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Bioinformatics Advance Access published online on September 16, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti010
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received June 25, 2004
Revised August 11, 2004
Accepted August 30, 2004

Article

PhenomicDB: a multi-species genotype/phenotype database for comparative phenomics

Abdullah Kahraman 1, Andrey Avramov 2, Lyubomir G. Nashev 2, Dimitar Popov 2, Rainer Ternes 3, Hans-Dieter Pohlenz 3, and Bertram Weiss 3*

1 Dept. 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. E-mail: bertram.weiss{at}schering.de.


  Abstract

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. Up to now these data have been available in distinct organism-specific databases (e.g. WormBase, OMIM, FlyBase or 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

Supplementary Information: database model, semantic mapping table.


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