This article is part of the supplement: Proceedings of Ontologies in Biomedicine and Life Sciences (OBML 2011)

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Quantitative comparison of mapping methods between Human and Mammalian Phenotype Ontology

Anika Oellrich1*, Georgios V Gkoutos23, Robert Hoehndorf23 and Dietrich Rebholz-Schuhmann1

Author Affiliations

1 European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK

2 Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK

3 Department of Computer Science, University of Aberystwyth, Old College, King Street, SY23 2AX, UK

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Journal of Biomedical Semantics 2012, 3(Suppl 2):S1  doi:10.1186/2041-1480-3-S2-S1

Published: 21 September 2012


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.