Plant, Animal & Microbe Genomes X Conference Plant, Animal & Microbe Genomes X ConferenceJanuary 12-16, 2002
Town & Country Convention Center
San Diego, CA
Workshop: Controlled Vocabulary/Ontology
Genes are expressed in temporally and spatially characteristic patterns. Their products are (often) located in specific cellular compartments and may be components of complexes. Gene products possess one or more functions which may play a role in one or more biological processes. We are developing a method to describe these attributes in a rigorous way that will allow researchers to consistently annotate and explore the universe of genomes. GO is a collaborative project between several model organism databases; FlyBase for the fruitfly, the Saccharomyces Genome Database for yeast, Mouse Genome Database for mouse, TAIR for Arabidopsis, WormBase for C. elegans and others. In addition the Swiss-Prot group at the EBI are using GO for the annotation of human genes. The three organizing principles of GO are function, process and cellular component. A gene product can have one or more functions and can be used in one or more processes; a gene product may be a component of one or more supra-molecular complexes. Function is what something does. It describes only what it can do without specifying where or when this usage actually occurs. Process is a biological objective. A process is accomplished via one or more ordered assemblies of functions. The model organism database curators assign controlled vocabulary terms to gene products based on current knowledge. This information describes the specific function(s) of a gene product, the role(s) it plays in cellular processes and its localization and associations. The structure of the Gene Ontology Database allows both attribution and querying at different levels of granularity. The Gene Ontology database provides annotation, definitions, and unique identifiers for all terms. The cooperation between the model organism databases ensures the use of a common ontology and, therefore, facilitates queries across all cooperating model organism databases. Gene Ontology, therefore, allows users to make queries exemplified by: What mouse genes encode products playing a role in RAS signal transduction ?; What fly genes encode products in this biological process ?; What genes in flies and yeast have products that are components of the mitochondrial inner membrane and function as enzymes ?. The GO database is open to all without restraint. The database and associated software tools are available from http:://www.geneontology.org/. GO is supported by funds from the NIH, the MRC, London, Astra Zeneca, and Incyte.