[2][3] GO is part of a larger classification effort, the Open Biomedical Ontologies, being one of the Initial Candidate Members of the OBO Foundry.

The Gene Ontology was originally constructed in 1998 by a consortium of researchers studying the genomes of three model organisms: Drosophila melanogaster (fruit fly), Mus musculus (mouse), and Saccharomyces cerevisiae (brewer's or baker's yeast).

The GO vocabulary is designed to be species-neutral and includes terms applicable to prokaryotes and eukaryotes, single and multicellular organisms.

GO is not static, and additions, corrections, and alterations are suggested by and solicited from members of the research and annotation communities, as well as by those directly involved in the GO project.

[8] For example, an annotator may request a specific term to represent a metabolic pathway, or a section of the ontology may be revised with the help of community experts (e.g.[9]).

The GO ontology and annotation files are freely available from the GO website in a number of formats or can be accessed online using the GO browser AmiGO.

[12] For example, Traceable Author Statement (TAS) means a curator has read a published scientific paper and the metadata for that annotation bears a citation to that paper; Inferred from Sequence Similarity (ISS) means a human curator has reviewed the output from a sequence similarity search and verified that it is biologically meaningful.

[13][14] As these annotations are not checked by a human, the GO Consortium considers them to be marginally less reliable and they are commonly to a higher level, less detailed terms.

AmiGO[19][11] is a web-based application that allows users to query, browse, and visualize ontologies and gene product annotation data.

OBO-Edit also has a reasoner that can infer links that have not been explicitly stated based on existing relationships and their properties.