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
slot_usage:
  id:
    name: id
    required: true
    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
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'
      interpolated: true
attributes:
  biomaterial_purity:
    name: biomaterial_purity
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: biomaterial_purity
    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
    alias: dna_absorb1
    owner: ProcessedSample
    domain_of:
    - Biosample
    - 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
    alias: dna_concentration
    owner: ProcessedSample
    domain_of:
    - Biosample
    - 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
    notes:
    - had tried ranges of external identifier and string
    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
    alias: external_database_identifiers
    owner: ProcessedSample
    domain_of:
    - ProcessedSample
    range: external_identifier
    multivalued: true
    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
  id:
    name: id
    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
    examples:
    - value: nmdc:mgmag-00-x012.1_7_c1
      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    identifier: true
    alias: id
    owner: ProcessedSample
    domain_of:
    - NamedThing
    range: uriorcurie
    required: true
    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
    structured_pattern:
      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'
      interpolated: true
  name:
    name: name
    description: A human readable label for an entity
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: name
    owner: ProcessedSample
    domain_of:
    - PersonValue
    - NamedThing
    - Protocol
    range: string
  description:
    name: description
    description: a human-readable description of a thing
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    slot_uri: dcterms:description
    alias: description
    owner: ProcessedSample
    domain_of:
    - ImageValue
    - NamedThing
    range: string
  alternative_identifiers:
    name: alternative_identifiers
    description: A list of alternative identifiers for the entity.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: alternative_identifiers
    owner: ProcessedSample
    domain_of:
    - MetaboliteIdentification
    - NamedThing
    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
    notes:
    - 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
    from_schema: https://w3id.org/nmdc/nmdc
    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
    rank: 1000
    slot_uri: rdf:type
    designates_type: true
    alias: type
    owner: ProcessedSample
    domain_of:
    - EukEval
    - FunctionalAnnotationAggMember
    - PeptideQuantification
    - ProteinQuantification
    - MobilePhaseSegment
    - PortionOfSubstance
    - MagBin
    - MetaboliteIdentification
    - GenomeFeature
    - FunctionalAnnotation
    - AttributeValue
    - NamedThing
    - OntologyRelation
    - FailureCategorization
    - Protocol
    - CreditAssociation
    - Doi
    range: uriorcurie
    required: true
class_uri: nmdc:ProcessedSample