- Communication -
| In Silico Biology 4, 0006 (2003); ©2003, Bioinformation Systems e.V. |
TRANSFAC®, TRANSPATH® and CYTOMER® as starting points for an ontology of regulatory networks
Edgar Wingender
Dept. of Bioinformatics, UKG, University of Göttingen, Goldschmidtstr. 1, D-37077 Göttingen, Germany
BIOBASE GmbH, Halchtersche Str. 33, D-38304 Wolfenbüttel, Germany
Email: e.wingender@med.uni-goettingen.de
Edited by T. Takai-Igarashi; received March 02, 2004; revised and accepted March 16; published March 16, 2004
Abstract
Building an ontology of a defined knowledge domain can help to model an appropriate database structure for the relevant contents. On the other hand, having a comprehensive overview of the knowledge of a certain domain as it may be provided by corresponding databases facilitates building an appropriate ontology, or ontologies with different granularities, which may then provide many additional benefits in handling the stored and in retrieving additional information from heterogenous sources. In this communication, the first steps are reported how we may derive an ontology for the domain of "molecular regulation" from our databases TRANSFAC® (transcriptional regulation), TRANSPATH® (signal transduction) and CYTOMER® (cellular locations).
Key words: regulatory networks, signal transduction pathways, transcriptional regulation, databases, ontological modeling