- Review -
| In Silico Biology 4, 0009 (2003); ©2003, Bioinformation Systems e.V. |
Notes on the use of ontologies in the biochemical domain
Isabel Rojas*, Esther Ratsch, Jasmin Saric and Ulrike Wittig
Scientific Databases and Visualisation Group,
EML Research, Heidelberg, Germany
Email: Isabel.Rojas@eml-r.villa-bosch.de
* corresponding author
Edited by H. Michael; received February 17, 2004; revised and accepted March 08, 2004; published March 15, 2004
Abstract
Although databases for cell signaling pathways include numbers of reaction data of the pathways, the reaction data cannot be used yet to deduce biological functions from them. For the deduction, we need systematic and consistent interpretation of biological functions of reactions in cell signaling pathways in the context of "information transmission". To address this issue, we have developed a functional ontology for cell signaling pathways, Cell Signaling Network Ontology (CSN-Ontology), which provides framework for the functional interpretation presenting some important concepts as information, selectivity, movability, and signaling rules including passage of time.
Key words: ontology, cell signaling pathway, biological function