Class: Processed Sample (ProcessedSample)

name: ProcessedSample
title: Processed Sample
from_schema: https://w3id.org/nmdc/nmdc
is_a: Sample
slots:
- biomaterial_purity
- dna_absorb1
- dna_concentration
- external_database_identifiers
- sampled_portion
- gradient_position
- gradient_pos_density
- gradient_pos_rel_am
- nucleobase_atom_frac
slot_usage:
  id:
    name: id
    examples:
    - value: nmdc:procsm-11-0013mk17
      description: a production ProcessedSample
    structured_pattern:
      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}'
      interpolated: true
class_uri: nmdc:ProcessedSample

name: ProcessedSample
title: Processed Sample
from_schema: https://w3id.org/nmdc/nmdc
is_a: Sample
slot_usage:
  id:
    name: id
    examples:
    - value: nmdc:procsm-11-0013mk17
      description: a production ProcessedSample
    structured_pattern:
      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}'
      interpolated: true
attributes:
  biomaterial_purity:
    name: biomaterial_purity
    description: A measure of the purity of a biomaterial sample
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    abstract: true
    owner: ProcessedSample
    domain_of:
    - ProcessedSample
    range: QuantityValue
  dna_absorb1:
    name: dna_absorb1
    description: 260/280 measurement of DNA sample purity
    title: DNA absorbance 260/280
    comments:
    - Recommended value is between 1 and 3.
    examples:
    - value: '2.02'
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 7
    is_a: biomaterial_purity
    owner: ProcessedSample
    domain_of:
    - ProcessedSample
    slot_group: JGI-Metagenomics
    range: float
    recommended: true
  dna_concentration:
    name: dna_concentration
    title: DNA concentration in ng/ul
    comments:
    - Units must be in ng/uL. Enter the numerical part only. Must be calculated using
      a fluorometric method. Acceptable values are 0-2000.
    examples:
    - value: '100'
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - nmdc:nucleic_acid_concentration
    rank: 5
    owner: ProcessedSample
    domain_of:
    - ProcessedSample
    slot_group: JGI-Metagenomics
    range: float
    recommended: true
    minimum_value: 0
    maximum_value: 2000
  external_database_identifiers:
    name: external_database_identifiers
    description: Link to corresponding identifier in external database
    comments:
    - The value of this field is always a registered CURIE
    from_schema: https://w3id.org/nmdc/nmdc
    close_mappings:
    - skos:closeMatch
    rank: 1000
    is_a: alternative_identifiers
    abstract: true
    owner: ProcessedSample
    domain_of:
    - ProcessedSample
    - OrganismSample
    range: external_identifier
    multivalued: true
    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
  sampled_portion:
    name: sampled_portion
    description: The portion of the sample that is taken for downstream activity.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    owner: ProcessedSample
    domain_of:
    - SubSamplingProcess
    - ProcessedSample
    range: SamplePortionEnum
    multivalued: true
  gradient_position:
    name: gradient_position
    description: A number designating the gradient position from heaviest (=1) to
      lightest. Unfractionated samples, from which fractionated samples were derived,
      should be denoted with -1.
    title: gradient position
    examples:
    - value: '1'
    - value: '-1'
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    slot_uri: MIXS:0001342
    owner: ProcessedSample
    domain_of:
    - ProcessedSample
    range: integer
    minimum_value: -1
  gradient_pos_density:
    name: gradient_pos_density
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: g/mL
      storage_units:
        tag: storage_units
        value: g/mL
    description: Buoyant density of this fraction
    title: density of gradient position
    examples:
    - object:
        type: nmdc:QuantityValue
        has_raw_value: 1.725 g/mL
        has_numeric_value: 1.725
        has_unit: g/mL
    - object:
        type: nmdc:QuantityValue
        has_raw_value: 1.725-1.735 g/mL
        has_minimum_numeric_value: 1.725
        has_maximum_numeric_value: 1.735
        has_unit: g/mL
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    slot_uri: MIXS:0001343
    owner: ProcessedSample
    domain_of:
    - ProcessedSample
    range: QuantityValue
    recommended: true
  gradient_pos_rel_am:
    name: gradient_pos_rel_am
    annotations:
      storage_units:
        tag: storage_units
        value: '1'
    description: The total nucleic acids loaded onto the column in this fraction as
      a decimal. If uploading 16S rRNA gene (or other amplicon) sequencing data, this
      value should be calculated from qPCR data. If uploading untargetted sequencing
      data, this value should be calculated from total DNA concentration.
    title: relative amount of nucleic acids in the gradient position
    examples:
    - object:
        type: nmdc:QuantityValue
        has_raw_value: '0.1'
        has_numeric_value: 0.1
        has_unit: '1'
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    slot_uri: MIXS:0001344
    owner: ProcessedSample
    domain_of:
    - ProcessedSample
    range: QuantityValue
    range_expression:
      slot_conditions:
        has_numeric_value:
          name: has_numeric_value
          minimum_value: 0
          maximum_value: 1
    recommended: true
  nucleobase_atom_frac:
    name: nucleobase_atom_frac
    description: Excess atom fraction of the nucleobases in this fraction.
    title: nucleobase excess atom fraction
    examples:
    - value: '0.25'
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    slot_uri: MIXS:0001349
    owner: ProcessedSample
    domain_of:
    - ProcessedSample
    range: float
    recommended: true
    minimum_value: 0
    maximum_value: 1
  id:
    name: id
    description: A unique identifier for a thing. Must be either a CURIE shorthand
      for a URI or a complete URI
    title: ID
    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
    - This slot has no examples on purpose. linkml 1.12 copies a slot's examples into
      every class that uses it, and no single id matches every class id pattern (https://github.com/microbiomedata/nmdc-schema/issues/3540).
      Id examples belong in each class's slot_usage.
    examples:
    - value: nmdc:procsm-11-0013mk17
      description: a production ProcessedSample
    from_schema: https://w3id.org/nmdc/nmdc
    structured_aliases:
    - literal_form: workflow_execution_id
      predicate: NARROW_SYNONYM
      notes:
      - JGI Analysis Tracker (JAT) macro nmdc_metadata.yaml, in an access-restricted
        Bitbucket repository (https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml);
        source is the public NMDC page describing how JAT is used.
      source: https://github.com/microbiomedata/nmdc_automation/blob/main/data_management/README.md
    - literal_form: data_object_id
      predicate: NARROW_SYNONYM
      notes:
      - JGI Analysis Tracker (JAT) macro nmdc_metadata.yaml, in an access-restricted
        Bitbucket repository (https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml);
        source is the public NMDC page describing how JAT is used.
      source: https://github.com/microbiomedata/nmdc_automation/blob/main/data_management/README.md
    rank: 1000
    identifier: true
    owner: ProcessedSample
    domain_of:
    - NamedThing
    range: uriorcurie
    required: true
    pattern: ^(?:(nmdc):procsm-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,}))$
    structured_pattern:
      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}'
      interpolated: true
  name:
    name: name
    description: A human readable label for an entity
    title: Name
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    owner: ProcessedSample
    domain_of:
    - Agent
    - NamedThing
    - Protocol
    range: string
  description:
    name: description
    description: a human-readable description of a thing
    title: Description
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    slot_uri: dcterms:description
    owner: ProcessedSample
    domain_of:
    - ImageValue
    - NamedThing
    - Protocol
    range: string
  alternative_identifiers:
    name: alternative_identifiers
    description: A list of alternative identifiers for the entity.
    title: Alternative Identifiers
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    owner: ProcessedSample
    domain_of:
    - NamedThing
    - MetaboliteIdentification
    range: uriorcurie
    multivalued: true
    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,\(\)\=\#]*$
  type:
    name: type
    description: the class_uri of the class that has been instantiated
    title: Type
    notes:
    - makes it easier to read example data files
    - required for polymorphic MongoDB collections
    comments:
    - 'Deprecating this slot was proposed and rejected: without it, a document read
      back from a polymorphic MongoDB collection cannot be resolved to the class it
      instantiates. It is required on every class for that reason, rather than as
      a convention inherited from LinkML.'
    examples:
    - value: nmdc:Biosample
    - value: nmdc:Study
    from_schema: https://w3id.org/nmdc/nmdc
    structured_aliases:
    - literal_form: workflow_execution_class
      predicate: NARROW_SYNONYM
      notes:
      - JGI Analysis Tracker (JAT) macro nmdc_metadata.yaml, in an access-restricted
        Bitbucket repository (https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml);
        source is the public NMDC page describing how JAT is used.
      source: https://github.com/microbiomedata/nmdc_automation/blob/main/data_management/README.md
    rank: 1000
    slot_uri: rdf:type
    designates_type: true
    owner: ProcessedSample
    domain_of:
    - Agent
    - EukEval
    - FunctionalAnnotationAggMember
    - IsotopologAddition
    - IsotopologComposition
    - PeptideQuantification
    - ProteinQuantification
    - GenomeFeature
    - FunctionalAnnotation
    - AttributeValue
    - NamedThing
    - OntologyRelation
    - FailureCategorization
    - Protocol
    - CreditAssociation
    - Doi
    - ProvenanceMetadata
    - MobilePhaseSegment
    - PortionOfSubstance
    - MagBin
    - MetaboliteIdentification
    range: uriorcurie
    required: true
class_uri: nmdc:ProcessedSample