ontology

Ontology related questions (e.g. structure, relations, subsets/slims...).

Does the GO ID have any meaning?

GO IDs are unique identifiers, however, they do not encode any information about a term or its position relative to other terms in the tree.

Can a term in one ontology have parents in one of the other two ontologies?

Yes - there are links between molecular function, biological process, and cellular component ontologies. Note that any one term will ONLY have is_a parentage up to one of the root terms.

What is an ontology?

Ontologies are 'specifications of a relational vocabulary'. In other words they are sets of defined terms like the sort that you would find in a dictionary, but the terms are given hierarchical relationships to one another. The terms in a given vocabulary are likely to be restricted to those used in a particular field or domain, and in the case of GO, the terms are all biological.

What is GO "content"?

GO content refers to the content of the ontologies themselves and the biology underlying it. It includes anything to do with terms and their organisation, definitions, synonyms and the relationships between terms.

How can I suggest new GO terms?

The GO vocabularies are updated on a regular basis, and suggestions from the community for additional terms or for other improvements are very welcome. Please visit the page "Contributing to the Ontology" for details on how to submit your contributions.

What is beyond the scope of the GO project?

Almost as important as understanding the scope of the GO project is understanding what the GO project is not. The most common misapprehensions are (1) that the GO is a system for naming genes and proteins and (2) that the GO attempts to describe all of biology. The GO neither names genes or gene products, nor does it attempt to provide structured vocabularies beyond its three domains: molecular function, biological process and cellular component.

Can I reason over GO?

It is possible to do some reasoning over GO now, and we expect to do much more in the future. We provide logical definitions or 'cross-products' for some terms as part of the extended GO file, which can be reasoned over. The OWL version of GO is described in a conference paper Use of OWL within the Gene Ontology.