libAnnotationSBML: a library for exploiting SBML annotations.

Abstract

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.