Class: FunctionalAnnotation
An assignment of a function term (e.g. reaction or pathway) that is executed by a gene product, or which the gene product plays an active role in. Functional annotations can be assigned manually by curators, or automatically in workflows. In the context of NMDC, all function annotation is performed automatically, typically using HMM or Blast type methods
URI: nmdc:FunctionalAnnotation
classDiagram
class FunctionalAnnotation
click FunctionalAnnotation href "../FunctionalAnnotation"
FunctionalAnnotation : feature_category
FunctionalAnnotation --> "0..1" ControlledIdentifiedTermValue : feature_category
click ControlledIdentifiedTermValue href "../ControlledIdentifiedTermValue"
FunctionalAnnotation : has_function
FunctionalAnnotation : subject
FunctionalAnnotation --> "0..1" GeneProduct : subject
click GeneProduct href "../GeneProduct"
FunctionalAnnotation : type
FunctionalAnnotation : was_generated_by
FunctionalAnnotation --> "0..1" MetagenomeAnnotation : was_generated_by
click MetagenomeAnnotation href "../MetagenomeAnnotation"
Slots
Name | Cardinality and Range | Description | Inheritance |
---|---|---|---|
has_function | 0..1 String |
direct | |
subject | 0..1 GeneProduct |
direct | |
was_generated_by | 0..1 MetagenomeAnnotation |
provenance for the annotation | direct |
type | 1 Uriorcurie |
the class_uri of the class that has been instantiated | direct |
feature_category | 0..1 ControlledIdentifiedTermValue |
A Sequence Ontology term that describes the category of a feature | direct |
Usages
used by | used in | type | used |
---|---|---|---|
Database | functional_annotation_set | range | FunctionalAnnotation |
See Also
- https://img.jgi.doe.gov/docs/functional-annotation.pdf
- https://github.com/microbiomedata/mg_annotation/blob/master/functional-annotation.wdl
Identifier and Mapping Information
Schema Source
- from schema: https://w3id.org/nmdc/nmdc
Mappings
Mapping Type | Mapped Value |
---|---|
self | nmdc:FunctionalAnnotation |
native | nmdc:FunctionalAnnotation |
narrow | biolink:GeneToGoTermAssociation |
LinkML Source
Direct
name: FunctionalAnnotation
description: An assignment of a function term (e.g. reaction or pathway) that is executed
by a gene product, or which the gene product plays an active role in. Functional
annotations can be assigned manually by curators, or automatically in workflows. In
the context of NMDC, all function annotation is performed automatically, typically
using HMM or Blast type methods
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://img.jgi.doe.gov/docs/functional-annotation.pdf
- https://github.com/microbiomedata/mg_annotation/blob/master/functional-annotation.wdl
narrow_mappings:
- biolink:GeneToGoTermAssociation
slots:
- has_function
- subject
- was_generated_by
- type
- feature_category
slot_usage:
has_function:
name: has_function
notes:
- Still missing patterns for COG and RetroRules
- These patterns are not yet tied to the listed prefixes. A discussion about that
possibility had been started, including the question of whether these lists
are intended to be open examples or closed
domain_of:
- FunctionalAnnotation
was_generated_by:
name: was_generated_by
description: provenance for the annotation.
notes:
- To be consistent with the rest of the NMDC schema we use the PROV annotation
model, rather than GPAD
domain_of:
- FunctionalAnnotation
- DataObject
range: MetagenomeAnnotation
structured_pattern:
syntax: '{id_nmdc_prefix}:(wfmgan)-{id_shoulder}-{id_blade}{id_version}$'
interpolated: true
class_uri: nmdc:FunctionalAnnotation
Induced
name: FunctionalAnnotation
description: An assignment of a function term (e.g. reaction or pathway) that is executed
by a gene product, or which the gene product plays an active role in. Functional
annotations can be assigned manually by curators, or automatically in workflows. In
the context of NMDC, all function annotation is performed automatically, typically
using HMM or Blast type methods
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://img.jgi.doe.gov/docs/functional-annotation.pdf
- https://github.com/microbiomedata/mg_annotation/blob/master/functional-annotation.wdl
narrow_mappings:
- biolink:GeneToGoTermAssociation
slot_usage:
has_function:
name: has_function
notes:
- Still missing patterns for COG and RetroRules
- These patterns are not yet tied to the listed prefixes. A discussion about that
possibility had been started, including the question of whether these lists
are intended to be open examples or closed
domain_of:
- FunctionalAnnotation
was_generated_by:
name: was_generated_by
description: provenance for the annotation.
notes:
- To be consistent with the rest of the NMDC schema we use the PROV annotation
model, rather than GPAD
domain_of:
- FunctionalAnnotation
- DataObject
range: MetagenomeAnnotation
structured_pattern:
syntax: '{id_nmdc_prefix}:(wfmgan)-{id_shoulder}-{id_blade}{id_version}$'
interpolated: true
attributes:
has_function:
name: has_function
notes:
- Still missing patterns for COG and RetroRules
- These patterns are not yet tied to the listed prefixes. A discussion about that
possibility had been started, including the question of whether these lists
are intended to be open examples or closed
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: has_function
owner: FunctionalAnnotation
domain_of:
- FunctionalAnnotation
range: string
pattern: ^(KEGG_PATHWAY:\w{2,4}\d{5}|KEGG.REACTION:R\d+|RHEA:\d{5}|MetaCyc:[A-Za-z0-9+_.%-:]+|EC:\d{1,2}(\.\d{0,3}){0,3}|GO:\d{7}|MetaNetX:(MNXR\d+|EMPTY)|SEED:\w+|KEGG\.ORTHOLOGY:K\d+|EGGNOG:\w+|PFAM:PF\d{5}|TIGRFAM:TIGR\d+|SUPFAM:\w+|CATH:[1-6]\.[0-9]+\.[0-9]+\.[0-9]+|PANTHER.FAMILY:PTHR\d{5}(\:SF\d{1,3})?)$
subject:
name: subject
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: subject
owner: FunctionalAnnotation
domain_of:
- FunctionalAnnotation
range: GeneProduct
was_generated_by:
name: was_generated_by
description: provenance for the annotation.
notes:
- To be consistent with the rest of the NMDC schema we use the PROV annotation
model, rather than GPAD
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: was_generated_by
owner: FunctionalAnnotation
domain_of:
- FunctionalAnnotation
- DataObject
range: MetagenomeAnnotation
structured_pattern:
syntax: '{id_nmdc_prefix}:(wfmgan)-{id_shoulder}-{id_blade}{id_version}$'
interpolated: true
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: FunctionalAnnotation
domain_of:
- EukEval
- FunctionalAnnotationAggMember
- MobilePhaseSegment
- PortionOfSubstance
- MagBin
- MetaboliteIdentification
- PeptideQuantification
- ProteinQuantification
- GenomeFeature
- FunctionalAnnotation
- AttributeValue
- NamedThing
- FailureCategorization
- Protocol
- CreditAssociation
- Doi
range: uriorcurie
required: true
feature_category:
name: feature_category
description: A Sequence Ontology term that describes the category of a feature
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: feature_category
owner: FunctionalAnnotation
domain_of:
- GenomeFeature
- FunctionalAnnotation
range: ControlledIdentifiedTermValue
class_uri: nmdc:FunctionalAnnotation