title: Annotation and merging of SBML models with semanticSBML.
abstract: CONCLUSIONS
  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.
  
  
  BACKGROUND
  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 http://www.semanticsbml.org. A preinstalled version can be found on the Linux live DVD SB.OS, available at http://www.sbos.eu.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Theoretische Biophysik, Humboldt-Universität zu Berlin, Invalidenstrasse 42, D-10115 Berlin, Germany.
authors.forename: Falko
authors.initials: F
authors.lastname: Krause
authors.forename: Jannis
authors.initials: J
authors.lastname: Uhlendorf
authors.forename: Timo
authors.initials: T
authors.lastname: Lubitz
authors.forename: Marvin
authors.initials: M
authors.lastname: Schulz
authors.forename: Edda
authors.initials: E
authors.lastname: Klipp
authors.forename: Wolfram
authors.initials: W
authors.lastname: Liebermeister
mesh_terms: D019295:Computational Biology / Q000379:methods*; D003628:Database Management Systems; D016208:Databases, Factual; D012660:Semantics; D012984:Software; D049490:Systems Biology / Q000379:methods*