COMODI: an ontology to characterise differences in versions of computational models in biology.

Journal: Journal of biomedical semantics
Published Date: Jul 11, 2016

Abstract

BACKGROUND: 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.

Authors

  • Martin Scharm
    Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany. martin.scharm@uni-rostock.de.
  • Dagmar Waltemath
    Department of Medical Informatics, Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany.
  • Pedro Mendes
    School of Computer Science and Manchester Institute of Biotechnology, University of Manchester, Manchester, Great Britain.
  • Olaf Wolkenhauer
    Department of Systems Biology and Bioinformatics, Institute of Computer Science, University of Rostock, Rostock, Germany.

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