Re: [Obo-phenotype] pato quality-->quantitative-->size

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On Wed, 2007-11-21 at 11:23 -0500, Alan Ruttenberg wrote:
> This worries me. Will "small" always be used as a relative quality?  
> What will the reference be. How can we be sure that "small" will be  
> used consistently?
Good point.

This and related questions have been troubing me since I first looked at
PATO.

David

> -Alan
> 
> On Nov 21, 2007, at 7:15 AM, 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
> >
> >
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