Class: Instrument

name: Instrument
description: A material entity that is designed to perform a function in a scientific
  investigation, but is not a reagent. This class models the make and model of the
  instrument, not the specific instance of the instrument.
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- device
exact_mappings:
- OBI:0000968
is_a: MaterialEntity
slots:
- vendor
- model
slot_usage:
  id:
    name: id
    examples:
    - value: nmdc:inst-11-075j3n79
      description: a production Instrument
    structured_pattern:
      syntax: '{id_nmdc_prefix}:inst-{id_shoulder}-{id_blade}'
      interpolated: true
class_uri: nmdc:Instrument
unique_keys:
  main:
    unique_key_name: main
    unique_key_slots:
    - vendor
    - model
    description: A unique instrument is defined by its vendor and model.

name: Instrument
description: A material entity that is designed to perform a function in a scientific
  investigation, but is not a reagent. This class models the make and model of the
  instrument, not the specific instance of the instrument.
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- device
exact_mappings:
- OBI:0000968
is_a: MaterialEntity
slot_usage:
  id:
    name: id
    examples:
    - value: nmdc:inst-11-075j3n79
      description: a production Instrument
    structured_pattern:
      syntax: '{id_nmdc_prefix}:inst-{id_shoulder}-{id_blade}'
      interpolated: true
attributes:
  vendor:
    name: vendor
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    owner: Instrument
    domain_of:
    - Instrument
    range: InstrumentVendorEnum
  model:
    name: model
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    owner: Instrument
    domain_of:
    - Instrument
    range: InstrumentModelEnum
  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:inst-11-075j3n79
      description: a production Instrument
    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: Instrument
    domain_of:
    - NamedThing
    range: uriorcurie
    required: true
    pattern: ^(?:(nmdc):inst-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,}))$
    structured_pattern:
      syntax: '{id_nmdc_prefix}:inst-{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: Instrument
    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: Instrument
    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: Instrument
    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: Instrument
    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:Instrument
unique_keys:
  main:
    unique_key_name: main
    unique_key_slots:
    - vendor
    - model
    description: A unique instrument is defined by its vendor and model.