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Re: [Obo-discuss] adding a Transmission Method and a Symptom ontology to OBO
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From: Lynn S. <lyn...@gm...> - 2008-01-25 20:47:34
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sounds good On Jan 25, 2008 2:49 PM, Smith, Barry <phi...@bu...> wrote: > At 12:55 PM 1/25/2008, you wrote: > >Thank you Barry, > >I will look at the manual and PDF. > > > > Have you had a chance to look at the Transmission Method vocabulary > ? > > can you press me again about this late next week (unless it is VERY > urgent)? > BS > > > >Lynn > > > > > >On Jan 25, 2008 12:28 PM, Smith, Barry > ><<mailto:phi...@bu...>phi...@bu...> wrote: > >You might find some useful pointers here: > ><http://www.ifomis.org/bfo/manual>http://www.ifomis.org/bfo/manual > >and some papers applying them to particular cases here: > > > ><http://ontology.buffalo.edu/medo/NCIT.pdf> > http://ontology.buffalo.edu/medo/NCIT.pdf > >http://ontology.buffalo.edu/medo/errors.pdf > > > >You need to distinguish qualities (temperature, sensitivity) which go in > PATO > >Processes, increasing this ... decreasing that > >And objects like cysts > > > >Look forward to the next steps. > >Barry > > > > > >At 10:25 AM 1/25/2008, you wrote: > > >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 > > ><<mailto:phi...@bu...><mailto:phi...@bu...>phismith > > @buffalo.edu > 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/>ht > > tp://gemina.cvs.sourceforge.net/gemina/Gemina/ontologies/>http: > > > > > //gemina.cvs.sourceforge.net/gemina/Gemina/ontologies/ ><http://gemi > > n>http://gemin > > > > > <http://a.cvs.sourceforge.net/gemina/Gemina/ontologies/> > a.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>h > > ttp://sourceforge.net/project/showfiles.php?group_id=191166>http > > > ://sourceforge.net/project/showfiles.php?group_id=191166> > > > > > <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...><mailto:lsc...@so... > ><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/>http:// > > clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/>http://clk > > > .atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > > > >_______________________________________________ > > > >Obo-discuss mailing list > > > ><mailto:Obo...@li...><mailto:Obo-discuss@lis > > ts.sourceforge.net>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/>http://cl > > k.atdmt.com/MRT/go/vse0120000070mrt/direct/01/> > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > > >_______________________________________________ > > >Obo-discuss mailing list > > ><mailto:Obo...@li...><mailto:Obo-discuss@lists > > .sourceforge.net>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/>http://clk > > .atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > > >_______________________________________________ > > >Obo-discuss mailing list > > ><mailto:Obo...@li...> > 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/> > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > >_______________________________________________ > >Obo-discuss mailing list > ><mailto:Obo...@li...> > 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 > > > > > ------------------------------------------------------------------------- > 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 > |