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Bioinformatics Advance Access published online on October 20, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn528
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

The Protein Feature Ontology: A Tool for the Unification of Protein Feature Annotations

Gabrielle A. Reeves 1,*, Karen Eilbeck 2, Michele Magrane 1, Claire O'Donovan 1, Luisa Montecchi-Palazzi 1, Midori A. Harris 1, Sandra Orchard 1, Rafael C. Jimenez 3, Andreas Prlic 4, Tim J.P. Hubbard 4, Henning Hermjakob 1 and Janet M. Thornton 1

1EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom.
2Eccles Institute of Human Genetics, 15 North, 2030 East, University of Utah, Salt Lake City, 84112
3Bioinformatics and Genomics Department, Centro de Investigacion Principe Felipe (CIPF), Valencia, Spain
4The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.

*To whom correspondence should be addressed. Dr. Gabrielle A. Reeves, E-mail: gabby{at}ebi.ac.uk


  Abstract

Motivation: The advent of sequencing and structural genomics projects has provided a dramatic boost in the number of uncharacterised protein structures and sequences. Consequently, many computational tools have been developed to help elucidate protein function. However such services are spread throughout the world, often with standalone web pages. Integration of these methods is needed and so far this has not been possible as there was no common vocabulary available that could be used as a standard language.

Results: The Protein Feature Ontology has been developed to provide a structured controlled vocabulary for features on a protein sequence or structure and comprises approximately 100 positional terms, now integrated into the Sequence Ontology (SO) and 40 non-positional terms which describe features relating to the whole protein sequence. In addition, post-translational modifications are described by using a pre-existing ontology, the Protein Modification Ontology (MOD). This ontology is being used to integrate over 150 distinct annotations provided by the BioSapiens Network of Excellence, a consortium comprising 19 partner sites in Europe.

Availability: The protein feature ontology can be browsed by ac-cessing the ontology lookup service at the European Bioinformatics Institute (http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=BS)

Associate Editor: Prof. Martin Bishop

Received on July 22, 2008; revised on September 21, 2008; accepted on October 7, 2008

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