Consistent Re-Modeling of Signaling Pathways and Its Implementation in the TRANSPATH Database

Claudia Choi[1] (cch@biobase.de)
Torsten Crass[2] (torsten.crass@med.uni-goettingen.de)
Alexander Kel[1] (ake@biobase.de)
Olga Kel-Margoulis[1] (oke@biobase.de)
Mathias Krull[1] (mkl@biobase.de)
Susanne Pistor[1] (spi@biobase.de)
Anatolij Potapov[1],[2] (anatolij.potapov)
Nico Voss[1] (nvo@biobase.de)
Edgar Wingender[1],[2] (ewi@biobase.de)

[1]BIOBASE GmbH, Halchtersche Str.33, D-38304 Wolfenbüttel, Germany
[2]Dept. of Bioinformatics, University of Göttingen, Medical School, Goldschmidtstr. 1, D-37077 Güttingen, Germany


Abstract

The data model of the signaling pathways database TRANSPATH has been re-engineered to a three-layer model comprising experimental evidences and summarized pathway information, both in a mechanistically detailed manner, and a “semantic” projection for the abstract overview. Each molecule is described in the context of a certain reaction in the multidimensional space of posttranslational modification, molecular family relationships, and the biological species of its origin. The new model makes the data better suitable for reconstructing signaling pathways and networks and mapping expression data, for instance from microarray experiments, onto regulatory networks.

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Japanese Society for Bioinformatics