Quantitative comparison of mapping methods between Human and Mammalian Phenotype Ontology

Anika Oellrich*, Georgios V. Gkoutos, Robert Hoehndorf, Dietrich Rebholz-Schuhmann

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

5 Scopus citations

Abstract

Researchers use animal studies to better understand human diseases. In recent years, large-scale phenotype studies such as Phenoscape and EuroPhenome have been initiated to identify genetic causes of a species' phenome. Species-specific phenotype ontologies are required to capture and report about all findings and to automatically infer results relevant to human diseases. The integration of the different phenotype ontologies into a coherent framework is necessary to achieve interoperability for cross-species research. Here, we investigate the quality and completeness of two different methods to align the Human Phenotype Ontology and the Mammalian Phenotype Ontology. The first method combines lexical matching with inference over the ontologies' taxonomic structures, while the second method uses a mapping algorithm based on the formal definitions of the ontologies. Neither method could map all concepts. Despite the formal definitions method provides mappings for more concepts than does the lexical matching method, it does not outperform the lexical matching in a biological use case. Our results suggest that combining both approaches will yield a better mappings in terms of completeness, specificity and application purposes.

Original languageEnglish (US)
Article numberS1
JournalJournal of Biomedical Semantics
Volume3
Issue number2
DOIs
StatePublished - Sep 21 2012
Externally publishedYes

Bibliographical note

Funding Information:
Funding for AO and DRS was provided by the European Bioinformatics Institute. Funding for RH was provided by the European Commission’s 7th Framework Programme, RICORDO project, grant number 248502. Funding for GVG was provided by BBSRC grant BBG0 043581. This article has been published as part of Journal of Biomedical Semantics Volume 3 Supplement 2, 2012: Proceedings of Ontologies in Biomedicine and Life Sciences (OBML 2011). The full contents of the supplement are available online at http://www.jbiomedsem.com/supplements/3/S2.

Publisher Copyright:
© 2012 Oellrich et al.; licensee BioMed Central Ltd.

ASJC Scopus subject areas

  • Information Systems
  • Computer Science Applications
  • Health Informatics
  • Computer Networks and Communications

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