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Bioinformatics Advance Access originally published online on June 26, 2009
Bioinformatics 2009 25(17):2292-2293; doi:10.1093/bioinformatics/btp392
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

libAnnotationSBML: a library for exploiting SBML annotations

Neil Swainston 1,* and Pedro Mendes 1,2

1 Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester M1 7DN, UK and 2 Virginia Bioinformatics Institute, Virginia Tech, Washington St. 0477, Blacksburg, VA 24061, USA

* To whom correspondence should be addressed.


  Abstract

Summary: The Systems Biology Markup Language (SBML) is an established community XML format for the markup of biochemical models. With the introduction of SBML level 2 version 3, specific model entities, such as species or reactions, can now be annotated using ontological terms. These annotations, which are encoded using the resource description framework (RDF), provide the facility to specify definite terms to individual components, allowing software to unambiguously identify such components and thus link the models to existing data resources.

libSBML is an application programming interface library for the manipulation of SBML files. While libSBML provides the facilities for reading and writing such annotations from and to models, it is beyond the scope of libSBML to provide interpretation of these terms. The libAnnotationSBML library introduced here acts as a layer on top of libSBML linking SBML annotations to the web services that describe these ontological terms. Two applications that use this library are described: SbmlSynonymExtractor finds name synonyms of SBML model entities and SbmlReactionBalancer checks SBML files to determine whether specifed reactions are elementally balanced.

Availability: http://mcisb.sourceforge.net/

Contact: neil.swainston{at}manchester.ac.uk

Associate Editor: Alfonso Valencia

Received on March 20, 2009; revised on May 22, 2009; accepted on June 21, 2009

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