title: COMODI: an ontology to characterise differences in versions of computational models in biology.
abstract: Open model repositories provide ready-to-reuse computational models of biological systems. Models within those repositories evolve over time, leading to different model versions. Taken together, the underlying changes reflect a model's provenance and thus can give valuable insights into the studied biology. Currently, however, changes cannot be semantically interpreted. To improve this situation, we developed an ontology of terms describing changes in models. The ontology can be used by scientists and within software to characterise model updates at the level of single changes. When studying or reusing a model, these annotations help with determining the relevance of a change in a given context.
  
  
  
  We manually studied changes in selected models from BioModels and the Physiome Model Repository. Using the BiVeS tool for difference detection, we then performed an automatic analysis of changes in all models published in these repositories. The resulting set of concepts led us to define candidate terms for the ontology. In a final step, we aggregated and classified these terms and built the first version of the ontology.
  
  
  
  We present COMODI, an ontology needed because COmputational MOdels DIffer. It empowers users and software to describe changes in a model on the semantic level. COMODI also enables software to implement user-specific filter options for the display of model changes. Finally, COMODI is a step towards predicting how a change in a model influences the simulation results.
  
  
  
  COMODI, coupled with our algorithm for difference detection, ensures the transparency of a model's evolution, and it enhances the traceability of updates and error corrections. COMODI is encoded in OWL. It is openly available at http://comodi.sems.uni-rostock.de/ .
authors.affiliation: Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany. martin.scharm@uni-rostock.de.
authors.forename: Martin
authors.initials: M
authors.lastname: Scharm
authors.affiliation: Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany.
authors.forename: Dagmar
authors.initials: D
authors.lastname: Waltemath
authors.affiliation: School of Computer Science and Manchester Institute of Biotechnology, University of Manchester, Manchester, Great Britain.|Center for Quantitative Medicine, School of Medicine, University of Connecticut, Farmington, CT, USA.
authors.forename: Pedro
authors.initials: P
authors.lastname: Mendes
authors.affiliation: Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany.|Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa.
authors.forename: Olaf
authors.initials: O
authors.lastname: Wolkenhauer
mesh_terms: D064229:Biological Ontologies; D020407:Internet; D008954:Models, Biological
keywords: CellML; Difference detection; Modelling; Ontology; SBML; Version control