Gene Ontology Consortium: going forward

Abstract

The Gene Ontology (GO; http://www.geneontology.org) is a community-based bioinformatics resource that supplies information about gene product function using ontologies to represent biological knowledge. Here we describe improvements and expansions to several branches of the ontology, as well as updates that have allowed us to more efficiently disseminate the GO and capture feedback from the research community. The Gene Ontology Consortium (GOC) has expanded areas of the ontology such as cilia-related terms, cell-cycle terms and multicellular organism processes. We have also implemented new tools for generating ontology terms based on a set of logical rules making use of templates, and we have made efforts to increase our use of logical definitions. The GOC has a new and improved web site summarizing new developments and documentation, serving as a portal to GO data. Users can perform GO enrichment analysis, and search the GO for terms, annotations to gene products, and associated metadata across multiple species using the all-new AmiGO 2 browser. We encourage and welcome the input of the research community in all biological areas in our continued effort to improve the Gene Ontology.

Figure 1.

The new Gene Ontology web page. In addition to access to documentation, ontologies, and annotation sets (drop-down menus on top), users can immediately search on GO data (terms and annotations) using the search box, and even perform gene enrichment analysis.

Figure 2.

The new Gene Ontology browser AmiGO 2. (A) The entry portal page, where simple or complex queries can be performed, as well as term enrichment analysis. (B) Sample output from a ‘Quick Search’ on a GO term (recombinational repair). (C) Graphical Display and (D) Tree View of this GO term and its placement within the ontology.

Figure 3.

Sample search results from AmiGO2. (A) Shows two annotations of the same gene to both ‘negative’ and ‘positive’ regulation of glycogen catabolic process; the difference between the two lies in data entry on the ‘Annotation Extension’ column, showing that the experiments were performed in different tissues, i.e. liver and skeletal muscle. (B) Shows two annotations that only differ on whether the gene product ‘does’ or ‘does not’ positively regulate transcription initiation from an RNA polymerase II promoter. The data in the ‘Isoform’ column represents that the unsumoylated form ‘does’, whereas the sumoylated from ‘does not’.