Class: Annotation

name: Annotation
description: 'An association between a gene product and a GO term, with an evidence
  code, a

  reference to support the association, and other data associated with the gene

  product or the annotation.'
from_schema: https://w3id.org/geneontology/go-standard-annotation-schema
slots:
- db_object_id
- negation
- relation
- ontology_class_id
- references
- evidence_type
- with_or_from
- interacting_taxon_id
- annotation_date
- assigned_by
- annotation_extensions
- annotation_properties

name: Annotation
description: 'An association between a gene product and a GO term, with an evidence
  code, a

  reference to support the association, and other data associated with the gene

  product or the annotation.'
from_schema: https://w3id.org/geneontology/go-standard-annotation-schema
attributes:
  db_object_id:
    name: db_object_id
    description: A unique identifier for the item being annotated.
    from_schema: https://w3id.org/geneontology/go-standard-annotation-schema
    rank: 1000
    owner: Annotation
    domain_of:
    - Annotation
    - Entity
    range: external_identifier
    required: true
  negation:
    name: negation
    description: A boolean indicating whether the annotation is negated.
    todos:
    - Decide if this should be required in the schema so that it is always explicitly
      set to true or false. Or, is it okay to have it be optional and assumed false
      if not present?
    from_schema: https://w3id.org/geneontology/go-standard-annotation-schema
    rank: 1000
    owner: Annotation
    domain_of:
    - Annotation
    range: boolean
    required: false
  relation:
    name: relation
    description: 'Relation from the Relation Ontology that describe how the annotated
      biological

      entity relates to the GO term with which it is associated.'
    todos:
    - The GPAD spec says that the "relation used SHOULD come from the allowed gene-product-to-term
      relations". Decide whether to enforce this in the schema via an enum.
    from_schema: https://w3id.org/geneontology/go-standard-annotation-schema
    rank: 1000
    owner: Annotation
    domain_of:
    - Annotation
    range: external_identifier
    required: true
  ontology_class_id:
    name: ontology_class_id
    description: The GO identifier for the term attributed to the DB object ID.
    from_schema: https://w3id.org/geneontology/go-standard-annotation-schema
    rank: 1000
    owner: Annotation
    domain_of:
    - Annotation
    range: go_identifier
    required: true
  references:
    name: references
    description: 'One or more unique identifiers for a single source cited as an authority
      for the

      attribution of the GO ID to the DB object ID. This may be a literature reference

      or a database record. Valid references are one of: PubMed, DOI, GO_REF, MOD

      reference.'
    from_schema: https://w3id.org/geneontology/go-standard-annotation-schema
    rank: 1000
    owner: Annotation
    domain_of:
    - Annotation
    range: external_identifier
    required: true
    multivalued: true
    minimum_cardinality: 1
  evidence_type:
    name: evidence_type
    description: 'The Evidence & Conclusion Ontology (ECO) identifier for the evidence
      code that

      supports the association between the DB object ID and the GO term.'
    from_schema: https://w3id.org/geneontology/go-standard-annotation-schema
    rank: 1000
    owner: Annotation
    domain_of:
    - Annotation
    range: eco_identifier
    required: true
  with_or_from:
    name: with_or_from
    description: 'Used with specific ECO codes to capture an additional identifier
      supporting the

      evidence for the annotation. For example, it can identify another gene product
      to

      which the annotated gene product is similar (ISS) or interacts with (IPI).

      Population of the With/From is mandatory for certain evidence codes.'
    todos:
    - The GPAD spec makes a distinction between pipe- and comma-separated lists of
      With/From values. Decide if and how this should be represented in the schema.
    comments:
    - Cardinality must be 0 for evidence codes IDA, TAS, NAS, or ND
    - Cardinality must be 1, >1 for IEA, IC, IGI, IPI, ISS & child terms of ISS
    from_schema: https://w3id.org/geneontology/go-standard-annotation-schema
    rank: 1000
    owner: Annotation
    domain_of:
    - Annotation
    range: external_identifier
    required: false
    multivalued: true
  interacting_taxon_id:
    name: interacting_taxon_id
    description: 'Taxonomic identifier for interacting organism to be used only in
      conjunction with

      terms that have the biological process term ''GO:0044419 biological process

      involved in interspecies interaction between organisms'' or the cellular component

      term ''GO:0018995 host cellular component'' as an ancestor. Identifiers must
      come

      from NCBI Taxonomy database.'
    from_schema: https://w3id.org/geneontology/go-standard-annotation-schema
    rank: 1000
    owner: Annotation
    domain_of:
    - Annotation
    range: ncbi_taxon_identifier
    required: false
    multivalued: true
  annotation_date:
    name: annotation_date
    description: Date on which the annotation was made
    todos:
    - The GPAD file description says that this is a date in the format `YYYY-MM-DD`.
      The spec says that it is a date or datetime. Decide whether to permit date,
      datetime, or both.
    from_schema: https://w3id.org/geneontology/go-standard-annotation-schema
    rank: 1000
    owner: Annotation
    domain_of:
    - Annotation
    range: date
    required: true
  assigned_by:
    name: assigned_by
    description: 'The database which made the annotation one of the values from the
      set of GOC

      groups; used for tracking the source of an individual annotation.'
    comments:
    - Value may differ from the DB:DB Object ID column. Any annotation that is made
      by one database and incorporated into another retains the original value.
    from_schema: https://w3id.org/geneontology/go-standard-annotation-schema
    rank: 1000
    owner: Annotation
    domain_of:
    - Annotation
    range: string
    required: true
  annotation_extensions:
    name: annotation_extensions
    description: 'Annotation extensions allow GO terms in annotations to be further
      specified, using

      gene products, chemicals, cell types, anatomical structures, to provide additional

      biological context. The cross-reference is prefaced by an appropriate relationship

      from the Relation Ontology.'
    todos:
    - The GPAD spec makes a distinction between pipe- and comma-separated lists of
      annotation extensions. Decide if and how this should be represented in the schema.
    - Annotation extensions do not have a unique identifier, so the schema indicates
      they are inlined as a list. This makes change operations that target a specific
      annotation extension more difficult.
    from_schema: https://w3id.org/geneontology/go-standard-annotation-schema
    rank: 1000
    owner: Annotation
    domain_of:
    - Annotation
    range: AnnotationExtension
    required: false
    multivalued: true
    inlined: true
    inlined_as_list: true
  annotation_properties:
    name: annotation_properties
    description: A list if key-value pairs that provide additional information about
      an annotation.
    todos:
    - Annotation properties do not have a unique identifier, so the schema indicates
      they are inlined as a list. This makes change operations that target a specific
      annotation property more difficult.
    from_schema: https://w3id.org/geneontology/go-standard-annotation-schema
    rank: 1000
    owner: Annotation
    domain_of:
    - Annotation
    range: AnnotationProperty
    required: false
    multivalued: true
    inlined: true
    inlined_as_list: true