Chemical Knowledge for the Semantic Web

  • Mykola Konyk
  • Alexander De Leon
  • Michel Dumontier
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5109)


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.


semantic web knowledge representation knowledge engineering ontology life sciences question answering OWL chemistry molecule mashup 


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Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Mykola Konyk
    • 1
  • Alexander De Leon
    • 1
  • Michel Dumontier
    • 1
    • 2
    • 3
  1. 1.School of Computer ScienceCarleton UniversityOttawaCanada
  2. 2.Department of BiologyCarleton UniversityOttawaCanada
  3. 3.Institute of BiochemistryCarleton UniversityOttawaCanada

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