The ontologies of GO are structured as a graph, with terms as nodes in the graph and the relations (also known as object properties) between the terms as edges (more ontology information at Gene Ontology Overview). Just as each GO term is defined, the relations between GO terms are also categorized and defined. Some of the commonly used relationships in GO are:
- is a (is a subtype of)
- part of
- regulates
- negatively regulates
- positively regulates
All terms (except from the root terms representing each aspect) have an is a sub-class relationship to another term; for example,
GO:1904659:glucose transport is a GO:0015749:monosaccharide transport.
Importantly, any one term will ONLY have is_a parentage up to one of the root terms- this is how the Aspect is determined.
The Gene Ontology employs a number of other relations, including part of, e.g.
GO:0031966:mitochondrial membrane is part of GO:0005740:mitochondrial envelope
and regulates, e.g:
GO:0098689:latency-replication decision regulates GO:0019046:release from viral latency
For more information, see Relations in the Gene Ontology.
There are three versions of the ontology available:
| go-basic.obo | Most basic version of the GO, filtered such that the graph is guaranteed to be acyclic and annotations can be propagated up the graph. The relations included are is a, part of, regulates, negatively regulates and positively regulates. | http://purl.obolibrary.org/obo/go/go-basic.obo |
|---|---|---|
| go.obo & go.owl | Includes relationships not in the filtered version of GO including has_part and occurs_in. | http://purl.obolibrary.org/obo/go.obo / http://purl.obolibrary.org/obo/go.owl |
| go-plus.owl | Fully axiomatised version of the GO. Includes cross-ontology relationships (axioms) and imports additional required ontologies including ChEBI, Cell Ontology and Uberon. It also includes a complete set of relationship types including some not in go.obo/go.owl. | http://purl.obolibrary.org/obo/go/extensions/go-plus.owl |