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libAnnotationSBML: a library for exploiting SBML annotations.

Neil Swainston1, Pedro Mendes

  • 1Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester M1 7DN, UK. neil.swainston@manchester.ac.uk

Bioinformatics (Oxford, England)
|June 30, 2009
PubMed
Summary
This summary is machine-generated.

A new library, libAnnotationSBML, enhances the Systems Biology Markup Language (SBML) by linking model annotations to ontological terms. This facilitates unambiguous component identification and data resource linking for biochemical models.

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Area of Science:

  • Systems Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Systems Biology Markup Language (SBML) is a standard XML format for biochemical models.
  • SBML Level 2 Version 3 allows annotations using ontological terms via Resource Description Framework (RDF).
  • libSBML facilitates reading/writing SBML annotations but lacks term interpretation.

Purpose of the Study:

  • Introduce libAnnotationSBML, a library enhancing SBML annotation interpretation.
  • Link SBML annotations to web services describing ontological terms.
  • Develop applications for utilizing these enhanced annotations.

Main Methods:

  • Developed libAnnotationSBML as a layer on top of libSBML.
  • Integrated web services for ontological term interpretation.
  • Created SbmlSynonymExtractor and SbmlReactionBalancer applications.

Main Results:

  • libAnnotationSBML successfully links SBML annotations to ontological web services.
  • SbmlSynonymExtractor identifies name synonyms for SBML model entities.
  • SbmlReactionBalancer validates elemental balance in SBML reactions.

Conclusions:

  • libAnnotationSBML enhances the utility of SBML models through improved annotation interpretation.
  • The developed applications demonstrate practical uses for the library.
  • This work facilitates unambiguous identification and data linking for biochemical models.