sample_id.yaml

name: sample_id
description: This file defines terms that appear in the 'Sample ID' section of the
  NMDC sample metadata submission portal, which is implemented with DataHarmonizer
  as of Spring 2022
title: 'NMDC Schema supplement for Submission Portal: Sample ID'
id: https://w3id.org/nmdc/portal/sample_id

imports:
  - linkml:types

todos:
  - the two remaining slots in this module, analysis_type and sample_link aren't really sample identifiers

license: https://creativecommons.org/publicdomain/zero/1.0/

prefixes:
  linkml: https://w3id.org/linkml/
  nmdc: https://w3id.org/nmdc/

default_prefix: nmdc
default_range: string

enums:
  AnalysisTypeEnum:
    from_schema: https://example.com/nmdc_dh
    permissible_values:
      metabolomics: { }
      metagenomics:
        title: Metagenomics
        description: Standard short-read metagenomic sequencing
      metagenomics_long_read:
        title: Metagenomics (long read)
        description: Long-read metagenomic sequencing
      metaproteomics: { }
      metatranscriptomics: { }
      natural organic matter: { }

slots:
  analysis_type:
    description: Select all the data types associated or available for this biosample
    title: analysis/data type
    examples:
      - value: metagenomics; metabolomics; proteomics
    from_schema: https://example.com/nmdc_dh
    see_also:
      - MIxS:investigation_type
    rank: 3
    multivalued: true
    slot_group: Sample ID
    range: AnalysisTypeEnum
    recommended: true

  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.
    comments:
      - 'This field allows multiple entries separated by ; (Examples: Soil collected
      from the field will link with the soil used in an incubation. The soil a plant
      was grown in links to the plant sample. An original culture sample was transferred
      to a new vial and generated a new sample)'
    examples:
      - value: IGSN:DSJ0284
    from_schema: https://example.com/nmdc_dh
    multivalued: true
    range: string
    rank: 5
    recommended: true
    slot_group: Sample ID
    string_serialization: '{text}:{text}'
    title: sample linkage