Difference between revisions of "An Introduction to Chemistry Ontology"
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'''Tutorial by Colin Batchelor (Royal Society of Chemistry)''' | '''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: | Topics to be addressed will include: | ||
| Line 9: | Line 11: | ||
:parts vs. structures vs. names | :parts vs. structures vs. names | ||
:the IUPAC nomenclature | :the IUPAC nomenclature | ||
| − | :ChEBI | + | :the past, present and future of the ChEBI ontology |
| − | : | + | :the Sequence Ontology |
:reasoning with chemistry ontology | :reasoning with chemistry ontology | ||
:extending ontology to chemical processes | :extending ontology to chemical processes | ||
| Line 21: | Line 23: | ||
'''References''' | '''References''' | ||
| − | Kirill Degtyarenko, | + | Kirill Degtyarenko, et al., "[http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl_1/D344 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. | + | Peter Corbett, Colin Batchelor and Ann Copestake, "[http://www.lrec-conf.org/proceedings/lrec2008/workshops/W4_Proceedings.pdf 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. | + | Colin Batchelor, "[http://www.tantallon.org.uk/preprints/fois-upperchemistry.pdf 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. | + | N. Villanueva-Rosales, M Dumontier, "[http://www.scs.carleton.ca/~nvillanu/papers/2007_OWLED_CFG.pdf 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. [http://genomebiology.com/2005/6/5/R46 "Relations in Biomedical Ontologies"], Genome Biology, 2005, 6:R46. | Smith B, et al. [http://genomebiology.com/2005/6/5/R46 "Relations in Biomedical Ontologies"], Genome Biology, 2005, 6:R46. | ||
| + | |||
| + | '''Links''' | ||
| + | |||
| + | [http://www.ebi.ac.uk/chebi/ ChEBI] | ||
| + | |||
| + | [http://www.sequenceontology.org/ Sequence Ontology] | ||
[http://goldbook.iupac.org/ IUPAC Compendium of Chemical Terminology (Gold Book)/] | [http://goldbook.iupac.org/ IUPAC Compendium of Chemical Terminology (Gold Book)/] | ||
[http://www.ifomis.uni-saarland.de/bfo/ Basic Formal Ontology]. | [http://www.ifomis.uni-saarland.de/bfo/ Basic Formal Ontology]. | ||
Latest revision as of 13:08, 9 November 2008
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
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