SemanticSBML: annotation, checking, and merging of systems biology models

Scope of semanticSBML. SBML (www.sbml.org) is the leading standard format for mathematical models in systems biology. Semantic annotations can be used to define - among other things - the biochemical meaning of model elements. The tool semanticSBML is made to handle such annotations. It helps you to edit them and to check and merge your models.

Accessing semanticSBML. There are several ways to use semanticSBML: the semanticSBML online website provides a limited basic functionality for model building, annotation, checking, and merging. In model merging, conflicts are resolved automatically based on a priority ranking of the input models. But this works only for models that have been carefully prepared. In all other cases, please use the stand-alone semanticSBML tool, which lets you control the merging process in more detail. SemanticSBML is also included in SB.OS, a free live DVD for Systems Biology, which allows you to test it without a permanent installation.

Further online services are available at semanticSBML 2.0.

Hints for SBML beginners. For getting started, visit the SBML web site www.sbml.org. Many SBML models are freely available in the model repositories BioModels Database or JWS online. To check SBML files for syntactic correctness, use the online SBML validator. For a list of software tools that support SBML, see the SBML software guide.

Reporting bugs. Please use our bug tracker at SourceForge to report any bugs or suggestions for improving semanticSBML.

Citing semanticSBML. For citing semanticSBML, please refer to: Krause F, Uhlendorf J., Lubitz T., Schulz M., Klipp E., Liebermeister W. (2010), Annotation and merging of SBML models with semanticSBML, Bioinformatics 26 (3), 421-422, doi:10.1093/bioinformatics/btp642.