_def.permissible_values.keys() -def test_main(tmp_path): +def test_ingest(tmp_path): # Define paths to the TSV files and expected enums file_enum_mappings = [ @@ -61,7 +61,10 @@ def test_main(tmp_path): # Run `main` with real file paths for tsv_path, enum_name in file_enum_mappings: - main(enum_name, tsv_path, BASE_SCHEMA_PATH, BASE_SCHEMA_PATH) + ingest(enum_name=enum_name, + values_file_path=tsv_path, + source_schema_yaml_path=BASE_SCHEMA_PATH, + target_schema_yaml_path=BASE_SCHEMA_PATH) # Verify that the output schema file contains the injected enums with the correct permissible values output_schema_view = SchemaView(str(BASE_SCHEMA_PATH)) From fd5b6b21efa03bb15dafe44a61878f56202ff844 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Wed, 6 Nov 2024 16:36:05 -0800 Subject: [PATCH 5/9] add functioning make targets --- ...ost_google_sheets_soil_env_broad_scale.tsv | 2 +- project.Makefile | 5 +++ pyproject.toml | 2 + .../schema/nmdc_submission_schema.yaml | 6 +-- .../scripts/generate_env_triad_enums.py | 39 +++++++++++++++++-- 5 files changed, 47 insertions(+), 7 deletions(-) diff --git a/notebooks/post_google_sheets_soil_env_broad_scale.tsv b/notebooks/post_google_sheets_soil_env_broad_scale.tsv index 146d35e6..8ca2f2fd 100644 --- a/notebooks/post_google_sheets_soil_env_broad_scale.tsv +++ b/notebooks/post_google_sheets_soil_env_broad_scale.tsv @@ -1,5 +1,5 @@ id label -ENVO:01000209 subtropical coniferous forest biome +ENVO:s01000209 subtropical coniferous forest biome ENVO:01000178 savanna biome ENVO:01001369 tidal mangrove shrubland ENVO:01000177 grassland biome diff --git a/project.Makefile b/project.Makefile index f4dc8981..1df1bdcc 100644 --- a/project.Makefile +++ b/project.Makefile @@ -181,6 +181,11 @@ local/nmdc.yaml --format yaml $@.raw > $@ - $(RUN) linkml-lint $@ > local/with_modifications.lint_report.txt +ingest_triad: notebooks/*.tsv + $(RUN) inject-env-triad-terms -f notebooks/post_google_sheets_soil_env_local_scale.tsv -i src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml -o src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml + $(RUN) inject-env-triad-terms -f notebooks/post_google_sheets_soil_env_medium_scale.tsv -i src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml -o src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml + $(RUN) inject-env-triad-terms -f notebooks/post_google_sheets_soil_env_broad_scale.tsv -i src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml -o src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml + src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml: local/with_modifications.yaml project/thirdparty/GoldEcosystemTree.json $(RUN) inject-gold-pathway-terms -g $(word 2,$^) -i $< -o $@ #cp $< $@ diff --git a/pyproject.toml b/pyproject.toml index 535cb997..7eaf86ec 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -76,3 +76,5 @@ oak-tree-to-pv-list = "nmdc_submission_schema.scripts.oak_tree_to_pv_list:main" dh-json2linkml = 'nmdc_submission_schema.scripts.dh_json2linkml:update_json' linkml-json2dh = 'nmdc_submission_schema.scripts.linkml_json2dh:extract_lists' inject-gold-pathway-terms = 'nmdc_submission_schema.scripts.gold:main' +inject-env-triad-terms = 'nmdc_submission_schema.scripts.generate_env_triad_enums:main' + diff --git a/src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml b/src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml index e9b6ba71..6b390c4a 100644 --- a/src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml +++ b/src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml @@ -7297,8 +7297,8 @@ enums: text: subpolar coniferous forest biome [ENVO:01000250] subtropical broadleaf forest biome [ENVO:01000201]: text: subtropical broadleaf forest biome [ENVO:01000201] - subtropical coniferous forest biome [ENVO:01000209]: - text: subtropical coniferous forest biome [ENVO:01000209] + subtropical coniferous forest biome [ENVO:s01000209]: + text: subtropical coniferous forest biome [ENVO:s01000209] subtropical dry broadleaf forest biome [ENVO:01000225]: text: subtropical dry broadleaf forest biome [ENVO:01000225] subtropical grassland biome [ENVO:01000191]: @@ -57047,4 +57047,4 @@ classes: - alternative_identifiers - type class_uri: nmdc:NamedThing -source_file: /Users/SMoxon/Documents/src/submission-schema/src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml +source_file: src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml diff --git a/src/nmdc_submission_schema/scripts/generate_env_triad_enums.py b/src/nmdc_submission_schema/scripts/generate_env_triad_enums.py index 45eb07d9..b262ccd1 100644 --- a/src/nmdc_submission_schema/scripts/generate_env_triad_enums.py +++ b/src/nmdc_submission_schema/scripts/generate_env_triad_enums.py @@ -3,12 +3,23 @@ from linkml_runtime.dumpers import yaml_dumper from linkml_runtime.linkml_model import EnumDefinition, EnumDefinitionName, PermissibleValue, SchemaDefinition import csv +import click repo_root = Path(__file__).resolve().parent.parent.parent.parent # Paths to the source and target schema files SOURCE_SCHEMA_YAML_PATH = repo_root / "src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml" TARGET_SCHEMA_YAML_PATH = repo_root / "src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml" +SOIL_ENV_LOCAL_PATH = "post_google_sheets_soil_env_local_scale.tsv" +SOIL_ENV_MEDIUM_PATH = "post_google_sheets_soil_env_medium_scale.tsv" +SOIL_ENV_BROAD_PATH = "post_google_sheets_soil_env_broad_scale.tsv" + + +enum_file_mappings = { + SOIL_ENV_LOCAL_PATH: "EnvLocalScaleSoilEnum", + SOIL_ENV_MEDIUM_PATH: "EnvMediumScaleSoilEnum", + SOIL_ENV_BROAD_PATH: "EnvBroadScaleSoilEnum" +} def parse_tsv_to_dict(file_path): @@ -57,9 +68,7 @@ def inject_terms_into_schema(values_file_path: Path, sv.add_enum(enum_def) return sv.schema - -def ingest(enum_name: str, - values_file_path: Path, +def ingest(values_file_path: Path, source_schema_yaml_path: Path = SOURCE_SCHEMA_YAML_PATH, target_schema_yaml_path: Path = TARGET_SCHEMA_YAML_PATH) -> None: """ @@ -72,6 +81,10 @@ def ingest(enum_name: str, """ # Define files and corresponding enumeration names + enum_name = enum_file_mappings.get(values_file_path.name) + if enum_name is None: + raise ValueError(f"Enumeration name not found for file: {values_file_path}") + sv = SchemaView(source_schema_yaml_path) # Load, inject terms, and save the updated schema for each file schema = inject_terms_into_schema(values_file_path, @@ -82,3 +95,23 @@ def ingest(enum_name: str, with target_schema_yaml_path.open("w", encoding="utf-8") as file: file.write(yaml_dumper.dumps(schema)) + +@click.command() +@click.option("-f", "--values-file-path", + type=click.Path(exists=True, path_type=Path), required=True, + help="Path to the TSV file containing the terms to replace the Enum PVs with.") +@click.option("-i", "--source-schema-yaml-path", + type=click.Path(exists=True, path_type=Path), + default=SOURCE_SCHEMA_YAML_PATH, + help="Path to the source schema YAML file.") +@click.option("-o", "--target-schema-yaml-path", + type=click.Path(path_type=Path), + default=TARGET_SCHEMA_YAML_PATH, + help="Path to the target schema YAML file.") +def main(values_file_path, source_schema_yaml_path, target_schema_yaml_path): + """CLI to inject terms from a TSV file into the schema.""" + + ingest(values_file_path, source_schema_yaml_path, target_schema_yaml_path) + +if __name__ == "__main__": + main() From 16d8797354ea1d02f6db9e359d8c277a5001938e Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Wed, 6 Nov 2024 16:50:04 -0800 Subject: [PATCH 6/9] update makefile to prevent self-reruns --- Makefile | 2 +- project.Makefile | 17 +- project/json/nmdc_submission_schema.json | 2066 +++++++++-------- .../nmdc_submission_schema.schema.json | 47 +- project/thirdparty/GoldEcosystemTree.json | 240 +- .../datamodel/nmdc_submission_schema.py | 1398 ++++------- .../schema/nmdc_submission_schema.yaml | 93 +- 7 files changed, 1694 insertions(+), 2169 deletions(-) diff --git a/Makefile b/Makefile index d5773a49..c9d30725 100644 --- a/Makefile +++ b/Makefile @@ -91,7 +91,7 @@ update-linkml: poetry add -D linkml@latest all: site -site: clean schema-clean src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml \ +site: clean schema-clean src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml ingest-triad \ gen-project gendoc project/json/nmdc_submission_schema.json %.yaml: gen-project diff --git a/project.Makefile b/project.Makefile index 1df1bdcc..d08266a7 100644 --- a/project.Makefile +++ b/project.Makefile @@ -181,10 +181,25 @@ local/nmdc.yaml --format yaml $@.raw > $@ - $(RUN) linkml-lint $@ > local/with_modifications.lint_report.txt -ingest_triad: notebooks/*.tsv + +########### ENV Triad PV generation ########## +# Specify that 'ingest-triad' is a phony target, meaning it doesn't correspond to an actual file +.PHONY: ingest-triad + +# Define an intermediate target to prevent re-triggering +.INTERMEDIATE: temp_target + +# Main target to run ingestion commands, depending on the intermediate target +ingest-triad: temp_target + +# Intermediate target that has all dependencies +temp_target: notebooks/*.tsv src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml $(RUN) inject-env-triad-terms -f notebooks/post_google_sheets_soil_env_local_scale.tsv -i src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml -o src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml $(RUN) inject-env-triad-terms -f notebooks/post_google_sheets_soil_env_medium_scale.tsv -i src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml -o src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml $(RUN) inject-env-triad-terms -f notebooks/post_google_sheets_soil_env_broad_scale.tsv -i src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml -o src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml + touch temp_target + +################################################ src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml: local/with_modifications.yaml project/thirdparty/GoldEcosystemTree.json $(RUN) inject-gold-pathway-terms -g $(word 2,$^) -i $< -o $@ diff --git a/project/json/nmdc_submission_schema.json b/project/json/nmdc_submission_schema.json index 1dbefdce..bb9c935d 100644 --- a/project/json/nmdc_submission_schema.json +++ b/project/json/nmdc_submission_schema.json @@ -458,19 +458,6 @@ "base": "str", "uri": "xsd:language" }, - "string": { - "name": "string", - "description": "A character string", - "notes": [ - "In RDF serializations, a slot with range of string is treated as a literal or type xsd:string. If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"string\"." - ], - "from_schema": "https://example.com/nmdc_submission_schema", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "xsd:string" - }, "integer": { "name": "integer", "description": "An integer", @@ -484,19 +471,18 @@ "base": "int", "uri": "xsd:integer" }, - "boolean": { - "name": "boolean", - "description": "A binary (true or false) value", + "double": { + "name": "double", + "description": "A real number that conforms to the xsd:double specification", "notes": [ - "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"boolean\"." + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"double\"." ], "from_schema": "https://example.com/nmdc_submission_schema", - "exact_mappings": [ - "schema:Boolean" + "close_mappings": [ + "schema:Float" ], - "base": "Bool", - "uri": "xsd:boolean", - "repr": "bool" + "base": "float", + "uri": "xsd:double" }, "float": { "name": "float", @@ -511,19 +497,6 @@ "base": "float", "uri": "xsd:float" }, - "double": { - "name": "double", - "description": "A real number that conforms to the xsd:double specification", - "notes": [ - "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"double\"." - ], - "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", @@ -537,6 +510,44 @@ "base": "Decimal", "uri": "xsd:decimal" }, + "uriorcurie": { + "name": "uriorcurie", + "description": "a URI or a CURIE", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"uriorcurie\"." + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "base": "URIorCURIE", + "uri": "xsd:anyURI", + "repr": "str" + }, + "string": { + "name": "string", + "description": "A character string", + "notes": [ + "In RDF serializations, a slot with range of string is treated as a literal or type xsd:string. If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"string\"." + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "exact_mappings": [ + "schema:Text" + ], + "base": "str", + "uri": "xsd:string" + }, + "boolean": { + "name": "boolean", + "description": "A binary (true or false) value", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"boolean\"." + ], + "from_schema": "https://example.com/nmdc_submission_schema", + "exact_mappings": [ + "schema:Boolean" + ], + "base": "Bool", + "uri": "xsd:boolean", + "repr": "bool" + }, "time": { "name": "time", "description": "A time object represents a (local) time of day, independent of any particular day", @@ -592,17 +603,6 @@ "uri": "linkml:DateOrDatetime", "repr": "str" }, - "uriorcurie": { - "name": "uriorcurie", - "description": "a URI or a CURIE", - "notes": [ - "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"uriorcurie\"." - ], - "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/", @@ -713,12 +713,10 @@ "enums": { "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", @@ -737,20 +735,16 @@ ] }, "free living": { - "text": "free living", - "description": "placeholder PV descr" + "text": "free living" }, "mutualism": { - "text": "mutualism", - "description": "placeholder PV descr" + "text": "mutualism" }, "parasitism": { - "text": "parasitism", - "description": "placeholder PV descr" + "text": "parasitism" }, "symbiotic": { - "text": "symbiotic", - "description": "placeholder enum descr" + "text": "symbiotic" } } }, @@ -768,59 +762,46 @@ }, "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" + "text": "10 mM Tris-HCl" }, "DNAStable": { - "text": "DNAStable", - "description": "placeholder PV descr" + "text": "DNAStable" }, "Ethanol": { - "text": "Ethanol", - "description": "placeholder PV descr" + "text": "Ethanol" }, "Low EDTA TE": { - "text": "Low EDTA TE", - "description": "placeholder PV descr" + "text": "Low EDTA TE" }, "MDA reaction buffer": { - "text": "MDA reaction buffer", - "description": "placeholder PV descr" + "text": "MDA reaction buffer" }, "PBS": { - "text": "PBS", - "description": "placeholder PV descr" + "text": "PBS" }, "Pellet": { - "text": "Pellet", - "description": "placeholder PV descr" + "text": "Pellet" }, "RNAStable": { - "text": "RNAStable", - "description": "placeholder PV descr" + "text": "RNAStable" }, "TE": { - "text": "TE", - "description": "placeholder PV descr" + "text": "TE" }, "Water": { - "text": "Water", - "description": "placeholder PV descr" + "text": "Water" } } }, "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" ] @@ -829,12 +810,10 @@ }, "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", @@ -849,47 +828,37 @@ ] }, "field": { - "text": "field", - "description": "placeholder PV descr" + "text": "field" }, "field_incubation": { - "text": "field_incubation", - "description": "placeholder PV descr" + "text": "field_incubation" }, "glasshouse": { - "text": "glasshouse", - "description": "placeholder PV descr" + "text": "glasshouse" }, "greenhouse": { - "text": "greenhouse", - "description": "placeholder PV descr" + "text": "greenhouse" }, "growth_chamber": { - "text": "growth_chamber", - "description": "placeholder PV descr" + "text": "growth_chamber" }, "lab_incubation": { - "text": "lab_incubation", - "description": "placeholder PV descr" + "text": "lab_incubation" }, "open_top_chamber": { - "text": "open_top_chamber", - "description": "placeholder PV descr" + "text": "open_top_chamber" }, "other": { - "text": "other", - "description": "placeholder PV descr" + "text": "other" } } }, "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", @@ -901,75 +870,58 @@ ] }, "anaerobe": { - "text": "anaerobe", - "description": "placeholder PV descr" + "text": "anaerobe" }, "facultative": { - "text": "facultative", - "description": "placeholder PV descr" + "text": "facultative" }, "microaerophilic": { - "text": "microaerophilic", - "description": "placeholder PV descr" + "text": "microaerophilic" }, "microanaerobe": { - "text": "microanaerobe", - "description": "placeholder PV descr" + "text": "microanaerobe" }, "obligate aerobe": { - "text": "obligate aerobe", - "description": "placeholder PV descr" + "text": "obligate aerobe" }, "obligate anaerobe": { - "text": "obligate anaerobe", - "description": "placeholder PV descr" + "text": "obligate anaerobe" } } }, "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" + "text": "10 mM Tris-HCl" }, "DNAStable": { - "text": "DNAStable", - "description": "placeholder PV descr" + "text": "DNAStable" }, "Ethanol": { - "text": "Ethanol", - "description": "placeholder PV descr" + "text": "Ethanol" }, "Low EDTA TE": { - "text": "Low EDTA TE", - "description": "placeholder PV descr" + "text": "Low EDTA TE" }, "MDA reaction buffer": { - "text": "MDA reaction buffer", - "description": "placeholder PV descr" + "text": "MDA reaction buffer" }, "PBS": { - "text": "PBS", - "description": "placeholder PV descr" + "text": "PBS" }, "Pellet": { - "text": "Pellet", - "description": "placeholder PV descr" + "text": "Pellet" }, "RNAStable": { - "text": "RNAStable", - "description": "placeholder PV descr" + "text": "RNAStable" }, "TE": { - "text": "TE", - "description": "placeholder PV descr" + "text": "TE" }, "Water": { - "text": "Water", - "description": "placeholder PV descr" + "text": "Water" } } }, @@ -996,12 +948,10 @@ }, "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", @@ -1013,16 +963,13 @@ ] }, "frozen": { - "text": "frozen", - "description": "placeholder PV descr" + "text": "frozen" }, "lyophilized": { - "text": "lyophilized", - "description": "placeholder PV descr" + "text": "lyophilized" }, "other": { - "text": "other", - "description": "placeholder PV descr" + "text": "other" } } }, @@ -1039,1035 +986,330 @@ } } }, - "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" + "text": "pathogen-suppressive soil [ENVO:03600036]" }, "mangrove biome soil [ENVO:02000138]": { - "text": "mangrove biome soil [ENVO:02000138]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "mangrove biome soil [ENVO:02000138]" }, "surface soil [ENVO:02000059]": { - "text": "surface soil [ENVO:02000059]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "surface soil [ENVO:02000059]" }, "frost-susceptible soil [ENVO:01001638]": { - "text": "frost-susceptible soil [ENVO:01001638]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "frost-susceptible soil [ENVO:01001638]" }, "bare soil [ENVO:01001616]": { - "text": "bare soil [ENVO:01001616]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "bare soil [ENVO:01001616]" }, "frozen soil [ENVO:01001526]": { - "text": "frozen soil [ENVO:01001526]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "frozen soil [ENVO:01001526]" }, "__friable-frozen soil [ENVO:01001528]": { - "text": "__friable-frozen soil [ENVO:01001528]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "__friable-frozen soil [ENVO:01001528]" }, "__plastic-frozen soil [ENVO:01001527]": { - "text": "__plastic-frozen soil [ENVO:01001527]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "__plastic-frozen soil [ENVO:01001527]" }, "__hard-frozen soil [ENVO:01001525]": { - "text": "__hard-frozen soil [ENVO:01001525]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "__hard-frozen soil [ENVO:01001525]" }, "__frozen compost soil [ENVO:00005765]": { - "text": "__frozen compost soil [ENVO:00005765]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "__frozen compost soil [ENVO:00005765]" }, "__cryosol [ENVO:00002236]": { - "text": "__cryosol [ENVO:00002236]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "__cryosol [ENVO:00002236]" }, "ultisol [ENVO:01001397]": { - "text": "ultisol [ENVO:01001397]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "ultisol [ENVO:01001397]" }, "__acrisol [ENVO:00002234]": { - "text": "__acrisol [ENVO:00002234]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "__acrisol [ENVO:00002234]" }, "acidic soil [ENVO:01001185]": { - "text": "acidic soil [ENVO:01001185]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "acidic soil [ENVO:01001185]" }, "bulk soil [ENVO:00005802]": { - "text": "bulk soil [ENVO:00005802]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "bulk soil [ENVO:00005802]" }, "red soil [ENVO:00005790]": { - "text": "red soil [ENVO:00005790]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "red soil [ENVO:00005790]" }, "upland soil [ENVO:00005786]": { - "text": "upland soil [ENVO:00005786]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "upland soil [ENVO:00005786]" }, "__mountain forest soil [ENVO:00005769]": { - "text": "__mountain forest soil [ENVO:00005769]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "__mountain forest soil [ENVO:00005769]" }, "__dune soil [ENVO:00002260]": { - "text": "__dune soil [ENVO:00002260]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "__dune soil [ENVO:00002260]" }, "ornithogenic soil [ENVO:00005782]": { - "text": "ornithogenic soil [ENVO:00005782]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "ornithogenic soil [ENVO:00005782]" }, "heat stressed soil [ENVO:00005781]": { - "text": "heat stressed soil [ENVO:00005781]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "heat stressed soil [ENVO:00005781]" }, "greenhouse soil [ENVO:00005780]": { - "text": "greenhouse soil [ENVO:00005780]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "greenhouse soil [ENVO:00005780]" }, "tropical soil [ENVO:00005778]": { - "text": "tropical soil [ENVO:00005778]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "tropical soil [ENVO:00005778]" }, "pasture soil [ENVO:00005773]": { - "text": "pasture soil [ENVO:00005773]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "pasture soil [ENVO:00005773]" }, "muddy soil [ENVO:00005771]": { - "text": "muddy soil [ENVO:00005771]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "muddy soil [ENVO:00005771]" }, "orchid soil [ENVO:00005768]": { - "text": "orchid soil [ENVO:00005768]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "orchid soil [ENVO:00005768]" }, "manured soil [ENVO:00005767]": { - "text": "manured soil [ENVO:00005767]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "manured soil [ENVO:00005767]" }, "limed soil [ENVO:00005766]": { - "text": "limed soil [ENVO:00005766]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "limed soil [ENVO:00005766]" }, "pond soil [ENVO:00005764]": { - "text": "pond soil [ENVO:00005764]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "pond soil [ENVO:00005764]" }, "meadow soil [ENVO:00005761]": { - "text": "meadow soil [ENVO:00005761]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "meadow soil [ENVO:00005761]" }, "burned soil [ENVO:00005760]": { - "text": "burned soil [ENVO:00005760]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "burned soil [ENVO:00005760]" }, "lawn soil [ENVO:00005756]": { - "text": "lawn soil [ENVO:00005756]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "lawn soil [ENVO:00005756]" }, "field soil [ENVO:00005755]": { - "text": "field soil [ENVO:00005755]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "field soil [ENVO:00005755]" }, "__paddy field soil [ENVO:00005740]": { - "text": "__paddy field soil [ENVO:00005740]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "__paddy field soil [ENVO:00005740]" }, "____peaty paddy field soil [ENVO:00005776]": { - "text": "____peaty paddy field soil [ENVO:00005776]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "____peaty paddy field soil [ENVO:00005776]" }, "____alluvial paddy field soil [ENVO:00005759]": { - "text": "____alluvial paddy field soil [ENVO:00005759]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "____alluvial paddy field soil [ENVO:00005759]" }, "fertilized soil [ENVO:00005754]": { - "text": "fertilized soil [ENVO:00005754]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "fertilized soil [ENVO:00005754]" }, "sawah soil [ENVO:00005752]": { - "text": "sawah soil [ENVO:00005752]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "sawah soil [ENVO:00005752]" }, "jungle soil [ENVO:00005751]": { - "text": "jungle soil [ENVO:00005751]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "jungle soil [ENVO:00005751]" }, "grassland soil [ENVO:00005750]": { - "text": "grassland soil [ENVO:00005750]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "grassland soil [ENVO:00005750]" }, "__steppe soil [ENVO:00005777]": { - "text": "__steppe soil [ENVO:00005777]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "__steppe soil [ENVO:00005777]" }, "__savanna soil [ENVO:00005746]": { - "text": "__savanna soil [ENVO:00005746]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "__savanna soil [ENVO:00005746]" }, "farm soil [ENVO:00005749]": { - "text": "farm soil [ENVO:00005749]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "farm soil [ENVO:00005749]" }, "__rubber plantation soil [ENVO:00005788]": { - "text": "__rubber plantation soil [ENVO:00005788]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "__rubber plantation soil [ENVO:00005788]" }, "__orchard soil [ENVO:00005772]": { - "text": "__orchard soil [ENVO:00005772]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "__orchard soil [ENVO:00005772]" }, "dry soil [ENVO:00005748]": { - "text": "dry soil [ENVO:00005748]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "dry soil [ENVO:00005748]" }, "compost soil [ENVO:00005747]": { - "text": "compost soil [ENVO:00005747]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "compost soil [ENVO:00005747]" }, "roadside soil [ENVO:00005743]": { - "text": "roadside soil [ENVO:00005743]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "roadside soil [ENVO:00005743]" }, "arable soil [ENVO:00005742]": { - "text": "arable soil [ENVO:00005742]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "arable soil [ENVO:00005742]" }, "alpine soil [ENVO:00005741]": { - "text": "alpine soil [ENVO:00005741]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "alpine soil [ENVO:00005741]" }, "alluvial soil [ENVO:00002871]": { - "text": "alluvial soil [ENVO:00002871]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "alluvial soil [ENVO:00002871]" }, "__alluvial paddy field soil [ENVO:00005759]": { - "text": "__alluvial paddy field soil [ENVO:00005759]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "__alluvial paddy field soil [ENVO:00005759]" }, "__alluvial swamp soil [ENVO:00005758]": { - "text": "__alluvial swamp soil [ENVO:00005758]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "__alluvial swamp soil [ENVO:00005758]" }, "technosol [ENVO:00002275]": { - "text": "technosol [ENVO:00002275]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "technosol [ENVO:00002275]" }, "stagnosol [ENVO:00002274]": { - "text": "stagnosol [ENVO:00002274]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "stagnosol [ENVO:00002274]" }, "fluvisol [ENVO:00002273]": { - "text": "fluvisol [ENVO:00002273]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "fluvisol [ENVO:00002273]" }, "garden soil [ENVO:00002263]": { - "text": "garden soil [ENVO:00002263]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "garden soil [ENVO:00002263]" }, "__vegetable garden soil [ENVO:00005779]": { - "text": "__vegetable garden soil [ENVO:00005779]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "__vegetable garden soil [ENVO:00005779]" }, "__allotment garden soil [ENVO:00005744]": { - "text": "__allotment garden soil [ENVO:00005744]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "__allotment garden soil [ENVO:00005744]" }, "clay soil [ENVO:00002262]": { - "text": "clay soil [ENVO:00002262]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "clay soil [ENVO:00002262]" }, "forest soil [ENVO:00002261]": { - "text": "forest soil [ENVO:00002261]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "forest soil [ENVO:00002261]" }, "__eucalyptus forest soil [ENVO:00005787]": { - "text": "__eucalyptus forest soil [ENVO:00005787]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "__eucalyptus forest soil [ENVO:00005787]" }, "__spruce forest soil [ENVO:00005784]": { - "text": "__spruce forest soil [ENVO:00005784]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "__spruce forest soil [ENVO:00005784]" }, "__leafy wood soil [ENVO:00005783]": { - "text": "__leafy wood soil [ENVO:00005783]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "__leafy wood soil [ENVO:00005783]" }, "__beech forest soil [ENVO:00005770]": { - "text": "__beech forest soil [ENVO:00005770]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "__beech forest soil [ENVO:00005770]" }, "agricultural soil [ENVO:00002259]": { - "text": "agricultural soil [ENVO:00002259]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "agricultural soil [ENVO:00002259]" }, "__bluegrass field soil [ENVO:00005789]": { - "text": "__bluegrass field soil [ENVO:00005789]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "__bluegrass field soil [ENVO:00005789]" }, "loam [ENVO:00002258]": { - "text": "loam [ENVO:00002258]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "loam [ENVO:00002258]" }, "__clay loam [ENVO:06105277]": { - "text": "__clay loam [ENVO:06105277]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "__clay loam [ENVO:06105277]" }, "____silty clay loam [ENVO:06105278]": { - "text": "____silty clay loam [ENVO:06105278]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "____silty clay loam [ENVO:06105278]" }, "____sandy clay loam [ENVO:06105276]": { - "text": "____sandy clay loam [ENVO:06105276]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "____sandy clay loam [ENVO:06105276]" }, "__silty loam [ENVO:06105275]": { - "text": "__silty loam [ENVO:06105275]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "__silty loam [ENVO:06105275]" }, "__sandy loam [ENVO:06105274]": { - "text": "__sandy loam [ENVO:06105274]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "__sandy loam [ENVO:06105274]" }, "podzol [ENVO:00002257]": { - "text": "podzol [ENVO:00002257]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "podzol [ENVO:00002257]" }, "regosol [ENVO:00002256]": { - "text": "regosol [ENVO:00002256]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "regosol [ENVO:00002256]" }, "solonetz [ENVO:00002255]": { - "text": "solonetz [ENVO:00002255]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "solonetz [ENVO:00002255]" }, "vertisol [ENVO:00002254]": { - "text": "vertisol [ENVO:00002254]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "vertisol [ENVO:00002254]" }, "umbrisol [ENVO:00002253]": { - "text": "umbrisol [ENVO:00002253]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "umbrisol [ENVO:00002253]" }, "solonchak [ENVO:00002252]": { - "text": "solonchak [ENVO:00002252]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "solonchak [ENVO:00002252]" }, "planosol [ENVO:00002251]": { - "text": "planosol [ENVO:00002251]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "planosol [ENVO:00002251]" }, "plinthosol [ENVO:00002250]": { - "text": "plinthosol [ENVO:00002250]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "plinthosol [ENVO:00002250]" }, "phaeozem [ENVO:00002249]": { - "text": "phaeozem [ENVO:00002249]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "phaeozem [ENVO:00002249]" }, "luvisol [ENVO:00002248]": { - "text": "luvisol [ENVO:00002248]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "luvisol [ENVO:00002248]" }, "nitisol [ENVO:00002247]": { - "text": "nitisol [ENVO:00002247]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "nitisol [ENVO:00002247]" }, "ferralsol [ENVO:00002246]": { - "text": "ferralsol [ENVO:00002246]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "ferralsol [ENVO:00002246]" }, "gypsisol [ENVO:00002245]": { - "text": "gypsisol [ENVO:00002245]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "gypsisol [ENVO:00002245]" }, "gleysol [ENVO:00002244]": { - "text": "gleysol [ENVO:00002244]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "gleysol [ENVO:00002244]" }, "histosol [ENVO:00002243]": { - "text": "histosol [ENVO:00002243]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "histosol [ENVO:00002243]" }, "__peat soil [ENVO:00005774]": { - "text": "__peat soil [ENVO:00005774]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "__peat soil [ENVO:00005774]" }, "lixisol [ENVO:00002242]": { - "text": "lixisol [ENVO:00002242]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "lixisol [ENVO:00002242]" }, "leptosol [ENVO:00002241]": { - "text": "leptosol [ENVO:00002241]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "leptosol [ENVO:00002241]" }, "kastanozem [ENVO:00002240]": { - "text": "kastanozem [ENVO:00002240]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "kastanozem [ENVO:00002240]" }, "calcisol [ENVO:00002239]": { - "text": "calcisol [ENVO:00002239]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "calcisol [ENVO:00002239]" }, "durisol [ENVO:00002238]": { - "text": "durisol [ENVO:00002238]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "durisol [ENVO:00002238]" }, "chernozem [ENVO:00002237]": { - "text": "chernozem [ENVO:00002237]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "chernozem [ENVO:00002237]" }, "cambisol [ENVO:00002235]": { - "text": "cambisol [ENVO:00002235]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "cambisol [ENVO:00002235]" }, "albeluvisol [ENVO:00002233]": { - "text": "albeluvisol [ENVO:00002233]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "albeluvisol [ENVO:00002233]" }, "andosol [ENVO:00002232]": { - "text": "andosol [ENVO:00002232]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "andosol [ENVO:00002232]" }, "__volcanic soil [ENVO:01001841]": { - "text": "__volcanic soil [ENVO:01001841]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "__volcanic soil [ENVO:01001841]" }, "alisol [ENVO:00002231]": { - "text": "alisol [ENVO:00002231]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "alisol [ENVO:00002231]" }, "anthrosol [ENVO:00002230]": { - "text": "anthrosol [ENVO:00002230]", - "description": "placeholder PV descr, DO NOT SORT" + "text": "anthrosol [ENVO:00002230]" }, "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" + "text": "arenosol [ENVO:00002229]" } } }, "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" + "text": "aerobic" }, "anaerobic": { - "text": "anaerobic", - "description": "placeholder PV descr, DO NOT SORT" + "text": "anaerobic" }, "other": { - "text": "other", - "description": "placeholder PV descr, DO NOT SORT" + "text": "other" } } }, @@ -6729,9 +5971,6 @@ "Digestive tube": { "text": "Digestive tube" }, - "Dinoflagellates": { - "text": "Dinoflagellates" - }, "Dissolved organics (aerobic)": { "text": "Dissolved organics (aerobic)" }, @@ -6912,6 +6151,9 @@ "Frozen seafood": { "text": "Frozen seafood" }, + "Fruit processing": { + "text": "Fruit processing" + }, "Fumaroles": { "text": "Fumaroles" }, @@ -7890,6 +7132,9 @@ "Smooth muscles": { "text": "Smooth muscles" }, + "Snow": { + "text": "Snow" + }, "Soda lake": { "text": "Soda lake" }, @@ -10095,6 +9340,9 @@ "Squamous cell carcinoma": { "text": "Squamous cell carcinoma" }, + "Stolon": { + "text": "Stolon" + }, "Stomach": { "text": "Stomach" }, @@ -10846,6 +10094,846 @@ "text": "Wetland zone" } } + }, + "EnvLocalScaleSoilEnum": { + "name": "EnvLocalScaleSoilEnum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "abandoned watercourse [ENVO:00000524]": { + "text": "abandoned watercourse [ENVO:00000524]" + }, + "active permafrost layer [ENVO:04000009]": { + "text": "active permafrost layer [ENVO:04000009]" + }, + "agricultural ecosystem [ENVO:00000077]": { + "text": "agricultural ecosystem [ENVO:00000077]" + }, + "agricultural field [ENVO:00000114]": { + "text": "agricultural field [ENVO:00000114]" + }, + "alas [ENVO:00000438]": { + "text": "alas [ENVO:00000438]" + }, + "apron [ENVO:00000530]": { + "text": "apron [ENVO:00000530]" + }, + "arable land [ENVO:01001177]": { + "text": "arable land [ENVO:01001177]" + }, + "arete [ENVO:00000429]": { + "text": "arete [ENVO:00000429]" + }, + "badland [ENVO:00000127]": { + "text": "badland [ENVO:00000127]" + }, + "beach [ENVO:00000091]": { + "text": "beach [ENVO:00000091]" + }, + "beach ridge [ENVO:00000529]": { + "text": "beach ridge [ENVO:00000529]" + }, + "biochar [ENVO:2000007]": { + "text": "biochar [ENVO:2000007]" + }, + "blowout [ENVO:00000313]": { + "text": "blowout [ENVO:00000313]" + }, + "booth [ENVO:03501309]": { + "text": "booth [ENVO:03501309]" + }, + "borehole [ENVO:00002226]": { + "text": "borehole [ENVO:00002226]" + }, + "boundary wall [ENVO:01000466]": { + "text": "boundary wall [ENVO:01000466]" + }, + "bridge [ENVO:00000075]": { + "text": "bridge [ENVO:00000075]" + }, + "burrow [ENVO:01000429]": { + "text": "burrow [ENVO:01000429]" + }, + "butte [ENVO:00000287]": { + "text": "butte [ENVO:00000287]" + }, + "calanque [ENVO:00000567]": { + "text": "calanque [ENVO:00000567]" + }, + "caldera [ENVO:00000096]": { + "text": "caldera [ENVO:00000096]" + }, + "campground [ENVO:01000935]": { + "text": "campground [ENVO:01000935]" + }, + "canyon [ENVO:00000169]": { + "text": "canyon [ENVO:00000169]" + }, + "causeway [ENVO:00000158]": { + "text": "causeway [ENVO:00000158]" + }, + "cave [ENVO:00000067]": { + "text": "cave [ENVO:00000067]" + }, + "channel [ENVO:03000117]": { + "text": "channel [ENVO:03000117]" + }, + "cirque [ENVO:00000155]": { + "text": "cirque [ENVO:00000155]" + }, + "cliff [ENVO:00000087]": { + "text": "cliff [ENVO:00000087]" + }, + "continental divide [ENVO:00000293]": { + "text": "continental divide [ENVO:00000293]" + }, + "crater [ENVO:00000514]": { + "text": "crater [ENVO:00000514]" + }, + "crevasse [ENVO:00000320]": { + "text": "crevasse [ENVO:00000320]" + }, + "crevice [ENVO:01000294]": { + "text": "crevice [ENVO:01000294]" + }, + "cryosphere [ENVO:03000143]": { + "text": "cryosphere [ENVO:03000143]" + }, + "dam [ENVO:00000074]": { + "text": "dam [ENVO:00000074]" + }, + "dell [ENVO:00000439]": { + "text": "dell [ENVO:00000439]" + }, + "desert [ENVO:01001357]": { + "text": "desert [ENVO:01001357]" + }, + "drainage basin [ENVO:00000291]": { + "text": "drainage basin [ENVO:00000291]" + }, + "drawbridge [ENVO:03501245]": { + "text": "drawbridge [ENVO:03501245]" + }, + "driveway [ENVO:01001280]": { + "text": "driveway [ENVO:01001280]" + }, + "drumlin [ENVO:00000276]": { + "text": "drumlin [ENVO:00000276]" + }, + "dry lake [ENVO:00000277]": { + "text": "dry lake [ENVO:00000277]" + }, + "dune [ENVO:00000170]": { + "text": "dune [ENVO:00000170]" + }, + "escarpment [ENVO:00000280]": { + "text": "escarpment [ENVO:00000280]" + }, + "esker [ENVO:00000282]": { + "text": "esker [ENVO:00000282]" + }, + "fairground [ENVO:01000985]": { + "text": "fairground [ENVO:01000985]" + }, + "farm [ENVO:00000078]": { + "text": "farm [ENVO:00000078]" + }, + "fen [ENVO:00000232]": { + "text": "fen [ENVO:00000232]" + }, + "fence [ENVO:01000468]": { + "text": "fence [ENVO:01000468]" + }, + "firebreak [ENVO:03000132]": { + "text": "firebreak [ENVO:03000132]" + }, + "fjord [ENVO:00000039]": { + "text": "fjord [ENVO:00000039]" + }, + "flood plain [ENVO:00000255]": { + "text": "flood plain [ENVO:00000255]" + }, + "floodway [ENVO:00000256]": { + "text": "floodway [ENVO:00000256]" + }, + "fomite [ENVO:00010358]": { + "text": "fomite [ENVO:00010358]" + }, + "ford [ENVO:00000411]": { + "text": "ford [ENVO:00000411]" + }, + "forest ecosystem [ENVO:01001243]": { + "text": "forest ecosystem [ENVO:01001243]" + }, + "forested area [ENVO:00000111]": { + "text": "forested area [ENVO:00000111]" + }, + "frost heave [ENVO:01001568]": { + "text": "frost heave [ENVO:01001568]" + }, + "frost-formed hummock [ENVO:01001538]": { + "text": "frost-formed hummock [ENVO:01001538]" + }, + "frozen land [ENVO:01001524]": { + "text": "frozen land [ENVO:01001524]" + }, + "fumarole [ENVO:00000216]": { + "text": "fumarole [ENVO:00000216]" + }, + "garden [ENVO:00000011]": { + "text": "garden [ENVO:00000011]" + }, + "gas well [ENVO:01001870]": { + "text": "gas well [ENVO:01001870]" + }, + "glacier [ENVO:00000133]": { + "text": "glacier [ENVO:00000133]" + }, + "graben [ENVO:00000290]": { + "text": "graben [ENVO:00000290]" + }, + "grassland area [ENVO:00000106]": { + "text": "grassland area [ENVO:00000106]" + }, + "greenhouse [ENVO:03600087]": { + "text": "greenhouse [ENVO:03600087]" + }, + "harbour [ENVO:00000463]": { + "text": "harbour [ENVO:00000463]" + }, + "hedge [ENVO:00000046]": { + "text": "hedge [ENVO:00000046]" + }, + "hill [ENVO:00000083]": { + "text": "hill [ENVO:00000083]" + }, + "hillock [ENVO:03501238]": { + "text": "hillock [ENVO:03501238]" + }, + "hillside [ENVO:01000333]": { + "text": "hillside [ENVO:01000333]" + }, + "horst [ENVO:00000289]": { + "text": "horst [ENVO:00000289]" + }, + "hummock [ENVO:00000516]": { + "text": "hummock [ENVO:00000516]" + }, + "ice wedge [ENVO:03600068]": { + "text": "ice wedge [ENVO:03600068]" + }, + "isthmus [ENVO:00000174]": { + "text": "isthmus [ENVO:00000174]" + }, + "landfill [ENVO:00000533]": { + "text": "landfill [ENVO:00000533]" + }, + "landslide [ENVO:00000520]": { + "text": "landslide [ENVO:00000520]" + }, + "lock [ENVO:00000357]": { + "text": "lock [ENVO:00000357]" + }, + "marsh [ENVO:00000035]": { + "text": "marsh [ENVO:00000035]" + }, + "massif [ENVO:00000381]": { + "text": "massif [ENVO:00000381]" + }, + "meadow ecosystem [ENVO:00000108]": { + "text": "meadow ecosystem [ENVO:00000108]" + }, + "mesa [ENVO:00000179]": { + "text": "mesa [ENVO:00000179]" + }, + "mine [ENVO:00000076]": { + "text": "mine [ENVO:00000076]" + }, + "mine drainage [ENVO:00001996]": { + "text": "mine drainage [ENVO:00001996]" + }, + "monadnock [ENVO:00000432]": { + "text": "monadnock [ENVO:00000432]" + }, + "moraine [ENVO:00000177]": { + "text": "moraine [ENVO:00000177]" + }, + "mound [ENVO:00000180]": { + "text": "mound [ENVO:00000180]" + }, + "mountain [ENVO:00000081]": { + "text": "mountain [ENVO:00000081]" + }, + "oil spill [ENVO:00002061]": { + "text": "oil spill [ENVO:00002061]" + }, + "orchard [ENVO:00000115]": { + "text": "orchard [ENVO:00000115]" + }, + "outcrop [ENVO:01000302]": { + "text": "outcrop [ENVO:01000302]" + }, + "overpass [ENVO:03501248]": { + "text": "overpass [ENVO:03501248]" + }, + "park [ENVO:00000562]": { + "text": "park [ENVO:00000562]" + }, + "pasture [ENVO:00000266]": { + "text": "pasture [ENVO:00000266]" + }, + "peatland [ENVO:00000044]": { + "text": "peatland [ENVO:00000044]" + }, + "permafrost [ENVO:00000134]": { + "text": "permafrost [ENVO:00000134]" + }, + "pier [ENVO:00000563]": { + "text": "pier [ENVO:00000563]" + }, + "pinnacle [ENVO:00000481]": { + "text": "pinnacle [ENVO:00000481]" + }, + "pit [ENVO:01001871]": { + "text": "pit [ENVO:01001871]" + }, + "plain [ENVO:00000086]": { + "text": "plain [ENVO:00000086]" + }, + "plateau [ENVO:00000182]": { + "text": "plateau [ENVO:00000182]" + }, + "playground [ENVO:03500001]": { + "text": "playground [ENVO:03500001]" + }, + "polje [ENVO:00000325]": { + "text": "polje [ENVO:00000325]" + }, + "pond [ENVO:00000033]": { + "text": "pond [ENVO:00000033]" + }, + "prairie [ENVO:00000260]": { + "text": "prairie [ENVO:00000260]" + }, + "quarry [ENVO:00000284]": { + "text": "quarry [ENVO:00000284]" + }, + "ranch [ENVO:01001207]": { + "text": "ranch [ENVO:01001207]" + }, + "ravine [ENVO:01000446]": { + "text": "ravine [ENVO:01000446]" + }, + "refinery [ENVO:02000141]": { + "text": "refinery [ENVO:02000141]" + }, + "residential backyard [ENVO:03600033]": { + "text": "residential backyard [ENVO:03600033]" + }, + "rhizosphere [ENVO:00005801]": { + "text": "rhizosphere [ENVO:00005801]" + }, + "ridge [ENVO:00000283]": { + "text": "ridge [ENVO:00000283]" + }, + "river [ENVO:00000022]": { + "text": "river [ENVO:00000022]" + }, + "riverfront [ENVO:03501239]": { + "text": "riverfront [ENVO:03501239]" + }, + "road [ENVO:00000064]": { + "text": "road [ENVO:00000064]" + }, + "roadside [ENVO:01000447]": { + "text": "roadside [ENVO:01000447]" + }, + "rockfall [ENVO:00000521]": { + "text": "rockfall [ENVO:00000521]" + }, + "savanna [ENVO:00000261]": { + "text": "savanna [ENVO:00000261]" + }, + "shore [ENVO:00000304]": { + "text": "shore [ENVO:00000304]" + }, + "sidewalk [ENVO:01001279]": { + "text": "sidewalk [ENVO:01001279]" + }, + "sinkhole [ENVO:00000195]": { + "text": "sinkhole [ENVO:00000195]" + }, + "slope [ENVO:00002000]": { + "text": "slope [ENVO:00002000]" + }, + "soil cryoturbate [ENVO:01001665]": { + "text": "soil cryoturbate [ENVO:01001665]" + }, + "spring [ENVO:00000027]": { + "text": "spring [ENVO:00000027]" + }, + "stack [ENVO:00000419]": { + "text": "stack [ENVO:00000419]" + }, + "steppe [ENVO:00000262]": { + "text": "steppe [ENVO:00000262]" + }, + "stream [ENVO:00000023]": { + "text": "stream [ENVO:00000023]" + }, + "swale [ENVO:00000543]": { + "text": "swale [ENVO:00000543]" + }, + "terrace [ENVO:00000508]": { + "text": "terrace [ENVO:00000508]" + }, + "terracette [ENVO:00000441]": { + "text": "terracette [ENVO:00000441]" + }, + "thermokarst [ENVO:03000085]": { + "text": "thermokarst [ENVO:03000085]" + }, + "trench [ENVO:01000649]": { + "text": "trench [ENVO:01000649]" + }, + "tunnel [ENVO:00000068]": { + "text": "tunnel [ENVO:00000068]" + }, + "valley [ENVO:00000100]": { + "text": "valley [ENVO:00000100]" + }, + "vein [ENVO:01000670]": { + "text": "vein [ENVO:01000670]" + }, + "volcano [ENVO:00000247]": { + "text": "volcano [ENVO:00000247]" + }, + "wadi [ENVO:00000031]": { + "text": "wadi [ENVO:00000031]" + }, + "watershed [ENVO:00000292]": { + "text": "watershed [ENVO:00000292]" + }, + "wave-cut platform [ENVO:00000421]": { + "text": "wave-cut platform [ENVO:00000421]" + }, + "weir [ENVO:00000535]": { + "text": "weir [ENVO:00000535]" + }, + "well [ENVO:00000026]": { + "text": "well [ENVO:00000026]" + }, + "wetland ecosystem [ENVO:01001209]": { + "text": "wetland ecosystem [ENVO:01001209]" + }, + "woodland area [ENVO:00000109]": { + "text": "woodland area [ENVO:00000109]" + }, + "woodland clearing [ENVO:00000444]": { + "text": "woodland clearing [ENVO:00000444]" + } + } + }, + "EnvMediumScaleSoilEnum": { + "name": "EnvMediumScaleSoilEnum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "acidic soil [ENVO:01001185]": { + "text": "acidic soil [ENVO:01001185]" + }, + "acrisol [ENVO:00002234]": { + "text": "acrisol [ENVO:00002234]" + }, + "albeluvisol [ENVO:00002233]": { + "text": "albeluvisol [ENVO:00002233]" + }, + "alisol [ENVO:00002231]": { + "text": "alisol [ENVO:00002231]" + }, + "allotment garden soil [ENVO:00005744]": { + "text": "allotment garden soil [ENVO:00005744]" + }, + "alluvial paddy field soil [ENVO:00005759]": { + "text": "alluvial paddy field soil [ENVO:00005759]" + }, + "alluvial soil [ENVO:00002871]": { + "text": "alluvial soil [ENVO:00002871]" + }, + "alluvial swamp soil [ENVO:00005758]": { + "text": "alluvial swamp soil [ENVO:00005758]" + }, + "alpine soil [ENVO:00005741]": { + "text": "alpine soil [ENVO:00005741]" + }, + "andosol [ENVO:00002232]": { + "text": "andosol [ENVO:00002232]" + }, + "anthrosol [ENVO:00002230]": { + "text": "anthrosol [ENVO:00002230]" + }, + "arable soil [ENVO:00005742]": { + "text": "arable soil [ENVO:00005742]" + }, + "arenosol [ENVO:00002229]": { + "text": "arenosol [ENVO:00002229]" + }, + "bare soil [ENVO:01001616]": { + "text": "bare soil [ENVO:01001616]" + }, + "beech forest soil [ENVO:00005770]": { + "text": "beech forest soil [ENVO:00005770]" + }, + "bluegrass field soil [ENVO:00005789]": { + "text": "bluegrass field soil [ENVO:00005789]" + }, + "bulk soil [ENVO:00005802]": { + "text": "bulk soil [ENVO:00005802]" + }, + "burned soil [ENVO:00005760]": { + "text": "burned soil [ENVO:00005760]" + }, + "calcisol [ENVO:00002239]": { + "text": "calcisol [ENVO:00002239]" + }, + "cambisol [ENVO:00002235]": { + "text": "cambisol [ENVO:00002235]" + }, + "chernozem [ENVO:00002237]": { + "text": "chernozem [ENVO:00002237]" + }, + "clay soil [ENVO:00002262]": { + "text": "clay soil [ENVO:00002262]" + }, + "compacted soil [ENVO:06105205]": { + "text": "compacted soil [ENVO:06105205]" + }, + "compost soil [ENVO:00005747]": { + "text": "compost soil [ENVO:00005747]" + }, + "cryosol [ENVO:00002236]": { + "text": "cryosol [ENVO:00002236]" + }, + "dry soil [ENVO:00005748]": { + "text": "dry soil [ENVO:00005748]" + }, + "durisol [ENVO:00002238]": { + "text": "durisol [ENVO:00002238]" + }, + "eucalyptus forest soil [ENVO:00005787]": { + "text": "eucalyptus forest soil [ENVO:00005787]" + }, + "ferralsol [ENVO:00002246]": { + "text": "ferralsol [ENVO:00002246]" + }, + "fertilized soil [ENVO:00005754]": { + "text": "fertilized soil [ENVO:00005754]" + }, + "fluvisol [ENVO:00002273]": { + "text": "fluvisol [ENVO:00002273]" + }, + "friable-frozen soil [ENVO:01001528]": { + "text": "friable-frozen soil [ENVO:01001528]" + }, + "frost-susceptible soil [ENVO:01001638]": { + "text": "frost-susceptible soil [ENVO:01001638]" + }, + "frozen compost soil [ENVO:00005765]": { + "text": "frozen compost soil [ENVO:00005765]" + }, + "gleysol [ENVO:00002244]": { + "text": "gleysol [ENVO:00002244]" + }, + "gypsisol [ENVO:00002245]": { + "text": "gypsisol [ENVO:00002245]" + }, + "hard-frozen soil [ENVO:01001525]": { + "text": "hard-frozen soil [ENVO:01001525]" + }, + "heat stressed soil [ENVO:00005781]": { + "text": "heat stressed soil [ENVO:00005781]" + }, + "histosol [ENVO:00002243]": { + "text": "histosol [ENVO:00002243]" + }, + "jungle soil [ENVO:00005751]": { + "text": "jungle soil [ENVO:00005751]" + }, + "kastanozem [ENVO:00002240]": { + "text": "kastanozem [ENVO:00002240]" + }, + "lawn soil [ENVO:00005756]": { + "text": "lawn soil [ENVO:00005756]" + }, + "leafy wood soil [ENVO:00005783]": { + "text": "leafy wood soil [ENVO:00005783]" + }, + "leptosol [ENVO:00002241]": { + "text": "leptosol [ENVO:00002241]" + }, + "limed soil [ENVO:00005766]": { + "text": "limed soil [ENVO:00005766]" + }, + "lixisol [ENVO:00002242]": { + "text": "lixisol [ENVO:00002242]" + }, + "loam [ENVO:00002258]": { + "text": "loam [ENVO:00002258]" + }, + "luvisol [ENVO:00002248]": { + "text": "luvisol [ENVO:00002248]" + }, + "manured soil [ENVO:00005767]": { + "text": "manured soil [ENVO:00005767]" + }, + "mountain forest soil [ENVO:00005769]": { + "text": "mountain forest soil [ENVO:00005769]" + }, + "muddy soil [ENVO:00005771]": { + "text": "muddy soil [ENVO:00005771]" + }, + "nitisol [ENVO:00002247]": { + "text": "nitisol [ENVO:00002247]" + }, + "orchid soil [ENVO:00005768]": { + "text": "orchid soil [ENVO:00005768]" + }, + "ornithogenic soil [ENVO:00005782]": { + "text": "ornithogenic soil [ENVO:00005782]" + }, + "paddy field soil [ENVO:00005740]": { + "text": "paddy field soil [ENVO:00005740]" + }, + "pathogen-suppressive soil [ENVO:03600036]": { + "text": "pathogen-suppressive soil [ENVO:03600036]" + }, + "phaeozem [ENVO:00002249]": { + "text": "phaeozem [ENVO:00002249]" + }, + "planosol [ENVO:00002251]": { + "text": "planosol [ENVO:00002251]" + }, + "plastic-frozen soil [ENVO:01001527]": { + "text": "plastic-frozen soil [ENVO:01001527]" + }, + "plinthosol [ENVO:00002250]": { + "text": "plinthosol [ENVO:00002250]" + }, + "podzol [ENVO:00002257]": { + "text": "podzol [ENVO:00002257]" + }, + "red soil [ENVO:00005790]": { + "text": "red soil [ENVO:00005790]" + }, + "regosol [ENVO:00002256]": { + "text": "regosol [ENVO:00002256]" + }, + "rubber plantation soil [ENVO:00005788]": { + "text": "rubber plantation soil [ENVO:00005788]" + }, + "sawah soil [ENVO:00005752]": { + "text": "sawah soil [ENVO:00005752]" + }, + "soil [ENVO:00001998]": { + "text": "soil [ENVO:00001998]" + }, + "solonchak [ENVO:00002252]": { + "text": "solonchak [ENVO:00002252]" + }, + "solonetz [ENVO:00002255]": { + "text": "solonetz [ENVO:00002255]" + }, + "spruce forest soil [ENVO:00005784]": { + "text": "spruce forest soil [ENVO:00005784]" + }, + "stagnosol [ENVO:00002274]": { + "text": "stagnosol [ENVO:00002274]" + }, + "surface soil [ENVO:02000059]": { + "text": "surface soil [ENVO:02000059]" + }, + "technosol [ENVO:00002275]": { + "text": "technosol [ENVO:00002275]" + }, + "tropical soil [ENVO:00005778]": { + "text": "tropical soil [ENVO:00005778]" + }, + "ultisol [ENVO:01001397]": { + "text": "ultisol [ENVO:01001397]" + }, + "umbrisol [ENVO:00002253]": { + "text": "umbrisol [ENVO:00002253]" + }, + "upland soil [ENVO:00005786]": { + "text": "upland soil [ENVO:00005786]" + }, + "vegetable garden soil [ENVO:00005779]": { + "text": "vegetable garden soil [ENVO:00005779]" + }, + "vertisol [ENVO:00002254]": { + "text": "vertisol [ENVO:00002254]" + } + } + }, + "EnvBroadScaleSoilEnum": { + "name": "EnvBroadScaleSoilEnum", + "from_schema": "https://example.com/nmdc_submission_schema", + "permissible_values": { + "alpine tundra biome [ENVO:01001505]": { + "text": "alpine tundra biome [ENVO:01001505]" + }, + "anthropogenic terrestrial biome [ENVO:01000219]": { + "text": "anthropogenic terrestrial biome [ENVO:01000219]" + }, + "broadleaf forest biome [ENVO:01000197]": { + "text": "broadleaf forest biome [ENVO:01000197]" + }, + "coniferous forest biome [ENVO:01000196]": { + "text": "coniferous forest biome [ENVO:01000196]" + }, + "cropland biome [ENVO:01000245]": { + "text": "cropland biome [ENVO:01000245]" + }, + "flooded grassland biome [ENVO:01000195]": { + "text": "flooded grassland biome [ENVO:01000195]" + }, + "flooded savanna biome [ENVO:01000190]": { + "text": "flooded savanna biome [ENVO:01000190]" + }, + "forest biome [ENVO:01000174]": { + "text": "forest biome [ENVO:01000174]" + }, + "grassland biome [ENVO:01000177]": { + "text": "grassland biome [ENVO:01000177]" + }, + "mangrove biome [ENVO:01000181]": { + "text": "mangrove biome [ENVO:01000181]" + }, + "mediterranean forest biome [ENVO:01000199]": { + "text": "mediterranean forest biome [ENVO:01000199]" + }, + "mediterranean grassland biome [ENVO:01000224]": { + "text": "mediterranean grassland biome [ENVO:01000224]" + }, + "mediterranean savanna biome [ENVO:01000229]": { + "text": "mediterranean savanna biome [ENVO:01000229]" + }, + "mediterranean shrubland biome [ENVO:01000217]": { + "text": "mediterranean shrubland biome [ENVO:01000217]" + }, + "mediterranean woodland biome [ENVO:01000208]": { + "text": "mediterranean woodland biome [ENVO:01000208]" + }, + "mixed forest biome [ENVO:01000198]": { + "text": "mixed forest biome [ENVO:01000198]" + }, + "montane grassland biome [ENVO:01000194]": { + "text": "montane grassland biome [ENVO:01000194]" + }, + "montane savanna biome [ENVO:01000223]": { + "text": "montane savanna biome [ENVO:01000223]" + }, + "montane shrubland biome [ENVO:01000216]": { + "text": "montane shrubland biome [ENVO:01000216]" + }, + "rangeland biome [ENVO:01000247]": { + "text": "rangeland biome [ENVO:01000247]" + }, + "savanna biome [ENVO:01000178]": { + "text": "savanna biome [ENVO:01000178]" + }, + "shrubland biome [ENVO:01000176]": { + "text": "shrubland biome [ENVO:01000176]" + }, + "subpolar coniferous forest biome [ENVO:01000250]": { + "text": "subpolar coniferous forest biome [ENVO:01000250]" + }, + "subtropical broadleaf forest biome [ENVO:01000201]": { + "text": "subtropical broadleaf forest biome [ENVO:01000201]" + }, + "subtropical coniferous forest biome [ENVO:s01000209]": { + "text": "subtropical coniferous forest biome [ENVO:s01000209]" + }, + "subtropical dry broadleaf forest biome [ENVO:01000225]": { + "text": "subtropical dry broadleaf forest biome [ENVO:01000225]" + }, + "subtropical grassland biome [ENVO:01000191]": { + "text": "subtropical grassland biome [ENVO:01000191]" + }, + "subtropical moist broadleaf forest biome [ENVO:01000226]": { + "text": "subtropical moist broadleaf forest biome [ENVO:01000226]" + }, + "subtropical savanna biome [ENVO:01000187]": { + "text": "subtropical savanna biome [ENVO:01000187]" + }, + "subtropical shrubland biome [ENVO:01000213]": { + "text": "subtropical shrubland biome [ENVO:01000213]" + }, + "subtropical woodland biome [ENVO:01000222]": { + "text": "subtropical woodland biome [ENVO:01000222]" + }, + "temperate broadleaf forest biome [ENVO:01000202]": { + "text": "temperate broadleaf forest biome [ENVO:01000202]" + }, + "temperate coniferous forest biome [ENVO:01000211]": { + "text": "temperate coniferous forest biome [ENVO:01000211]" + }, + "temperate grassland biome [ENVO:01000193]": { + "text": "temperate grassland biome [ENVO:01000193]" + }, + "temperate mixed forest biome [ENVO:01000212]": { + "text": "temperate mixed forest biome [ENVO:01000212]" + }, + "temperate savanna biome [ENVO:01000189]": { + "text": "temperate savanna biome [ENVO:01000189]" + }, + "temperate shrubland biome [ENVO:01000215]": { + "text": "temperate shrubland biome [ENVO:01000215]" + }, + "temperate woodland biome [ENVO:01000221]": { + "text": "temperate woodland biome [ENVO:01000221]" + }, + "terrestrial biome [ENVO:00000446]": { + "text": "terrestrial biome [ENVO:00000446]" + }, + "tidal mangrove shrubland [ENVO:01001369]": { + "text": "tidal mangrove shrubland [ENVO:01001369]" + }, + "tropical broadleaf forest biome [ENVO:01000200]": { + "text": "tropical broadleaf forest biome [ENVO:01000200]" + }, + "tropical coniferous forest biome [ENVO:01000210]": { + "text": "tropical coniferous forest biome [ENVO:01000210]" + }, + "tropical dry broadleaf forest biome [ENVO:01000227]": { + "text": "tropical dry broadleaf forest biome [ENVO:01000227]" + }, + "tropical grassland biome [ENVO:01000192]": { + "text": "tropical grassland biome [ENVO:01000192]" + }, + "tropical mixed forest biome [ENVO:01001798]": { + "text": "tropical mixed forest biome [ENVO:01001798]" + }, + "tropical moist broadleaf forest biome [ENVO:01000228]": { + "text": "tropical moist broadleaf forest biome [ENVO:01000228]" + }, + "tropical savanna biome [ENVO:01000188]": { + "text": "tropical savanna biome [ENVO:01000188]" + }, + "tropical shrubland biome [ENVO:01000214]": { + "text": "tropical shrubland biome [ENVO:01000214]" + }, + "tropical woodland biome [ENVO:01000220]": { + "text": "tropical woodland biome [ENVO:01000220]" + }, + "tundra biome [ENVO:01000180]": { + "text": "tundra biome [ENVO:01000180]" + }, + "woodland biome [ENVO:01000175]": { + "text": "woodland biome [ENVO:01000175]" + }, + "xeric shrubland biome [ENVO:01000218]": { + "text": "xeric shrubland biome [ENVO:01000218]" + } + } } }, "slots": { @@ -11039,7 +11127,6 @@ }, "emsl_section": { "name": "emsl_section", - "description": "placeholder", "title": "EMSL", "from_schema": "https://example.com/nmdc_submission_schema", "rank": 2, @@ -11047,7 +11134,6 @@ }, "jgi_metagenomics_section": { "name": "jgi_metagenomics_section", - "description": "placeholder", "title": "JGI-Metagenomics", "from_schema": "https://example.com/nmdc_submission_schema", "rank": 3, @@ -11055,7 +11141,6 @@ }, "jgi_metatranscriptomics_section": { "name": "jgi_metatranscriptomics_section", - "description": "placeholder", "title": "JGI-Metatranscriptomics", "from_schema": "https://example.com/nmdc_submission_schema", "rank": 4, @@ -11063,7 +11148,6 @@ }, "mixs_core_section": { "name": "mixs_core_section", - "description": "placeholder", "title": "MIxS Core", "from_schema": "https://example.com/nmdc_submission_schema", "rank": 10, @@ -11071,7 +11155,6 @@ }, "mixs_inspired_section": { "name": "mixs_inspired_section", - "description": "placeholder", "title": "MIxS Inspired", "from_schema": "https://example.com/nmdc_submission_schema", "rank": 7, @@ -11079,14 +11162,12 @@ }, "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, @@ -11094,14 +11175,12 @@ }, "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, @@ -11109,7 +11188,6 @@ }, "sample_id_section": { "name": "sample_id_section", - "description": "placeholder", "title": "Sample ID", "from_schema": "https://example.com/nmdc_submission_schema", "rank": 1, @@ -29764,7 +29842,7 @@ "range": "string", "required": true, "multivalued": false, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" }, "methane": { "name": "methane", @@ -31790,7 +31868,7 @@ "range": "string", "required": true, "multivalued": false, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" }, "methane": { "name": "methane", @@ -34742,7 +34820,7 @@ "range": "string", "required": true, "multivalued": false, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" }, "magnesium": { "name": "magnesium", @@ -38425,7 +38503,7 @@ "range": "string", "required": true, "multivalued": false, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" }, "magnesium": { "name": "magnesium", @@ -44278,7 +44356,7 @@ "range": "string", "required": true, "multivalued": false, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" }, "light_type": { "name": "light_type", @@ -51029,7 +51107,7 @@ "range": "string", "required": true, "multivalued": false, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" }, "light_type": { "name": "light_type", @@ -56914,7 +56992,7 @@ "range": "string", "required": true, "multivalued": false, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" }, "lithology": { "name": "lithology", @@ -61213,7 +61291,7 @@ "range": "string", "required": true, "multivalued": false, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" }, "lithology": { "name": "lithology", @@ -66071,7 +66149,7 @@ "range": "string", "required": true, "multivalued": false, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" }, "lithology": { "name": "lithology", @@ -70569,7 +70647,7 @@ "range": "string", "required": true, "multivalued": false, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" }, "lithology": { "name": "lithology", @@ -75202,7 +75280,7 @@ "range": "string", "required": true, "multivalued": false, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" }, "misc_param": { "name": "misc_param", @@ -77962,7 +78040,7 @@ "range": "string", "required": true, "multivalued": false, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" }, "misc_param": { "name": "misc_param", @@ -79305,7 +79383,8 @@ "range": "string", "required": true, "recommended": false, - "multivalued": false + "multivalued": false, + "pattern": "^[_a-zA-Z0-9-]*$" }, "dna_seq_project": { "name": "dna_seq_project", @@ -79768,7 +79847,8 @@ "range": "string", "required": true, "recommended": false, - "multivalued": false + "multivalued": false, + "pattern": "^[_a-zA-Z0-9-]*$" }, "dna_seq_project": { "name": "dna_seq_project", @@ -80476,7 +80556,8 @@ "range": "string", "required": true, "recommended": false, - "multivalued": false + "multivalued": false, + "pattern": "^[_a-zA-Z0-9-]*$" }, "dna_seq_project": { "name": "dna_seq_project", @@ -80941,7 +81022,8 @@ "range": "string", "required": true, "recommended": false, - "multivalued": false + "multivalued": false, + "pattern": "^[_a-zA-Z0-9-]*$" }, "dna_seq_project": { "name": "dna_seq_project", @@ -81619,7 +81701,8 @@ "recommended": false, "multivalued": false, "minimum_value": 0, - "maximum_value": 2000 + "maximum_value": 2000, + "pattern": "^[_a-zA-Z0-9-]*$" }, "rna_seq_project": { "name": "rna_seq_project", @@ -82067,7 +82150,8 @@ "recommended": false, "multivalued": false, "minimum_value": 0, - "maximum_value": 2000 + "maximum_value": 2000, + "pattern": "^[_a-zA-Z0-9-]*$" }, "rna_seq_project": { "name": "rna_seq_project", @@ -83790,7 +83874,7 @@ "range": "string", "required": true, "multivalued": false, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" }, "misc_param": { "name": "misc_param", @@ -86646,7 +86730,7 @@ "range": "string", "required": true, "multivalued": false, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" }, "misc_param": { "name": "misc_param", @@ -90506,7 +90590,7 @@ "range": "string", "required": true, "multivalued": false, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" }, "light_regm": { "name": "light_regm", @@ -94505,7 +94589,7 @@ "range": "string", "required": true, "multivalued": false, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" }, "light_regm": { "name": "light_regm", @@ -98809,7 +98893,7 @@ "range": "string", "required": true, "multivalued": false, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" }, "light_regm": { "name": "light_regm", @@ -103775,7 +103859,7 @@ "range": "string", "required": true, "multivalued": false, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" }, "light_regm": { "name": "light_regm", @@ -109008,7 +109092,7 @@ "range": "string", "required": true, "multivalued": false, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" }, "lbc_thirty": { "name": "lbc_thirty", @@ -113852,7 +113936,7 @@ "range": "string", "required": true, "multivalued": false, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" }, "lbc_thirty": { "name": "lbc_thirty", @@ -117889,7 +117973,7 @@ "range": "string", "required": true, "multivalued": false, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" }, "misc_param": { "name": "misc_param", @@ -120402,7 +120486,7 @@ "range": "string", "required": true, "multivalued": false, - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$" + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$" }, "misc_param": { "name": "misc_param", diff --git a/project/jsonschema/nmdc_submission_schema.schema.json b/project/jsonschema/nmdc_submission_schema.schema.json index d4bb233c..2d170407 100644 --- a/project/jsonschema/nmdc_submission_schema.schema.json +++ b/project/jsonschema/nmdc_submission_schema.schema.json @@ -129,7 +129,7 @@ }, "lat_lon": { "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$", + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$", "type": "string" }, "methane": { @@ -613,7 +613,7 @@ }, "lat_lon": { "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$", + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$", "type": "string" }, "magnesium": { @@ -1616,7 +1616,7 @@ }, "lat_lon": { "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$", + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$", "type": "string" }, "light_type": { @@ -2351,7 +2351,7 @@ "type": "object" }, "DnaSampleFormatEnum": { - "description": "placeholder enum descr", + "description": "", "enum": [ "10 mM Tris-HCl", "DNAStable", @@ -2744,7 +2744,6 @@ "Digestate", "Digestive system", "Digestive tube", - "Dinoflagellates", "Dissolved organics (aerobic)", "Dissolved organics (anaerobic)", "Distilled water", @@ -2805,6 +2804,7 @@ "Freshwater debries", "Frozen remains", "Frozen seafood", + "Fruit processing", "Fumaroles", "Fungi", "Galls", @@ -3131,6 +3131,7 @@ "Small intestine", "Smooth muscle", "Smooth muscles", + "Snow", "Soda lake", "Soft tissue", "Soft tissues", @@ -3679,7 +3680,7 @@ "type": "object" }, "EnvBroadScaleSoilEnum": { - "description": "placeholder enum descr, DO NOT SORT", + "description": "", "enum": [ "arid biome [ENVO:01001838]", "subalpine biome [ENVO:01001837]", @@ -3740,7 +3741,7 @@ "type": "string" }, "EnvLocalScaleSoilEnum": { - "description": "placeholder enum descr, DO NOT SORT", + "description": "", "enum": [ "astronomical body part [ENVO:01000813]", "__coast [ENVO:01000687]", @@ -3839,7 +3840,7 @@ "type": "string" }, "EnvMediumSoilEnum": { - "description": "placeholder enum descr, DO NOT SORT", + "description": "", "enum": [ "pathogen-suppressive soil [ENVO:03600036]", "mangrove biome soil [ENVO:02000138]", @@ -3948,7 +3949,7 @@ "type": "string" }, "EnvPackageEnum": { - "description": "placeholder enum descr", + "description": "", "enum": [ "soil" ], @@ -4122,7 +4123,7 @@ "type": "string" }, "GrowthFacilEnum": { - "description": "placeholder enum descr", + "description": "", "enum": [ "experimental_garden", "field", @@ -4447,7 +4448,7 @@ }, "lat_lon": { "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$", + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$", "type": "string" }, "lithology": { @@ -5240,7 +5241,7 @@ }, "lat_lon": { "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$", + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$", "type": "string" }, "lithology": { @@ -6056,7 +6057,7 @@ }, "lat_lon": { "description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$", + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$", "type": "string" }, "misc_param": { @@ -6377,6 +6378,7 @@ }, "dna_sample_name": { "description": "Give the DNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", + "pattern": "^[_a-zA-Z0-9-]*$", "type": "string" }, "dna_seq_project": { @@ -6488,6 +6490,7 @@ }, "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.", + "pattern": "^[_a-zA-Z0-9-]*$", "type": "string" }, "dna_seq_project": { @@ -6658,6 +6661,7 @@ "description": "Give the RNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.", "maximum": 2000, "minimum": 0, + "pattern": "^[_a-zA-Z0-9-]*$", "type": "string" }, "rna_seq_project": { @@ -6957,7 +6961,7 @@ }, "lat_lon": { "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", - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$", + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$", "type": "string" }, "misc_param": { @@ -7586,7 +7590,7 @@ }, "lat_lon": { "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", - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$", + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$", "type": "string" }, "light_regm": { @@ -8027,7 +8031,7 @@ "type": "string" }, "RelToOxygenEnum": { - "description": "placeholder enum descr", + "description": "", "enum": [ "aerobe", "anaerobe", @@ -8041,7 +8045,7 @@ "type": "string" }, "RnaSampleFormatEnum": { - "description": "placeholder enum descr", + "description": "", "enum": [ "10 mM Tris-HCl", "DNAStable", @@ -8723,7 +8727,7 @@ }, "lat_lon": { "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", - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$", + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$", "type": "string" }, "light_regm": { @@ -9642,7 +9646,7 @@ }, "lat_lon": { "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", - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$", + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$", "type": "string" }, "lbc_thirty": { @@ -10806,6 +10810,7 @@ "Spring", "Spring sediment", "Squamous cell carcinoma", + "Stolon", "Stomach", "Stomach content", "Stomach: Cardiac", @@ -11061,7 +11066,7 @@ "type": "string" }, "StoreCondEnum": { - "description": "placeholder enum descr", + "description": "", "enum": [ "fresh", "frozen", @@ -11412,7 +11417,7 @@ }, "lat_lon": { "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", - "pattern": "^[-+]?([1-8]?\\d(\\.\\d+)?|90(\\.0+)?)\\s[-+]?(180(\\.0+)?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d+)?)$", + "pattern": "^[-+]?([1-8]?\\d(\\.\\d{1,8})?|90(\\.0{1,8})?)\\s[-+]?(180(\\.0{1,8})?|((1[0-7]\\d)|([1-9]?\\d))(\\.\\d{1,8})?)$", "type": "string" }, "misc_param": { diff --git a/project/thirdparty/GoldEcosystemTree.json b/project/thirdparty/GoldEcosystemTree.json index 8185ceec..3c6d281c 100644 --- a/project/thirdparty/GoldEcosystemTree.json +++ b/project/thirdparty/GoldEcosystemTree.json @@ -2,7 +2,7 @@ "name": "Ecosystems", "children": [ -{"name": "Engineered", "count": "17399" , "url": "search?Biosample.Ecosystem=Engineered" , "children" : [ +{"name": "Engineered", "count": "17892" , "url": "search?Biosample.Ecosystem=Engineered" , "children" : [ {"name": "Animal feed production" , "count": "0" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Animal feed production" , "children" : [ {"name": "Fermentation" , "count": "0" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Animal feed production&Biosample.Ecosystem+Type=Fermentation" , "children" : [ {"name": "Swine waste with corn" , "count": "0" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Animal feed production&Biosample.Ecosystem+Type=Fermentation&Biosample.Ecosystem+Subtype=Swine waste with corn" , "children" : [ @@ -261,7 +261,7 @@ }] }, - {"name": "Bioreactor" , "count": "1748" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Bioreactor" , "children" : [ + {"name": "Bioreactor" , "count": "2235" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Bioreactor" , "children" : [ {"name": "Aerobic" , "count": "163" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Bioreactor&Biosample.Ecosystem+Type=Aerobic" , "children" : [ {"name": "AGS (Aerobic granular sludge)" , "count": "0" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Bioreactor&Biosample.Ecosystem+Type=Aerobic&Biosample.Ecosystem+Subtype=AGS (Aerobic granular sludge)" , "children" : [ {"name": "Unclassified" , "count": "0" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Bioreactor&Biosample.Ecosystem+Type=Aerobic&Biosample.Ecosystem+Subtype=AGS (Aerobic granular sludge)&Biosample.Specific Ecosystem=Unclassified" }] @@ -280,7 +280,7 @@ }] }, - {"name": "Anaerobic" , "count": "1200" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Bioreactor&Biosample.Ecosystem+Type=Anaerobic" , "children" : [ + {"name": "Anaerobic" , "count": "1687" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Bioreactor&Biosample.Ecosystem+Type=Anaerobic" , "children" : [ {"name": "Biofilm" , "count": "3" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Bioreactor&Biosample.Ecosystem+Type=Anaerobic&Biosample.Ecosystem+Subtype=Biofilm" , "children" : [ {"name": "Unclassified" , "count": "3" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Bioreactor&Biosample.Ecosystem+Type=Anaerobic&Biosample.Ecosystem+Subtype=Biofilm&Biosample.Specific Ecosystem=Unclassified" }] }, @@ -317,18 +317,18 @@ {"name": "Unclassified" , "count": "2" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Bioreactor&Biosample.Ecosystem+Type=Anaerobic&Biosample.Ecosystem+Subtype=Settled granule&Biosample.Specific Ecosystem=Unclassified" }] }, - {"name": "Sludge" , "count": "86" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Bioreactor&Biosample.Ecosystem+Type=Anaerobic&Biosample.Ecosystem+Subtype=Sludge" , "children" : [ + {"name": "Sludge" , "count": "463" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Bioreactor&Biosample.Ecosystem+Type=Anaerobic&Biosample.Ecosystem+Subtype=Sludge" , "children" : [ {"name": "Granular sludge" , "count": "0" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Bioreactor&Biosample.Ecosystem+Type=Anaerobic&Biosample.Ecosystem+Subtype=Sludge&Biosample.Specific Ecosystem=Granular sludge" }, - {"name": "Unclassified" , "count": "86" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Bioreactor&Biosample.Ecosystem+Type=Anaerobic&Biosample.Ecosystem+Subtype=Sludge&Biosample.Specific Ecosystem=Unclassified" }] + {"name": "Unclassified" , "count": "463" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Bioreactor&Biosample.Ecosystem+Type=Anaerobic&Biosample.Ecosystem+Subtype=Sludge&Biosample.Specific Ecosystem=Unclassified" }] }, {"name": "Thermophilic digester" , "count": "0" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Bioreactor&Biosample.Ecosystem+Type=Anaerobic&Biosample.Ecosystem+Subtype=Thermophilic digester" , "children" : [ {"name": "Unclassified" , "count": "0" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Bioreactor&Biosample.Ecosystem+Type=Anaerobic&Biosample.Ecosystem+Subtype=Thermophilic digester&Biosample.Specific Ecosystem=Unclassified" }] }, - {"name": "Unclassified" , "count": "651" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Bioreactor&Biosample.Ecosystem+Type=Anaerobic&Biosample.Ecosystem+Subtype=Unclassified" , "children" : [ - {"name": "Unclassified" , "count": "651" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Bioreactor&Biosample.Ecosystem+Type=Anaerobic&Biosample.Ecosystem+Subtype=Unclassified&Biosample.Specific Ecosystem=Unclassified" }] + {"name": "Unclassified" , "count": "761" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Bioreactor&Biosample.Ecosystem+Type=Anaerobic&Biosample.Ecosystem+Subtype=Unclassified" , "children" : [ + {"name": "Unclassified" , "count": "761" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Bioreactor&Biosample.Ecosystem+Type=Anaerobic&Biosample.Ecosystem+Subtype=Unclassified&Biosample.Specific Ecosystem=Unclassified" }] }, {"name": "Wastewater" , "count": "0" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Bioreactor&Biosample.Ecosystem+Type=Anaerobic&Biosample.Ecosystem+Subtype=Wastewater" , "children" : [ @@ -1227,14 +1227,14 @@ }] }, - {"name": "Industrial production" , "count": "772" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Industrial production" , "children" : [ + {"name": "Industrial production" , "count": "774" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Industrial production" , "children" : [ {"name": "Biochar" , "count": "5" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Industrial production&Biosample.Ecosystem+Type=Biochar" , "children" : [ {"name": "Unclassified" , "count": "5" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Industrial production&Biosample.Ecosystem+Type=Biochar&Biosample.Ecosystem+Subtype=Unclassified" , "children" : [ {"name": "Unclassified" , "count": "5" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Industrial production&Biosample.Ecosystem+Type=Biochar&Biosample.Ecosystem+Subtype=Unclassified&Biosample.Specific Ecosystem=Unclassified" }] }] }, - {"name": "Chemical products" , "count": "570" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Industrial production&Biosample.Ecosystem+Type=Chemical products" , "children" : [ + {"name": "Chemical products" , "count": "572" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Industrial production&Biosample.Ecosystem+Type=Chemical products" , "children" : [ {"name": "Buffer" , "count": "9" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Industrial production&Biosample.Ecosystem+Type=Chemical products&Biosample.Ecosystem+Subtype=Buffer" , "children" : [ {"name": "Unclassified" , "count": "9" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Industrial production&Biosample.Ecosystem+Type=Chemical products&Biosample.Ecosystem+Subtype=Buffer&Biosample.Specific Ecosystem=Unclassified" }] }, @@ -1263,8 +1263,8 @@ {"name": "Unclassified" , "count": "5" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Industrial production&Biosample.Ecosystem+Type=Chemical products&Biosample.Ecosystem+Subtype=PCR blank control&Biosample.Specific Ecosystem=Unclassified" }] }, - {"name": "Reagent blank" , "count": "129" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Industrial production&Biosample.Ecosystem+Type=Chemical products&Biosample.Ecosystem+Subtype=Reagent blank" , "children" : [ - {"name": "Unclassified" , "count": "129" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Industrial production&Biosample.Ecosystem+Type=Chemical products&Biosample.Ecosystem+Subtype=Reagent blank&Biosample.Specific Ecosystem=Unclassified" }] + {"name": "Reagent blank" , "count": "131" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Industrial production&Biosample.Ecosystem+Type=Chemical products&Biosample.Ecosystem+Subtype=Reagent blank" , "children" : [ + {"name": "Unclassified" , "count": "131" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Industrial production&Biosample.Ecosystem+Type=Chemical products&Biosample.Ecosystem+Subtype=Reagent blank&Biosample.Specific Ecosystem=Unclassified" }] }, {"name": "Sheath fluid" , "count": "23" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Industrial production&Biosample.Ecosystem+Type=Chemical products&Biosample.Ecosystem+Subtype=Sheath fluid" , "children" : [ @@ -1339,22 +1339,22 @@ }] }, - {"name": "Lab culture" , "count": "191" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Lab culture" , "children" : [ - {"name": "Culture media" , "count": "191" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Lab culture&Biosample.Ecosystem+Type=Culture media" , "children" : [ + {"name": "Lab culture" , "count": "194" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Lab culture" , "children" : [ + {"name": "Culture media" , "count": "194" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Lab culture&Biosample.Ecosystem+Type=Culture media" , "children" : [ {"name": "Algae" , "count": "6" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Lab culture&Biosample.Ecosystem+Type=Culture media&Biosample.Ecosystem+Subtype=Algae" , "children" : [ {"name": "Contaminated" , "count": "6" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Lab culture&Biosample.Ecosystem+Type=Culture media&Biosample.Ecosystem+Subtype=Algae&Biosample.Specific Ecosystem=Contaminated" }] }, - {"name": "Archaea" , "count": "0" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Lab culture&Biosample.Ecosystem+Type=Culture media&Biosample.Ecosystem+Subtype=Archaea" , "children" : [ + {"name": "Archaea" , "count": "2" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Lab culture&Biosample.Ecosystem+Type=Culture media&Biosample.Ecosystem+Subtype=Archaea" , "children" : [ {"name": "Contaminated" , "count": "0" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Lab culture&Biosample.Ecosystem+Type=Culture media&Biosample.Ecosystem+Subtype=Archaea&Biosample.Specific Ecosystem=Contaminated" }, - {"name": "Unclassified" , "count": "0" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Lab culture&Biosample.Ecosystem+Type=Culture media&Biosample.Ecosystem+Subtype=Archaea&Biosample.Specific Ecosystem=Unclassified" }] + {"name": "Unclassified" , "count": "2" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Lab culture&Biosample.Ecosystem+Type=Culture media&Biosample.Ecosystem+Subtype=Archaea&Biosample.Specific Ecosystem=Unclassified" }] }, - {"name": "Bacteria" , "count": "114" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Lab culture&Biosample.Ecosystem+Type=Culture media&Biosample.Ecosystem+Subtype=Bacteria" , "children" : [ + {"name": "Bacteria" , "count": "115" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Lab culture&Biosample.Ecosystem+Type=Culture media&Biosample.Ecosystem+Subtype=Bacteria" , "children" : [ {"name": "Co-culture" , "count": "0" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Lab culture&Biosample.Ecosystem+Type=Culture media&Biosample.Ecosystem+Subtype=Bacteria&Biosample.Specific Ecosystem=Co-culture" }, - {"name": "Contaminated" , "count": "5" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Lab culture&Biosample.Ecosystem+Type=Culture media&Biosample.Ecosystem+Subtype=Bacteria&Biosample.Specific Ecosystem=Contaminated" }, + {"name": "Contaminated" , "count": "6" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Lab culture&Biosample.Ecosystem+Type=Culture media&Biosample.Ecosystem+Subtype=Bacteria&Biosample.Specific Ecosystem=Contaminated" }, {"name": "Unclassified" , "count": "109" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Lab culture&Biosample.Ecosystem+Type=Culture media&Biosample.Ecosystem+Subtype=Bacteria&Biosample.Specific Ecosystem=Unclassified" }] }, @@ -1683,6 +1683,10 @@ {"name": "Unclassified" , "count": "0" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Solid waste&Biosample.Ecosystem+Type=Industrial waste&Biosample.Ecosystem+Subtype=Composting&Biosample.Specific Ecosystem=Unclassified" }] }, + {"name": "Fruit processing" , "count": "0" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Solid waste&Biosample.Ecosystem+Type=Industrial waste&Biosample.Ecosystem+Subtype=Fruit processing" , "children" : [ + {"name": "Unclassified" , "count": "0" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Solid waste&Biosample.Ecosystem+Type=Industrial waste&Biosample.Ecosystem+Subtype=Fruit processing&Biosample.Specific Ecosystem=Unclassified" }] +}, + {"name": "Radioactive waste" , "count": "0" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Solid waste&Biosample.Ecosystem+Type=Industrial waste&Biosample.Ecosystem+Subtype=Radioactive waste" , "children" : [ {"name": "Unclassified" , "count": "0" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=Solid waste&Biosample.Ecosystem+Type=Industrial waste&Biosample.Ecosystem+Subtype=Radioactive waste&Biosample.Specific Ecosystem=Unclassified" }] }, @@ -1777,7 +1781,7 @@ }] }, - {"name": "WWTP" , "count": "1476" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=WWTP" , "children" : [ + {"name": "WWTP" , "count": "1477" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=WWTP" , "children" : [ {"name": "A/O treatment system" , "count": "0" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=WWTP&Biosample.Ecosystem+Type=A/O treatment system" , "children" : [ {"name": "A/O bioreactor" , "count": "0" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=WWTP&Biosample.Ecosystem+Type=A/O treatment system&Biosample.Ecosystem+Subtype=A/O bioreactor" , "children" : [ {"name": "Activated sludge" , "count": "0" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=WWTP&Biosample.Ecosystem+Type=A/O treatment system&Biosample.Ecosystem+Subtype=A/O bioreactor&Biosample.Specific Ecosystem=Activated sludge" }, @@ -1836,9 +1840,9 @@ }] }, - {"name": "Mixed liquor" , "count": "100" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=WWTP&Biosample.Ecosystem+Type=Mixed liquor" , "children" : [ - {"name": "Unclassified" , "count": "100" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=WWTP&Biosample.Ecosystem+Type=Mixed liquor&Biosample.Ecosystem+Subtype=Unclassified" , "children" : [ - {"name": "Unclassified" , "count": "100" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=WWTP&Biosample.Ecosystem+Type=Mixed liquor&Biosample.Ecosystem+Subtype=Unclassified&Biosample.Specific Ecosystem=Unclassified" }] + {"name": "Mixed liquor" , "count": "101" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=WWTP&Biosample.Ecosystem+Type=Mixed liquor" , "children" : [ + {"name": "Unclassified" , "count": "101" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=WWTP&Biosample.Ecosystem+Type=Mixed liquor&Biosample.Ecosystem+Subtype=Unclassified" , "children" : [ + {"name": "Unclassified" , "count": "101" , "url": "search?Biosample.Ecosystem=Engineered&Biosample.Ecosystem+Category=WWTP&Biosample.Ecosystem+Type=Mixed liquor&Biosample.Ecosystem+Subtype=Unclassified&Biosample.Specific Ecosystem=Unclassified" }] }] }, @@ -2032,7 +2036,7 @@ }] } , -{"name": "Environmental", "count": "96802" , "url": "search?Biosample.Ecosystem=Environmental" , "children" : [ +{"name": "Environmental", "count": "97020" , "url": "search?Biosample.Ecosystem=Environmental" , "children" : [ {"name": "Air" , "count": "1638" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Air" , "children" : [ {"name": "Indoor Air" , "count": "349" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Air&Biosample.Ecosystem+Type=Indoor Air" , "children" : [ {"name": "Air scrubber" , "count": "0" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Air&Biosample.Ecosystem+Type=Indoor Air&Biosample.Ecosystem+Subtype=Air scrubber" , "children" : [ @@ -2075,7 +2079,7 @@ }] }, - {"name": "Aquatic" , "count": "56006" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic" , "children" : [ + {"name": "Aquatic" , "count": "56103" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic" , "children" : [ {"name": "Acidic" , "count": "0" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Acidic" , "children" : [ {"name": "Acidic hypersaline lake" , "count": "0" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Acidic&Biosample.Ecosystem+Subtype=Acidic hypersaline lake" , "children" : [ {"name": "Microbial mat" , "count": "0" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Acidic&Biosample.Ecosystem+Subtype=Acidic hypersaline lake&Biosample.Specific Ecosystem=Microbial mat" }, @@ -2202,7 +2206,7 @@ }] }, - {"name": "Freshwater" , "count": "19834" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater" , "children" : [ + {"name": "Freshwater" , "count": "19874" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater" , "children" : [ {"name": "Agricultural field" , "count": "1" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Agricultural field" , "children" : [ {"name": "Unclassified" , "count": "1" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Agricultural field&Biosample.Specific Ecosystem=Unclassified" }] }, @@ -2225,8 +2229,8 @@ {"name": "Unclassified" , "count": "1" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Bog lake&Biosample.Specific Ecosystem=Unclassified" }] }, - {"name": "Creek" , "count": "1215" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Creek" , "children" : [ - {"name": "Biofilm" , "count": "66" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Creek&Biosample.Specific Ecosystem=Biofilm" }, + {"name": "Creek" , "count": "1221" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Creek" , "children" : [ + {"name": "Biofilm" , "count": "72" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Creek&Biosample.Specific Ecosystem=Biofilm" }, {"name": "Microbial mat" , "count": "0" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Creek&Biosample.Specific Ecosystem=Microbial mat" }, @@ -2331,7 +2335,7 @@ {"name": "Unclassified" , "count": "98" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Kettle hole&Biosample.Specific Ecosystem=Unclassified" }] }, - {"name": "Lake" , "count": "9163" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Lake" , "children" : [ + {"name": "Lake" , "count": "9165" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Lake" , "children" : [ {"name": "Algal bloom" , "count": "8" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Lake&Biosample.Specific Ecosystem=Algal bloom" }, {"name": "Anoxic zone" , "count": "27" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Lake&Biosample.Specific Ecosystem=Anoxic zone" }, @@ -2362,7 +2366,7 @@ {"name": "Sediment" , "count": "1445" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Lake&Biosample.Specific Ecosystem=Sediment" }, - {"name": "Unclassified" , "count": "6673" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Lake&Biosample.Specific Ecosystem=Unclassified" }] + {"name": "Unclassified" , "count": "6675" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Lake&Biosample.Specific Ecosystem=Unclassified" }] }, {"name": "Lentic" , "count": "101" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Lentic" , "children" : [ @@ -2391,10 +2395,10 @@ {"name": "Unclassified" , "count": "14" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Microbialites&Biosample.Specific Ecosystem=Unclassified" }] }, - {"name": "Pond" , "count": "697" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Pond" , "children" : [ + {"name": "Pond" , "count": "699" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Pond" , "children" : [ {"name": "Sediment" , "count": "306" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Pond&Biosample.Specific Ecosystem=Sediment" }, - {"name": "Unclassified" , "count": "391" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Pond&Biosample.Specific Ecosystem=Unclassified" }] + {"name": "Unclassified" , "count": "393" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Pond&Biosample.Specific Ecosystem=Unclassified" }] }, {"name": "Puddle" , "count": "4" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Puddle" , "children" : [ @@ -2413,18 +2417,18 @@ {"name": "Unclassified" , "count": "292" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Reservoir&Biosample.Specific Ecosystem=Unclassified" }] }, - {"name": "River" , "count": "3977" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=River" , "children" : [ + {"name": "River" , "count": "4007" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=River" , "children" : [ {"name": "Microbial mats" , "count": "203" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=River&Biosample.Specific Ecosystem=Microbial mats" }, {"name": "Periphyton" , "count": "9" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=River&Biosample.Specific Ecosystem=Periphyton" }, {"name": "Plankton" , "count": "112" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=River&Biosample.Specific Ecosystem=Plankton" }, - {"name": "River biofilm" , "count": "40" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=River&Biosample.Specific Ecosystem=River biofilm" }, + {"name": "River biofilm" , "count": "41" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=River&Biosample.Specific Ecosystem=River biofilm" }, {"name": "Sediment" , "count": "859" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=River&Biosample.Specific Ecosystem=Sediment" }, - {"name": "Unclassified" , "count": "2754" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=River&Biosample.Specific Ecosystem=Unclassified" }] + {"name": "Unclassified" , "count": "2783" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=River&Biosample.Specific Ecosystem=Unclassified" }] }, {"name": "Sediment" , "count": "95" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Sediment" , "children" : [ @@ -2443,6 +2447,10 @@ {"name": "Unclassified" , "count": "29" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Sinkhole&Biosample.Specific Ecosystem=Unclassified" }] }, + {"name": "Snow" , "count": "0" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Snow" , "children" : [ + {"name": "Unclassified" , "count": "0" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Snow&Biosample.Specific Ecosystem=Unclassified" }] +}, + {"name": "Sterile water" , "count": "39" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Sterile water" , "children" : [ {"name": "Unclassified" , "count": "39" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Freshwater&Biosample.Ecosystem+Subtype=Sterile water&Biosample.Specific Ecosystem=Unclassified" }] }, @@ -2500,7 +2508,7 @@ }] }, - {"name": "Marine" , "count": "27329" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine" , "children" : [ + {"name": "Marine" , "count": "27380" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine" , "children" : [ {"name": "Abyssopelagic" , "count": "7" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Abyssopelagic" , "children" : [ {"name": "Unclassified" , "count": "7" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Abyssopelagic&Biosample.Specific Ecosystem=Unclassified" }] }, @@ -2537,12 +2545,12 @@ {"name": "Unclassified" , "count": "0" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Biofouling&Biosample.Specific Ecosystem=Unclassified" }] }, - {"name": "Coastal" , "count": "4690" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Coastal" , "children" : [ + {"name": "Coastal" , "count": "4693" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Coastal" , "children" : [ {"name": "Brine" , "count": "12" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Coastal&Biosample.Specific Ecosystem=Brine" }, {"name": "Phytoplankton bloom" , "count": "0" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Coastal&Biosample.Specific Ecosystem=Phytoplankton bloom" }, - {"name": "Sediment" , "count": "569" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Coastal&Biosample.Specific Ecosystem=Sediment" }, + {"name": "Sediment" , "count": "572" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Coastal&Biosample.Specific Ecosystem=Sediment" }, {"name": "Unclassified" , "count": "4109" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Coastal&Biosample.Specific Ecosystem=Unclassified" }] }, @@ -2641,7 +2649,7 @@ {"name": "Unclassified" , "count": "1278" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Inlet&Biosample.Specific Ecosystem=Unclassified" }] }, - {"name": "Intertidal zone" , "count": "3498" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Intertidal zone" , "children" : [ + {"name": "Intertidal zone" , "count": "3520" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Intertidal zone" , "children" : [ {"name": "Beach/Shore" , "count": "750" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Intertidal zone&Biosample.Specific Ecosystem=Beach/Shore" }, {"name": "Coral reef" , "count": "229" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Intertidal zone&Biosample.Specific Ecosystem=Coral reef" }, @@ -2666,7 +2674,7 @@ {"name": "Oil-contaminated sediment" , "count": "0" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Intertidal zone&Biosample.Specific Ecosystem=Oil-contaminated sediment" }, - {"name": "Salt marsh" , "count": "513" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Intertidal zone&Biosample.Specific Ecosystem=Salt marsh" }, + {"name": "Salt marsh" , "count": "535" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Intertidal zone&Biosample.Specific Ecosystem=Salt marsh" }, {"name": "Salt marsh sediment" , "count": "197" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Intertidal zone&Biosample.Specific Ecosystem=Salt marsh sediment" }, @@ -2753,13 +2761,13 @@ {"name": "Unclassified" , "count": "247" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Neritic zone/Coastal water&Biosample.Specific Ecosystem=Unclassified" }] }, - {"name": "Ocean trench" , "count": "82" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Ocean trench" , "children" : [ + {"name": "Ocean trench" , "count": "85" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Ocean trench" , "children" : [ {"name": "Sediment" , "count": "5" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Ocean trench&Biosample.Specific Ecosystem=Sediment" }, - {"name": "Unclassified" , "count": "77" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Ocean trench&Biosample.Specific Ecosystem=Unclassified" }] + {"name": "Unclassified" , "count": "80" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Ocean trench&Biosample.Specific Ecosystem=Unclassified" }] }, - {"name": "Oceanic" , "count": "5964" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Oceanic" , "children" : [ + {"name": "Oceanic" , "count": "5972" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Oceanic" , "children" : [ {"name": "Abyssal plane" , "count": "77" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Oceanic&Biosample.Specific Ecosystem=Abyssal plane" }, {"name": "Aphotic zone" , "count": "64" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Oceanic&Biosample.Specific Ecosystem=Aphotic zone" }, @@ -2784,19 +2792,19 @@ {"name": "Sediment" , "count": "383" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Oceanic&Biosample.Specific Ecosystem=Sediment" }, - {"name": "Unclassified" , "count": "5053" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Oceanic&Biosample.Specific Ecosystem=Unclassified" }] + {"name": "Unclassified" , "count": "5061" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Oceanic&Biosample.Specific Ecosystem=Unclassified" }] }, {"name": "Oil seeps" , "count": "8" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Oil seeps" , "children" : [ {"name": "Unclassified" , "count": "8" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Oil seeps&Biosample.Specific Ecosystem=Unclassified" }] }, - {"name": "Pelagic zone" , "count": "912" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Pelagic zone" , "children" : [ + {"name": "Pelagic zone" , "count": "925" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Pelagic zone" , "children" : [ {"name": "Abyssopelagic/Abyssal zone" , "count": "27" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Pelagic zone&Biosample.Specific Ecosystem=Abyssopelagic/Abyssal zone" }, {"name": "Bathypelagic/Bathyal zone" , "count": "5" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Pelagic zone&Biosample.Specific Ecosystem=Bathypelagic/Bathyal zone" }, - {"name": "Epipelagic/Euphotic zone" , "count": "289" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Pelagic zone&Biosample.Specific Ecosystem=Epipelagic/Euphotic zone" }, + {"name": "Epipelagic/Euphotic zone" , "count": "302" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Pelagic zone&Biosample.Specific Ecosystem=Epipelagic/Euphotic zone" }, {"name": "Hadopelagic zone/Ocean trenches" , "count": "2" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Pelagic zone&Biosample.Specific Ecosystem=Hadopelagic zone/Ocean trenches" }, @@ -2813,12 +2821,12 @@ {"name": "Unclassified" , "count": "0" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=River plume&Biosample.Specific Ecosystem=Unclassified" }] }, - {"name": "Sea ice" , "count": "103" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Sea ice" , "children" : [ + {"name": "Sea ice" , "count": "104" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Sea ice" , "children" : [ {"name": "Cryoconite" , "count": "3" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Sea ice&Biosample.Specific Ecosystem=Cryoconite" }, {"name": "Melt pond" , "count": "6" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Sea ice&Biosample.Specific Ecosystem=Melt pond" }, - {"name": "Unclassified" , "count": "94" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Sea ice&Biosample.Specific Ecosystem=Unclassified" }] + {"name": "Unclassified" , "count": "95" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Sea ice&Biosample.Specific Ecosystem=Unclassified" }] }, {"name": "Seaweed" , "count": "90" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Seaweed" , "children" : [ @@ -2851,8 +2859,8 @@ {"name": "Unclassified" , "count": "0" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Supratidal zone&Biosample.Specific Ecosystem=Unclassified" }] }, - {"name": "Unclassified" , "count": "5248" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Unclassified" , "children" : [ - {"name": "Unclassified" , "count": "5248" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Unclassified&Biosample.Specific Ecosystem=Unclassified" }] + {"name": "Unclassified" , "count": "5249" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Unclassified" , "children" : [ + {"name": "Unclassified" , "count": "5249" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Unclassified&Biosample.Specific Ecosystem=Unclassified" }] }, {"name": "Volcanic" , "count": "25" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Marine&Biosample.Ecosystem+Subtype=Volcanic" , "children" : [ @@ -3026,7 +3034,7 @@ }] }, - {"name": "Thermal springs" , "count": "3512" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Thermal springs" , "children" : [ + {"name": "Thermal springs" , "count": "3518" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Thermal springs" , "children" : [ {"name": "Acid lake" , "count": "2" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Thermal springs&Biosample.Ecosystem+Subtype=Acid lake" , "children" : [ {"name": "Sediment" , "count": "1" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Thermal springs&Biosample.Ecosystem+Subtype=Acid lake&Biosample.Specific Ecosystem=Sediment" }, @@ -3039,7 +3047,7 @@ {"name": "Unclassified" , "count": "0" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Thermal springs&Biosample.Ecosystem+Subtype=Geothermal pool/Hot lake&Biosample.Specific Ecosystem=Unclassified" }] }, - {"name": "Hot (42-90C)" , "count": "3145" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Thermal springs&Biosample.Ecosystem+Subtype=Hot (42-90C)" , "children" : [ + {"name": "Hot (42-90C)" , "count": "3148" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Thermal springs&Biosample.Ecosystem+Subtype=Hot (42-90C)" , "children" : [ {"name": "Acidic" , "count": "350" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Thermal springs&Biosample.Ecosystem+Subtype=Hot (42-90C)&Biosample.Specific Ecosystem=Acidic" }, {"name": "Alkaline" , "count": "16" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Thermal springs&Biosample.Ecosystem+Subtype=Hot (42-90C)&Biosample.Specific Ecosystem=Alkaline" }, @@ -3048,13 +3056,13 @@ {"name": "Neutral" , "count": "23" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Thermal springs&Biosample.Ecosystem+Subtype=Hot (42-90C)&Biosample.Specific Ecosystem=Neutral" }, - {"name": "Sediment" , "count": "1270" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Thermal springs&Biosample.Ecosystem+Subtype=Hot (42-90C)&Biosample.Specific Ecosystem=Sediment" }, + {"name": "Sediment" , "count": "1273" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Thermal springs&Biosample.Ecosystem+Subtype=Hot (42-90C)&Biosample.Specific Ecosystem=Sediment" }, {"name": "Unclassified" , "count": "558" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Thermal springs&Biosample.Ecosystem+Subtype=Hot (42-90C)&Biosample.Specific Ecosystem=Unclassified" }] }, - {"name": "Microbial mats" , "count": "8" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Thermal springs&Biosample.Ecosystem+Subtype=Microbial mats" , "children" : [ - {"name": "Unclassified" , "count": "8" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Thermal springs&Biosample.Ecosystem+Subtype=Microbial mats&Biosample.Specific Ecosystem=Unclassified" }] + {"name": "Microbial mats" , "count": "10" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Thermal springs&Biosample.Ecosystem+Subtype=Microbial mats" , "children" : [ + {"name": "Unclassified" , "count": "10" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Thermal springs&Biosample.Ecosystem+Subtype=Microbial mats&Biosample.Specific Ecosystem=Unclassified" }] }, {"name": "Near-boiling (>90C)" , "count": "20" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Thermal springs&Biosample.Ecosystem+Subtype=Near-boiling (>90C)" , "children" : [ @@ -3070,6 +3078,8 @@ {"name": "Microbial mats" , "count": "0" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Thermal springs&Biosample.Ecosystem+Subtype=Runoff channel&Biosample.Specific Ecosystem=Microbial mats" }, + {"name": "Sediment" , "count": "0" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Thermal springs&Biosample.Ecosystem+Subtype=Runoff channel&Biosample.Specific Ecosystem=Sediment" }, + {"name": "Unclassified" , "count": "36" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Thermal springs&Biosample.Ecosystem+Subtype=Runoff channel&Biosample.Specific Ecosystem=Unclassified" }] }, @@ -3083,8 +3093,8 @@ {"name": "Unclassified" , "count": "109" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Thermal springs&Biosample.Ecosystem+Subtype=Tepid (25-34C)&Biosample.Specific Ecosystem=Unclassified" }] }, - {"name": "Unclassified" , "count": "123" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Thermal springs&Biosample.Ecosystem+Subtype=Unclassified" , "children" : [ - {"name": "Unclassified" , "count": "123" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Thermal springs&Biosample.Ecosystem+Subtype=Unclassified&Biosample.Specific Ecosystem=Unclassified" }] + {"name": "Unclassified" , "count": "124" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Thermal springs&Biosample.Ecosystem+Subtype=Unclassified" , "children" : [ + {"name": "Unclassified" , "count": "124" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Thermal springs&Biosample.Ecosystem+Subtype=Unclassified&Biosample.Specific Ecosystem=Unclassified" }] }, {"name": "Warm (34-42C)" , "count": "38" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Aquatic&Biosample.Ecosystem+Type=Thermal springs&Biosample.Ecosystem+Subtype=Warm (34-42C)" , "children" : [ @@ -3105,7 +3115,7 @@ }] }, - {"name": "Terrestrial" , "count": "39158" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial" , "children" : [ + {"name": "Terrestrial" , "count": "39279" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial" , "children" : [ {"name": "Agricultural field" , "count": "0" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Agricultural field" , "children" : [ {"name": "Unclassified" , "count": "0" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Agricultural field&Biosample.Ecosystem+Subtype=Unclassified" , "children" : [ {"name": "Unclassified" , "count": "0" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Agricultural field&Biosample.Ecosystem+Subtype=Unclassified&Biosample.Specific Ecosystem=Unclassified" }] @@ -3134,19 +3144,19 @@ }] }, - {"name": "Deep subsurface" , "count": "758" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Deep subsurface" , "children" : [ + {"name": "Deep subsurface" , "count": "759" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Deep subsurface" , "children" : [ {"name": "Aquifer" , "count": "88" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Deep subsurface&Biosample.Ecosystem+Subtype=Aquifer" , "children" : [ {"name": "Rock core/Sediment" , "count": "62" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Deep subsurface&Biosample.Ecosystem+Subtype=Aquifer&Biosample.Specific Ecosystem=Rock core/Sediment" }, {"name": "Unclassified" , "count": "26" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Deep subsurface&Biosample.Ecosystem+Subtype=Aquifer&Biosample.Specific Ecosystem=Unclassified" }] }, - {"name": "Cave" , "count": "15" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Deep subsurface&Biosample.Ecosystem+Subtype=Cave" , "children" : [ + {"name": "Cave" , "count": "16" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Deep subsurface&Biosample.Ecosystem+Subtype=Cave" , "children" : [ {"name": "Floor sediment" , "count": "0" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Deep subsurface&Biosample.Ecosystem+Subtype=Cave&Biosample.Specific Ecosystem=Floor sediment" }, {"name": "Speleothems" , "count": "0" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Deep subsurface&Biosample.Ecosystem+Subtype=Cave&Biosample.Specific Ecosystem=Speleothems" }, - {"name": "Unclassified" , "count": "1" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Deep subsurface&Biosample.Ecosystem+Subtype=Cave&Biosample.Specific Ecosystem=Unclassified" }, + {"name": "Unclassified" , "count": "2" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Deep subsurface&Biosample.Ecosystem+Subtype=Cave&Biosample.Specific Ecosystem=Unclassified" }, {"name": "Wall biofilm" , "count": "8" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Deep subsurface&Biosample.Ecosystem+Subtype=Cave&Biosample.Specific Ecosystem=Wall biofilm" }, @@ -3370,11 +3380,11 @@ }] }, - {"name": "Soil" , "count": "36125" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil" , "children" : [ - {"name": "Agricultural land" , "count": "7439" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Agricultural land" , "children" : [ - {"name": "Bulk soil" , "count": "4305" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Agricultural land&Biosample.Specific Ecosystem=Bulk soil" }, + {"name": "Soil" , "count": "36245" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil" , "children" : [ + {"name": "Agricultural land" , "count": "7441" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Agricultural land" , "children" : [ + {"name": "Bulk soil" , "count": "4306" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Agricultural land&Biosample.Specific Ecosystem=Bulk soil" }, - {"name": "Unclassified" , "count": "3134" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Agricultural land&Biosample.Specific Ecosystem=Unclassified" }] + {"name": "Unclassified" , "count": "3135" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Agricultural land&Biosample.Specific Ecosystem=Unclassified" }] }, {"name": "Alpine" , "count": "15" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Alpine" , "children" : [ @@ -3459,12 +3469,12 @@ {"name": "Uranium contaminated" , "count": "45" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Contaminated&Biosample.Specific Ecosystem=Uranium contaminated" }] }, - {"name": "Desert" , "count": "411" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Desert" , "children" : [ + {"name": "Desert" , "count": "412" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Desert" , "children" : [ {"name": "Dry permafrost" , "count": "0" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Desert&Biosample.Specific Ecosystem=Dry permafrost" }, {"name": "Gibber plain" , "count": "10" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Desert&Biosample.Specific Ecosystem=Gibber plain" }, - {"name": "Unclassified" , "count": "401" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Desert&Biosample.Specific Ecosystem=Unclassified" }] + {"name": "Unclassified" , "count": "402" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Desert&Biosample.Specific Ecosystem=Unclassified" }] }, {"name": "Drainage basin" , "count": "0" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Drainage basin" , "children" : [ @@ -3499,8 +3509,8 @@ {"name": "Unclassified" , "count": "0" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Geothermal field&Biosample.Specific Ecosystem=Unclassified" }] }, - {"name": "Glacial till" , "count": "152" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Glacial till" , "children" : [ - {"name": "Unclassified" , "count": "152" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Glacial till&Biosample.Specific Ecosystem=Unclassified" }] + {"name": "Glacial till" , "count": "153" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Glacial till" , "children" : [ + {"name": "Unclassified" , "count": "153" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Glacial till&Biosample.Specific Ecosystem=Unclassified" }] }, {"name": "Glacier" , "count": "125" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Glacier" , "children" : [ @@ -3517,22 +3527,22 @@ {"name": "Unclassified" , "count": "94" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Glacier&Biosample.Specific Ecosystem=Unclassified" }] }, - {"name": "Grasslands" , "count": "3543" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Grasslands" , "children" : [ + {"name": "Grasslands" , "count": "3581" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Grasslands" , "children" : [ {"name": "Bulk soil" , "count": "354" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Grasslands&Biosample.Specific Ecosystem=Bulk soil" }, {"name": "Pasture" , "count": "137" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Grasslands&Biosample.Specific Ecosystem=Pasture" }, - {"name": "Unclassified" , "count": "3052" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Grasslands&Biosample.Specific Ecosystem=Unclassified" }] + {"name": "Unclassified" , "count": "3090" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Grasslands&Biosample.Specific Ecosystem=Unclassified" }] }, {"name": "Gravesite" , "count": "2" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Gravesite" , "children" : [ {"name": "Sediment" , "count": "2" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Gravesite&Biosample.Specific Ecosystem=Sediment" }] }, - {"name": "Greenhouse" , "count": "117" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Greenhouse" , "children" : [ + {"name": "Greenhouse" , "count": "119" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Greenhouse" , "children" : [ {"name": "Agricultural land" , "count": "17" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Greenhouse&Biosample.Specific Ecosystem=Agricultural land" }, - {"name": "Unclassified" , "count": "100" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Greenhouse&Biosample.Specific Ecosystem=Unclassified" }] + {"name": "Unclassified" , "count": "102" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Greenhouse&Biosample.Specific Ecosystem=Unclassified" }] }, {"name": "Intertidal zone" , "count": "0" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Intertidal zone" , "children" : [ @@ -3741,12 +3751,12 @@ {"name": "Unclassified" , "count": "1" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Tailings&Biosample.Specific Ecosystem=Unclassified" }] }, - {"name": "Temperate forest" , "count": "3870" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Temperate forest" , "children" : [ + {"name": "Temperate forest" , "count": "3927" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Temperate forest" , "children" : [ {"name": "A horizon/Topsoil" , "count": "12" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Temperate forest&Biosample.Specific Ecosystem=A horizon/Topsoil" }, {"name": "B horizon/Subsoil" , "count": "11" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Temperate forest&Biosample.Specific Ecosystem=B horizon/Subsoil" }, - {"name": "Bulk soil" , "count": "2563" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Temperate forest&Biosample.Specific Ecosystem=Bulk soil" }, + {"name": "Bulk soil" , "count": "2572" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Temperate forest&Biosample.Specific Ecosystem=Bulk soil" }, {"name": "C horizon/Substratum" , "count": "0" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Temperate forest&Biosample.Specific Ecosystem=C horizon/Substratum" }, @@ -3754,11 +3764,11 @@ {"name": "Humus" , "count": "33" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Temperate forest&Biosample.Specific Ecosystem=Humus" }, - {"name": "Mineral soil" , "count": "338" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Temperate forest&Biosample.Specific Ecosystem=Mineral soil" }, + {"name": "Mineral soil" , "count": "339" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Temperate forest&Biosample.Specific Ecosystem=Mineral soil" }, - {"name": "O horizon/Organic" , "count": "463" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Temperate forest&Biosample.Specific Ecosystem=O horizon/Organic" }, + {"name": "O horizon/Organic" , "count": "472" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Temperate forest&Biosample.Specific Ecosystem=O horizon/Organic" }, - {"name": "Unclassified" , "count": "450" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Temperate forest&Biosample.Specific Ecosystem=Unclassified" }] + {"name": "Unclassified" , "count": "488" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Temperate forest&Biosample.Specific Ecosystem=Unclassified" }] }, {"name": "Tree plantation" , "count": "111" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Tree plantation" , "children" : [ @@ -3795,7 +3805,7 @@ {"name": "Unclassified" , "count": "455" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Tundra&Biosample.Specific Ecosystem=Unclassified" }] }, - {"name": "Unclassified" , "count": "10453" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Unclassified" , "children" : [ + {"name": "Unclassified" , "count": "10472" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Unclassified" , "children" : [ {"name": "Agricultural land" , "count": "1325" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Unclassified&Biosample.Specific Ecosystem=Agricultural land" }, {"name": "Alpine" , "count": "46" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Unclassified&Biosample.Specific Ecosystem=Alpine" }, @@ -3834,7 +3844,7 @@ {"name": "Tropical rainforest" , "count": "86" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Unclassified&Biosample.Specific Ecosystem=Tropical rainforest" }, - {"name": "Unclassified" , "count": "6863" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Unclassified&Biosample.Specific Ecosystem=Unclassified" }] + {"name": "Unclassified" , "count": "6882" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Unclassified&Biosample.Specific Ecosystem=Unclassified" }] }, {"name": "Urban forest" , "count": "0" , "url": "search?Biosample.Ecosystem=Environmental&Biosample.Ecosystem+Category=Terrestrial&Biosample.Ecosystem+Type=Soil&Biosample.Ecosystem+Subtype=Urban forest" , "children" : [ @@ -3910,8 +3920,8 @@ }] } , -{"name": "Host-associated", "count": "94954" , "url": "search?Biosample.Ecosystem=Host-associated" , "children" : [ - {"name": "Algae" , "count": "661" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Algae" , "children" : [ +{"name": "Host-associated", "count": "95659" , "url": "search?Biosample.Ecosystem=Host-associated" , "children" : [ + {"name": "Algae" , "count": "667" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Algae" , "children" : [ {"name": "Biocrust" , "count": "0" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Algae&Biosample.Ecosystem+Type=Biocrust" , "children" : [ {"name": "Unclassified" , "count": "0" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Algae&Biosample.Ecosystem+Type=Biocrust&Biosample.Ecosystem+Subtype=Unclassified" , "children" : [ {"name": "Unclassified" , "count": "0" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Algae&Biosample.Ecosystem+Type=Biocrust&Biosample.Ecosystem+Subtype=Unclassified&Biosample.Specific Ecosystem=Unclassified" }] @@ -3964,13 +3974,13 @@ }] }, - {"name": "Green algae" , "count": "130" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Algae&Biosample.Ecosystem+Type=Green algae" , "children" : [ + {"name": "Green algae" , "count": "136" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Algae&Biosample.Ecosystem+Type=Green algae" , "children" : [ {"name": "Ectosymbionts" , "count": "45" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Algae&Biosample.Ecosystem+Type=Green algae&Biosample.Ecosystem+Subtype=Ectosymbionts" , "children" : [ {"name": "Unclassified" , "count": "45" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Algae&Biosample.Ecosystem+Type=Green algae&Biosample.Ecosystem+Subtype=Ectosymbionts&Biosample.Specific Ecosystem=Unclassified" }] }, - {"name": "Unclassified" , "count": "85" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Algae&Biosample.Ecosystem+Type=Green algae&Biosample.Ecosystem+Subtype=Unclassified" , "children" : [ - {"name": "Unclassified" , "count": "85" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Algae&Biosample.Ecosystem+Type=Green algae&Biosample.Ecosystem+Subtype=Unclassified&Biosample.Specific Ecosystem=Unclassified" }] + {"name": "Unclassified" , "count": "91" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Algae&Biosample.Ecosystem+Type=Green algae&Biosample.Ecosystem+Subtype=Unclassified" , "children" : [ + {"name": "Unclassified" , "count": "91" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Algae&Biosample.Ecosystem+Type=Green algae&Biosample.Ecosystem+Subtype=Unclassified&Biosample.Specific Ecosystem=Unclassified" }] }] }, @@ -4124,8 +4134,6 @@ }, {"name": "Subcuticular space" , "count": "0" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Annelida&Biosample.Ecosystem+Type=Integument&Biosample.Ecosystem+Subtype=Subcuticular space" , "children" : [ - {"name": "Extracellular symbionts" , "count": "0" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Annelida&Biosample.Ecosystem+Type=Integument&Biosample.Ecosystem+Subtype=Subcuticular space&Biosample.Specific Ecosystem=Extracellular symbionts" }, - {"name": "Unclassified" , "count": "0" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Annelida&Biosample.Ecosystem+Type=Integument&Biosample.Ecosystem+Subtype=Subcuticular space&Biosample.Specific Ecosystem=Unclassified" }] }, @@ -4379,7 +4387,7 @@ }] }, - {"name": "Arthropoda: Insects" , "count": "2402" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Arthropoda: Insects" , "children" : [ + {"name": "Arthropoda: Insects" , "count": "2406" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Arthropoda: Insects" , "children" : [ {"name": "Abdomen" , "count": "152" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Arthropoda: Insects&Biosample.Ecosystem+Type=Abdomen" , "children" : [ {"name": "Metasoma" , "count": "1" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Arthropoda: Insects&Biosample.Ecosystem+Type=Abdomen&Biosample.Ecosystem+Subtype=Metasoma" , "children" : [ {"name": "Gaster" , "count": "1" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Arthropoda: Insects&Biosample.Ecosystem+Type=Abdomen&Biosample.Ecosystem+Subtype=Metasoma&Biosample.Specific Ecosystem=Gaster" }] @@ -4510,17 +4518,17 @@ }] }, - {"name": "Larva" , "count": "263" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Arthropoda: Insects&Biosample.Ecosystem+Type=Larva" , "children" : [ + {"name": "Larva" , "count": "267" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Arthropoda: Insects&Biosample.Ecosystem+Type=Larva" , "children" : [ {"name": "Abdomen" , "count": "0" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Arthropoda: Insects&Biosample.Ecosystem+Type=Larva&Biosample.Ecosystem+Subtype=Abdomen" , "children" : [ {"name": "Unclassified" , "count": "0" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Arthropoda: Insects&Biosample.Ecosystem+Type=Larva&Biosample.Ecosystem+Subtype=Abdomen&Biosample.Specific Ecosystem=Unclassified" }] }, - {"name": "Gut" , "count": "85" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Arthropoda: Insects&Biosample.Ecosystem+Type=Larva&Biosample.Ecosystem+Subtype=Gut" , "children" : [ + {"name": "Gut" , "count": "89" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Arthropoda: Insects&Biosample.Ecosystem+Type=Larva&Biosample.Ecosystem+Subtype=Gut" , "children" : [ {"name": "Frass" , "count": "0" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Arthropoda: Insects&Biosample.Ecosystem+Type=Larva&Biosample.Ecosystem+Subtype=Gut&Biosample.Specific Ecosystem=Frass" }, {"name": "Gastric caeca" , "count": "2" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Arthropoda: Insects&Biosample.Ecosystem+Type=Larva&Biosample.Ecosystem+Subtype=Gut&Biosample.Specific Ecosystem=Gastric caeca" }, - {"name": "Unclassified" , "count": "83" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Arthropoda: Insects&Biosample.Ecosystem+Type=Larva&Biosample.Ecosystem+Subtype=Gut&Biosample.Specific Ecosystem=Unclassified" }] + {"name": "Unclassified" , "count": "87" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Arthropoda: Insects&Biosample.Ecosystem+Type=Larva&Biosample.Ecosystem+Subtype=Gut&Biosample.Specific Ecosystem=Unclassified" }] }, {"name": "Head" , "count": "0" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Arthropoda: Insects&Biosample.Ecosystem+Type=Larva&Biosample.Ecosystem+Subtype=Head" , "children" : [ @@ -5405,7 +5413,7 @@ }] }, - {"name": "Fungi" , "count": "1149" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Fungi" , "children" : [ + {"name": "Fungi" , "count": "1150" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Fungi" , "children" : [ {"name": "Appressorium" , "count": "3" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Fungi&Biosample.Ecosystem+Type=Appressorium" , "children" : [ {"name": "Unclassified" , "count": "3" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Fungi&Biosample.Ecosystem+Type=Appressorium&Biosample.Ecosystem+Subtype=Unclassified" , "children" : [ {"name": "Unclassified" , "count": "3" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Fungi&Biosample.Ecosystem+Type=Appressorium&Biosample.Ecosystem+Subtype=Unclassified&Biosample.Specific Ecosystem=Unclassified" }] @@ -5434,9 +5442,9 @@ }] }, - {"name": "Mycelium" , "count": "1002" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Fungi&Biosample.Ecosystem+Type=Mycelium" , "children" : [ - {"name": "Unclassified" , "count": "1002" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Fungi&Biosample.Ecosystem+Type=Mycelium&Biosample.Ecosystem+Subtype=Unclassified" , "children" : [ - {"name": "Unclassified" , "count": "1002" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Fungi&Biosample.Ecosystem+Type=Mycelium&Biosample.Ecosystem+Subtype=Unclassified&Biosample.Specific Ecosystem=Unclassified" }] + {"name": "Mycelium" , "count": "1003" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Fungi&Biosample.Ecosystem+Type=Mycelium" , "children" : [ + {"name": "Unclassified" , "count": "1003" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Fungi&Biosample.Ecosystem+Type=Mycelium&Biosample.Ecosystem+Subtype=Unclassified" , "children" : [ + {"name": "Unclassified" , "count": "1003" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Fungi&Biosample.Ecosystem+Type=Mycelium&Biosample.Ecosystem+Subtype=Unclassified&Biosample.Specific Ecosystem=Unclassified" }] }] }, @@ -7537,10 +7545,10 @@ }] }, - {"name": "Microbial" , "count": "534" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Microbial" , "children" : [ - {"name": "Bacteria" , "count": "522" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Microbial&Biosample.Ecosystem+Type=Bacteria" , "children" : [ - {"name": "Unclassified" , "count": "522" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Microbial&Biosample.Ecosystem+Type=Bacteria&Biosample.Ecosystem+Subtype=Unclassified" , "children" : [ - {"name": "Unclassified" , "count": "522" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Microbial&Biosample.Ecosystem+Type=Bacteria&Biosample.Ecosystem+Subtype=Unclassified&Biosample.Specific Ecosystem=Unclassified" }] + {"name": "Microbial" , "count": "546" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Microbial" , "children" : [ + {"name": "Bacteria" , "count": "544" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Microbial&Biosample.Ecosystem+Type=Bacteria" , "children" : [ + {"name": "Unclassified" , "count": "544" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Microbial&Biosample.Ecosystem+Type=Bacteria&Biosample.Ecosystem+Subtype=Unclassified" , "children" : [ + {"name": "Unclassified" , "count": "544" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Microbial&Biosample.Ecosystem+Type=Bacteria&Biosample.Ecosystem+Subtype=Unclassified&Biosample.Specific Ecosystem=Unclassified" }] }] }, @@ -7550,13 +7558,13 @@ }] }, - {"name": "Dinoflagellates" , "count": "10" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Microbial&Biosample.Ecosystem+Type=Dinoflagellates" , "children" : [ - {"name": "Endosymbionts" , "count": "1" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Microbial&Biosample.Ecosystem+Type=Dinoflagellates&Biosample.Ecosystem+Subtype=Endosymbionts" , "children" : [ - {"name": "Unclassified" , "count": "1" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Microbial&Biosample.Ecosystem+Type=Dinoflagellates&Biosample.Ecosystem+Subtype=Endosymbionts&Biosample.Specific Ecosystem=Unclassified" }] + {"name": "Dinoflagellates" , "count": "0" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Microbial&Biosample.Ecosystem+Type=Dinoflagellates" , "children" : [ + {"name": "Endosymbionts" , "count": "0" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Microbial&Biosample.Ecosystem+Type=Dinoflagellates&Biosample.Ecosystem+Subtype=Endosymbionts" , "children" : [ + {"name": "Unclassified" , "count": "0" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Microbial&Biosample.Ecosystem+Type=Dinoflagellates&Biosample.Ecosystem+Subtype=Endosymbionts&Biosample.Specific Ecosystem=Unclassified" }] }, - {"name": "Unclassified" , "count": "9" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Microbial&Biosample.Ecosystem+Type=Dinoflagellates&Biosample.Ecosystem+Subtype=Unclassified" , "children" : [ - {"name": "Unclassified" , "count": "9" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Microbial&Biosample.Ecosystem+Type=Dinoflagellates&Biosample.Ecosystem+Subtype=Unclassified&Biosample.Specific Ecosystem=Unclassified" }] + {"name": "Unclassified" , "count": "0" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Microbial&Biosample.Ecosystem+Type=Dinoflagellates&Biosample.Ecosystem+Subtype=Unclassified" , "children" : [ + {"name": "Unclassified" , "count": "0" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Microbial&Biosample.Ecosystem+Type=Dinoflagellates&Biosample.Ecosystem+Subtype=Unclassified&Biosample.Specific Ecosystem=Unclassified" }] }] }, @@ -7705,7 +7713,7 @@ }] }, - {"name": "Plants" , "count": "22628" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Plants" , "children" : [ + {"name": "Plants" , "count": "23300" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Plants" , "children" : [ {"name": "Bryophytes" , "count": "0" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Plants&Biosample.Ecosystem+Type=Bryophytes" , "children" : [ {"name": "Hornworts" , "count": "0" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Plants&Biosample.Ecosystem+Type=Bryophytes&Biosample.Ecosystem+Subtype=Hornworts" , "children" : [ {"name": "Rhizoids" , "count": "0" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Plants&Biosample.Ecosystem+Type=Bryophytes&Biosample.Ecosystem+Subtype=Hornworts&Biosample.Specific Ecosystem=Rhizoids" }, @@ -7778,7 +7786,7 @@ }] }, - {"name": "Phyllosphere" , "count": "4382" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Plants&Biosample.Ecosystem+Type=Phyllosphere" , "children" : [ + {"name": "Phyllosphere" , "count": "4384" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Plants&Biosample.Ecosystem+Type=Phyllosphere" , "children" : [ {"name": "Anthosphere" , "count": "5" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Plants&Biosample.Ecosystem+Type=Phyllosphere&Biosample.Ecosystem+Subtype=Anthosphere" , "children" : [ {"name": "Nectar" , "count": "0" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Plants&Biosample.Ecosystem+Type=Phyllosphere&Biosample.Ecosystem+Subtype=Anthosphere&Biosample.Specific Ecosystem=Nectar" }, @@ -7811,7 +7819,7 @@ {"name": "Unclassified" , "count": "0" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Plants&Biosample.Ecosystem+Type=Phyllosphere&Biosample.Ecosystem+Subtype=Petiole&Biosample.Specific Ecosystem=Unclassified" }] }, - {"name": "Phylloplane/Leaf" , "count": "3139" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Plants&Biosample.Ecosystem+Type=Phyllosphere&Biosample.Ecosystem+Subtype=Phylloplane/Leaf" , "children" : [ + {"name": "Phylloplane/Leaf" , "count": "3141" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Plants&Biosample.Ecosystem+Type=Phyllosphere&Biosample.Ecosystem+Subtype=Phylloplane/Leaf" , "children" : [ {"name": "Endophytes" , "count": "26" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Plants&Biosample.Ecosystem+Type=Phyllosphere&Biosample.Ecosystem+Subtype=Phylloplane/Leaf&Biosample.Specific Ecosystem=Endophytes" }, {"name": "Endosphere" , "count": "30" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Plants&Biosample.Ecosystem+Type=Phyllosphere&Biosample.Ecosystem+Subtype=Phylloplane/Leaf&Biosample.Specific Ecosystem=Endosphere" }, @@ -7830,7 +7838,7 @@ {"name": "Pitcher fluid" , "count": "0" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Plants&Biosample.Ecosystem+Type=Phyllosphere&Biosample.Ecosystem+Subtype=Phylloplane/Leaf&Biosample.Specific Ecosystem=Pitcher fluid" }, - {"name": "Unclassified" , "count": "3083" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Plants&Biosample.Ecosystem+Type=Phyllosphere&Biosample.Ecosystem+Subtype=Phylloplane/Leaf&Biosample.Specific Ecosystem=Unclassified" }, + {"name": "Unclassified" , "count": "3085" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Plants&Biosample.Ecosystem+Type=Phyllosphere&Biosample.Ecosystem+Subtype=Phylloplane/Leaf&Biosample.Specific Ecosystem=Unclassified" }, {"name": "Xylem vessels" , "count": "0" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Plants&Biosample.Ecosystem+Type=Phyllosphere&Biosample.Ecosystem+Subtype=Phylloplane/Leaf&Biosample.Specific Ecosystem=Xylem vessels" }] }, @@ -7844,6 +7852,8 @@ }, {"name": "Stem" , "count": "26" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Plants&Biosample.Ecosystem+Type=Phyllosphere&Biosample.Ecosystem+Subtype=Stem" , "children" : [ + {"name": "Stolon" , "count": "0" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Plants&Biosample.Ecosystem+Type=Phyllosphere&Biosample.Ecosystem+Subtype=Stem&Biosample.Specific Ecosystem=Stolon" }, + {"name": "Unclassified" , "count": "1" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Plants&Biosample.Ecosystem+Type=Phyllosphere&Biosample.Ecosystem+Subtype=Stem&Biosample.Specific Ecosystem=Unclassified" }, {"name": "Wood decay" , "count": "13" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Plants&Biosample.Ecosystem+Type=Phyllosphere&Biosample.Ecosystem+Subtype=Stem&Biosample.Specific Ecosystem=Wood decay" }, @@ -7894,7 +7904,7 @@ }] }, - {"name": "Roots" , "count": "17097" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Plants&Biosample.Ecosystem+Type=Roots" , "children" : [ + {"name": "Roots" , "count": "17767" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Plants&Biosample.Ecosystem+Type=Roots" , "children" : [ {"name": "Aerial root" , "count": "0" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Plants&Biosample.Ecosystem+Type=Roots&Biosample.Ecosystem+Subtype=Aerial root" , "children" : [ {"name": "Mucilage" , "count": "0" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Plants&Biosample.Ecosystem+Type=Roots&Biosample.Ecosystem+Subtype=Aerial root&Biosample.Specific Ecosystem=Mucilage" }, @@ -7923,8 +7933,8 @@ {"name": "Unclassified" , "count": "112" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Plants&Biosample.Ecosystem+Type=Roots&Biosample.Ecosystem+Subtype=Rhizoplane&Biosample.Specific Ecosystem=Unclassified" }] }, - {"name": "Rhizosphere" , "count": "11266" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Plants&Biosample.Ecosystem+Type=Roots&Biosample.Ecosystem+Subtype=Rhizosphere" , "children" : [ - {"name": "Soil" , "count": "2190" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Plants&Biosample.Ecosystem+Type=Roots&Biosample.Ecosystem+Subtype=Rhizosphere&Biosample.Specific Ecosystem=Soil" }, + {"name": "Rhizosphere" , "count": "11936" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Plants&Biosample.Ecosystem+Type=Roots&Biosample.Ecosystem+Subtype=Rhizosphere" , "children" : [ + {"name": "Soil" , "count": "2860" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Plants&Biosample.Ecosystem+Type=Roots&Biosample.Ecosystem+Subtype=Rhizosphere&Biosample.Specific Ecosystem=Soil" }, {"name": "Unclassified" , "count": "9076" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Plants&Biosample.Ecosystem+Type=Roots&Biosample.Ecosystem+Subtype=Rhizosphere&Biosample.Specific Ecosystem=Unclassified" }] }, @@ -7999,7 +8009,7 @@ }] }, - {"name": "Protists" , "count": "167" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Protists" , "children" : [ + {"name": "Protists" , "count": "177" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Protists" , "children" : [ {"name": "Amoebozoa" , "count": "78" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Protists&Biosample.Ecosystem+Type=Amoebozoa" , "children" : [ {"name": "Unclassified" , "count": "78" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Protists&Biosample.Ecosystem+Type=Amoebozoa&Biosample.Ecosystem+Subtype=Unclassified" , "children" : [ {"name": "Unclassified" , "count": "78" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Protists&Biosample.Ecosystem+Type=Amoebozoa&Biosample.Ecosystem+Subtype=Unclassified&Biosample.Specific Ecosystem=Unclassified" }] @@ -8007,18 +8017,14 @@ }, {"name": "Breviatea" , "count": "1" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Protists&Biosample.Ecosystem+Type=Breviatea" , "children" : [ - {"name": "Dinoflagellates" , "count": "0" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Protists&Biosample.Ecosystem+Type=Breviatea&Biosample.Ecosystem+Subtype=Dinoflagellates" , "children" : [ - {"name": "Unclassified" , "count": "0" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Protists&Biosample.Ecosystem+Type=Breviatea&Biosample.Ecosystem+Subtype=Dinoflagellates&Biosample.Specific Ecosystem=Unclassified" }] -}, - {"name": "Unclassified" , "count": "1" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Protists&Biosample.Ecosystem+Type=Breviatea&Biosample.Ecosystem+Subtype=Unclassified" , "children" : [ {"name": "Unclassified" , "count": "1" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Protists&Biosample.Ecosystem+Type=Breviatea&Biosample.Ecosystem+Subtype=Unclassified&Biosample.Specific Ecosystem=Unclassified" }] }] }, - {"name": "Dinoflagellates" , "count": "1" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Protists&Biosample.Ecosystem+Type=Dinoflagellates" , "children" : [ - {"name": "Unclassified" , "count": "1" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Protists&Biosample.Ecosystem+Type=Dinoflagellates&Biosample.Ecosystem+Subtype=Unclassified" , "children" : [ - {"name": "Unclassified" , "count": "1" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Protists&Biosample.Ecosystem+Type=Dinoflagellates&Biosample.Ecosystem+Subtype=Unclassified&Biosample.Specific Ecosystem=Unclassified" }] + {"name": "Dinoflagellates" , "count": "11" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Protists&Biosample.Ecosystem+Type=Dinoflagellates" , "children" : [ + {"name": "Unclassified" , "count": "11" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Protists&Biosample.Ecosystem+Type=Dinoflagellates&Biosample.Ecosystem+Subtype=Unclassified" , "children" : [ + {"name": "Unclassified" , "count": "11" , "url": "search?Biosample.Ecosystem=Host-associated&Biosample.Ecosystem+Category=Protists&Biosample.Ecosystem+Type=Dinoflagellates&Biosample.Ecosystem+Subtype=Unclassified&Biosample.Specific Ecosystem=Unclassified" }] }] }, diff --git a/src/nmdc_submission_schema/datamodel/nmdc_submission_schema.py b/src/nmdc_submission_schema/datamodel/nmdc_submission_schema.py index 90655c9e..a850b1bb 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: 2024-10-08T12:54:01 +# Generation date: 2024-11-06T16:44:48 # Schema: nmdc_submission_schema # # id: https://example.com/nmdc_submission_schema @@ -8,20 +8,55 @@ import dataclasses import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any from dataclasses import dataclass -from datetime import date, datetime, time -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int +from datetime import ( + date, + datetime, + time +) +from typing import ( + Any, + ClassVar, + Dict, + List, + Optional, + Union +) + +from jsonasobj2 import ( + JsonObj, + as_dict +) +from linkml_runtime.linkml_model.meta import ( + EnumDefinition, + PermissibleValue, + PvFormulaOptions +) +from linkml_runtime.utils.curienamespace import CurieNamespace from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace +from linkml_runtime.utils.formatutils import ( + camelcase, + sfx, + underscore +) +from linkml_runtime.utils.metamodelcore import ( + bnode, + empty_dict, + empty_list +) +from linkml_runtime.utils.slot import Slot +from linkml_runtime.utils.yamlutils import ( + YAMLRoot, + extended_float, + extended_int, + extended_str +) +from rdflib import ( + Namespace, + URIRef +) + from linkml_runtime.utils.metamodelcore import Bool, Curie, Decimal, ElementIdentifier, NCName, NodeIdentifier, URI, URIorCURIE, XSDDate, XSDDateTime, XSDTime metamodel_version = "1.7.0" @@ -147,14 +182,6 @@ class LanguageCode(str): type_model_uri = NMDC_SUB_SCHEMA.LanguageCode -class String(str): - """ A character string """ - type_class_uri = XSD["string"] - type_class_curie = "xsd:string" - type_name = "string" - type_model_uri = NMDC_SUB_SCHEMA.String - - class Integer(int): """ An integer """ type_class_uri = XSD["integer"] @@ -163,12 +190,12 @@ class Integer(int): type_model_uri = NMDC_SUB_SCHEMA.Integer -class Boolean(Bool): - """ A binary (true or false) value """ - type_class_uri = XSD["boolean"] - type_class_curie = "xsd:boolean" - type_name = "boolean" - type_model_uri = NMDC_SUB_SCHEMA.Boolean +class Double(float): + """ A real number that conforms to the xsd:double specification """ + type_class_uri = XSD["double"] + type_class_curie = "xsd:double" + type_name = "double" + type_model_uri = NMDC_SUB_SCHEMA.Double class Float(float): @@ -179,14 +206,6 @@ class Float(float): type_model_uri = NMDC_SUB_SCHEMA.Float -class Double(float): - """ A real number that conforms to the xsd:double specification """ - type_class_uri = XSD["double"] - type_class_curie = "xsd:double" - type_name = "double" - type_model_uri = NMDC_SUB_SCHEMA.Double - - class Decimal(Decimal): """ A real number with arbitrary precision that conforms to the xsd:decimal specification """ type_class_uri = XSD["decimal"] @@ -195,6 +214,30 @@ class Decimal(Decimal): type_model_uri = NMDC_SUB_SCHEMA.Decimal +class Uriorcurie(URIorCURIE): + """ a URI or a CURIE """ + type_class_uri = XSD["anyURI"] + type_class_curie = "xsd:anyURI" + type_name = "uriorcurie" + type_model_uri = NMDC_SUB_SCHEMA.Uriorcurie + + +class String(str): + """ A character string """ + type_class_uri = XSD["string"] + type_class_curie = "xsd:string" + type_name = "string" + type_model_uri = NMDC_SUB_SCHEMA.String + + +class Boolean(Bool): + """ A binary (true or false) value """ + type_class_uri = XSD["boolean"] + type_class_curie = "xsd:boolean" + type_name = "boolean" + type_model_uri = NMDC_SUB_SCHEMA.Boolean + + class Time(XSDTime): """ A time object represents a (local) time of day, independent of any particular day """ type_class_uri = XSD["time"] @@ -227,14 +270,6 @@ class DateOrDatetime(str): type_model_uri = NMDC_SUB_SCHEMA.DateOrDatetime -class Uriorcurie(URIorCURIE): - """ a URI or a CURIE """ - type_class_uri = XSD["anyURI"] - type_class_curie = "xsd:anyURI" - type_name = "uriorcurie" - type_model_uri = NMDC_SUB_SCHEMA.Uriorcurie - - class Curie(Curie): """ a compact URI """ type_class_uri = XSD["string"] @@ -9704,33 +9739,20 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): # Enumerations class BioticRelationshipEnum(EnumDefinitionImpl): - """ - placeholder enum descr - """ - commensalism = PermissibleValue( - text="commensalism", - description="placeholder PV descr") - mutualism = PermissibleValue( - text="mutualism", - description="placeholder PV descr") - parasitism = PermissibleValue( - text="parasitism", - description="placeholder PV descr") - symbiotic = PermissibleValue( - text="symbiotic", - description="placeholder enum descr") + + commensalism = PermissibleValue(text="commensalism") + mutualism = PermissibleValue(text="mutualism") + parasitism = PermissibleValue(text="parasitism") + symbiotic = PermissibleValue(text="symbiotic") _defn = EnumDefinition( name="BioticRelationshipEnum", - description="placeholder enum descr", ) @classmethod def _addvals(cls): setattr(cls, "free living", - PermissibleValue( - text="free living", - description="placeholder PV descr")) + PermissibleValue(text="free living")) class JgiContTypeEnum(EnumDefinitionImpl): @@ -9742,182 +9764,93 @@ class JgiContTypeEnum(EnumDefinitionImpl): ) class DnaSampleFormatEnum(EnumDefinitionImpl): - """ - placeholder enum descr - """ - DNAStable = PermissibleValue( - text="DNAStable", - description="placeholder PV descr") - Ethanol = PermissibleValue( - text="Ethanol", - description="placeholder PV descr") - PBS = PermissibleValue( - text="PBS", - description="placeholder PV descr") - Pellet = PermissibleValue( - text="Pellet", - description="placeholder PV descr") - RNAStable = PermissibleValue( - text="RNAStable", - description="placeholder PV descr") - TE = PermissibleValue( - text="TE", - description="placeholder PV descr") - Water = PermissibleValue( - text="Water", - description="placeholder PV descr") + + DNAStable = PermissibleValue(text="DNAStable") + Ethanol = PermissibleValue(text="Ethanol") + PBS = PermissibleValue(text="PBS") + Pellet = PermissibleValue(text="Pellet") + RNAStable = PermissibleValue(text="RNAStable") + TE = PermissibleValue(text="TE") + Water = PermissibleValue(text="Water") _defn = EnumDefinition( name="DnaSampleFormatEnum", - description="placeholder enum descr", ) @classmethod def _addvals(cls): setattr(cls, "10 mM Tris-HCl", - PermissibleValue( - text="10 mM Tris-HCl", - description="placeholder PV descr")) + PermissibleValue(text="10 mM Tris-HCl")) setattr(cls, "Low EDTA TE", - PermissibleValue( - text="Low EDTA TE", - description="placeholder PV descr")) + PermissibleValue(text="Low EDTA TE")) setattr(cls, "MDA reaction buffer", - PermissibleValue( - text="MDA reaction buffer", - description="placeholder PV descr")) + PermissibleValue(text="MDA reaction buffer")) class EnvPackageEnum(EnumDefinitionImpl): - """ - placeholder enum descr - """ - soil = PermissibleValue( - text="soil", - description="placeholder PV descr") + + soil = PermissibleValue(text="soil") _defn = EnumDefinition( name="EnvPackageEnum", - description="placeholder enum descr", ) class GrowthFacilEnum(EnumDefinitionImpl): - """ - placeholder enum descr - """ - experimental_garden = PermissibleValue( - text="experimental_garden", - description="placeholder PV descr") - field = PermissibleValue( - text="field", - description="placeholder PV descr") - field_incubation = PermissibleValue( - text="field_incubation", - description="placeholder PV descr") - glasshouse = PermissibleValue( - text="glasshouse", - description="placeholder PV descr") - greenhouse = PermissibleValue( - text="greenhouse", - description="placeholder PV descr") - growth_chamber = PermissibleValue( - text="growth_chamber", - description="placeholder PV descr") - lab_incubation = PermissibleValue( - text="lab_incubation", - description="placeholder PV descr") - open_top_chamber = PermissibleValue( - text="open_top_chamber", - description="placeholder PV descr") - other = PermissibleValue( - text="other", - description="placeholder PV descr") + + experimental_garden = PermissibleValue(text="experimental_garden") + field = PermissibleValue(text="field") + field_incubation = PermissibleValue(text="field_incubation") + glasshouse = PermissibleValue(text="glasshouse") + greenhouse = PermissibleValue(text="greenhouse") + growth_chamber = PermissibleValue(text="growth_chamber") + lab_incubation = PermissibleValue(text="lab_incubation") + open_top_chamber = PermissibleValue(text="open_top_chamber") + other = PermissibleValue(text="other") _defn = EnumDefinition( name="GrowthFacilEnum", - description="placeholder enum descr", ) class RelToOxygenEnum(EnumDefinitionImpl): - """ - placeholder enum descr - """ - aerobe = PermissibleValue( - text="aerobe", - description="placeholder PV descr") - anaerobe = PermissibleValue( - text="anaerobe", - description="placeholder PV descr") - facultative = PermissibleValue( - text="facultative", - description="placeholder PV descr") - microaerophilic = PermissibleValue( - text="microaerophilic", - description="placeholder PV descr") - microanaerobe = PermissibleValue( - text="microanaerobe", - description="placeholder PV descr") + + aerobe = PermissibleValue(text="aerobe") + anaerobe = PermissibleValue(text="anaerobe") + facultative = PermissibleValue(text="facultative") + microaerophilic = PermissibleValue(text="microaerophilic") + microanaerobe = PermissibleValue(text="microanaerobe") _defn = EnumDefinition( name="RelToOxygenEnum", - description="placeholder enum descr", ) @classmethod def _addvals(cls): setattr(cls, "obligate aerobe", - PermissibleValue( - text="obligate aerobe", - description="placeholder PV descr")) + PermissibleValue(text="obligate aerobe")) setattr(cls, "obligate anaerobe", - PermissibleValue( - text="obligate anaerobe", - description="placeholder PV descr")) + PermissibleValue(text="obligate anaerobe")) class RnaSampleFormatEnum(EnumDefinitionImpl): - """ - placeholder enum descr - """ - DNAStable = PermissibleValue( - text="DNAStable", - description="placeholder PV descr") - Ethanol = PermissibleValue( - text="Ethanol", - description="placeholder PV descr") - PBS = PermissibleValue( - text="PBS", - description="placeholder PV descr") - Pellet = PermissibleValue( - text="Pellet", - description="placeholder PV descr") - RNAStable = PermissibleValue( - text="RNAStable", - description="placeholder PV descr") - TE = PermissibleValue( - text="TE", - description="placeholder PV descr") - Water = PermissibleValue( - text="Water", - description="placeholder PV descr") + + DNAStable = PermissibleValue(text="DNAStable") + Ethanol = PermissibleValue(text="Ethanol") + PBS = PermissibleValue(text="PBS") + Pellet = PermissibleValue(text="Pellet") + RNAStable = PermissibleValue(text="RNAStable") + TE = PermissibleValue(text="TE") + Water = PermissibleValue(text="Water") _defn = EnumDefinition( name="RnaSampleFormatEnum", - description="placeholder enum descr", ) @classmethod def _addvals(cls): setattr(cls, "10 mM Tris-HCl", - PermissibleValue( - text="10 mM Tris-HCl", - description="placeholder PV descr")) + PermissibleValue(text="10 mM Tris-HCl")) setattr(cls, "Low EDTA TE", - PermissibleValue( - text="Low EDTA TE", - description="placeholder PV descr")) + PermissibleValue(text="Low EDTA TE")) setattr(cls, "MDA reaction buffer", - PermissibleValue( - text="MDA reaction buffer", - description="placeholder PV descr")) + PermissibleValue(text="MDA reaction buffer")) class SampleTypeEnum(EnumDefinitionImpl): @@ -9937,25 +9870,14 @@ def _addvals(cls): PermissibleValue(text="plant associated")) class StoreCondEnum(EnumDefinitionImpl): - """ - placeholder enum descr - """ - fresh = PermissibleValue( - text="fresh", - description="placeholder PV descr") - frozen = PermissibleValue( - text="frozen", - description="placeholder PV descr") - lyophilized = PermissibleValue( - text="lyophilized", - description="placeholder PV descr") - other = PermissibleValue( - text="other", - description="placeholder PV descr") + + fresh = PermissibleValue(text="fresh") + frozen = PermissibleValue(text="frozen") + lyophilized = PermissibleValue(text="lyophilized") + other = PermissibleValue(text="other") _defn = EnumDefinition( name="StoreCondEnum", - description="placeholder enum descr", ) class YesNoEnum(EnumDefinitionImpl): @@ -9971,1050 +9893,536 @@ class YesNoEnum(EnumDefinitionImpl): ) class EnvBroadScaleSoilEnum(EnumDefinitionImpl): - """ - placeholder enum descr, DO NOT SORT - """ + _defn = EnumDefinition( name="EnvBroadScaleSoilEnum", - description="placeholder enum descr, DO NOT SORT", ) @classmethod def _addvals(cls): setattr(cls, "arid biome [ENVO:01001838]", - PermissibleValue( - text="arid biome [ENVO:01001838]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="arid biome [ENVO:01001838]")) setattr(cls, "subalpine biome [ENVO:01001837]", - PermissibleValue( - text="subalpine biome [ENVO:01001837]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="subalpine biome [ENVO:01001837]")) setattr(cls, "montane biome [ENVO:01001836]", - PermissibleValue( - text="montane biome [ENVO:01001836]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="montane biome [ENVO:01001836]")) setattr(cls, "__montane savanna biome [ENVO:01000223]", - PermissibleValue( - text="__montane savanna biome [ENVO:01000223]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__montane savanna biome [ENVO:01000223]")) setattr(cls, "__montane shrubland biome [ENVO:01000216]", - PermissibleValue( - text="__montane shrubland biome [ENVO:01000216]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__montane shrubland biome [ENVO:01000216]")) setattr(cls, "alpine biome [ENVO:01001835]", - PermissibleValue( - text="alpine biome [ENVO:01001835]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="alpine biome [ENVO:01001835]")) setattr(cls, "__alpine tundra biome [ENVO:01001505]", - PermissibleValue( - text="__alpine tundra biome [ENVO:01001505]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__alpine tundra biome [ENVO:01001505]")) setattr(cls, "subpolar biome [ENVO:01001834]", - PermissibleValue( - text="subpolar biome [ENVO:01001834]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="subpolar biome [ENVO:01001834]")) setattr(cls, "subtropical biome [ENVO:01001832]", - PermissibleValue( - text="subtropical biome [ENVO:01001832]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="subtropical biome [ENVO:01001832]")) setattr(cls, "__mediterranean biome [ENVO:01001833]", - PermissibleValue( - text="__mediterranean biome [ENVO:01001833]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__mediterranean biome [ENVO:01001833]")) setattr(cls, "____mediterranean savanna biome [ENVO:01000229]", - PermissibleValue( - text="____mediterranean savanna biome [ENVO:01000229]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="____mediterranean savanna biome [ENVO:01000229]")) setattr(cls, "____mediterranean shrubland biome [ENVO:01000217]", - PermissibleValue( - text="____mediterranean shrubland biome [ENVO:01000217]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="____mediterranean shrubland biome [ENVO:01000217]")) setattr(cls, "____mediterranean woodland biome [ENVO:01000208]", - PermissibleValue( - text="____mediterranean woodland biome [ENVO:01000208]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="____mediterranean woodland biome [ENVO:01000208]")) setattr(cls, "__subtropical woodland biome [ENVO:01000222]", - PermissibleValue( - text="__subtropical woodland biome [ENVO:01000222]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__subtropical woodland biome [ENVO:01000222]")) setattr(cls, "__subtropical shrubland biome [ENVO:01000213]", - PermissibleValue( - text="__subtropical shrubland biome [ENVO:01000213]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__subtropical shrubland biome [ENVO:01000213]")) setattr(cls, "__subtropical savanna biome [ENVO:01000187]", - PermissibleValue( - text="__subtropical savanna biome [ENVO:01000187]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__subtropical savanna biome [ENVO:01000187]")) setattr(cls, "temperate biome [ENVO:01001831]", - PermissibleValue( - text="temperate biome [ENVO:01001831]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="temperate biome [ENVO:01001831]")) setattr(cls, "__temperate woodland biome [ENVO:01000221]", - PermissibleValue( - text="__temperate woodland biome [ENVO:01000221]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__temperate woodland biome [ENVO:01000221]")) setattr(cls, "__temperate shrubland biome [ENVO:01000215]", - PermissibleValue( - text="__temperate shrubland biome [ENVO:01000215]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__temperate shrubland biome [ENVO:01000215]")) setattr(cls, "__temperate savanna biome [ENVO:01000189]", - PermissibleValue( - text="__temperate savanna biome [ENVO:01000189]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__temperate savanna biome [ENVO:01000189]")) setattr(cls, "tropical biome [ENVO:01001830]", - PermissibleValue( - text="tropical biome [ENVO:01001830]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="tropical biome [ENVO:01001830]")) setattr(cls, "__tropical woodland biome [ENVO:01000220]", - PermissibleValue( - text="__tropical woodland biome [ENVO:01000220]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__tropical woodland biome [ENVO:01000220]")) setattr(cls, "__tropical shrubland biome [ENVO:01000214]", - PermissibleValue( - text="__tropical shrubland biome [ENVO:01000214]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__tropical shrubland biome [ENVO:01000214]")) setattr(cls, "__tropical savanna biome [ENVO:01000188]", - PermissibleValue( - text="__tropical savanna biome [ENVO:01000188]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__tropical savanna biome [ENVO:01000188]")) setattr(cls, "polar biome [ENVO:01000339]", - PermissibleValue( - text="polar biome [ENVO:01000339]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="polar biome [ENVO:01000339]")) setattr(cls, "terrestrial biome [ENVO:00000446]", - PermissibleValue( - text="terrestrial biome [ENVO:00000446]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="terrestrial biome [ENVO:00000446]")) setattr(cls, "__anthropogenic terrestrial biome [ENVO:01000219]", - PermissibleValue( - text="__anthropogenic terrestrial biome [ENVO:01000219]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__anthropogenic terrestrial biome [ENVO:01000219]")) setattr(cls, "____dense settlement biome [ENVO:01000248]", - PermissibleValue( - text="____dense settlement biome [ENVO:01000248]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="____dense settlement biome [ENVO:01000248]")) setattr(cls, "______urban biome [ENVO:01000249]", - PermissibleValue( - text="______urban biome [ENVO:01000249]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="______urban biome [ENVO:01000249]")) setattr(cls, "____rangeland biome [ENVO:01000247]", - PermissibleValue( - text="____rangeland biome [ENVO:01000247]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="____rangeland biome [ENVO:01000247]")) setattr(cls, "____village biome [ENVO:01000246]", - PermissibleValue( - text="____village biome [ENVO:01000246]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="____village biome [ENVO:01000246]")) setattr(cls, "__mangrove biome [ENVO:01000181]", - PermissibleValue( - text="__mangrove biome [ENVO:01000181]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__mangrove biome [ENVO:01000181]")) setattr(cls, "__tundra biome [ENVO:01000180]", - PermissibleValue( - text="__tundra biome [ENVO:01000180]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__tundra biome [ENVO:01000180]")) setattr(cls, "____alpine tundra biome [ENVO:01001505]", - PermissibleValue( - text="____alpine tundra biome [ENVO:01001505]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="____alpine tundra biome [ENVO:01001505]")) setattr(cls, "__shrubland biome [ENVO:01000176]", - PermissibleValue( - text="__shrubland biome [ENVO:01000176]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__shrubland biome [ENVO:01000176]")) setattr(cls, "____tidal mangrove shrubland [ENVO:01001369]", - PermissibleValue( - text="____tidal mangrove shrubland [ENVO:01001369]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="____tidal mangrove shrubland [ENVO:01001369]")) setattr(cls, "____xeric shrubland biome [ENVO:01000218]", - PermissibleValue( - text="____xeric shrubland biome [ENVO:01000218]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="____xeric shrubland biome [ENVO:01000218]")) setattr(cls, "____montane shrubland biome [ENVO:01000216]", - PermissibleValue( - text="____montane shrubland biome [ENVO:01000216]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="____montane shrubland biome [ENVO:01000216]")) setattr(cls, "____temperate shrubland biome [ENVO:01000215]", - PermissibleValue( - text="____temperate shrubland biome [ENVO:01000215]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="____temperate shrubland biome [ENVO:01000215]")) setattr(cls, "____tropical shrubland biome [ENVO:01000214]", - PermissibleValue( - text="____tropical shrubland biome [ENVO:01000214]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="____tropical shrubland biome [ENVO:01000214]")) setattr(cls, "____subtropical shrubland biome [ENVO:01000213]", - PermissibleValue( - text="____subtropical shrubland biome [ENVO:01000213]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="____subtropical shrubland biome [ENVO:01000213]")) setattr(cls, "______mediterranean shrubland biome [ENVO:01000217]", - PermissibleValue( - text="______mediterranean shrubland biome [ENVO:01000217]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="______mediterranean shrubland biome [ENVO:01000217]")) setattr(cls, "__woodland biome [ENVO:01000175]", - PermissibleValue( - text="__woodland biome [ENVO:01000175]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__woodland biome [ENVO:01000175]")) setattr(cls, "____subtropical woodland biome [ENVO:01000222]", - PermissibleValue( - text="____subtropical woodland biome [ENVO:01000222]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="____subtropical woodland biome [ENVO:01000222]")) setattr(cls, "______mediterranean woodland biome [ENVO:01000208]", - PermissibleValue( - text="______mediterranean woodland biome [ENVO:01000208]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="______mediterranean woodland biome [ENVO:01000208]")) setattr(cls, "____temperate woodland biome [ENVO:01000221]", - PermissibleValue( - text="____temperate woodland biome [ENVO:01000221]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="____temperate woodland biome [ENVO:01000221]")) setattr(cls, "____tropical woodland biome [ENVO:01000220]", - PermissibleValue( - text="____tropical woodland biome [ENVO:01000220]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="____tropical woodland biome [ENVO:01000220]")) setattr(cls, "____savanna biome [ENVO:01000178]", - PermissibleValue( - text="____savanna biome [ENVO:01000178]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="____savanna biome [ENVO:01000178]")) setattr(cls, "______montane savanna biome [ENVO:01000223]", - PermissibleValue( - text="______montane savanna biome [ENVO:01000223]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="______montane savanna biome [ENVO:01000223]")) setattr(cls, "______flooded savanna biome [ENVO:01000190]", - PermissibleValue( - text="______flooded savanna biome [ENVO:01000190]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="______flooded savanna biome [ENVO:01000190]")) setattr(cls, "______temperate savanna biome [ENVO:01000189]", - PermissibleValue( - text="______temperate savanna biome [ENVO:01000189]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="______temperate savanna biome [ENVO:01000189]")) setattr(cls, "______tropical savanna biome [ENVO:01000188]", - PermissibleValue( - text="______tropical savanna biome [ENVO:01000188]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="______tropical savanna biome [ENVO:01000188]")) setattr(cls, "______subtropical savanna biome [ENVO:01000187]", - PermissibleValue( - text="______subtropical savanna biome [ENVO:01000187]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="______subtropical savanna biome [ENVO:01000187]")) setattr(cls, "________mediterranean savanna biome [ENVO:01000229]", - PermissibleValue( - text="________mediterranean savanna biome [ENVO:01000229]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="________mediterranean savanna biome [ENVO:01000229]")) class EnvMediumSoilEnum(EnumDefinitionImpl): - """ - placeholder enum descr, DO NOT SORT - """ + _defn = EnumDefinition( name="EnvMediumSoilEnum", - description="placeholder enum descr, DO NOT SORT", ) @classmethod def _addvals(cls): setattr(cls, "pathogen-suppressive soil [ENVO:03600036]", - PermissibleValue( - text="pathogen-suppressive soil [ENVO:03600036]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="pathogen-suppressive soil [ENVO:03600036]")) setattr(cls, "mangrove biome soil [ENVO:02000138]", - PermissibleValue( - text="mangrove biome soil [ENVO:02000138]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="mangrove biome soil [ENVO:02000138]")) setattr(cls, "surface soil [ENVO:02000059]", - PermissibleValue( - text="surface soil [ENVO:02000059]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="surface soil [ENVO:02000059]")) setattr(cls, "frost-susceptible soil [ENVO:01001638]", - PermissibleValue( - text="frost-susceptible soil [ENVO:01001638]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="frost-susceptible soil [ENVO:01001638]")) setattr(cls, "bare soil [ENVO:01001616]", - PermissibleValue( - text="bare soil [ENVO:01001616]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="bare soil [ENVO:01001616]")) setattr(cls, "frozen soil [ENVO:01001526]", - PermissibleValue( - text="frozen soil [ENVO:01001526]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="frozen soil [ENVO:01001526]")) setattr(cls, "__friable-frozen soil [ENVO:01001528]", - PermissibleValue( - text="__friable-frozen soil [ENVO:01001528]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__friable-frozen soil [ENVO:01001528]")) setattr(cls, "__plastic-frozen soil [ENVO:01001527]", - PermissibleValue( - text="__plastic-frozen soil [ENVO:01001527]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__plastic-frozen soil [ENVO:01001527]")) setattr(cls, "__hard-frozen soil [ENVO:01001525]", - PermissibleValue( - text="__hard-frozen soil [ENVO:01001525]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__hard-frozen soil [ENVO:01001525]")) setattr(cls, "__frozen compost soil [ENVO:00005765]", - PermissibleValue( - text="__frozen compost soil [ENVO:00005765]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__frozen compost soil [ENVO:00005765]")) setattr(cls, "__cryosol [ENVO:00002236]", - PermissibleValue( - text="__cryosol [ENVO:00002236]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__cryosol [ENVO:00002236]")) setattr(cls, "ultisol [ENVO:01001397]", - PermissibleValue( - text="ultisol [ENVO:01001397]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="ultisol [ENVO:01001397]")) setattr(cls, "__acrisol [ENVO:00002234]", - PermissibleValue( - text="__acrisol [ENVO:00002234]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__acrisol [ENVO:00002234]")) setattr(cls, "acidic soil [ENVO:01001185]", - PermissibleValue( - text="acidic soil [ENVO:01001185]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="acidic soil [ENVO:01001185]")) setattr(cls, "bulk soil [ENVO:00005802]", - PermissibleValue( - text="bulk soil [ENVO:00005802]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="bulk soil [ENVO:00005802]")) setattr(cls, "red soil [ENVO:00005790]", - PermissibleValue( - text="red soil [ENVO:00005790]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="red soil [ENVO:00005790]")) setattr(cls, "upland soil [ENVO:00005786]", - PermissibleValue( - text="upland soil [ENVO:00005786]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="upland soil [ENVO:00005786]")) setattr(cls, "__mountain forest soil [ENVO:00005769]", - PermissibleValue( - text="__mountain forest soil [ENVO:00005769]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__mountain forest soil [ENVO:00005769]")) setattr(cls, "__dune soil [ENVO:00002260]", - PermissibleValue( - text="__dune soil [ENVO:00002260]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__dune soil [ENVO:00002260]")) setattr(cls, "ornithogenic soil [ENVO:00005782]", - PermissibleValue( - text="ornithogenic soil [ENVO:00005782]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="ornithogenic soil [ENVO:00005782]")) setattr(cls, "heat stressed soil [ENVO:00005781]", - PermissibleValue( - text="heat stressed soil [ENVO:00005781]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="heat stressed soil [ENVO:00005781]")) setattr(cls, "greenhouse soil [ENVO:00005780]", - PermissibleValue( - text="greenhouse soil [ENVO:00005780]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="greenhouse soil [ENVO:00005780]")) setattr(cls, "tropical soil [ENVO:00005778]", - PermissibleValue( - text="tropical soil [ENVO:00005778]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="tropical soil [ENVO:00005778]")) setattr(cls, "pasture soil [ENVO:00005773]", - PermissibleValue( - text="pasture soil [ENVO:00005773]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="pasture soil [ENVO:00005773]")) setattr(cls, "muddy soil [ENVO:00005771]", - PermissibleValue( - text="muddy soil [ENVO:00005771]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="muddy soil [ENVO:00005771]")) setattr(cls, "orchid soil [ENVO:00005768]", - PermissibleValue( - text="orchid soil [ENVO:00005768]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="orchid soil [ENVO:00005768]")) setattr(cls, "manured soil [ENVO:00005767]", - PermissibleValue( - text="manured soil [ENVO:00005767]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="manured soil [ENVO:00005767]")) setattr(cls, "limed soil [ENVO:00005766]", - PermissibleValue( - text="limed soil [ENVO:00005766]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="limed soil [ENVO:00005766]")) setattr(cls, "pond soil [ENVO:00005764]", - PermissibleValue( - text="pond soil [ENVO:00005764]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="pond soil [ENVO:00005764]")) setattr(cls, "meadow soil [ENVO:00005761]", - PermissibleValue( - text="meadow soil [ENVO:00005761]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="meadow soil [ENVO:00005761]")) setattr(cls, "burned soil [ENVO:00005760]", - PermissibleValue( - text="burned soil [ENVO:00005760]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="burned soil [ENVO:00005760]")) setattr(cls, "lawn soil [ENVO:00005756]", - PermissibleValue( - text="lawn soil [ENVO:00005756]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="lawn soil [ENVO:00005756]")) setattr(cls, "field soil [ENVO:00005755]", - PermissibleValue( - text="field soil [ENVO:00005755]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="field soil [ENVO:00005755]")) setattr(cls, "__paddy field soil [ENVO:00005740]", - PermissibleValue( - text="__paddy field soil [ENVO:00005740]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__paddy field soil [ENVO:00005740]")) setattr(cls, "____peaty paddy field soil [ENVO:00005776]", - PermissibleValue( - text="____peaty paddy field soil [ENVO:00005776]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="____peaty paddy field soil [ENVO:00005776]")) setattr(cls, "____alluvial paddy field soil [ENVO:00005759]", - PermissibleValue( - text="____alluvial paddy field soil [ENVO:00005759]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="____alluvial paddy field soil [ENVO:00005759]")) setattr(cls, "fertilized soil [ENVO:00005754]", - PermissibleValue( - text="fertilized soil [ENVO:00005754]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="fertilized soil [ENVO:00005754]")) setattr(cls, "sawah soil [ENVO:00005752]", - PermissibleValue( - text="sawah soil [ENVO:00005752]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="sawah soil [ENVO:00005752]")) setattr(cls, "jungle soil [ENVO:00005751]", - PermissibleValue( - text="jungle soil [ENVO:00005751]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="jungle soil [ENVO:00005751]")) setattr(cls, "grassland soil [ENVO:00005750]", - PermissibleValue( - text="grassland soil [ENVO:00005750]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="grassland soil [ENVO:00005750]")) setattr(cls, "__steppe soil [ENVO:00005777]", - PermissibleValue( - text="__steppe soil [ENVO:00005777]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__steppe soil [ENVO:00005777]")) setattr(cls, "__savanna soil [ENVO:00005746]", - PermissibleValue( - text="__savanna soil [ENVO:00005746]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__savanna soil [ENVO:00005746]")) setattr(cls, "farm soil [ENVO:00005749]", - PermissibleValue( - text="farm soil [ENVO:00005749]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="farm soil [ENVO:00005749]")) setattr(cls, "__rubber plantation soil [ENVO:00005788]", - PermissibleValue( - text="__rubber plantation soil [ENVO:00005788]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__rubber plantation soil [ENVO:00005788]")) setattr(cls, "__orchard soil [ENVO:00005772]", - PermissibleValue( - text="__orchard soil [ENVO:00005772]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__orchard soil [ENVO:00005772]")) setattr(cls, "dry soil [ENVO:00005748]", - PermissibleValue( - text="dry soil [ENVO:00005748]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="dry soil [ENVO:00005748]")) setattr(cls, "compost soil [ENVO:00005747]", - PermissibleValue( - text="compost soil [ENVO:00005747]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="compost soil [ENVO:00005747]")) setattr(cls, "roadside soil [ENVO:00005743]", - PermissibleValue( - text="roadside soil [ENVO:00005743]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="roadside soil [ENVO:00005743]")) setattr(cls, "arable soil [ENVO:00005742]", - PermissibleValue( - text="arable soil [ENVO:00005742]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="arable soil [ENVO:00005742]")) setattr(cls, "alpine soil [ENVO:00005741]", - PermissibleValue( - text="alpine soil [ENVO:00005741]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="alpine soil [ENVO:00005741]")) setattr(cls, "alluvial soil [ENVO:00002871]", - PermissibleValue( - text="alluvial soil [ENVO:00002871]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="alluvial soil [ENVO:00002871]")) setattr(cls, "__alluvial paddy field soil [ENVO:00005759]", - PermissibleValue( - text="__alluvial paddy field soil [ENVO:00005759]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__alluvial paddy field soil [ENVO:00005759]")) setattr(cls, "__alluvial swamp soil [ENVO:00005758]", - PermissibleValue( - text="__alluvial swamp soil [ENVO:00005758]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__alluvial swamp soil [ENVO:00005758]")) setattr(cls, "technosol [ENVO:00002275]", - PermissibleValue( - text="technosol [ENVO:00002275]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="technosol [ENVO:00002275]")) setattr(cls, "stagnosol [ENVO:00002274]", - PermissibleValue( - text="stagnosol [ENVO:00002274]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="stagnosol [ENVO:00002274]")) setattr(cls, "fluvisol [ENVO:00002273]", - PermissibleValue( - text="fluvisol [ENVO:00002273]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="fluvisol [ENVO:00002273]")) setattr(cls, "garden soil [ENVO:00002263]", - PermissibleValue( - text="garden soil [ENVO:00002263]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="garden soil [ENVO:00002263]")) setattr(cls, "__vegetable garden soil [ENVO:00005779]", - PermissibleValue( - text="__vegetable garden soil [ENVO:00005779]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__vegetable garden soil [ENVO:00005779]")) setattr(cls, "__allotment garden soil [ENVO:00005744]", - PermissibleValue( - text="__allotment garden soil [ENVO:00005744]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__allotment garden soil [ENVO:00005744]")) setattr(cls, "clay soil [ENVO:00002262]", - PermissibleValue( - text="clay soil [ENVO:00002262]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="clay soil [ENVO:00002262]")) setattr(cls, "forest soil [ENVO:00002261]", - PermissibleValue( - text="forest soil [ENVO:00002261]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="forest soil [ENVO:00002261]")) setattr(cls, "__eucalyptus forest soil [ENVO:00005787]", - PermissibleValue( - text="__eucalyptus forest soil [ENVO:00005787]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__eucalyptus forest soil [ENVO:00005787]")) setattr(cls, "__spruce forest soil [ENVO:00005784]", - PermissibleValue( - text="__spruce forest soil [ENVO:00005784]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__spruce forest soil [ENVO:00005784]")) setattr(cls, "__leafy wood soil [ENVO:00005783]", - PermissibleValue( - text="__leafy wood soil [ENVO:00005783]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__leafy wood soil [ENVO:00005783]")) setattr(cls, "__beech forest soil [ENVO:00005770]", - PermissibleValue( - text="__beech forest soil [ENVO:00005770]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__beech forest soil [ENVO:00005770]")) setattr(cls, "agricultural soil [ENVO:00002259]", - PermissibleValue( - text="agricultural soil [ENVO:00002259]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="agricultural soil [ENVO:00002259]")) setattr(cls, "__bluegrass field soil [ENVO:00005789]", - PermissibleValue( - text="__bluegrass field soil [ENVO:00005789]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__bluegrass field soil [ENVO:00005789]")) setattr(cls, "loam [ENVO:00002258]", - PermissibleValue( - text="loam [ENVO:00002258]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="loam [ENVO:00002258]")) setattr(cls, "__clay loam [ENVO:06105277]", - PermissibleValue( - text="__clay loam [ENVO:06105277]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__clay loam [ENVO:06105277]")) setattr(cls, "____silty clay loam [ENVO:06105278]", - PermissibleValue( - text="____silty clay loam [ENVO:06105278]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="____silty clay loam [ENVO:06105278]")) setattr(cls, "____sandy clay loam [ENVO:06105276]", - PermissibleValue( - text="____sandy clay loam [ENVO:06105276]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="____sandy clay loam [ENVO:06105276]")) setattr(cls, "__silty loam [ENVO:06105275]", - PermissibleValue( - text="__silty loam [ENVO:06105275]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__silty loam [ENVO:06105275]")) setattr(cls, "__sandy loam [ENVO:06105274]", - PermissibleValue( - text="__sandy loam [ENVO:06105274]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__sandy loam [ENVO:06105274]")) setattr(cls, "podzol [ENVO:00002257]", - PermissibleValue( - text="podzol [ENVO:00002257]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="podzol [ENVO:00002257]")) setattr(cls, "regosol [ENVO:00002256]", - PermissibleValue( - text="regosol [ENVO:00002256]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="regosol [ENVO:00002256]")) setattr(cls, "solonetz [ENVO:00002255]", - PermissibleValue( - text="solonetz [ENVO:00002255]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="solonetz [ENVO:00002255]")) setattr(cls, "vertisol [ENVO:00002254]", - PermissibleValue( - text="vertisol [ENVO:00002254]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="vertisol [ENVO:00002254]")) setattr(cls, "umbrisol [ENVO:00002253]", - PermissibleValue( - text="umbrisol [ENVO:00002253]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="umbrisol [ENVO:00002253]")) setattr(cls, "solonchak [ENVO:00002252]", - PermissibleValue( - text="solonchak [ENVO:00002252]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="solonchak [ENVO:00002252]")) setattr(cls, "planosol [ENVO:00002251]", - PermissibleValue( - text="planosol [ENVO:00002251]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="planosol [ENVO:00002251]")) setattr(cls, "plinthosol [ENVO:00002250]", - PermissibleValue( - text="plinthosol [ENVO:00002250]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="plinthosol [ENVO:00002250]")) setattr(cls, "phaeozem [ENVO:00002249]", - PermissibleValue( - text="phaeozem [ENVO:00002249]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="phaeozem [ENVO:00002249]")) setattr(cls, "luvisol [ENVO:00002248]", - PermissibleValue( - text="luvisol [ENVO:00002248]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="luvisol [ENVO:00002248]")) setattr(cls, "nitisol [ENVO:00002247]", - PermissibleValue( - text="nitisol [ENVO:00002247]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="nitisol [ENVO:00002247]")) setattr(cls, "ferralsol [ENVO:00002246]", - PermissibleValue( - text="ferralsol [ENVO:00002246]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="ferralsol [ENVO:00002246]")) setattr(cls, "gypsisol [ENVO:00002245]", - PermissibleValue( - text="gypsisol [ENVO:00002245]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="gypsisol [ENVO:00002245]")) setattr(cls, "gleysol [ENVO:00002244]", - PermissibleValue( - text="gleysol [ENVO:00002244]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="gleysol [ENVO:00002244]")) setattr(cls, "histosol [ENVO:00002243]", - PermissibleValue( - text="histosol [ENVO:00002243]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="histosol [ENVO:00002243]")) setattr(cls, "__peat soil [ENVO:00005774]", - PermissibleValue( - text="__peat soil [ENVO:00005774]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__peat soil [ENVO:00005774]")) setattr(cls, "lixisol [ENVO:00002242]", - PermissibleValue( - text="lixisol [ENVO:00002242]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="lixisol [ENVO:00002242]")) setattr(cls, "leptosol [ENVO:00002241]", - PermissibleValue( - text="leptosol [ENVO:00002241]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="leptosol [ENVO:00002241]")) setattr(cls, "kastanozem [ENVO:00002240]", - PermissibleValue( - text="kastanozem [ENVO:00002240]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="kastanozem [ENVO:00002240]")) setattr(cls, "calcisol [ENVO:00002239]", - PermissibleValue( - text="calcisol [ENVO:00002239]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="calcisol [ENVO:00002239]")) setattr(cls, "durisol [ENVO:00002238]", - PermissibleValue( - text="durisol [ENVO:00002238]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="durisol [ENVO:00002238]")) setattr(cls, "chernozem [ENVO:00002237]", - PermissibleValue( - text="chernozem [ENVO:00002237]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="chernozem [ENVO:00002237]")) setattr(cls, "cambisol [ENVO:00002235]", - PermissibleValue( - text="cambisol [ENVO:00002235]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="cambisol [ENVO:00002235]")) setattr(cls, "albeluvisol [ENVO:00002233]", - PermissibleValue( - text="albeluvisol [ENVO:00002233]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="albeluvisol [ENVO:00002233]")) setattr(cls, "andosol [ENVO:00002232]", - PermissibleValue( - text="andosol [ENVO:00002232]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="andosol [ENVO:00002232]")) setattr(cls, "__volcanic soil [ENVO:01001841]", - PermissibleValue( - text="__volcanic soil [ENVO:01001841]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__volcanic soil [ENVO:01001841]")) setattr(cls, "alisol [ENVO:00002231]", - PermissibleValue( - text="alisol [ENVO:00002231]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="alisol [ENVO:00002231]")) setattr(cls, "anthrosol [ENVO:00002230]", - PermissibleValue( - text="anthrosol [ENVO:00002230]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="anthrosol [ENVO:00002230]")) setattr(cls, "arenosol [ENVO:00002229]", - PermissibleValue( - text="arenosol [ENVO:00002229]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="arenosol [ENVO:00002229]")) class EnvLocalScaleSoilEnum(EnumDefinitionImpl): - """ - placeholder enum descr, DO NOT SORT - """ + _defn = EnumDefinition( name="EnvLocalScaleSoilEnum", - description="placeholder enum descr, DO NOT SORT", ) @classmethod def _addvals(cls): setattr(cls, "astronomical body part [ENVO:01000813]", - PermissibleValue( - text="astronomical body part [ENVO:01000813]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="astronomical body part [ENVO:01000813]")) setattr(cls, "__coast [ENVO:01000687]", - PermissibleValue( - text="__coast [ENVO:01000687]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__coast [ENVO:01000687]")) setattr(cls, "__solid astronomical body part [ENVO:00000191]", - PermissibleValue( - text="__solid astronomical body part [ENVO:00000191]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__solid astronomical body part [ENVO:00000191]")) setattr(cls, "______landform [ENVO:01001886]", - PermissibleValue( - text="______landform [ENVO:01001886]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="______landform [ENVO:01001886]")) setattr(cls, "______channel [ENVO:03000117]", - PermissibleValue( - text="______channel [ENVO:03000117]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="______channel [ENVO:03000117]")) setattr(cls, "________tunnel [ENVO:00000068]", - PermissibleValue( - text="________tunnel [ENVO:00000068]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="________tunnel [ENVO:00000068]")) setattr(cls, "______surface landform [ENVO:01001884]", - PermissibleValue( - text="______surface landform [ENVO:01001884]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="______surface landform [ENVO:01001884]")) setattr(cls, "________desert [ENVO:01001357]", - PermissibleValue( - text="________desert [ENVO:01001357]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="________desert [ENVO:01001357]")) setattr(cls, "________outcrop [ENVO:01000302]", - PermissibleValue( - text="________outcrop [ENVO:01000302]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="________outcrop [ENVO:01000302]")) setattr(cls, "________boulder field [ENVO:00000537]", - PermissibleValue( - text="________boulder field [ENVO:00000537]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="________boulder field [ENVO:00000537]")) setattr(cls, "________landfill [ENVO:00000533]", - PermissibleValue( - text="________landfill [ENVO:00000533]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="________landfill [ENVO:00000533]")) setattr(cls, "________hummock [ENVO:00000516]", - PermissibleValue( - text="________hummock [ENVO:00000516]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="________hummock [ENVO:00000516]")) setattr(cls, "________terrace [ENVO:00000508]", - PermissibleValue( - text="________terrace [ENVO:00000508]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="________terrace [ENVO:00000508]")) setattr(cls, "________peninsula [ENVO:00000305]", - PermissibleValue( - text="________peninsula [ENVO:00000305]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="________peninsula [ENVO:00000305]")) setattr(cls, "________shore [ENVO:00000304]", - PermissibleValue( - text="________shore [ENVO:00000304]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="________shore [ENVO:00000304]")) setattr(cls, "__________lake shore [ENVO:00000382]", - PermissibleValue( - text="__________lake shore [ENVO:00000382]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__________lake shore [ENVO:00000382]")) setattr(cls, "________dry lake [ENVO:00000277]", - PermissibleValue( - text="________dry lake [ENVO:00000277]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="________dry lake [ENVO:00000277]")) setattr(cls, "________karst [ENVO:00000175]", - PermissibleValue( - text="________karst [ENVO:00000175]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="________karst [ENVO:00000175]")) setattr(cls, "________isthmus [ENVO:00000174]", - PermissibleValue( - text="________isthmus [ENVO:00000174]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="________isthmus [ENVO:00000174]")) setattr(cls, "________badland [ENVO:00000127]", - PermissibleValue( - text="________badland [ENVO:00000127]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="________badland [ENVO:00000127]")) setattr(cls, "________volcanic feature [ENVO:00000094]", - PermissibleValue( - text="________volcanic feature [ENVO:00000094]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="________volcanic feature [ENVO:00000094]")) setattr(cls, "__________volcanic cone [ENVO:00000398]", - PermissibleValue( - text="__________volcanic cone [ENVO:00000398]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__________volcanic cone [ENVO:00000398]")) setattr(cls, "____________tuff cone [ENVO:01000664]", - PermissibleValue( - text="____________tuff cone [ENVO:01000664]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="____________tuff cone [ENVO:01000664]")) setattr(cls, "________beach [ENVO:00000091]", - PermissibleValue( - text="________beach [ENVO:00000091]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="________beach [ENVO:00000091]")) setattr(cls, "________plain [ENVO:00000086]", - PermissibleValue( - text="________plain [ENVO:00000086]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="________plain [ENVO:00000086]")) setattr(cls, "________cave [ENVO:00000067]", - PermissibleValue( - text="________cave [ENVO:00000067]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="________cave [ENVO:00000067]")) setattr(cls, "________spring [ENVO:00000027]", - PermissibleValue( - text="________spring [ENVO:00000027]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="________spring [ENVO:00000027]")) setattr(cls, "______slope [ENVO:00002000]", - PermissibleValue( - text="______slope [ENVO:00002000]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="______slope [ENVO:00002000]")) setattr(cls, "________talus slope [ENVO:01000334]", - PermissibleValue( - text="________talus slope [ENVO:01000334]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="________talus slope [ENVO:01000334]")) setattr(cls, "________hillside [ENVO:01000333]", - PermissibleValue( - text="________hillside [ENVO:01000333]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="________hillside [ENVO:01000333]")) setattr(cls, "________levee [ENVO:00000178]", - PermissibleValue( - text="________levee [ENVO:00000178]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="________levee [ENVO:00000178]")) setattr(cls, "________bank [ENVO:00000141]", - PermissibleValue( - text="________bank [ENVO:00000141]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="________bank [ENVO:00000141]")) setattr(cls, "________cliff [ENVO:00000087]", - PermissibleValue( - text="________cliff [ENVO:00000087]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="________cliff [ENVO:00000087]")) setattr(cls, "______peak [ENVO:00000480]", - PermissibleValue( - text="______peak [ENVO:00000480]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="______peak [ENVO:00000480]")) setattr(cls, "______depressed landform [ENVO:00000309]", - PermissibleValue( - text="______depressed landform [ENVO:00000309]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="______depressed landform [ENVO:00000309]")) setattr(cls, "________geographic basin [ENVO:03000015]", - PermissibleValue( - text="________geographic basin [ENVO:03000015]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="________geographic basin [ENVO:03000015]")) setattr(cls, "__________valley [ENVO:00000100]", - PermissibleValue( - text="__________valley [ENVO:00000100]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__________valley [ENVO:00000100]")) setattr(cls, "____________canyon [ENVO:00000169]", - PermissibleValue( - text="____________canyon [ENVO:00000169]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="____________canyon [ENVO:00000169]")) setattr(cls, "____________dry valley [ENVO:00000128]", - PermissibleValue( - text="____________dry valley [ENVO:00000128]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="____________dry valley [ENVO:00000128]")) setattr(cls, "____________glacial valley [ENVO:00000248]", - PermissibleValue( - text="____________glacial valley [ENVO:00000248]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="____________glacial valley [ENVO:00000248]")) setattr(cls, "________pit [ENVO:01001871]", - PermissibleValue( - text="________pit [ENVO:01001871]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="________pit [ENVO:01001871]")) setattr(cls, "________trench [ENVO:01000649]", - PermissibleValue( - text="________trench [ENVO:01000649]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="________trench [ENVO:01000649]")) setattr(cls, "________swale [ENVO:00000543]", - PermissibleValue( - text="________swale [ENVO:00000543]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="________swale [ENVO:00000543]")) setattr(cls, "________crater [ENVO:00000514]", - PermissibleValue( - text="________crater [ENVO:00000514]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="________crater [ENVO:00000514]")) setattr(cls, "__________impact crater [ENVO:01001071]", - PermissibleValue( - text="__________impact crater [ENVO:01001071]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__________impact crater [ENVO:01001071]")) setattr(cls, "__________volcanic crater [ENVO:00000246]", - PermissibleValue( - text="__________volcanic crater [ENVO:00000246]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__________volcanic crater [ENVO:00000246]")) setattr(cls, "__________caldera [ENVO:00000096]", - PermissibleValue( - text="__________caldera [ENVO:00000096]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__________caldera [ENVO:00000096]")) setattr(cls, "________channel of a watercourse [ENVO:00000395]", - PermissibleValue( - text="________channel of a watercourse [ENVO:00000395]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="________channel of a watercourse [ENVO:00000395]")) setattr(cls, "__________strait [ENVO:00000394]", - PermissibleValue( - text="__________strait [ENVO:00000394]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__________strait [ENVO:00000394]")) setattr(cls, "__________dry stream [ENVO:00000278]", - PermissibleValue( - text="__________dry stream [ENVO:00000278]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__________dry stream [ENVO:00000278]")) setattr(cls, "____________dry river [ENVO:01000995]", - PermissibleValue( - text="____________dry river [ENVO:01000995]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="____________dry river [ENVO:01000995]")) setattr(cls, "__________artificial channel [ENVO:00000121]", - PermissibleValue( - text="__________artificial channel [ENVO:00000121]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__________artificial channel [ENVO:00000121]")) setattr(cls, "____________plumbing drain [ENVO:01000924]", - PermissibleValue( - text="____________plumbing drain [ENVO:01000924]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="____________plumbing drain [ENVO:01000924]")) setattr(cls, "____________ditch [ENVO:00000037]", - PermissibleValue( - text="____________ditch [ENVO:00000037]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="____________ditch [ENVO:00000037]")) setattr(cls, "________sinkhole [ENVO:00000195]", - PermissibleValue( - text="________sinkhole [ENVO:00000195]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="________sinkhole [ENVO:00000195]")) setattr(cls, "______elevated landform [ENVO:00000176]", - PermissibleValue( - text="______elevated landform [ENVO:00000176]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="______elevated landform [ENVO:00000176]")) setattr(cls, "________flattened elevation [ENVO:01001491]", - PermissibleValue( - text="________flattened elevation [ENVO:01001491]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="________flattened elevation [ENVO:01001491]")) setattr(cls, "__________butte [ENVO:00000287]", - PermissibleValue( - text="__________butte [ENVO:00000287]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__________butte [ENVO:00000287]")) setattr(cls, "__________plateau [ENVO:00000182]", - PermissibleValue( - text="__________plateau [ENVO:00000182]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__________plateau [ENVO:00000182]")) setattr(cls, "__________mesa [ENVO:00000179]", - PermissibleValue( - text="__________mesa [ENVO:00000179]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__________mesa [ENVO:00000179]")) setattr(cls, "________pinnacle [ENVO:00000481]", - PermissibleValue( - text="________pinnacle [ENVO:00000481]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="________pinnacle [ENVO:00000481]")) setattr(cls, "________mount [ENVO:00000477]", - PermissibleValue( - text="________mount [ENVO:00000477]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="________mount [ENVO:00000477]")) setattr(cls, "__________hill [ENVO:00000083]", - PermissibleValue( - text="__________hill [ENVO:00000083]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__________hill [ENVO:00000083]")) setattr(cls, "____________dune [ENVO:00000170]", - PermissibleValue( - text="____________dune [ENVO:00000170]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="____________dune [ENVO:00000170]")) setattr(cls, "__________mountain [ENVO:00000081]", - PermissibleValue( - text="__________mountain [ENVO:00000081]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__________mountain [ENVO:00000081]")) setattr(cls, "________ridge [ENVO:00000283]", - PermissibleValue( - text="________ridge [ENVO:00000283]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="________ridge [ENVO:00000283]")) setattr(cls, "____part of a landmass [ENVO:01001781]", - PermissibleValue( - text="____part of a landmass [ENVO:01001781]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="____part of a landmass [ENVO:01001781]")) setattr(cls, "______peninsula [ENVO:00000305]", - PermissibleValue( - text="______peninsula [ENVO:00000305]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="______peninsula [ENVO:00000305]")) setattr(cls, "____geological fracture [ENVO:01000667]", - PermissibleValue( - text="____geological fracture [ENVO:01000667]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="____geological fracture [ENVO:01000667]")) setattr(cls, "______vein [ENVO:01000670]", - PermissibleValue( - text="______vein [ENVO:01000670]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="______vein [ENVO:01000670]")) setattr(cls, "______geological fault [ENVO:01000668]", - PermissibleValue( - text="______geological fault [ENVO:01000668]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="______geological fault [ENVO:01000668]")) setattr(cls, "________active geological fault [ENVO:01000669]", - PermissibleValue( - text="________active geological fault [ENVO:01000669]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="________active geological fault [ENVO:01000669]")) setattr(cls, "______volcano [ENVO:00000247]", - PermissibleValue( - text="______volcano [ENVO:00000247]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="______volcano [ENVO:00000247]")) setattr(cls, "__field [ENVO:01000352]", - PermissibleValue( - text="__field [ENVO:01000352]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__field [ENVO:01000352]")) setattr(cls, "____lava field [ENVO:01000437]", - PermissibleValue( - text="____lava field [ENVO:01000437]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="____lava field [ENVO:01000437]")) setattr(cls, "____gravel field [ENVO:00000548]", - PermissibleValue( - text="____gravel field [ENVO:00000548]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="____gravel field [ENVO:00000548]")) setattr(cls, "____woodland clearing [ENVO:00000444]", - PermissibleValue( - text="____woodland clearing [ENVO:00000444]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="____woodland clearing [ENVO:00000444]")) setattr(cls, "____agricultural field [ENVO:00000114]", - PermissibleValue( - text="____agricultural field [ENVO:00000114]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="____agricultural field [ENVO:00000114]")) setattr(cls, "____snow field [ENVO:00000146]", - PermissibleValue( - text="____snow field [ENVO:00000146]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="____snow field [ENVO:00000146]")) setattr(cls, "__geographic feature [ENVO:00000000]", - PermissibleValue( - text="__geographic feature [ENVO:00000000]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="__geographic feature [ENVO:00000000]")) setattr(cls, "____hydrographic feature [ENVO:00000012]", - PermissibleValue( - text="____hydrographic feature [ENVO:00000012]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="____hydrographic feature [ENVO:00000012]")) setattr(cls, "______reef [ENVO:01001899]", - PermissibleValue( - text="______reef [ENVO:01001899]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="______reef [ENVO:01001899]")) setattr(cls, "______inlet [ENVO:00000475]", - PermissibleValue( - text="______inlet [ENVO:00000475]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="______inlet [ENVO:00000475]")) setattr(cls, "______bar [ENVO:00000167]", - PermissibleValue( - text="______bar [ENVO:00000167]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="______bar [ENVO:00000167]")) setattr(cls, "________tombolo [ENVO:00000420]", - PermissibleValue( - text="________tombolo [ENVO:00000420]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="________tombolo [ENVO:00000420]")) setattr(cls, "____anthropogenic geographic feature [ENVO:00000002]", - PermissibleValue( - text="____anthropogenic geographic feature [ENVO:00000002]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="____anthropogenic geographic feature [ENVO:00000002]")) setattr(cls, "______yard [ENVO:03600053]", - PermissibleValue( - text="______yard [ENVO:03600053]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="______yard [ENVO:03600053]")) setattr(cls, "________residential backyard [ENVO:03600033]", - PermissibleValue( - text="________residential backyard [ENVO:03600033]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="________residential backyard [ENVO:03600033]")) setattr(cls, "______market [ENVO:01000987]", - PermissibleValue( - text="______market [ENVO:01000987]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="______market [ENVO:01000987]")) setattr(cls, "______park [ENVO:00000562]", - PermissibleValue( - text="______park [ENVO:00000562]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="______park [ENVO:00000562]")) setattr(cls, "______well [ENVO:00000026]", - PermissibleValue( - text="______well [ENVO:00000026]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="______well [ENVO:00000026]")) setattr(cls, "______garden [ENVO:00000011]", - PermissibleValue( - text="______garden [ENVO:00000011]", - description="placeholder PV descr, DO NOT SORT")) + PermissibleValue(text="______garden [ENVO:00000011]")) class OxyStatSampEnum(EnumDefinitionImpl): - """ - placeholder enum descr, DO NOT SORT - """ - aerobic = PermissibleValue( - text="aerobic", - description="placeholder PV descr, DO NOT SORT") - anaerobic = PermissibleValue( - text="anaerobic", - description="placeholder PV descr, DO NOT SORT") - other = PermissibleValue( - text="other", - description="placeholder PV descr, DO NOT SORT") + + aerobic = PermissibleValue(text="aerobic") + anaerobic = PermissibleValue(text="anaerobic") + other = PermissibleValue(text="other") _defn = EnumDefinition( name="OxyStatSampEnum", - description="placeholder enum descr, DO NOT SORT", ) class ArchStrucEnum(EnumDefinitionImpl): @@ -13608,7 +13016,6 @@ class EcosystemSubtypeEnum(EnumDefinitionImpl): Desert = PermissibleValue(text="Desert") Diaphragm = PermissibleValue(text="Diaphragm") Digestate = PermissibleValue(text="Digestate") - Dinoflagellates = PermissibleValue(text="Dinoflagellates") Doormat = PermissibleValue(text="Doormat") Dust = PermissibleValue(text="Dust") Ear = PermissibleValue(text="Ear") @@ -13773,6 +13180,7 @@ class EcosystemSubtypeEnum(EnumDefinitionImpl): Sinkhole = PermissibleValue(text="Sinkhole") Skin = PermissibleValue(text="Skin") Sludge = PermissibleValue(text="Sludge") + Snow = PermissibleValue(text="Snow") Soil = PermissibleValue(text="Soil") Spacecraft = PermissibleValue(text="Spacecraft") Spat = PermissibleValue(text="Spat") @@ -14040,6 +13448,8 @@ def _addvals(cls): PermissibleValue(text="Frozen remains")) setattr(cls, "Frozen seafood", PermissibleValue(text="Frozen seafood")) + setattr(cls, "Fruit processing", + PermissibleValue(text="Fruit processing")) setattr(cls, "Geothermal field", PermissibleValue(text="Geothermal field")) setattr(cls, "Geothermal pool/Hot lake", @@ -14756,6 +14166,7 @@ class SpecificEcosystemEnum(EnumDefinitionImpl): Spores = PermissibleValue(text="Spores") Sporophytes = PermissibleValue(text="Sporophytes") Spring = PermissibleValue(text="Spring") + Stolon = PermissibleValue(text="Stolon") Stomach = PermissibleValue(text="Stomach") Stromatolites = PermissibleValue(text="Stromatolites") Stye = PermissibleValue(text="Stye") @@ -17839,7 +17250,7 @@ class slots: slots.AirInterface_lat_lon = Slot(uri=MIXS['0000009'], name="AirInterface_lat_lon", curie=MIXS.curie('0000009'), model_uri=NMDC_SUB_SCHEMA.AirInterface_lat_lon, domain=AirInterface, range=str, - pattern=re.compile(r'^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$')) + pattern=re.compile(r'^[-+]?([1-8]?\d(\.\d{1,8})?|90(\.0{1,8})?)\s[-+]?(180(\.0{1,8})?|((1[0-7]\d)|([1-9]?\d))(\.\d{1,8})?)$')) slots.AirInterface_methane = Slot(uri=MIXS['0000101'], name="AirInterface_methane", curie=MIXS.curie('0000101'), model_uri=NMDC_SUB_SCHEMA.AirInterface_methane, domain=AirInterface, range=Optional[str], @@ -18065,7 +17476,7 @@ class slots: 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+)?)$')) + pattern=re.compile(r'^[-+]?([1-8]?\d(\.\d{1,8})?|90(\.0{1,8})?)\s[-+]?(180(\.0{1,8})?|((1[0-7]\d)|([1-9]?\d))(\.\d{1,8})?)$')) slots.BiofilmInterface_magnesium = Slot(uri=MIXS['0000431'], name="BiofilmInterface_magnesium", curie=MIXS.curie('0000431'), model_uri=NMDC_SUB_SCHEMA.BiofilmInterface_magnesium, domain=BiofilmInterface, range=Optional[str], @@ -18536,7 +17947,7 @@ class slots: slots.BuiltEnvInterface_lat_lon = Slot(uri=MIXS['0000009'], name="BuiltEnvInterface_lat_lon", curie=MIXS.curie('0000009'), model_uri=NMDC_SUB_SCHEMA.BuiltEnvInterface_lat_lon, domain=BuiltEnvInterface, range=str, - pattern=re.compile(r'^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$')) + pattern=re.compile(r'^[-+]?([1-8]?\d(\.\d{1,8})?|90(\.0{1,8})?)\s[-+]?(180(\.0{1,8})?|((1[0-7]\d)|([1-9]?\d))(\.\d{1,8})?)$')) slots.BuiltEnvInterface_light_type = Slot(uri=MIXS['0000769'], name="BuiltEnvInterface_light_type", curie=MIXS.curie('0000769'), model_uri=NMDC_SUB_SCHEMA.BuiltEnvInterface_light_type, domain=BuiltEnvInterface, range=Optional[Union[Union[str, "LightTypeEnum"], List[Union[str, "LightTypeEnum"]]]]) @@ -19003,7 +18414,7 @@ class slots: 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+)?)$')) + pattern=re.compile(r'^[-+]?([1-8]?\d(\.\d{1,8})?|90(\.0{1,8})?)\s[-+]?(180(\.0{1,8})?|((1[0-7]\d)|([1-9]?\d))(\.\d{1,8})?)$')) slots.HcrCoresInterface_lithology = Slot(uri=MIXS['0000990'], name="HcrCoresInterface_lithology", curie=MIXS.curie('0000990'), model_uri=NMDC_SUB_SCHEMA.HcrCoresInterface_lithology, domain=HcrCoresInterface, range=Optional[Union[str, "LithologyEnum"]]) @@ -19387,7 +18798,7 @@ class slots: slots.HcrFluidsSwabsInterface_lat_lon = Slot(uri=MIXS['0000009'], name="HcrFluidsSwabsInterface_lat_lon", curie=MIXS.curie('0000009'), model_uri=NMDC_SUB_SCHEMA.HcrFluidsSwabsInterface_lat_lon, domain=HcrFluidsSwabsInterface, range=str, - pattern=re.compile(r'^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$')) + pattern=re.compile(r'^[-+]?([1-8]?\d(\.\d{1,8})?|90(\.0{1,8})?)\s[-+]?(180(\.0{1,8})?|((1[0-7]\d)|([1-9]?\d))(\.\d{1,8})?)$')) slots.HcrFluidsSwabsInterface_lithology = Slot(uri=MIXS['0000990'], name="HcrFluidsSwabsInterface_lithology", curie=MIXS.curie('0000990'), model_uri=NMDC_SUB_SCHEMA.HcrFluidsSwabsInterface_lithology, domain=HcrFluidsSwabsInterface, range=Optional[Union[str, "LithologyEnum"]]) @@ -19758,7 +19169,7 @@ class slots: slots.HostAssociatedInterface_lat_lon = Slot(uri=MIXS['0000009'], name="HostAssociatedInterface_lat_lon", curie=MIXS.curie('0000009'), model_uri=NMDC_SUB_SCHEMA.HostAssociatedInterface_lat_lon, domain=HostAssociatedInterface, range=str, - pattern=re.compile(r'^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$')) + pattern=re.compile(r'^[-+]?([1-8]?\d(\.\d{1,8})?|90(\.0{1,8})?)\s[-+]?(180(\.0{1,8})?|((1[0-7]\d)|([1-9]?\d))(\.\d{1,8})?)$')) slots.HostAssociatedInterface_misc_param = Slot(uri=MIXS['0000752'], name="HostAssociatedInterface_misc_param", curie=MIXS.curie('0000752'), model_uri=NMDC_SUB_SCHEMA.HostAssociatedInterface_misc_param, domain=HostAssociatedInterface, range=Optional[str], @@ -19860,7 +19271,8 @@ class slots: model_uri=NMDC_SUB_SCHEMA.JgiMgInterface_dna_sample_format, domain=JgiMgInterface, range=Union[str, "DNASampleFormatEnum"]) slots.JgiMgInterface_dna_sample_name = Slot(uri=NMDC['nmdc/dna_sample_name'], name="JgiMgInterface_dna_sample_name", curie=NMDC.curie('nmdc/dna_sample_name'), - model_uri=NMDC_SUB_SCHEMA.JgiMgInterface_dna_sample_name, domain=JgiMgInterface, range=str) + model_uri=NMDC_SUB_SCHEMA.JgiMgInterface_dna_sample_name, domain=JgiMgInterface, range=str, + pattern=re.compile(r'^[_a-zA-Z0-9-]*$')) slots.JgiMgInterface_dna_seq_project = Slot(uri=NMDC['nmdc/dna_seq_project'], name="JgiMgInterface_dna_seq_project", curie=NMDC.curie('nmdc/dna_seq_project'), model_uri=NMDC_SUB_SCHEMA.JgiMgInterface_dna_seq_project, domain=JgiMgInterface, range=str) @@ -19916,7 +19328,8 @@ class slots: model_uri=NMDC_SUB_SCHEMA.JgiMgLrInterface_dna_sample_format, domain=JgiMgLrInterface, range=Union[str, "DNASampleFormatEnum"]) slots.JgiMgLrInterface_dna_sample_name = Slot(uri=NMDC['nmdc/dna_sample_name'], name="JgiMgLrInterface_dna_sample_name", curie=NMDC.curie('nmdc/dna_sample_name'), - model_uri=NMDC_SUB_SCHEMA.JgiMgLrInterface_dna_sample_name, domain=JgiMgLrInterface, range=str) + model_uri=NMDC_SUB_SCHEMA.JgiMgLrInterface_dna_sample_name, domain=JgiMgLrInterface, range=str, + pattern=re.compile(r'^[_a-zA-Z0-9-]*$')) slots.JgiMgLrInterface_dna_seq_project = Slot(uri=NMDC['nmdc/dna_seq_project'], name="JgiMgLrInterface_dna_seq_project", curie=NMDC.curie('nmdc/dna_seq_project'), model_uri=NMDC_SUB_SCHEMA.JgiMgLrInterface_dna_seq_project, domain=JgiMgLrInterface, range=str) @@ -19975,7 +19388,8 @@ class slots: model_uri=NMDC_SUB_SCHEMA.JgiMtInterface_rna_sample_format, domain=JgiMtInterface, range=Union[str, "RNASampleFormatEnum"]) slots.JgiMtInterface_rna_sample_name = Slot(uri=NMDC['nmdc/rna_sample_name'], name="JgiMtInterface_rna_sample_name", curie=NMDC.curie('nmdc/rna_sample_name'), - model_uri=NMDC_SUB_SCHEMA.JgiMtInterface_rna_sample_name, domain=JgiMtInterface, range=str) + model_uri=NMDC_SUB_SCHEMA.JgiMtInterface_rna_sample_name, domain=JgiMtInterface, range=str, + pattern=re.compile(r'^[_a-zA-Z0-9-]*$')) slots.JgiMtInterface_rna_seq_project = Slot(uri=NMDC['nmdc/rna_seq_project'], name="JgiMtInterface_rna_seq_project", curie=NMDC.curie('nmdc/rna_seq_project'), model_uri=NMDC_SUB_SCHEMA.JgiMtInterface_rna_seq_project, domain=JgiMtInterface, range=str) @@ -20100,7 +19514,7 @@ class slots: slots.MiscEnvsInterface_lat_lon = Slot(uri=MIXS['0000009'], name="MiscEnvsInterface_lat_lon", curie=MIXS.curie('0000009'), model_uri=NMDC_SUB_SCHEMA.MiscEnvsInterface_lat_lon, domain=MiscEnvsInterface, range=str, - pattern=re.compile(r'^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$')) + pattern=re.compile(r'^[-+]?([1-8]?\d(\.\d{1,8})?|90(\.0{1,8})?)\s[-+]?(180(\.0{1,8})?|((1[0-7]\d)|([1-9]?\d))(\.\d{1,8})?)$')) slots.MiscEnvsInterface_misc_param = Slot(uri=MIXS['0000752'], name="MiscEnvsInterface_misc_param", curie=MIXS.curie('0000752'), model_uri=NMDC_SUB_SCHEMA.MiscEnvsInterface_misc_param, domain=MiscEnvsInterface, range=Optional[str], @@ -20392,7 +19806,7 @@ class slots: slots.PlantAssociatedInterface_lat_lon = Slot(uri=MIXS['0000009'], name="PlantAssociatedInterface_lat_lon", curie=MIXS.curie('0000009'), model_uri=NMDC_SUB_SCHEMA.PlantAssociatedInterface_lat_lon, domain=PlantAssociatedInterface, range=str, - pattern=re.compile(r'^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$')) + pattern=re.compile(r'^[-+]?([1-8]?\d(\.\d{1,8})?|90(\.0{1,8})?)\s[-+]?(180(\.0{1,8})?|((1[0-7]\d)|([1-9]?\d))(\.\d{1,8})?)$')) slots.PlantAssociatedInterface_light_regm = Slot(uri=MIXS['0000569'], name="PlantAssociatedInterface_light_regm", curie=MIXS.curie('0000569'), model_uri=NMDC_SUB_SCHEMA.PlantAssociatedInterface_light_regm, domain=PlantAssociatedInterface, range=Optional[str], @@ -20726,7 +20140,7 @@ class slots: slots.SedimentInterface_lat_lon = Slot(uri=MIXS['0000009'], name="SedimentInterface_lat_lon", curie=MIXS.curie('0000009'), model_uri=NMDC_SUB_SCHEMA.SedimentInterface_lat_lon, domain=SedimentInterface, range=str, - pattern=re.compile(r'^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$')) + pattern=re.compile(r'^[-+]?([1-8]?\d(\.\d{1,8})?|90(\.0{1,8})?)\s[-+]?(180(\.0{1,8})?|((1[0-7]\d)|([1-9]?\d))(\.\d{1,8})?)$')) slots.SedimentInterface_light_regm = Slot(uri=MIXS['0000569'], name="SedimentInterface_light_regm", curie=MIXS.curie('0000569'), model_uri=NMDC_SUB_SCHEMA.SedimentInterface_light_regm, domain=SedimentInterface, range=Optional[str], @@ -21135,7 +20549,7 @@ class slots: slots.SoilInterface_lat_lon = Slot(uri=MIXS['0000009'], name="SoilInterface_lat_lon", curie=MIXS.curie('0000009'), model_uri=NMDC_SUB_SCHEMA.SoilInterface_lat_lon, domain=SoilInterface, range=str, - pattern=re.compile(r'^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$')) + pattern=re.compile(r'^[-+]?([1-8]?\d(\.\d{1,8})?|90(\.0{1,8})?)\s[-+]?(180(\.0{1,8})?|((1[0-7]\d)|([1-9]?\d))(\.\d{1,8})?)$')) slots.SoilInterface_lbc_thirty = Slot(uri=NMDC['nmdc/lbc_thirty'], name="SoilInterface_lbc_thirty", curie=NMDC.curie('nmdc/lbc_thirty'), model_uri=NMDC_SUB_SCHEMA.SoilInterface_lbc_thirty, domain=SoilInterface, range=Optional[str], @@ -21458,7 +20872,7 @@ class slots: slots.WastewaterSludgeInterface_lat_lon = Slot(uri=MIXS['0000009'], name="WastewaterSludgeInterface_lat_lon", curie=MIXS.curie('0000009'), model_uri=NMDC_SUB_SCHEMA.WastewaterSludgeInterface_lat_lon, domain=WastewaterSludgeInterface, range=str, - pattern=re.compile(r'^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$')) + pattern=re.compile(r'^[-+]?([1-8]?\d(\.\d{1,8})?|90(\.0{1,8})?)\s[-+]?(180(\.0{1,8})?|((1[0-7]\d)|([1-9]?\d))(\.\d{1,8})?)$')) slots.WastewaterSludgeInterface_misc_param = Slot(uri=MIXS['0000752'], name="WastewaterSludgeInterface_misc_param", curie=MIXS.curie('0000752'), model_uri=NMDC_SUB_SCHEMA.WastewaterSludgeInterface_misc_param, domain=WastewaterSludgeInterface, range=Optional[str], diff --git a/src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml b/src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml index 6b390c4a..eaaab81a 100644 --- a/src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml +++ b/src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml @@ -353,39 +353,6 @@ types: from_schema: https://example.com/nmdc_submission_schema base: str uri: xsd:language - float: - name: float - description: A real number that conforms to the xsd:float specification - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "float". - from_schema: https://example.com/nmdc_submission_schema - exact_mappings: - - schema:Float - base: float - uri: xsd:float - string: - name: string - description: A character string - notes: - - In RDF serializations, a slot with range of string is treated as a literal or - type xsd:string. If you are authoring schemas in LinkML YAML, the type is - referenced with the lower case "string". - from_schema: https://example.com/nmdc_submission_schema - exact_mappings: - - schema:Text - base: str - uri: xsd:string - uriorcurie: - name: uriorcurie - description: a URI or a CURIE - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "uriorcurie". - from_schema: https://example.com/nmdc_submission_schema - base: URIorCURIE - uri: xsd:anyURI - repr: str integer: name: integer description: An integer @@ -408,6 +375,17 @@ types: - schema:Float base: float uri: xsd:double + float: + name: float + description: A real number that conforms to the xsd:float specification + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "float". + from_schema: https://example.com/nmdc_submission_schema + exact_mappings: + - schema:Float + base: float + uri: xsd:float decimal: name: decimal description: A real number with arbitrary precision that conforms to the xsd:decimal @@ -420,6 +398,28 @@ types: - schema:Number base: Decimal uri: xsd:decimal + uriorcurie: + name: uriorcurie + description: a URI or a CURIE + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "uriorcurie". + from_schema: https://example.com/nmdc_submission_schema + base: URIorCURIE + uri: xsd:anyURI + repr: str + string: + name: string + description: A character string + notes: + - In RDF serializations, a slot with range of string is treated as a literal or + type xsd:string. If you are authoring schemas in LinkML YAML, the type is + referenced with the lower case "string". + from_schema: https://example.com/nmdc_submission_schema + exact_mappings: + - schema:Text + base: str + uri: xsd:string boolean: name: boolean description: A binary (true or false) value @@ -4052,8 +4052,6 @@ enums: text: Digestive system Digestive tube: text: Digestive tube - Dinoflagellates: - text: Dinoflagellates Dissolved organics (aerobic): text: Dissolved organics (aerobic) Dissolved organics (anaerobic): @@ -21470,7 +21468,7 @@ classes: range: string required: true multivalued: false - pattern: ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$ + pattern: ^[-+]?([1-8]?\d(\.\d{1,8})?|90(\.0{1,8})?)\s[-+]?(180(\.0{1,8})?|((1[0-7]\d)|([1-9]?\d))(\.\d{1,8})?)$ methane: name: methane annotations: @@ -23370,7 +23368,7 @@ classes: range: string required: true multivalued: false - pattern: ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$ + pattern: ^[-+]?([1-8]?\d(\.\d{1,8})?|90(\.0{1,8})?)\s[-+]?(180(\.0{1,8})?|((1[0-7]\d)|([1-9]?\d))(\.\d{1,8})?)$ magnesium: name: magnesium annotations: @@ -27370,7 +27368,7 @@ classes: range: string required: true multivalued: false - pattern: ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$ + pattern: ^[-+]?([1-8]?\d(\.\d{1,8})?|90(\.0{1,8})?)\s[-+]?(180(\.0{1,8})?|((1[0-7]\d)|([1-9]?\d))(\.\d{1,8})?)$ light_type: name: light_type annotations: @@ -31221,7 +31219,7 @@ classes: range: string required: true multivalued: false - pattern: ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$ + pattern: ^[-+]?([1-8]?\d(\.\d{1,8})?|90(\.0{1,8})?)\s[-+]?(180(\.0{1,8})?|((1[0-7]\d)|([1-9]?\d))(\.\d{1,8})?)$ lithology: name: lithology annotations: @@ -34506,7 +34504,7 @@ classes: range: string required: true multivalued: false - pattern: ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$ + pattern: ^[-+]?([1-8]?\d(\.\d{1,8})?|90(\.0{1,8})?)\s[-+]?(180(\.0{1,8})?|((1[0-7]\d)|([1-9]?\d))(\.\d{1,8})?)$ lithology: name: lithology annotations: @@ -37643,7 +37641,7 @@ classes: range: string required: true multivalued: false - pattern: ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$ + pattern: ^[-+]?([1-8]?\d(\.\d{1,8})?|90(\.0{1,8})?)\s[-+]?(180(\.0{1,8})?|((1[0-7]\d)|([1-9]?\d))(\.\d{1,8})?)$ misc_param: name: misc_param annotations: @@ -38414,6 +38412,7 @@ classes: required: true recommended: false multivalued: false + pattern: ^[_a-zA-Z0-9-]*$ dna_seq_project: name: dna_seq_project title: DNA seq project ID @@ -38819,6 +38818,7 @@ classes: required: true recommended: false multivalued: false + pattern: ^[_a-zA-Z0-9-]*$ dna_seq_project: name: dna_seq_project title: DNA seq project ID @@ -39212,6 +39212,7 @@ classes: multivalued: false minimum_value: 0 maximum_value: 2000 + pattern: ^[_a-zA-Z0-9-]*$ rna_seq_project: name: rna_seq_project title: RNA seq project ID @@ -40319,7 +40320,7 @@ classes: range: string required: true multivalued: false - pattern: ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$ + pattern: ^[-+]?([1-8]?\d(\.\d{1,8})?|90(\.0{1,8})?)\s[-+]?(180(\.0{1,8})?|((1[0-7]\d)|([1-9]?\d))(\.\d{1,8})?)$ misc_param: name: misc_param annotations: @@ -42895,7 +42896,7 @@ classes: range: string required: true multivalued: false - pattern: ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$ + pattern: ^[-+]?([1-8]?\d(\.\d{1,8})?|90(\.0{1,8})?)\s[-+]?(180(\.0{1,8})?|((1[0-7]\d)|([1-9]?\d))(\.\d{1,8})?)$ light_regm: name: light_regm annotations: @@ -45805,7 +45806,7 @@ classes: range: string required: true multivalued: false - pattern: ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$ + pattern: ^[-+]?([1-8]?\d(\.\d{1,8})?|90(\.0{1,8})?)\s[-+]?(180(\.0{1,8})?|((1[0-7]\d)|([1-9]?\d))(\.\d{1,8})?)$ light_regm: name: light_regm annotations: @@ -49320,7 +49321,7 @@ classes: range: string required: true multivalued: false - pattern: ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$ + pattern: ^[-+]?([1-8]?\d(\.\d{1,8})?|90(\.0{1,8})?)\s[-+]?(180(\.0{1,8})?|((1[0-7]\d)|([1-9]?\d))(\.\d{1,8})?)$ lbc_thirty: name: lbc_thirty annotations: @@ -52019,7 +52020,7 @@ classes: range: string required: true multivalued: false - pattern: ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$ + pattern: ^[-+]?([1-8]?\d(\.\d{1,8})?|90(\.0{1,8})?)\s[-+]?(180(\.0{1,8})?|((1[0-7]\d)|([1-9]?\d))(\.\d{1,8})?)$ misc_param: name: misc_param annotations: From 11629b82ff1dceb19f83a3822e3cb46d4e7277ce Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Mon, 11 Nov 2024 10:58:29 -0800 Subject: [PATCH 7/9] fix makefile target to rerun with new file locations --- .../post_google_sheets_soil_env_local_scale.ipynb | 2 +- ... => post_google_sheets_soil_env_medium_scale.ipynb} | 2 +- ...sv => post_google_sheets_soil_env_medium_scale.tsv} | 0 ..._soil_env_medium_scale_retention_justification.tsv} | 0 project.Makefile | 10 ++++++---- .../schema/nmdc_submission_schema.yaml | 4 ++-- 6 files changed, 10 insertions(+), 8 deletions(-) rename notebooks/environmental_context_value_sets/soil/env_medium/{post_google_sheets_soil_env_medium.ipynb => post_google_sheets_soil_env_medium_scale.ipynb} (99%) rename notebooks/environmental_context_value_sets/soil/env_medium/{post_google_sheets_soil_env_medium.tsv => post_google_sheets_soil_env_medium_scale.tsv} (100%) rename notebooks/environmental_context_value_sets/soil/env_medium/{post_google_sheets_soil_env_medium_retention_justification.tsv => post_google_sheets_soil_env_medium_scale_retention_justification.tsv} (100%) diff --git a/notebooks/environmental_context_value_sets/soil/env_local_scale/post_google_sheets_soil_env_local_scale.ipynb b/notebooks/environmental_context_value_sets/soil/env_local_scale/post_google_sheets_soil_env_local_scale.ipynb index 5437cf63..b5da5aad 100644 --- a/notebooks/environmental_context_value_sets/soil/env_local_scale/post_google_sheets_soil_env_local_scale.ipynb +++ b/notebooks/environmental_context_value_sets/soil/env_local_scale/post_google_sheets_soil_env_local_scale.ipynb @@ -306,7 +306,7 @@ "# for the sake of 'soils whose differentia can be expressed in the broad or local scale slots\n", "\n", "# run this after discover_excludable_soils.ipynb\n", - "# and before post_google_sheets_soil_env_medium.ipynb\n", + "# and before post_google_sheets_soil_env_medium_scale.ipynb\n", "\n", "# see discover_excludable_soils.tsv with relation_is_reasonable filtered to true\n", "# then remove blanks from sole_reasonable_other and sole_soil" diff --git a/notebooks/environmental_context_value_sets/soil/env_medium/post_google_sheets_soil_env_medium.ipynb b/notebooks/environmental_context_value_sets/soil/env_medium/post_google_sheets_soil_env_medium_scale.ipynb similarity index 99% rename from notebooks/environmental_context_value_sets/soil/env_medium/post_google_sheets_soil_env_medium.ipynb rename to notebooks/environmental_context_value_sets/soil/env_medium/post_google_sheets_soil_env_medium_scale.ipynb index 64373ef6..b806912b 100644 --- a/notebooks/environmental_context_value_sets/soil/env_medium/post_google_sheets_soil_env_medium.ipynb +++ b/notebooks/environmental_context_value_sets/soil/env_medium/post_google_sheets_soil_env_medium_scale.ipynb @@ -80,7 +80,7 @@ } }, "cell_type": "code", - "source": "output_file = \"post_google_sheets_soil_env_medium.tsv\"", + "source": "output_file = \"post_google_sheets_soil_env_medium_scale.tsv\"", "id": "4737c7dfdaa5400e", "outputs": [], "execution_count": 6 diff --git a/notebooks/environmental_context_value_sets/soil/env_medium/post_google_sheets_soil_env_medium.tsv b/notebooks/environmental_context_value_sets/soil/env_medium/post_google_sheets_soil_env_medium_scale.tsv similarity index 100% rename from notebooks/environmental_context_value_sets/soil/env_medium/post_google_sheets_soil_env_medium.tsv rename to notebooks/environmental_context_value_sets/soil/env_medium/post_google_sheets_soil_env_medium_scale.tsv diff --git a/notebooks/environmental_context_value_sets/soil/env_medium/post_google_sheets_soil_env_medium_retention_justification.tsv b/notebooks/environmental_context_value_sets/soil/env_medium/post_google_sheets_soil_env_medium_scale_retention_justification.tsv similarity index 100% rename from notebooks/environmental_context_value_sets/soil/env_medium/post_google_sheets_soil_env_medium_retention_justification.tsv rename to notebooks/environmental_context_value_sets/soil/env_medium/post_google_sheets_soil_env_medium_scale_retention_justification.tsv diff --git a/project.Makefile b/project.Makefile index d08266a7..543c4a67 100644 --- a/project.Makefile +++ b/project.Makefile @@ -185,6 +185,8 @@ local/nmdc.yaml ########### ENV Triad PV generation ########## # Specify that 'ingest-triad' is a phony target, meaning it doesn't correspond to an actual file .PHONY: ingest-triad +WATCHED_DIR := notebooks/environmental_context_value_sets +WATCHED_FILES := $(shell find $(WATCHED_DIR) -type f) # Define an intermediate target to prevent re-triggering .INTERMEDIATE: temp_target @@ -193,10 +195,10 @@ local/nmdc.yaml ingest-triad: temp_target # Intermediate target that has all dependencies -temp_target: notebooks/*.tsv src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml - $(RUN) inject-env-triad-terms -f notebooks/post_google_sheets_soil_env_local_scale.tsv -i src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml -o src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml - $(RUN) inject-env-triad-terms -f notebooks/post_google_sheets_soil_env_medium_scale.tsv -i src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml -o src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml - $(RUN) inject-env-triad-terms -f notebooks/post_google_sheets_soil_env_broad_scale.tsv -i src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml -o src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml +temp_target: $(WATCHED_FILES) src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml + $(RUN) inject-env-triad-terms -f notebooks/environmental_context_value_sets/soil/env_local_scale/post_google_sheets_soil_env_local_scale.tsv -i src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml -o src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml + $(RUN) inject-env-triad-terms -f notebooks/environmental_context_value_sets/soil/env_medium/post_google_sheets_soil_env_medium_scale.tsv -i src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml -o src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml + $(RUN) inject-env-triad-terms -f notebooks/environmental_context_value_sets/soil/env_broad_scale/post_google_sheets_soil_env_broad_scale.tsv -i src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml -o src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml touch temp_target ################################################ diff --git a/src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml b/src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml index eaaab81a..c53195d6 100644 --- a/src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml +++ b/src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml @@ -7295,8 +7295,8 @@ enums: text: subpolar coniferous forest biome [ENVO:01000250] subtropical broadleaf forest biome [ENVO:01000201]: text: subtropical broadleaf forest biome [ENVO:01000201] - subtropical coniferous forest biome [ENVO:s01000209]: - text: subtropical coniferous forest biome [ENVO:s01000209] + subtropical coniferous forest biome [ENVO:01000209]: + text: subtropical coniferous forest biome [ENVO:01000209] subtropical dry broadleaf forest biome [ENVO:01000225]: text: subtropical dry broadleaf forest biome [ENVO:01000225] subtropical grassland biome [ENVO:01000191]: From 46a1d542e84d2b0b1df96338830be7edb7fa1a79 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Mon, 11 Nov 2024 11:38:05 -0800 Subject: [PATCH 8/9] convert to pytest, make sure test is running successfully --- Makefile | 2 +- .../scripts/generate_env_triad_enums.py | 11 +++-- tests/test_env_triad.py | 47 ++++++++++--------- 3 files changed, 33 insertions(+), 27 deletions(-) diff --git a/Makefile b/Makefile index c9d30725..8136d9df 100644 --- a/Makefile +++ b/Makefile @@ -124,7 +124,7 @@ test-schema: $(RUN) gen-project ${GEN_PARGS} -d tmp $(SOURCE_SCHEMA_PATH) test-python: - $(RUN) python -m unittest discover + $(RUN) pytest lint: $(RUN) linkml-lint $(SOURCE_SCHEMA_PATH) diff --git a/src/nmdc_submission_schema/scripts/generate_env_triad_enums.py b/src/nmdc_submission_schema/scripts/generate_env_triad_enums.py index b262ccd1..99287031 100644 --- a/src/nmdc_submission_schema/scripts/generate_env_triad_enums.py +++ b/src/nmdc_submission_schema/scripts/generate_env_triad_enums.py @@ -68,22 +68,25 @@ def inject_terms_into_schema(values_file_path: Path, sv.add_enum(enum_def) return sv.schema + def ingest(values_file_path: Path, source_schema_yaml_path: Path = SOURCE_SCHEMA_YAML_PATH, - target_schema_yaml_path: Path = TARGET_SCHEMA_YAML_PATH) -> None: + target_schema_yaml_path: Path = TARGET_SCHEMA_YAML_PATH, + enum_name: str = None) -> None: """ Inject terms from multiple TSV files into the schema, each under a specified enumeration name. - :param enum_name : Name of the enumeration to add or update in the schema. :param values_file_path: Path to the TSV file containing the terms to replace the Enum PVs with :param source_schema_yaml_path: Path to the source schema YAML file. :param target_schema_yaml_path: Path to the target schema YAML file. + :param enum_name: Dictionary mapping TSV file paths to enumeration names. """ # Define files and corresponding enumeration names - enum_name = enum_file_mappings.get(values_file_path.name) if enum_name is None: - raise ValueError(f"Enumeration name not found for file: {values_file_path}") + enum_name = enum_file_mappings.get(values_file_path) + if enum_name is None: + raise ValueError(f"Enumeration name not found for file: {values_file_path.name}") sv = SchemaView(source_schema_yaml_path) # Load, inject terms, and save the updated schema for each file diff --git a/tests/test_env_triad.py b/tests/test_env_triad.py index d77a7bcf..4235fb8b 100644 --- a/tests/test_env_triad.py +++ b/tests/test_env_triad.py @@ -8,11 +8,12 @@ repo_root = Path(__file__).resolve().parent.parent +test_files_root = repo_root / "tests" / "inputs" # Define the paths to the test input files -SOIL_ENV_LOCAL_PATH = repo_root / "tests/inputs/soil_env_local_test.tsv" -SOIL_ENV_MEDIUM_PATH = repo_root / "tests/inputs/soil_env_medium_test.tsv" -SOIL_ENV_BROAD_PATH = repo_root / "tests/inputs/soil_env_broad_test.tsv" +SOIL_ENV_LOCAL_PATH = test_files_root / "soil_env_local_test.tsv" +SOIL_ENV_MEDIUM_PATH = test_files_root / "soil_env_medium_test.tsv" +SOIL_ENV_BROAD_PATH = test_files_root / "soil_env_broad_test.tsv" BASE_SCHEMA_PATH = repo_root / "tests/inputs/base_schema.yaml" OUTPUT_SCHEMA_PATH = repo_root / "tests/inputs/output_schema.yaml" # Location for output schema @@ -52,31 +53,33 @@ def test_inject_terms_into_schema(sample_schema_view): def test_ingest(tmp_path): # Define paths to the TSV files and expected enums - file_enum_mappings = [ - (SOIL_ENV_LOCAL_PATH, "EnvLocalScaleSoilEnum"), - (SOIL_ENV_MEDIUM_PATH, "EnvMediumScaleSoilEnum"), - (SOIL_ENV_BROAD_PATH, "EnvBroadScaleSoilEnum") + {SOIL_ENV_LOCAL_PATH: "EnvLocalScaleSoilEnum"}, + {SOIL_ENV_MEDIUM_PATH: "EnvMediumScaleSoilEnum"}, + {SOIL_ENV_BROAD_PATH: "EnvBroadScaleSoilEnum"} ] - # Run `main` with real file paths - for tsv_path, enum_name in file_enum_mappings: - ingest(enum_name=enum_name, - values_file_path=tsv_path, - source_schema_yaml_path=BASE_SCHEMA_PATH, - target_schema_yaml_path=BASE_SCHEMA_PATH) - + # Run `ingest` with real file paths + for mapping in file_enum_mappings: + for tsv_path, enum_name in mapping.items(): # Iterate over each dictionary and get path and enum name + ingest( + values_file_path=tsv_path, + source_schema_yaml_path=BASE_SCHEMA_PATH, + target_schema_yaml_path=BASE_SCHEMA_PATH, + enum_name=enum_name # Pass the specific enum name + ) # Verify that the output schema file contains the injected enums with the correct permissible values output_schema_view = SchemaView(str(BASE_SCHEMA_PATH)) # Check that each enum exists with expected permissible values - for tsv_path, enum_name in file_enum_mappings: - assert enum_name in output_schema_view.schema.enums, f"Enum '{enum_name}' not found in output schema" + for mapping in file_enum_mappings: + for tsv_path, enum_name in mapping.items(): + assert enum_name in output_schema_view.schema.enums, f"Enum '{enum_name}' not found in output schema" - # Load and check permissible values - expected_data = parse_tsv_to_dict(tsv_path) - sorted_data = sorted(expected_data, key=lambda x: x["term_name"]) - expected_pvs = [PermissibleValue(text=f"{term['term_name']} [{term['term_id']}]") for term in sorted_data] + # Load and check permissible values + expected_data = parse_tsv_to_dict(tsv_path) + sorted_data = sorted(expected_data, key=lambda x: x["term_name"]) + expected_pvs = [PermissibleValue(text=f"{term['term_name']} [{term['term_id']}]") for term in sorted_data] - enum_def = output_schema_view.schema.enums[enum_name] - assert list(enum_def.permissible_values.values()) == expected_pvs, f"Permissible values for '{enum_name}' do not match expected data" + enum_def = output_schema_view.schema.enums[enum_name] + assert list(enum_def.permissible_values.values()) == expected_pvs, f"Permissible values for '{enum_name}' do not match expected data" From 3aeeff1be3bfea9dd9ed190594829a5b5708351f Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Mon, 11 Nov 2024 11:54:31 -0800 Subject: [PATCH 9/9] fix test --- pyproject.toml | 1 + src/nmdc_submission_schema/scripts/generate_env_triad_enums.py | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index f8f5bfb9..f17c1543 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -75,3 +75,4 @@ oak-tree-to-pv-list = "nmdc_submission_schema.scripts.oak_tree_to_pv_list:main" dh-json2linkml = 'nmdc_submission_schema.scripts.dh_json2linkml:update_json' linkml-json2dh = 'nmdc_submission_schema.scripts.linkml_json2dh:extract_lists' inject-gold-pathway-terms = 'nmdc_submission_schema.scripts.gold:main' +inject-env-triad-terms = 'nmdc_submission_schema.scripts.generate_env_triad_enums:main' \ No newline at end of file diff --git a/src/nmdc_submission_schema/scripts/generate_env_triad_enums.py b/src/nmdc_submission_schema/scripts/generate_env_triad_enums.py index 99287031..4953c98e 100644 --- a/src/nmdc_submission_schema/scripts/generate_env_triad_enums.py +++ b/src/nmdc_submission_schema/scripts/generate_env_triad_enums.py @@ -84,7 +84,7 @@ def ingest(values_file_path: Path, # Define files and corresponding enumeration names if enum_name is None: - enum_name = enum_file_mappings.get(values_file_path) + enum_name = enum_file_mappings.get(values_file_path.name) if enum_name is None: raise ValueError(f"Enumeration name not found for file: {values_file_path.name}")