From: Chris M. <cj...@fr...> - 2007-11-21 18:03:48
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I answered the part about the OWL translation of the .obo on the obo- format list if anyone's interested. Cheers 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: >> >> 1) 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 >> >> 2) 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. >> >> <oboInOwl:hasRelatedSynonym> >> <oboInOwl:Synonym> >> <rdfs:label xml:lang="en">small</rdfs:label> >> </oboInOwl:Synonym> >> </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 >>> 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: >>>> >>>> quality >>>> quantitative >>>> amount >>>> decreased >>>> increased >>>> >>>> It would be helpful to also have >>>> >>>> quality >>>> quantitative >>>> size >>>> small >>>> large >>>> >>>> at least for those observations where that is all that is >>>> specified. >>>> >>>> Has this issue come up before? >>>> >>>> Cheers, >>>> Bill >>>> >>>> >>>> William Bug, M.S., M.Phil. >>>> email: wb...@nc... >>>> Ontological Engineer (Programmer Analyst III) work: (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 >>>> >>>> >>>> >>> >>> -- >>> 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. >> email: wb...@nc... >> Ontological Engineer (Programmer Analyst III) work: (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 >> >> >> > > -- > 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 > > ------------------------------------------------------ > > > > > ---------------------------------------------------------------------- > --- > 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 > |