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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, ...
Entity An annotatable biological entity for an organism: protein-coding genes, non-c...
Property A key-value pair that provides additional information about an annotation or
        AnnotationProperty A key-value pair that provides additional information about an annotation
        EntityProperty A key-value pair that provides additional information about an entity

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 A list if key-value pairs that provide additional information about an annota...
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
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_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 A list of key-value pairs that provide additional information about an entity
interacting_taxon_id Taxonomic identifier for interacting organism to be used only in conjunction ...
negation A boolean indicating whether the annotation is negated
ontology_class_id The GO identifier for the term attributed to the DB object ID
property_key The key of an annotation property
property_value The value of an annotation property
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 describe how the annotated biologica...
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
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
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