The Gene Ontology (GO) project in 2006

Abstract

The Gene Ontology (GO) project (http://www.geneontology.org) develops and uses a set of structured, controlled vocabularies for community use in annotating genes, gene products and sequences (also see http://song.sourceforge.net/). The GO Consortium continues to improve to the vocabulary content, reflecting the impact of several novel mechanisms of incorporating community input. A growing number of model organism databases and genome annotation groups contribute annotation sets using GO terms to GO's public repository. Updates to the AmiGO browser have improved access to contributed genome annotations. As the GO project continues to grow, the use of the GO vocabularies is becoming more varied as well as more widespread. The GO project provides an ontological annotation system that enables biologists to infer knowledge from large amounts of data.

Figure 1

Improved AmiGO interface. For all search results, the string matching the search query is highlighted to help identify why a specific result was returned. (A) The gene product search result display has been expanded to provide hyperlinks to documentation, references and other databases that contain information that support each annotation. Readability is greatly improved, such that for each search result, a sentence can be constructed from the tabular format, e.g. gene X from species S is annotated to term Y based on evidence of type Z from publications A, B and C. (B) The term search now includes comments; the search result display shows matches to synonyms as well as term names. Obsolete terms are grayed out and any suggested replacement terms are highlighted (data not shown).