Bioinformatics Advance Access originally published online on September 16, 2004
Bioinformatics 2005 21(3):418-420; doi:10.1093/bioinformatics/bti010
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Bioinformatics vol. 21 issue 3 © Oxford University Press 2005; all rights reserved.
PhenomicDB: a multi-species genotype/phenotype database for comparative phenomics
1 Department of Bioinformatics, University of Applied Science Giessen 35596 Giessen, Germany
2 Metalife AG Im Metapark 1, 79297 Winden, Germany
3 Research Laboratories, Schering AG 13342 Berlin, Germany
*To whom correspondence should be addressed.
Summary: We have created PhenomicDB, a multi-species genotype/phenotype database by merging public genotype/phenotype data from a wide range of model organisms and Homo sapiens. Until now these data were available in distinct organism-specific databases (e.g. WormBase, OMIM, FlyBase and MGI). We compiled this wealth of data into a single integrated resource by coarse-grained semantic mapping of the phenotypic data fields, by including common gene indices (NCBI Gene), and by the use of associated orthology relationships. With its use-case-oriented user interface, PhenomicDB allows scientists to compare and browse known phenotypes for a given gene or a set of genes from different organisms simultaneously.
Availability: PhenomicDB has been implemented at Schering AG as described below. A PhenomicDB implementation differing in some technical details has been set up for the public at Metalife AG http://www.phenomicDB.de
Contact: bertram.weiss{at}schering.de
Supplementary information: database model, semantic mapping table.
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