Chemical knowledge for the semantic web

M. Konyk; AS Leon; M. Dumontier

doi:10.1007/978-3-540-69828-9_17

Chemical knowledge for the semantic web

M. Konyk, AS Leon, M. Dumontier

Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceeding › Academic › peer-review

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.keywordssemantic webknowledge representationknowledge engineeringontologylife sciencesquestion answeringowlchemistrymoleculemashup.

Original language	English
Title of host publication	Data Integration in the Life Sciences
Subtitle of host publication	5th International Workshop, DILS 2008, Evry, France, June 25-27, 2008. Proceedings
Publisher	Springer
Pages	169-176
Number of pages	8
ISBN (Electronic)	9783540698289
ISBN (Print)	9783540698272
DOIs	https://doi.org/10.1007/978-3-540-69828-9_17
Publication status	Published - 2008
Externally published	Yes

Publication series

Series	Lecture Notes in Computer Science
Volume	5109
ISSN	0302-9743

Access to Document

10.1007/978-3-540-69828-9_17

Cite this

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title = "Chemical knowledge for the semantic web",

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.keywordssemantic webknowledge representationknowledge engineeringontologylife sciencesquestion answeringowlchemistrymoleculemashup.",

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Chemical knowledge for the semantic web. / Konyk, M.; Leon, AS; Dumontier, M.
Data Integration in the Life Sciences: 5th International Workshop, DILS 2008, Evry, France, June 25-27, 2008. Proceedings. Springer, 2008. p. 169-176 (Lecture Notes in Computer Science, Vol. 5109).

Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceeding › Academic › peer-review

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AB - 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.keywordssemantic webknowledge representationknowledge engineeringontologylife sciencesquestion answeringowlchemistrymoleculemashup.

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