Class: FunctionalAnnotation

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
  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
    range: MetagenomeAnnotation
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(wfmgan)-{id_shoulder}-{id_blade}{id_version}$'
      interpolated: true
class_uri: nmdc:FunctionalAnnotation

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
  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
    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
    mappings:
    - prov:wasGeneratedBy
    rank: 1000
    alias: was_generated_by
    owner: FunctionalAnnotation
    domain_of:
    - FunctionalAnnotationAggMember
    - FunctionalAnnotation
    - DataObject
    range: MetagenomeAnnotation
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(wfmgan)-{id_shoulder}-{id_blade}{id_version}$'
      interpolated: true
    any_of:
    - range: WorkflowExecution
    - range: DataGeneration
  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