SemanticSBML: a tool for annotation, checking, and merging of biochemical models

Scope of semanticSBML. SBML (www.sbml.org) is the leading standard format for mathematical models in systems biology. Semantic annotations in SBML models define, e.g., the biochemical meaning of model elements. SemanticSBML helps you to edit such annotations and uses them for model checking and merging.

Using semanticSBML. There are several ways to use semanticSBML: SemanticSBML online provides a limited basic functionality for model building, annotation, checks, and merging. In model merging, conflicts are resolved automatically based on a priority ranking of the input models; this works only for models that have been carefully prepared. In all other cases, please use the installable 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 on your computer without a permanent installation.

Annotating non-SBML models. Models in other formats (including Matlab, Java, R, C/C++, Python) can be annotated here.

main gui annotation gui

Hints for SBML beginners. Many SBML models are freely available at the model repositories Biomodels.net 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. (2009), Annotation and merging of SBML models with semanticSBML, Bioinformatics 2009, doi:10.1093/bioinformatics/btp642