Class: Isolate (IsolateInterface)

name: IsolateInterface
annotations:
  excel_worksheet_name:
    tag: excel_worksheet_name
    value: Isolate
description: 'Metadata for microbial isolate samples submitted to NMDC. Captures core
  biological identity slots (taxonomy, strain, culture collection) that NMDC stores
  and queries. Slots are sourced from nmdc-schema OrganismSample and Organism classes;
  depends on nmdc-schema PR #2977 and #2975 merging.'
title: Isolate
from_schema: https://example.com/nmdc_submission_schema
is_a: DhInterface
mixins:
- DhMultiviewCommonColumnsMixin
slots:
- isolate_single_colony
- isolate_known_contaminants
- collection_date
- source_mat_id
- organism_genus
- organism_species
- strain_name
- isolate_name
- classified_as
- gc_content
- ploidy
slot_usage:
  isolate_single_colony:
    name: isolate_single_colony
    slot_group: organism_section
  isolate_known_contaminants:
    name: isolate_known_contaminants
    slot_group: organism_section
  collection_date:
    name: collection_date
    notes:
    - JGI requires all three date components, so the full YYYY-MM-DD is mandatory
      on the isolate interface. The export layer splits it into Collection Year, Collection
      Month, and Collection Day columns.
    comments:
    - Use the date the sample was collected from its natural habitat, not the date
      of purchase or culturing. Full date (YYYY-MM-DD) is required.
    examples:
    - value: '2017-01-20'
    - value: '2013-03-25'
    aliases:
    - Collection Year
    - Collection Month
    - Collection Day
    pattern: ^[12]\d{3}-(?:0[1-9]|1[0-2])-(?:0[1-9]|[12]\d|3[01])$

name: IsolateInterface
annotations:
  excel_worksheet_name:
    tag: excel_worksheet_name
    value: Isolate
description: 'Metadata for microbial isolate samples submitted to NMDC. Captures core
  biological identity slots (taxonomy, strain, culture collection) that NMDC stores
  and queries. Slots are sourced from nmdc-schema OrganismSample and Organism classes;
  depends on nmdc-schema PR #2977 and #2975 merging.'
title: Isolate
from_schema: https://example.com/nmdc_submission_schema
is_a: DhInterface
mixins:
- DhMultiviewCommonColumnsMixin
slot_usage:
  isolate_single_colony:
    name: isolate_single_colony
    slot_group: organism_section
  isolate_known_contaminants:
    name: isolate_known_contaminants
    slot_group: organism_section
  collection_date:
    name: collection_date
    notes:
    - JGI requires all three date components, so the full YYYY-MM-DD is mandatory
      on the isolate interface. The export layer splits it into Collection Year, Collection
      Month, and Collection Day columns.
    comments:
    - Use the date the sample was collected from its natural habitat, not the date
      of purchase or culturing. Full date (YYYY-MM-DD) is required.
    examples:
    - value: '2017-01-20'
    - value: '2013-03-25'
    aliases:
    - Collection Year
    - Collection Month
    - Collection Day
    pattern: ^[12]\d{3}-(?:0[1-9]|1[0-2])-(?:0[1-9]|[12]\d|3[01])$
attributes:
  isolate_single_colony:
    name: isolate_single_colony
    description: Was the sample isolated from a single colony or equivalent axenic/pure
      culture?
    title: single colony isolation
    comments:
    - Answer yes if the sample originated from a single colony pick, single-cell isolation,
      or equivalent process expected to yield a genetically homogeneous culture.
    examples:
    - value: 'yes'
    from_schema: https://example.com/nmdc_submission_schema
    aliases:
    - Is the sample isolated from a single colony or equivalent?
    rank: 30
    alias: isolate_single_colony
    owner: IsolateInterface
    domain_of:
    - IsolateInterface
    slot_group: organism_section
    range: YesNoEnum
    required: true
  isolate_known_contaminants:
    name: isolate_known_contaminants
    description: List any organisms known or suspected to grow in co-culture or that
      may be contaminating the culture, along with an estimate of the percentage.
    title: known or suspected organisms
    comments:
    - Leave blank if no contaminants are known or suspected.
    examples:
    - value: Bacillus subtilis ~5%
    from_schema: https://example.com/nmdc_submission_schema
    aliases:
    - Known / Suspected Organisms
    rank: 31
    alias: isolate_known_contaminants
    owner: IsolateInterface
    domain_of:
    - IsolateInterface
    slot_group: organism_section
    range: string
    recommended: true
  collection_date:
    name: collection_date
    description: The date of sampling
    title: collection date
    notes:
    - JGI requires all three date components, so the full YYYY-MM-DD is mandatory
      on the isolate interface. The export layer splits it into Collection Year, Collection
      Month, and Collection Day columns.
    comments:
    - Use the date the sample was collected from its natural habitat, not the date
      of purchase or culturing. Full date (YYYY-MM-DD) is required.
    examples:
    - value: '2017-01-20'
    - value: '2013-03-25'
    from_schema: https://example.com/nmdc_submission_schema
    aliases:
    - Collection Year
    - Collection Month
    - Collection Day
    rank: 3
    keywords:
    - date
    slot_uri: MIXS:0000011
    alias: collection_date
    owner: IsolateInterface
    domain_of:
    - AirInterface
    - BiofilmInterface
    - BuiltEnvInterface
    - HcrCoresInterface
    - HcrFluidsSwabsInterface
    - HostAssociatedInterface
    - MiscEnvsInterface
    - PlantAssociatedInterface
    - SedimentInterface
    - SoilInterface
    - WastewaterSludgeInterface
    - WaterInterface
    - IsolateInterface
    slot_group: mixs_modified_section
    range: string
    required: true
    pattern: ^[12]\d{3}-(?:0[1-9]|1[0-2])-(?:0[1-9]|[12]\d|3[01])$
  source_mat_id:
    name: source_mat_id
    annotations:
      Expected_value:
        tag: Expected_value
        value: 'for cultures of microorganisms: identifiers for two culture collections;
          for other material a unique arbitrary identifer'
    description: A globally unique identifier assigned to the parent sample or sample
      that is the source of this 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.
    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/).
    - 'Prefixed FAIR identifiers are preferred where available: `igsn` for International
      Generic Sample Numbers (http://www.geosamples.org/getigsn), `biosample` for
      NCBI biosample accession IDs, `gold` for GOLD identifiers. The format is not
      constrained, so culture collection identifiers such as "DSM 6724" or "ATCC 5680"
      are also accepted.'
    examples:
    - value: igsn:AU1243
    - value: biosample:SAMEA2397676
    from_schema: https://example.com/nmdc_submission_schema
    rank: 2
    keywords:
    - identifier
    - material
    - source
    slot_uri: MIXS:0000026
    alias: source_mat_id
    owner: IsolateInterface
    domain_of:
    - DhMultiviewCommonColumnsMixin
    - IsolateInterface
    slot_group: sample_id_section
    range: string
    multivalued: false
  organism_genus:
    name: organism_genus
    description: Genus of the organism.
    comments:
    - Free-text submitter-provided genus name. For an ontology-grounded classification,
      use `classified_as` with a NcbiTaxon instance on the parent Organism class.
    examples:
    - value: Shewanella
      description: GOLD organism_v2 Go0000189 (Shewanella loihica PV-4, queried 2026-04-21)
    - value: Ruegeria
      description: GOLD organism_v2 Go0000514 (Ruegeria pomeroyi DSS-3, queried 2026-04-21)
    - value: Campylobacter
      description: GOLD organism_v2 (Go0000058, queried 2026-04-14)
    in_subset:
    - jgi_isolate
    from_schema: https://example.com/nmdc_submission_schema
    structured_aliases:
      Genus:
        literal_form: Genus
        predicate: EXACT_SYNONYM
        notes:
        - Exact JGI form template is access-restricted; source is the public submission
          overview.
        source: https://jgi.doe.gov/user-programs/pmo-overview/project-materials-submission-overview/
    rank: 106
    alias: organism_genus
    owner: IsolateInterface
    domain_of:
    - IsolateInterface
    slot_group: organism_section
    range: string
    required: true
  organism_species:
    name: organism_species
    description: Species of the organism.
    comments:
    - Free-text submitter-provided species name. For an ontology-grounded classification,
      use `classified_as` with a NcbiTaxon instance on the parent Organism class.
    examples:
    - value: loihica
      description: GOLD organism_v2 Go0000189 (Shewanella loihica PV-4, queried 2026-04-21)
    - value: pomeroyi
      description: GOLD organism_v2 Go0000514 (Ruegeria pomeroyi DSS-3, queried 2026-04-21)
    - value: sp.
      description: GOLD organism_v2.species (n=37 records, queried 2026-04-30) — used
        when the isolate has not yet been assigned a species name
    in_subset:
    - jgi_isolate
    from_schema: https://example.com/nmdc_submission_schema
    structured_aliases:
      Species:
        literal_form: Species
        predicate: EXACT_SYNONYM
        notes:
        - Exact JGI form template is access-restricted; source is the public submission
          overview.
        source: https://jgi.doe.gov/user-programs/pmo-overview/project-materials-submission-overview/
    rank: 107
    alias: organism_species
    owner: IsolateInterface
    domain_of:
    - IsolateInterface
    slot_group: organism_section
    range: string
    required: true
  strain_name:
    name: strain_name
    description: Strain or cultivar name of the organism.
    comments:
    - 'Microbial strain identifiers and plant cultivar names (governed by the International
      Code of Nomenclature for Cultivated Plants, ICNCP) are nomenclaturally distinct,
      but this slot accepts both for now to match the JGI Isolate (NA) v19 form''s
      combined "Strain or cultivar" field. A separate `cultivar_name` slot may be
      added if a plant-specific use case emerges; see #3056.'
    - MIxS `subspecf_gen_lin` (MIXS:0000020) covers this concept along with cultivar,
      serovar, biotype, ecotype, and other sub-species lineage types in a single slot
      using a rank-prefix encoding (e.g. "strain:PV-4"). NMDC splits the concept into
      separate slots; this slot covers the strain rank specifically.
    examples:
    - value: PV-4
      description: GOLD organism_v2 Go0000189 (Shewanella loihica PV-4, queried 2026-04-21)
    - value: DSS-3
      description: GOLD organism_v2 Go0000514 (Ruegeria pomeroyi DSS-3, queried 2026-04-21)
    - value: DSM 6724
      description: GOLD organism_v2 Dictyoglomus turgidum (Go0000002, queried 2026-04-14)
    in_subset:
    - jgi_isolate
    from_schema: https://example.com/nmdc_submission_schema
    structured_aliases:
      Strain or cultivar:
        literal_form: Strain or cultivar
        predicate: EXACT_SYNONYM
        notes:
        - Exact JGI form template is access-restricted; source is the public submission
          overview.
        source: https://jgi.doe.gov/user-programs/pmo-overview/project-materials-submission-overview/
    related_mappings:
    - MIXS:0000020
    rank: 108
    alias: strain_name
    owner: IsolateInterface
    domain_of:
    - IsolateInterface
    slot_group: organism_section
    range: string
    required: true
  isolate_name:
    name: isolate_name
    description: Isolate or mutant name.
    comments:
    - MIxS `subspecf_gen_lin` (MIXS:0000020) covers this concept along with strain,
      cultivar, serovar, biotype, ecotype, and other sub-species lineage types in
      a single slot using a rank-prefix encoding. NMDC uses a separate slot for the
      isolate rank specifically.
    examples:
    - value: Bd21-3
      description: GOLD dw_sample_taxonomy_info.isolate (n=260 records, queried 2026-04-30)
        — Brachypodium distachyon Bd21-3 reference accession
    - value: MR164
      description: GOLD dw_sample_taxonomy_info.isolate (n=555 records, queried 2026-04-30)
    - value: Isolate
      description: GOLD dw_sample_taxonomy_info.isolate (n=918 records, queried 2026-04-30)
        — generic placeholder used when no specific mutant/isolate name is recorded
    in_subset:
    - jgi_isolate
    from_schema: https://example.com/nmdc_submission_schema
    structured_aliases:
      Isolate:
        literal_form: Isolate
        predicate: EXACT_SYNONYM
        notes:
        - Exact JGI form template is access-restricted; source is the public submission
          overview.
        source: https://jgi.doe.gov/user-programs/pmo-overview/project-materials-submission-overview/
    related_mappings:
    - MIXS:0000020
    rank: 109
    alias: isolate_name
    owner: IsolateInterface
    domain_of:
    - IsolateInterface
    slot_group: organism_section
    range: string
  classified_as:
    name: classified_as
    description: 'Taxonomic classification of this organism. Narrowed from the global
      OntologyClass range (defined on the slot itself) to NcbiTaxon, since organism
      identity at NMDC is anchored to NCBI Taxonomy. Per #3016 — the broader pattern
      is to narrow `classified_as` to `NcbiTaxon` on all organism-oriented classes
      via slot_usage.'
    comments:
    - 'Taxonomy-oriented uses (e.g. on Organism) should point to NcbiTaxon instances.
      OrganismSample reaches taxonomy indirectly via expected_organism.classified_as.
      The global range stays OntologyClass; narrowing to NcbiTaxon via slot_usage
      is tracked in #3016.'
    examples:
    - value: NCBITaxon:562
    - value: NCBITaxon:1392
    from_schema: https://example.com/nmdc_submission_schema
    see_also:
    - https://github.com/microbiomedata/nmdc-schema/issues/2959
    narrow_mappings:
    - biolink:in_taxon
    rank: 111
    alias: classified_as
    owner: IsolateInterface
    domain_of:
    - IsolateInterface
    slot_group: organism_section
    range: string
    required: true
    multivalued: false
    pattern: NCBITaxon:\d+
    structured_pattern:
      syntax: NCBITaxon:\d+
      interpolated: false
  gc_content:
    name: gc_content
    description: Estimated GC content as a percentage.
    in_subset:
    - jgi_isolate
    from_schema: https://example.com/nmdc_submission_schema
    structured_aliases:
      GC Content %:
        literal_form: GC Content %
        predicate: EXACT_SYNONYM
        notes:
        - Exact JGI form template is access-restricted; source is the public submission
          overview.
        source: https://jgi.doe.gov/user-programs/pmo-overview/project-materials-submission-overview/
    rank: 113
    alias: gc_content
    owner: IsolateInterface
    domain_of:
    - IsolateInterface
    slot_group: organism_section
    range: float
    minimum_value: 0
    maximum_value: 100
    unit:
      ucum_code: '%'
  ploidy:
    name: ploidy
    description: The ploidy level of the genome (e.g. allopolyploid, haploid, diploid,
      triploid, tetraploid). It has implications for the downstream study of duplicated
      gene and regions of the genomes (and perhaps for difficulties in assembly).
      For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic
      Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer
      to http://purl.bioontology.org/ontology/PATO
    title: ploidy
    from_schema: https://example.com/nmdc_submission_schema
    rank: 114
    slot_uri: MIXS:0000021
    alias: ploidy
    owner: IsolateInterface
    domain_of:
    - IsolateInterface
    slot_group: organism_section
    range: PloidyEnum
  analysis_type:
    name: analysis_type
    description: Select all the data types associated or available for this biosample
    title: analysis/data type
    comments:
    - MIxS:investigation_type was included as a `see_also` but that term doesn't resolve
      any more
    examples:
    - value: metagenomics; metabolomics; metaproteomics
    from_schema: https://example.com/nmdc_submission_schema
    rank: 3
    alias: analysis_type
    owner: IsolateInterface
    domain_of:
    - DhMultiviewCommonColumnsMixin
    slot_group: sample_id_section
    range: AnalysisTypeEnum
    required: true
    multivalued: true
  samp_name:
    name: samp_name
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: ''
    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.
    - If multiple sample environments (soil, water, etc) are used, these values must
      be unique across all environments.
    examples:
    - value: Rock core CB1178(5-6) from NSW
    from_schema: https://example.com/nmdc_submission_schema
    rank: 1
    keywords:
    - sample
    slot_uri: MIXS:0001107
    identifier: true
    alias: samp_name
    owner: IsolateInterface
    domain_of:
    - DhMultiviewCommonColumnsMixin
    slot_group: sample_id_section
    range: string
    required: true