COnto-Diff: generation of complex evolution mappings for life science ontologies

  • Authors:

  • Michael Hartung;Anika Groí;Erhard Rahm

  • Affiliations:

  • Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraíe 16-18, 04107 Leipzig, Germany and Department of Computer Science, University of Leipzig, P.O. Box 100920, ...;Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraíe 16-18, 04107 Leipzig, Germany and Department of Computer Science, University of Leipzig, P.O. Box 100920, ...;Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraíe 16-18, 04107 Leipzig, Germany and Department of Computer Science, University of Leipzig, P.O. Box 100920, ...

  • Venue:
  • Journal of Biomedical Informatics
  • Year:
  • 2013

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Abstract

Life science ontologies evolve frequently to meet new requirements or to better reflect the current domain knowledge. The development and adaptation of large and complex ontologies is typically performed collaboratively by several curators. To effectively manage the evolution of ontologies it is essential to identify the difference (Diff) between ontology versions. Such a Diff supports the synchronization of changes in collaborative curation, the adaptation of dependent data such as annotations, and ontology version management. We propose a novel approach COnto-Diff to determine an expressive and invertible diff evolution mapping between given versions of an ontology. Our approach first matches the ontology versions and determines an initial evolution mapping consisting of basic change operations (insert/update/delete). To semantically enrich the evolution mapping we adopt a rule-based approach to transform the basic change operations into a smaller set of more complex change operations, such as merge, split, or changes of entire subgraphs. The proposed algorithm is customizable in different ways to meet the requirements of diverse ontologies and application scenarios. We evaluate the proposed approach for large life science ontologies including the Gene Ontology and the NCI Thesaurus and compare it with PromptDiff. We further show how the Diff results can be used for version management and annotation migration in collaborative curation.