Chemical Knowledge for the Semantic Web

Authors:
Mykola Konyk;Alexander Leon;Michel Dumontier
Affiliations:
School of Computer Science, Carleton University, Ottawa, Canada K1S 5B6;School of Computer Science, Carleton University, Ottawa, Canada K1S 5B6;School of Computer Science, Carleton University, Ottawa, Canada K1S 5B6 and Department of Biology, Carleton University, Ottawa, Canada K1S 5B6 and Institute of Biochemistry, Carleton University, O ...
Venue:
DILS '08 Proceedings of the 5th international workshop on Data Integration in the Life Sciences
Year:
2008

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Abstract

With over 80 file formats to represent various chemical attributes, the conversion between one format and another is invariably lossy due to informal specifications. In contrast, the use of a formal knowledge representation language such as the Web Ontology Language (OWL) enables precise molecular descriptions that can be reasoned about in a logically valid manner. In this paper, we describe a chemical knowledge representation using OWL. We demonstrate its utility in querying a new drug repository created from PubChem, DrugBank and DBpedia. By leveraging Semantic Web technologies, it becomes possible to integrate chemical information at differing levels of detail and granularity, opening new avenues for life science knowledge discovery.