From: Lynn S. <lyn...@gm...> - 2008-01-25 15:24:59
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Hello Barry, thank you for the constructive comments. It is good to get a larger perspective. We'll work on improving the ontology. I will work on these points and send it to you for re-review. A general symptom, is a symptom that is not localized to a specific body system. Can you tell me what is the process, for entering our ontologies to OBO. Is there documentation posted that I can look at ? I would also like to submit our Transmission Method vocabulary. Thank you, Lynn On Jan 24, 2008 9:16 PM, Smith, Barry <phi...@bu...> wrote: > Lynn > I looked at the symptom ontology. > One problem is that you switch back and forth between singular and plural. > Another problem is that you use 'and' and 'or' to form names of types, as > in > > > neck symptoms > is_a: head and neck symptoms > > > weight gain > 2121 is_a: SYMP:473 ! nutrition, metabolism, and development symptoms > > > A third problem is that you introduce names of types which (I think) > could not be sensible defined, as in > > > dyspareunia > 2128 is_a: SYMP:567 ! general symptoms > > or > > 2161 name: neurological and physiological symptoms > 2162 is_a: SYMP:567 ! general symptoms > > > what is a 'general symptoms'? > > A fourth problem is that you are sometimes classifying symptoms on > the basis of anatomy, sometimes on another sort of basis. > > A fifth problem is that you do not address the methodology being > tested in PATO for dealing with phenotypic qualities (some, at least, > of your symptoms, would have to fit there, e.g. > light sensitivity). Others (e.g. brain cyst) would go rather under > pathological anatomy -- perhaps the symptom is having-a-brain-cyst, > not the brain cyst itself. > > Needs more work. But it is a very impressive start. > BS > > > > > > At 08:00 PM 1/24/2008, you wrote: > > >Hello All, > > > > As part of the Gemina project, we've devised a Transmission > > Method controlled vocabulary > > > >and a Symptom Ontology which we would like to add to the set of OBO > >vocabularies. > > > > > > > >To our knowledge these no not overlap domain space with other ontology > work. > > > >I had heard last year at a conference that someone at the CDC was > >working on a transmission > > > >method ontology. The transmission method terms were derived from > >epidemiological text books. > > > > He mentioned this after seeing my poster. I've not seen any > > publications following the discussion. > > > >For symptoms, the ontology was derived from nodes extracted from > >ICD-9, ICD-10, terms were utilized > > > > From MeSH and the structure follows that of version 2 of the > > Disease Ontology, where the symptoms > > > >Are divided by body systems. > > > > > > > > > > > > > > > ><http://gemina.cvs.sourceforge.net/gemina/Gemina/ontologies/> > http://gemina.cvs.sourceforge.net/gemina/Gemina/ontologies/ > > > > > >Should we have a link to this page (above) on our the Gemina sourceforge > page > > > ><http://sourceforge.net/project/showfiles.php?group_id=191166> > http://sourceforge.net/project/showfiles.php?group_id=191166 > > > > > > > >Lynn M. Schriml, Ph.D. > > > >Assistant Professor > > > >Institute for Genome Sciences > > > >Department of Epidemiology and Preventive Medicine > > > >University of Maryland, School of Medicine > > > >685 West Baltimore Street > > > >HSF-I, Room 164 > > > >Baltimore, MD 21209 > > > > > > > >email: <mailto:lsc...@so...>lsc...@so... > > > >phone: 410-706-6776 > > > >fax: 410-706-6756 > > > > > >------------------------------------------------------------------------- > >This SF.net email is sponsored by: Microsoft > >Defy all challenges. Microsoft(R) Visual Studio 2008. > >http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > >_______________________________________________ > >Obo-discuss mailing list > >Obo...@li... > >https://lists.sourceforge.net/lists/listinfo/obo-discuss > > > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Obo-discuss mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-discuss > |