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

Journal of Biomedical Informatics
Michael HartungErhard Rahm

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 on...Continue Reading

References

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Jan 10, 2003·Nucleic Acids Research·Brigitte BoeckmannMichel Schneider
May 16, 2006·Journal of Biomedical Informatics·Nicholas SioutosLawrence W Wright
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Jun 2, 2009·Nucleic Acids Research·Natalya F NoyMark A Musen
Aug 15, 2009·BMC Bioinformatics·Michael HartungErhard Rahm
Mar 11, 2011·Journal of Biomedical Semantics·Syed Hamid TirmiziDaniel P Miranker
Jan 19, 2012·Bioinformatics·Michael HartungErhard Rahm

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Citations

Apr 19, 2015·Journal of Biomedical Informatics·Julio Cesar Dos ReisChantal Reynaud-Delaître
Jun 3, 2015·Journal of Biomedical Semantics·Victor ChristenAnika Groß
Dec 23, 2014·Artificial Intelligence in Medicine·Julio Cesar Dos ReisChantal Reynaud-Delaître
Dec 12, 2012·Journal of Biomedical Informatics·Tudor GrozaMichel Dumontier
Sep 20, 2016·Computational and Structural Biotechnology Journal·Anika GroßErhard Rahm
Nov 8, 2014·PloS One·Daniel FariaFrancisco M Couto
Sep 19, 2019·NPJ Digital Medicine·Maulik R KamdarMark A Musen
Mar 8, 2017·PeerJ·Simon Kocbek, Jin-Dong Kim

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