Class: GeneProduct
A molecule encoded by a gene that has an evolved function
URI: nmdc:GeneProduct
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
- MobilePhaseSegment
- PortionOfSubstance
- MagBin
- MetaboliteIdentification
- PeptideQuantification
- ProteinQuantification
- GenomeFeature
- FunctionalAnnotation
- AttributeValue
- NamedThing
- FailureCategorization
- Protocol
- CreditAssociation
- Doi
range: uriorcurie
required: true
class_uri: nmdc:GeneProduct