From: Bill B. <wb...@nc...> - 2007-11-22 04:15:51
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This is true, Daniel. Unfortunately, that feature does not present ALL annotation properties as available for searching - at least not in Protege v3.4b bld 104. It only presents a small subset of protege, rdfs, owl, and PAL properties as searchable - unless I'm missing something. We have quite a few other lexical variant annotation properties we use in BIRNLex - some from SKOS, some of our own making - that we'd need to make searchable. In the interim - as Gary Bader suggested - we can use the EBI OLS for those ontologies loaded in that system, which is certainly true for PATO. It appears searching other properties - like synonymies - even when represented as classes as they are doing in PATO and you are doing in RadLex - is also possible in the NCBO BioPortal as well, if you select the "attribute" option in the search form. Cheers, Bill On Nov 21, 2007, at 9:57 PM, Daniel Rubin wrote: > Hi everyone, > > See below for a response to the comment about protege search-- > protege does allow you to search slot values. > > At 04:15 AM 11/21/2007, 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 > > To search on particular properties, you have to tell Protege which > are those properties. This can be done in OWL menu -> Preferences - > > Searching > and you add there the properties of interest. Then, whatever search > you do, the values of those properties will also be searched. This > works for classes and properties. You can search the individuals by > name or display text. > > >> 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 >> >> >> --------------------------------------------------------------------- >> ---- >> 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 > 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 |