An Introduction to Chemistry Ontology

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Tutorial by Colin Batchelor (Royal Society of Chemistry)

Tuesday, July 21, 2009: 1-5p.m.

We provide an introduction to the development and use of chemistry ontology, with special focus on ChEBI (Chemical Entities of Biological Interest) and the Sequence Ontology.

Topics to be addressed will include:

chemical entities as continuants
the productivity of chemical nomenclature
parts vs. structures vs. names
the IUPAC nomenclature
the past, present and future of the ChEBI ontology
the Sequence Ontology
reasoning with chemistry ontology
extending ontology to chemical processes
experimental methods in chemistry


Colin Batchelor is team leader, Informatics Research and Development, at Royal Society of Chemistry Publishing in Cambridge, UK. He has a DPhil in physical and theoretical chemistry and is presently working on natural language processing and ontology development as applied to the chemical literature.


Kirill Degtyarenko, et al., "ChEBI: a database and ontology for chemical entities of biological interest", Nucleic Acids Research, 2008, 36(Database issue), D344-D350, doi:10.1093/nar/gkm791

Peter Corbett, Colin Batchelor and Ann Copestake, "Pyridines, Pyridine and Pyridine Rings: Disambiguating Chemical Named Entities", Proceedings of Building and Evaluating Resources for Biomedical Text Mining at LREC 2008, Marrakech, Morocco.

Colin Batchelor, "An Upper-Level Ontology for Chemistry", in 5th International Conference on Formal Ontology in Information Systems, Saarbrücken, Germany, October 31st to 3rd November 2008.

N. Villanueva-Rosales, M Dumontier, "Describing chemical functional groups in OWL-DL for the classification of chemical compounds", OWL: Experiences and Directions (OWLED 2007), colocated with European Semantic Web Conference (ESWC2007), Innsbruck, Austria, 2007.

Smith B, et al. "Relations in Biomedical Ontologies", Genome Biology, 2005, 6:R46.



Sequence Ontology

IUPAC Compendium of Chemical Terminology (Gold Book)/

Basic Formal Ontology.