From: Georgios V. G. (Genetics) <gg...@ca...> - 2007-11-21 18:11:49
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On Nov 21 2007, Chris Mungall wrote: > >I answered the part about the OWL translation of the .obo on the obo-=20 >format list if anyone's interested. > >Cheers >Chris Thanks Chris ! > >On Nov 21, 2007, at 4:33 AM, Georgios V. Gkoutos (Genetics) wrote: > >> >> Hi Bill, >> >> I see what happend... Maybe we can ask Alan (Rector) about this one... >> >> Best wishes, >> >> George >> >> >> >> On Nov 21 2007, Bill Bug wrote: >> >>> Hi George, >>> >>> That's perfect. I'd thought I remembered seeing this before when I >>> browsed through PATO. Thanks, George. >>> >>> I wonder why they didn't come up when I searched in BIRNLex (which >>> imports all of PATO). >>> >>> Ah - two reasons: >>> >>> =091) Protege will only search the "DISPLAY SLOT" property, which I had >>> set to "rdfs:label". Not being able to search synonyms along with >>> the preferred label is definitely a problem in Protege >>> >>> =092) There may also be something about the way obo properties >>> translate into OWL (OBOinOWL) that is also problematic. As you can >>> see in the OWL/RDF/XML below, synonyms are not given simply as >>> string literal annotation properties such as is done with rdfs:label, >>> but rather they are specified as individuals of the class "synonym" >>> and related via a "hasRelatedSynonym" property. >>> >>> =09=09 <oboInOwl:hasRelatedSynonym> >>> =09=09=09<oboInOwl:Synonym> >>> =09=09=09<rdfs:label xml:lang=3D"en">small</rdfs:label> >>> =09=09=09</oboInOwl:Synonym> >>> =09 </oboInOwl:hasRelatedSynonym> >>> >>> This adds a level of abstraction that might make it more difficult to >>> search for a class using synonyms, even once Protege is able to index >>> more than a single DISPLAY_SLOT annotation property, which I believe >>> is in the works. >>> >>> Thanks again for pointing me in the right direction, George. >>> >>> Cheers, >>> Bill >>> >>> On Nov 21, 2007, at 5:27 AM, Georgios V. Gkoutos (Genetics) wrote: >>> >>>> >>>> Hi Bill, >>>> >>>> we have "decreased size" (PATO:0000587) and "increased size" (PATO: >>>> 0000587) in PATO with synonyms "small" and "large". Would this be =20 >>>> OK? >>>> >>>> George >>>> >>>> On Nov 21 2007, Bill Bug wrote: >>>> >>>>> Hi All, >>>>> >>>>> I realize this is a problematic quality to address, but in BIRN >>>>> we have a need to qualify aspects of specific observations as >>>>> "small" and "large". Now, obviously these are relative measures >>>>> - measures that really only can apply to continuants. >>>>> >>>>> Still - I noticed at the base of PATO there are these simple >>>>> qualities: >>>>> >>>>> =09quality >>>>> =09=09quantitative >>>>> =09=09=09amount >>>>> =09=09=09=09decreased >>>>> =09=09=09=09increased >>>>> >>>>> It would be helpful to also have >>>>> >>>>> =09quality >>>>> =09=09quantitative >>>>> =09=09=09size >>>>> =09=09=09=09small >>>>> =09=09=09=09large >>>>> >>>>> at least for those observations where that is all that is =20 >>>>> specified. >>>>> >>>>> Has this issue come up before? >>>>> >>>>> Cheers, >>>>> Bill >>>>> >>>>> >>>>> William Bug, M.S., M.Phil. >>>>> =09=09 email: wb...@nc... >>>>> Ontological Engineer (Programmer Analyst III)=09=09work: (610) 457-04= 43 >>>>> Biomedical Informatics Research Network (BIRN) >>>>> and >>>>> National Center for Microscopy & Imaging Research (NCMIR) >>>>> Dept. of Neuroscience, School of Medicine >>>>> University of California, San Diego >>>>> 9500 Gilman Drive >>>>> La Jolla, CA 92093 >>>>> >>>>> Please note my email has recently changed >>>>> >>>>> >>>>> >>>> >>>> --=20 >>>> George Gkoutos >>>> >>>> ---------------------------------------------------- >>>> Dr. G.V.Gkoutos >>>> >>>> University of Cambridge >>>> Department of Genetics >>>> Downing Site, Downing Street >>>> Cambridge, CB2 3EH >>>> >>>> Tel: +44 [0] 1223 333963 >>>> Fax: + 44 [0] 1223 333992 >>>> >>>> email (direct): gg...@ca... >>>> email (departmental): g.g...@ge... >>>> url: http://www.gen.cam.ac.uk >>>> >>>> ------------------------------------------------------ >>>> >>>> >>>> >>> >>> William Bug, M.S., M.Phil. =09= =09 >>> email: wb...@nc... >>> Ontological Engineer (Programmer Analyst III)=09=09work: (610) 457-0443 >>> Biomedical Informatics Research Network (BIRN) >>> and >>> National Center for Microscopy & Imaging Research (NCMIR) >>> Dept. of Neuroscience, School of Medicine >>> University of California, San Diego >>> 9500 Gilman Drive >>> La Jolla, CA 92093 >>> >>> Please note my email has recently changed >>> >>> >>> >> >> --=20 >> George Gkoutos >> >> ---------------------------------------------------- >> Dr. G.V.Gkoutos >> >> University of Cambridge >> Department of Genetics >> Downing Site, Downing Street >> Cambridge, CB2 3EH >> >> Tel: +44 [0] 1223 333963 >> Fax: + 44 [0] 1223 333992 >> >> email (direct): gg...@ca... >> email (departmental): g.g...@ge... >> url: http://www.gen.cam.ac.uk >> >> ------------------------------------------------------ >> >> >> >> >> ----------------------------------------------------------------------= =20 >> --- >> This SF.net email is sponsored by: Microsoft >> Defy all challenges. Microsoft(R) Visual Studio 2005. >> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >> _______________________________________________ >> Obo-phenotype mailing list >> Obo...@li... >> https://lists.sourceforge.net/lists/listinfo/obo-phenotype >> > > --=20 George Gkoutos ---------------------------------------------------- Dr. G.V.Gkoutos University of Cambridge Department of Genetics Downing Site, Downing Street Cambridge, CB2 3EH Tel: +44 [0] 1223 333963 Fax: + 44 [0] 1223 333992 email (direct): gg...@ca... email (departmental): g.g...@ge... url: http://www.gen.cam.ac.uk ------------------------------------------------------ |