SemanticSBML

Frequently asked questions

How can I annotate an SBML model?

The names in SBML can be chosen arbitrarily; to identify the biological meaning of the model components, semanticSBML requires annotations: species, parameter, compartment, reaction and event tags should be specified by an annotation in a MIRIAM-compliant RDF format according to the proposal by N. LeNovere and A. Finney. If annotations are missing, semanticSBML can be used to add them.

Which kind of annotations can be handled by semanticSBML?

SemanticSBML allows you to assign annotations from various databases listed in the resource file. For automatic matching of elements, it has to rely on cross-references between the databases. Currently, the following databases are supported: GO, KEGG, ChEBI, PubChem, 3DMET, and CAS.

What happens to non-annotated elements during merging?

By default, non-annotated elements are treated as if they had no semantic relation to the other elements, i.e., they as individual elements. In the interactive merging process, the user can match them to other elements.

SemanticSBML is is free software distributed under the GNU public license. It is developed by the semanticSBML team at Humboldt University Berlin with financial support from the European integrated project BaSysBio. For feedback, please use our bug tracker at SourceForge or send us an email (general comments and suggestions to Wolfram Liebermeister, technical questions and bug reports to Timo Lubitz, Falko Krause, or Jannis Uhlendorf).