An Introduction to Chemistry Ontology

Tutorial by Colin Batchelor (Royal Society of Chemistry)

This tutorial will provide an introduction to chemistry ontology with special focus on the ChEBI (Chemical Entities of Biological Interest) ontology resource.

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

reasoning with chemistry ontology

extending ontology to chemical processes

experimental methods in chemistry

Faculty

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.

References

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.

Links

ChEBI ontology

IUPAC Compendium of Chemical Terminology (Gold Book)/

Basic Formal Ontology.