TRANSFAC©, TRANSPATH© and CYTOMER© as Starting Points for an Ontology of Regulatory Networks

Article type: Research Article

Authors: Wingender, Edgar

Affiliations: Department of Bioinformatics, UKG, University of Göttingen, Goldschmidtstr. 1, D-37077 Göttingen, Germany. BIOBASE GmbH, Halchtersche Str. 33, D-38304 Wolfenbüttel, Germany. E-mail: e.wingender@med.uni-goettingen.de.

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).

Keywords: regulatory networks, signal transduction pathways, transcriptional regulation, databases, ontological modeling

Journal: In Silico Biology, vol. 4, no. 1, pp. 55-61, 2004