On Mon, May 17, 2010 at 12:58 PM, Ola Spjuth <[email protected]> wrote: > Hi, > I asked this question > on http://blueobelisk.shapado.com/questions/is-there-a-chemical-ontology-which-i-can-use-to-annotate-my-chemical-reactions > but I am not sure that it reaches everyone (hence the double-posting). > Basically what I am after is to classify a set of reactions and I would like > to use a chemical ontology (or controlled vocabulary) rather than making up > my own reaction-type-names (such as "n-dealkylation", "s-dealkylation" etc). > Could anyone maybe recommend such an ontology? > Cheers,
We published an ontology in the CMLReact paper J Chem Inf Model. 2006 Jan-Feb;46(1):145-57. Chemical markup, XML, and the world wide web. 6. CMLReact, an XML vocabulary for chemical reactions. Holliday GL, Murray-Rust P, Rzepa HS. http://pubs.acs.org/doi/pdf/10.1021/ci0502698 (cost 30USD for 48 hours if you don't subscribe) The ontology was taken from IUPAC sources and rendered in XML (we would do this differently now). We are currently extracting reactions from the literature and will hope to present a phenomenological ontology I don't think there will be a single approach that satisfies everyone and we shall need multiple ontologies. P. > /Ola > -- > Ola Spjuth, PhD > Department of Pharmaceutical Biosciences > Box 541, Uppsala University > Sweden > Email: [email protected] > Web: http://www.farmbio.uu.se > Bioclipse: http://www.bioclipse.net > > ------------------------------------------------------------------------------ > > > _______________________________________________ > Blueobelisk-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss > > -- Peter Murray-Rust Reader in Molecular Informatics Unilever Centre, Dep. Of Chemistry University of Cambridge CB2 1EW, UK +44-1223-763069 ------------------------------------------------------------------------------ _______________________________________________ Blueobelisk-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
