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GO Standard Annotation Schema

LinkML schema for GO Standard Annotations

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

Name: go-standard-annotation-schema

Classes

Class Description
Annotation An association between a gene product and a GO term, with an evidence code, a...
AnnotationExtension Annotation extensions allow GO terms in annotations to be further specified, ...
AnnotationProperties The closed set of properties associated with an annotation
Entity An annotatable biological entity for an organism: protein-coding genes, non-c...
GeneProductProperties The closed set of properties associated with an entity in a GPI row

Slots

Slot Description
annotation_date Date on which the annotation was made
annotation_extensions Annotation extensions allow GO terms in annotations to be further specified, ...
annotation_properties Additional properties associated with an annotation
assigned_by The database which made the annotation one of the values from the set of GOC ...
canonical_object_id If the entity being annotated is a gene, gene-centric reference protein or a ...
comment Free text about a specific annotation
contributor_id The identifier of a curator or user who entered or changed an annotation
creation_date The date on which the annotation was created
db_object_id A unique identifier for the item being annotated
db_object_name The name of the entity being annotated
db_object_symbol The symbol of the entity being annotated
db_object_synonyms Alternative names for the entity being annotated
db_object_taxon_id The NCBI Taxonomy identifier for the organism (species or strain) encoding th...
db_object_type The class of biological entity being annotated
db_subset The status of a UniProtKB accession with respect to curator review
db_xrefs Cross-references to other databases for the entity being annotated
encoded_by For proteins and transcripts, the gene that encodes the entity being annotate...
evidence_type The Evidence & Conclusion Ontology (ECO) identifier for the evidence code tha...
extension_relation A term from the Relation Ontology that describes how the GO term in the exten...
extension_term The gene product, chemical, cell type, anatomical structure, or other entity ...
gene_product_properties The properties associated with an entity in a GPI row
go_annotation_complete The date on which a curator determined that the set of GO annotations for an ...
go_annotation_summary A textual gene or gene-product description
id The contributing database's unique identifier for an annotation
interacting_taxon_id Taxonomic identifier for interacting organism to be used only in conjunction ...
model_state The GO-CAM model state
modification_date A date on which the annotation was modified
negation A boolean indicating whether the annotation is negated
noctua_model_id The unique identifier of the associated GO-CAM model
ontology_class_id The GO identifier for the term attributed to the DB object ID
protein_containing_complex_members If the entity being annotated is a protein-containing complex, this should li...
references One or more unique identifiers for a single source cited as an authority for ...
relation Relation from the Relation Ontology that describes how the annotated biologic...
reviewed_date A date on which the annotation was reviewed
reviewer_id The identifier of a curator or user who last reviewed an annotation
uniprot_proteome The UniProt proteome accession for the set of proteins that constitute an org...
with_or_from Used with specific ECO codes to capture an additional identifier supporting t...

Enumerations

Enumeration Description

Types

Type Description
Boolean A binary (true or false) value
ContributorIdentifier An identifier of a contributor, such as a curator or user who entered or chan...
Curie a compact URI
Date a date (year, month and day) in an idealized calendar
DateOrDatetime Either a date or a datetime
Datetime The combination of a date and time
Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci...
Double A real number that conforms to the xsd:double specification
EcoIdentifier An identifier of an ECO term
ExternalIdentifier An identifier of an object from an external source, such as a gene product, a...
Float A real number that conforms to the xsd:float specification
GoIdentifier An identifier of a GO term
Integer An integer
Jsonpath A string encoding a JSON Path
Jsonpointer A string encoding a JSON Pointer
NcbiTaxonIdentifier An identifier of a taxon from the NCBI Taxonomy database
Ncname Prefix part of CURIE
Nodeidentifier A URI, CURIE or BNODE that represents a node in a model
Objectidentifier A URI or CURIE that represents an object in the model
RoIdentifier An identifier of a Relation Ontology term
Sparqlpath A string encoding a SPARQL Property Path
String A character string
Time A time object represents a (local) time of day, independent of any particular...
Uri a complete URI
Uriorcurie a URI or a CURIE

Subsets

Subset Description