Class: GeneProduct

A molecule encoded by a gene that has an evolved function

classDiagram class GeneProduct click GeneProduct href "../GeneProduct" NamedThing <|-- GeneProduct click NamedThing href "../NamedThing" GeneProduct : alternative_identifiers GeneProduct : description GeneProduct : id GeneProduct : name GeneProduct : type

Inheritance

NamedThing
- GeneProduct

Slots

Name	Cardinality and Range	Description	Inheritance
id	1 Uriorcurie	A unique identifier for a thing	NamedThing
name	0..1 String	A human readable label for an entity	NamedThing
description	0..1 String	a human-readable description of a thing	NamedThing
alternative_identifiers	* Uriorcurie	A list of alternative identifiers for the entity	NamedThing
type	1 Uriorcurie	the class_uri of the class that has been instantiated	NamedThing

Usages

used by	used in	type	used
PeptideQuantification	all_proteins	range	GeneProduct
PeptideQuantification	best_protein	range	GeneProduct
ProteinQuantification	all_proteins	range	GeneProduct
ProteinQuantification	best_protein	range	GeneProduct
GenomeFeature	encodes	range	GeneProduct
FunctionalAnnotation	subject	range	GeneProduct

Identifier and Mapping Information

Valid ID Prefixes

Instances of this class should have identifiers with one of the following prefixes:

PR
UniProtKB
gtpo

Schema Source

from schema: https://w3id.org/nmdc/nmdc

Mappings

Mapping Type	Mapped Value
self	nmdc:GeneProduct
native	nmdc:GeneProduct
exact	biolink:GeneProduct

LinkML Source

Direct

name: GeneProduct
id_prefixes:
- PR
- UniProtKB
- gtpo
description: A molecule encoded by a gene that has an evolved function
notes:
- we may include a more general gene product class in future to allow for ncRNA annotation
from_schema: https://w3id.org/nmdc/nmdc
exact_mappings:
- biolink:GeneProduct
is_a: NamedThing
class_uri: nmdc:GeneProduct

Induced

name: GeneProduct
id_prefixes:
- PR
- UniProtKB
- gtpo
description: A molecule encoded by a gene that has an evolved function
notes:
- we may include a more general gene product class in future to allow for ncRNA annotation
from_schema: https://w3id.org/nmdc/nmdc
exact_mappings:
- biolink:GeneProduct
is_a: NamedThing
attributes:
  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: GeneProduct
    domain_of:
    - NamedThing
    range: uriorcurie
    required: true
    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
  name:
    name: name
    description: A human readable label for an entity
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: name
    owner: GeneProduct
    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: GeneProduct
    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: GeneProduct
    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: GeneProduct
    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:GeneProduct