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

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Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes

Georgios V Gkoutos12* and Robert Hoehndorf12

Author Affiliations

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

2 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):S6  doi:10.1186/2041-1480-3-S2-S6

Published: 21 September 2012


Ontologies are widely used in the biomedical community for annotation and integration of databases. Formal definitions can relate classes from different ontologies and thereby integrate data across different levels of granularity, domains and species. We have applied this methodology to the Ascomycete Phenotype Ontology (APO), enabling the reuse of various orthogonal ontologies and we have converted the phenotype associated data found in the SGD following our proposed patterns. We have integrated the resulting data in the cross-species phenotype network PhenomeNET, and we make both the cross-species integration of yeast phenotypes and a similarity-based comparison of yeast phenotypes across species available in the PhenomeBrowser. Furthermore, we utilize our definitions and the yeast phenotype annotations to suggest novel functional annotations of gene products in yeast.