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Bioinformatics Advance Access published online on April 4, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn122
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

UniProtJAPI: A remote API for accessing UniProt data

Samuel Patient *, Daniela Wieser , Michael Kleen , Ernst Kretschmann , Maria Jesus Martin and Rolf Apweiler

The European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK

*To whom correspondence should be addressed. Samuel Patient, E-mail: spatient{at}ebi.ac.uk


  Abstract

Summary: Programmatic access to the UniProt Knowledgebase is essential for many bioinformatics applications dealing with protein data. We have created a Java library named UniProtJAPI, which facilitates the integration of UniProt data into Java-based software applications. The library supports queries and similarity searches that return UniProt Knowledgebase entries in the form of Java objects. These objects contain functional annotations or sequence information associated with a UniProt entry. Here, we briefly describe the UniProtJAPI and demonstrate its usage.

Availability: http://www.ebi.ac.uk/uniprot/remotingAPI

Contact: spatient{at}ebi.ac.uk, apweiler{at}ebi.ac.uk

Associate Editor: Prof. Martin Bishop

Received on December 6, 2007; revised on April 1, 2008; accepted on April 3, 2008

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