Creating the gene ontology resource: design and implementation

Abstract

The exponential growth in the volume of accessible biological information has generated a confusion of voices surrounding the annotation of molecular information about genes and their products. The Gene Ontology (GO) project seeks to provide a set of structured vocabularies for specific biological domains that can be used to describe gene products in any organism. This work includes building three extensive ontologies to describe molecular function, biological process, and cellular component, and providing a community database resource that supports the use of these ontologies. The GO Consortium was initiated by scientists associated with three model organism databases: SGD, the Saccharomyces Genome database; FlyBase, the Drosophila genome database; and MGD/GXD, the Mouse Genome Informatics databases. Additional model organism database groups are joining the project. Each of these model organism information systems is annotating genes and gene products using GO vocabulary terms and incorporating these annotations into their respective model organism databases. Each database contributes its annotation files to a shared GO data resource accessible to the public at http://www.geneontology.org/. The GO site can be used by the community both to recover the GO vocabularies and to access the annotated gene product data sets from the model organism databases. The GO Consortium supports the development of the GO database resource and provides tools enabling curators and researchers to query and manipulate the vocabularies. We believe that the shared development of this molecular annotation resource will contribute to the unification of biological information.

Figure 1

Multiple pathways. This figure illustrates the different pathways that represent the biological process of DNA replication. Viewed in the GO Browser, the relationships between the terms, the GO ID for DNA replication, and information about the number of pathways incorporating this biological process are displayed.

Figure 2

Extension of GO to reflect multiple uses of the term “chitin”. The “chitin” example illustrates the development of the GO structure to accurately reflect the understanding of the relationships. Cuticle chitin metabolism is a process independent of cell wall chitin metabolism. This illustration utilizes the BDGP GO Browser, which supports links to gene products annotated to a given GO term. Here, the genes annotated with the term “cell wall chitin biosynthesis” are represented, with links back to the SGD database representations for these genes.