Gene Ontology

The goal of the Gene Ontology project is to design a set of structured-controlled vocabulary terms to describe gene products in any organism. The vocabulary terms are used as attributes of genes in databases from a wide variety of species and facilitate computational queries across species. All the information about the GO consortium (including the lists of the current ontologies, extensive documentation, definition of terms, and detailed discussions) is available at the web site: www.geneontology.org

Currently the Gene Ontology Project comprises of three separate ontologies to describe the attributes of gene product or gene product groups, these are:

1. Molecular Function: This describes what a gene product does at biochemical level.
2. Biological Process: This refers to a biological objective to which a gene product contributes.
3. Cellular Component: This refers to the place in the cell where a gene product is found.

These ontologies are structured vocabularies which are in the form of direct acyclic graphs (DAGs) that represent a network in which each term maybe a 'child' of one or more than one 'parent'. A link to AmiGO is included on each GO (Gene Ontology) annotation. The BDGP Java-based GO browser provides a query interface to the ontologies that allows users to use either regular expressions or simple 'wild card' characters to query the database. The display includes a full DAG representation of the query results. AmiGO was developed at BDGP (Berkeley Drosophila Genome Project), and allows the user to view gene products from yeast and other species annotated to a specific GO term. In the future GO may expand and incorporate other sophisticated biological concepts, here this effort is an essential start to creating a shared language of Biology.

Related Publications describing the Gene Ontology

• Creating the gene ontology resource: design and implementation. The Gene Ontology Consortium (2001) Genome Res. 11:1425-1433
• Gene Ontology: tool for the unification of biology. The Gene Ontology Consortium (2000) Nature Genet. 25: 25-29

GO Annotations in RGD

A sample annotation from RGD is shown below (from gene F2, RGD ID: 61996). Five columns are shown for each GO Term annotated to a given gene product:

Using AmiGO links for more information

The AmiGO browser is an ontology browser that has the added benefit of listing all other genes annotated with the same GO Term that have been provided to GeneOntology.org. All GO Terms from RGD are hyperlinked to the corresponding AmiGO browser page allowing the RGD user access to a comprehensive list of gene products from other organisms that have been annotated with the same GO Term.