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UniProtKB - Gene Ontology Annotation


NAR Molecular Biology Database Collection entry number 389
Dimmer, Emily; Huntley, Rachael; Alam-Faruque, Yasmin; Sawford, Tony; O'Donovan, Claire; Martin, Maria; Auchincloss, Andrea; Axelsen, Kristian; Blatter, Marie-Claude; Boutet, Emmanuel; Braconi-Quintaje, Silvia; Breuza, Lionel; Argoud-Puy, Ghislaine; Bely, Benoit; Bridge, Alan; Browne, Paul; Chan, Wei Mun; Coudert, Elisabeth; Cusin, Isabelle; Duek Roggli, Paula; Eberhardt, Ruth; Estreicher, Anne; Famiglietti, Livia; Ferro Rojas, Serenella; Feuermann, Marc; Gardner, Michael; Gos, Arnaud; Gruaz-Gumowski, Nadine; Hinz, Ursula; Hulo, Chantal; James, Janet; Jimenez, Silvia; Jungo, Florence; Keller, Guillaume; Laiho, Kati; Legge, Duncan; Le Mercier, Philippe; Lieberherr, Damien; Magrane, Michele; Masson, Patrick; Moinat, Madelaine; Pedruzzi, Ivo; Pichler, Klemens; Poggioli, Diego; Poux, Sylvain; Rivoire, Catherine; Roechert, Bernd; Schneider, Michel; Sehra, Harminder; Stanley, Eleanor; Stutz, Andre; Sundaram, Shyamala; Michael, Tognolli; Bougueleret, Lydie; Xenarios, Ioannis; Apweiler, Rolf
EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

Database Description

he Gene Onotology Annotation (GOA) database is maintained by the European Bioinformatics Institute (EBI) and aims to provide assignments of gene products to the Gene Ontology (GO) resource - a dynamic controlled vocabulary that encourages the consistent description of a protein's function, process and location of action. In the GOA project, this vocabulary is being applied to a non-redundant set of proteins described in the EBI's core genome and proteome databases (UniProt Knowledgebase, InterPro and Ensembl) that collectively provide complete and incomplete proteomes for human (GOA-Human), mouse (GOA-Mouse) and rat (GOA-Rat) as well as many other organisms (GOA-UniProt). GOA is produced by electronic and manual techniques and is updated monthly, in accordance with the latest data released by its core databases. The production of GOA-Human is in keeping with our GO Consortium agreement to fast track the functional annotation of the human proteome and with our Human Proteomics Initiative. The release of all our annotation (for >76,000 species) via GOA-UniProt has made the EBI one of the largest resources of GO annotation by providing nearly 5 million annotations (see Statistics on GOA home page). The GOA project also ensures maintenance and sharing of GO mappings to Swiss-Prot keywords and InterPro. These mappings provide a useful resource of functional information for the analysis of microarray and mass spectrometry data. The GOA project also ensures that at least some of the existing corpus of scientific knowledge in our core databases is converted into a computationally accessible form. By annotating all characterized proteins with GO terms and facilitating the transfer of this knowledge to similar uncharacterized proteins, we hope to contribute to a better understanding of all proteomes.

The success and accuracy of our GO annotations rely on frequent electronic and manual checking. We actively encourage updates or corrections and new collaborations from the scientific community to improve this shared resource. For further information about how to use GOA please refer to our home page: http://www.ebi.ac.uk/GOA or contact us by e-mail to goa@ebi.ac.uk.

Recent Developments

GOA has spent many months providing the community and in-house databases with GO annotation and improving update cycles. More recently we have supplemented our dataset with other GO Consortium annotations. The aims of the GOA project have been achieved; the UniProt Knowledgebase has shared knowledge and integrated knowledge from specialised databases using a structured vocabulary. Initially we have integrated manual GO annotation from FlyBase, SGD, MGI, GeneDB, RGD and HGNC and will extend integration to other GO Consortium members over the next year. GOA has recruited new curators to annotate GO terms to the Human Proteome and is setting up collaborations with other groups, (e. g. Reactome, IntAct) who wish to contribute GO annotations.

GOA data is now available directly in UniProt entries and is cross-referenced in EMBL/DDBJ/GenBank flatfiles. GOA data is also displayed via LocusLink. The final potential of GO is to allow complicated queries with GO across all our databases. Improvements in this regard are well underway. GOA has also been used to provide training and test sets of manual GO annotation for the BioCreative text mining competition discussed at ISMB 2004. GOA curators took part in the evaluation.

Acknowledgements

We are very grateful to the GO consortium and in particular to the UniProt curators and programmers at the EBI. This work was supported by Grants QRLT-2001-00015 and QLRI-2000-00981 of the European Commission and a supplementary NIH grant, 1R01HGO2273-01.

References

Camon, E., Barrell, D., Brooksbank, C., Magrane, M. and Apweiler, R. (2003) The Gene Ontology Annotation (GOA) Project: Application of GO in Swiss-Prot, TrEMBL and InterPro. Comp. Funct. Genom. 4, 71-74.

Camon, E., Magrane, M., Barrell, D., Binns, D., Fleischmann, W., Kersey, P., Mulder, N., Oinn, T., Maslen, J., Cox, A. and Apweiler, R. (2003) The Gene Ontology Annotation (GOA) project: implementation of GO in Swiss-Prot, TrEMBL and InterPro. Genome Research 13(4), 662-72.

Camon, E, Magrane, M, Barrell, D, Lee, V, Dimmer, E, Maslen, J, Binns, D, Harte, N, Lopez, R, Apweiler, R. (2004) The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology. Nucleic Acids Res. 32, D262-D266.


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