Journal Article

Annotation and merging of SBML models with semanticSBML

Falko Krause, Jannis Uhlendorf, Timo Lubitz, Marvin Schulz, Edda Klipp and Wolfram Liebermeister

in Bioinformatics

Volume 26, issue 3, pages 421-422
Published in print February 2010 | ISSN: 1367-4803
Published online November 2009 | e-ISSN: 1460-2059 | DOI:
Annotation and merging of SBML models with semanticSBML

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Summary: Systems Biology Markup Language (SBML) is the leading exchange format for mathematical models in Systems Biology. Semantic annotations link model elements with external knowledge via unique database identifiers and ontology terms, enabling software to check and process models by their biochemical meaning. Such information is essential for model merging, one of the key steps towards the construction of large kinetic models. SemanticSBML is a tool that helps users to check and edit MIRIAM annotations and SBO terms in SBML models. Using a large collection of biochemical names and database identifiers, it supports modellers in finding the right annotations and in merging existing models. Initially, an element matching is derived from the MIRIAM annotations and conflicting element attributes are categorized and highlighted. Conflicts can then be resolved automatically or manually, allowing the user to control the merging process in detail.

Availability: SemanticSBML comes as a free software written in Python and released under the GPL 3. A Debian package, a source package for other Linux distributions, a Windows installer and an online version of semanticSBML with limited functionality are available at A preinstalled version can be found on the Linux live DVD SB.OS, available at


Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  1176 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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