The Gene Ontology (GO) database and informatics resource

M A Harris

J Clark

A Ireland

J Lomax

B Marshall+51 authors

GO-EBI, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

^{Correspondence should be addressed to GO-EBI, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. Tel. +44 1223 494667; Fax: +44 1223 494468; Email:}ku.ca.ibe@irodim

^{Current members of the GO Consortium are: M. A. Harris, J. Clark, A. Ireland, J. Lomax (GO-EBI, Hinxton, UK); M. Ashburner, R. Foulger (FlyBase, Department of Genetics, University of Cambridge, Cambridge, UK); K. Eilbeck, S. Lewis, B. Marshall, C. Mungall, J. Richter, G. M. Rubin (BDGP, UC-Berkeley, Berkeley, CA, USA), J. A. Blake, C. Bult, M. Dolan, H. Drabkin, J. T. Eppig, D. P. Hill, L. Ni, M. Ringwald (MGI, Jackson Laboratory, Bar Harbor, ME, USA); R. Balakrishnan, J. M. Cherry, K. R. Christie, M. C. Costanzo, S. S. Dwight, S. Engel, D. G. Fisk, J. E. Hirschman, E. L. Hong, R. S. Nash, A. Sethuraman, C. L. Theesfeld (SGD, Department of Genetics, Stanford University, Stanford, CA, USA); D. Botstein, K. Dolinski, B. Feierbach (Genomics Institute, Princeton University, Princeton, NJ, USA); T. Berardini, S. Mundodi, S. Y. Rhee (TAIR, Carnegie Institution, Department of Plant Biology, Stanford, CA, USA); R. Apweiler, D. Barrell, E. Camon, E. Dimmer, V. Lee (GOA database, UniProt, EBI, Hinxton, UK); R. Chisholm, P. Gaudet, W. Kibbe (DictyBase, Northwestern University, Chicago, IL, USA); R. Kishore, E. M. Schwarz, P. Sternberg (WormBase, California Institute of Technology, Pasadena, CA, USA); M. Gwinn, L. Hannick, J. Wortman (Institute for Genome Research, Rockville, MD, USA); M. Berriman, V. Wood (Wellcome Trust Sanger Institute, Hinxton, UK); N. de la Cruz, P. Tonellato (RGD, Medical College of Wisconsin, Milwaukee, WI, USA); P. Jaiswal (Gramene, Department of Plant Breeding, Cornell University, Ithaca, NY, USA); T. Seigfried (Maize DB, Iowa State University, Ames, IA, USA); R. White (Incyte Genomics, Palo Alto, CA, USA).}

Received 2003 Aug 21; Revised 2003 Sep 12; Accepted 2003 Sep 12.

Abstract

The Gene Ontology (GO) project (http://www.geneontology.org/) provides structured, controlled vocabularies and classifications that cover several domains of molecular and cellular biology and are freely available for community use in the annotation of genes, gene products and sequences. Many model organism databases and genome annotation groups use the GO and contribute their annotation sets to the GO resource. The GO database integrates the vocabularies and contributed annotations and provides full access to this information in several formats. Members of the GO Consortium continually work collectively, involving outside experts as needed, to expand and update the GO vocabularies. The GO Web resource also provides access to extensive documentation about the GO project and links to applications that use GO data for functional analyses.

Abstract

^{Excludes obsolete terms.}

^{Individual associations between any gene product and any GO term.}

^{Parent–child relationships traced from any GO term to the root (molecular function, biological process or cellular component).}

Click here to view.

ACKNOWLEDGEMENTS

The Gene Ontology Consortium is supported by NIH/NHGRI grant HG02273, and by grants from the European Union RTD Programme ‘Quality of Life and Management of Living Resources’ (QLRI-CT-2001-00981 and QLRI-CT-2001-00015).

ACKNOWLEDGEMENTS

REFERENCES

References

1. Gruber T.R(1993) A translational approach to portable ontologies. Knowl. Acq., 5, 199–220. [PubMed][Google Scholar]
2. Jones D.M. and Paton,R.C. (1999) Toward principles for the representation of hierarchical knowledge in formal ontologies. Data Knowl. Eng., 31, 102–105. [PubMed]
3. Schulze-Kremer S(1998) Ontologies for molecular biology. Pac. Symp. Biocomput., 3, 695–706. [[PubMed][Google Scholar]
4. Stevens R., Goble,C.A., and Bechhofer.S(2000) Ontology-based knowledge representation for bioinformatics. Brief. Bioinform., 1, 398–414. [[PubMed][Google Scholar]
5. Blake J.A. and Harris,M. (2003) The Gene Ontology Project: Structured vocabularies for molecular biology and their application to genome and expression analysis. In Baxevanis,A.D., Davison,D.B., Page,R., Stormo,G. and Stein,L. (eds), Current Protocols in Bioinformatics. Wiley and Sons, Inc., New York. [PubMed]
6. The Gene Ontology Consortium (2001) Creating the gene ontology resource: design and implementation. Genome Res., 11, 1425–1433.
7. The Gene Ontology Consortium (2000) Gene Ontology: tool for the unification of biology. Nature Genet., 25, 25–29.
8. Camon E., Magrane,M., Barrell,D., Binns,D., Fleischmann,W., Kersey,P., Mulder,N., Oinn,T., Maslen,J., Cox,A. et al. (2003) The Gene Ontology Annotation (GOA) Project: Implementation of GO in SWISS-PROT, TrEMBL, and InterPro. Genome Res., 13, 662–672.
9. Mi H., Vandergriff,J., Campbell,M., Narechania,A., Majoros,W., Lewis,S., Thomas,P.D. and Ashburner,M. (2003) Assessment of genome-wide protein function classification for Drosophila melanogaster. Genome Res., 13, 2118–2128.
10. Pouliot Y., Gao,J., Su,Q.J., Liu,G.G. and Ling,X.B. (2001) DIAN: a novel algorithm for genome ontological classification. Genome Res., 11, 1766–1779.
11. Okazaki Y., Furuno,M., Kasukawa,T., Adachi,J., Bono,H., Kondo,S., Nikaido,I., Osato,N., Saito,Rand Suzuki,H. et al. (2002) Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature, 420, 563–573. [[PubMed][Google Scholar]
12. Xie H., Wasserman,A., Levine,Z., Novik,A., Grebinskiy,V., Shoshan,A. and Mintz,L. (2002) Large scale protein annotation through Gene Ontology. Genome Res., 12, 785–794.
13. Adams M.D., Celniker,S.E., Holt,R.A., Evans,C.A., Gocayne,J.D., Amanatides,P.G., Scherer,S.E., Li,P.W., Hoskins,R.A., Galle,R.F. et al. (2000) The genome sequence of Drosophila melanogaster. Science, 287, 2185–2195. [[PubMed]