Class: Entity

name: Entity
description: 'An annotatable biological entity for an organism: protein-coding genes,
  non-coding

  RNA genes, protein isoforms (i. e., splice variants) and modified forms, such as

  cleaved forms or proteins modified by post-translational modifications.'
from_schema: https://w3id.org/geneontology/go-standard-annotation-schema
slots:
- db_object_id
- db_object_symbol
- db_object_name
- db_object_synonyms
- db_object_type
- db_object_taxon_id
- encoded_by
- canonical_object_id
- protein_containing_complex_members
- db_xrefs
- gene_product_properties

name: Entity
description: 'An annotatable biological entity for an organism: protein-coding genes,
  non-coding

  RNA genes, protein isoforms (i. e., splice variants) and modified forms, such as

  cleaved forms or proteins modified by post-translational modifications.'
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: Entity
    domain_of:
    - Annotation
    - Entity
    range: external_identifier
    required: true
  db_object_symbol:
    name: db_object_symbol
    description: The symbol of the entity being annotated.
    todos:
    - The GPI spec says that this is required, but in practice it is missing in many
      rows of existing GPI files. Decide whether this should be required in the schema
      and handled in the file parsing code if it is missing.
    from_schema: https://w3id.org/geneontology/go-standard-annotation-schema
    rank: 1000
    owner: Entity
    domain_of:
    - Entity
    range: string
    required: false
  db_object_name:
    name: db_object_name
    description: The name of the entity being annotated.
    from_schema: https://w3id.org/geneontology/go-standard-annotation-schema
    rank: 1000
    owner: Entity
    domain_of:
    - Entity
    range: string
    required: false
  db_object_synonyms:
    name: db_object_synonyms
    description: Alternative names for the entity being annotated.
    from_schema: https://w3id.org/geneontology/go-standard-annotation-schema
    rank: 1000
    owner: Entity
    domain_of:
    - Entity
    range: string
    required: false
    multivalued: true
  db_object_type:
    name: db_object_type
    description: The class of biological entity being annotated.
    notes:
    - This field should describe the type of biological object as defined by the contributing
      database. For example, WormBase identifiers represent genes, PomBase identifiers
      represent protein-coding genes, and SGD identifiers represent proteins.
    - GO does not allow 'gene' and 'gene product' as biological entity types, as this
      does not allow to differentiate between proteins and ncRNAs products.
    from_schema: https://w3id.org/geneontology/go-standard-annotation-schema
    rank: 1000
    owner: Entity
    domain_of:
    - Entity
    range: external_identifier
    required: true
  db_object_taxon_id:
    name: db_object_taxon_id
    description: 'The NCBI Taxonomy identifier for the organism (species or strain)
      encoding the

      entity being annotated.'
    from_schema: https://w3id.org/geneontology/go-standard-annotation-schema
    rank: 1000
    owner: Entity
    domain_of:
    - Entity
    range: ncbi_taxon_identifier
    required: true
  encoded_by:
    name: encoded_by
    description: For proteins and transcripts, the gene that encodes the entity being
      annotated.
    from_schema: https://w3id.org/geneontology/go-standard-annotation-schema
    rank: 1000
    owner: Entity
    domain_of:
    - Entity
    range: external_identifier
    required: false
    multivalued: true
  canonical_object_id:
    name: canonical_object_id
    description: 'If the entity being annotated is a gene, gene-centric reference
      protein or a

      protein complex, this should repeat the ID of the object being annotated. If
      the

      entity being annotated is derived from a gene product such as a protein isoform,
      a

      modified protein or a processed transcript (e. g. miRNA), then this refers to
      the

      gene-centric ID of the annotated entity.'
    from_schema: https://w3id.org/geneontology/go-standard-annotation-schema
    rank: 1000
    owner: Entity
    domain_of:
    - Entity
    range: external_identifier
    required: true
  protein_containing_complex_members:
    name: protein_containing_complex_members
    description: 'If the entity being annotated is a protein-containing complex, this
      should list

      the gene-centric canonical protein identifiers.'
    from_schema: https://w3id.org/geneontology/go-standard-annotation-schema
    rank: 1000
    owner: Entity
    domain_of:
    - Entity
    range: external_identifier
    required: false
    multivalued: true
  db_xrefs:
    name: db_xrefs
    description: Cross-references to other databases for the entity being annotated.
    notes:
    - 'This field is mandatory if the prefix of the annotated entity''s identifier
      is

      not one of: UniProtKB, RNACentral, ComplexPortal. In these cases, db_xrefs must

      include the corresponding UniProtKB ID, RNACentral, or ComplexPortal as

      appropriate according to the Object Type.'
    - Additional cross references such as NCBI gene or protein IDs, HGNC, etc, may
      also be included.
    from_schema: https://w3id.org/geneontology/go-standard-annotation-schema
    rank: 1000
    owner: Entity
    domain_of:
    - Entity
    range: external_identifier
    required: false
    multivalued: true
  gene_product_properties:
    name: gene_product_properties
    description: A list of key-value pairs that provide additional information about
      an entity.
    from_schema: https://w3id.org/geneontology/go-standard-annotation-schema
    rank: 1000
    owner: Entity
    domain_of:
    - Entity
    range: EntityProperty
    required: false
    multivalued: true
    inlined: true
    inlined_as_list: true