Merging of systems biology models with semanticSBML

Model repositories like BioModels.net or JWS online provide a large number of biochemical pathway models in the data format SBML (Systems Biology Markup Language). We have developed semanticSBML, an interactive model merging tool that helps users build, annotate, check, and combine SBML models. It supports the current standard for biological annotations within SBML and uses a large collection of synonyms and database identifiers for the matching and comparison of model elements. During model merging, semanticSBML automatically detects the various kinds of syntactic and semantic conflicts and guides the user in resolving them. Here we demonstrate its use with a simple example: following a work by Snoep et al., we merge three models describing the glycolytic pathway, the production of glycerol, and the degradation of the toxic byproduct methylglyoxal. The example shows typical issues that arise in automatic model merging and emphasises the importance of extensive and detailed biological annotations. SemanticSBML can be freely downloaded at http://semanticsbml.sourceforge.net.