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.
    notes:
    - The GPI grammar and narrative spec both say 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
    pattern: ^\S+$
  db_object_name:
    name: db_object_name
    description: The name of the entity being annotated.
    notes:
    - The GPI grammar implies that column 3 is required, but the narrative spec says
      that it is optional. The narrative spec seems more appropriate, so that is what
      is implemented here. Decide if that is correct.
    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:
    - The GPI grammar says that column 5 has cardinality 1..*, `ID ( '|' ID )*` but
      the narrative spec says that it has cardinality 1. The narrative spec seems
      more appropriate, so that is what is implemented here. Decide if that is correct.
    comments:
    - 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.
    - The entity type value must be provided as an ontology term identifier from Sequence
      Ontology, Protein Ontology, or GO, and must correspond to one of the permitted
      GPI entity types or a more granular child term. Common entries include PR:000000001
      (protein), GO:0032991 (protein-containing complex), SO:0001217 (protein-coding
      gene), SO:0000655 (ncRNA) or any SO child term, SO:0001263 (ncRNA-coding gene)
      or any SO child term, SO:0000336 (pseudogene).
    - 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.
    notes:
    - The GPI grammar says that column 8 has cardinality 0..*, `( ID ( '|' ID )* )?`
      but the narrative spec says that it has cardinality 1. The narrative spec seems
      more appropriate, so that is what is implemented here. Decide if that is correct.
    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.
    comments:
    - This field is mandatory if the prefix of the annotated entity's identifier is
      not UniProtKB, RNACentral, or 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: The properties associated with an entity in a GPI row.
    from_schema: https://w3id.org/geneontology/go-standard-annotation-schema
    rank: 1000
    owner: Entity
    domain_of:
    - Entity
    range: GeneProductProperties
    required: false
    inlined: true