Thanks Peter - this is helpful. What software packages currently support the ontology you describe?
On Tue, May 18, 2010 at 3:15 AM, Peter Murray-Rust <[email protected]> wrote: > 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 > -- Jean-Claude Bradley, Ph. D. E-Learning Coordinator for the College of Arts and Sciences Associate Professor of Chemistry Drexel University http://usefulchem.blogspot.com http://drexel-coas-elearning.blogspot.com http://drexel-coas-talks-mp3-podcast.blogspot.com/ http://friendfeed.com/jcbradley
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