Slot: db_object_type

The class of biological entity being annotated.

URI: go_standard_annotation_schema:db_object_type

Applicable Classes

Name	Description	Modifies Slot
Entity	An annotatable biological entity for an organism: protein-coding genes, non-c...	no

Properties

Type and Range

Property	Value
Range	ExternalIdentifier
Domain Of	Entity

Cardinality and Requirements

Property	Value
Required	Yes

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.

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.

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/geneontology/go-standard-annotation-schema

Mappings

Mapping Type	Mapped Value
self	go_standard_annotation_schema:db_object_type
native	go_standard_annotation_schema:db_object_type

LinkML Source

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
domain_of:
- Entity
range: external_identifier
required: true