From: Melissa H. <mha...@uo...> - 2007-11-27 00:35:12
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Hi, Thought maybe some examples would help. Under most circumstances, PATO terms are used to relate deviation from a population, normal state, wild-type, or taxon. For example, at ZFIN when we state that E=bone + Q=small size, we imply that the small size is relative to wild type state, and the genotype of the deviant population is specified. We can also specify the genotype of the background, but it is still implied that this is what is being compared to. In an evolutionary comparison, you'd often need to annotate things like: for Taxon A: E=bone X + Q=smaller_size_than E=bone Y for Taxon B: E=bone X + Q=larger_size_than E=bone Y where the states are compared between taxons. Melissa David Sutherland wrote: > On Wed, 2007-11-21 at 10:27 -0800, Raymond wrote: > >> perhaps we could make it more explicit which terms are 'comparative' in >> PATO. >> >> > I think that's the key. Some terms are explicitly comparative already > (relational qualities), but 'small' ('decreased size' in the latest > PATO) and many similar terms are categorised as a 'mondaic quality of a > continuant'. There may well be a useful distinction though, between > terms like 'decreased size' and those already categorised as relational > qualities... > > David > > > >> just to play with words, "small" really should be "smaller" and "tiny", >> "smallest"? :) >> >> raymond >> >> >> Alan Ruttenberg wrote: >> >>> [Term] >>> id: PATO:0000587 >>> name: decreased size >>> def: "A size which is lesser relative to the normal or >>> average." [PATOC:GVG] >>> subset: value_slim >>> related_synonym: "small" [] >>> related_synonym: "tiny" [] >>> is_a: PATO:0000117 ! size >>> >>> The question is: what defines the normal from which the average is >>> computed. >>> Can the definition be phrased in terms of exceed some number of >>> standard deviations from an explicitly defined population? >>> >>> Some uses in the wild: >>> http://arabidopsis.info/StockInfo?NASC_id=6262 Presumably the >>> population is some normal strain? Which one? >>> >>> In the example in the pheno representation doc (http:// >>> www.fruitfly.org/~cjm/obd/pheno-representation.html) we have >>> >>> >>>> <phenotype> >>>> <phenotype_character> >>>> <bearer> >>>> <!-- heart --> >>>> <typeref about="MA:0000072"/> >>>> </bearer> >>>> <quality> >>>> <!-- small --> >>>> <typeref about="PATO:0000587"/> >>>> </quality> >>>> </phenotype_character> >>>> </phenotype> >>>> In PS this is represented as: >>>> >>>> E= MA:0000072 Q= PATO:0000587 >>>> >>>> >>> Is this in reference to all mouse hearts, as use to describe a >>> strain? Or with respect to a particular animal, within a litter, in >>> relation to the litter? >>> >>> Do you see the problem? >>> >>> >>> -Alan >>> >>> On Nov 21, 2007, at 11:23 AM, 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? >>>> -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 >>>>> >>>>> >>>>> --------------------------------------------------------------------- >>>>> ---- >>>>> 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 >>>>> >>>>> >>> ------------------------------------------------------------------------- >>> 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 >>> >>> >> ------------------------------------------------------------------------- >> 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 >> > > > ------------------------------------------------------------------------- > 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 > -- Melissa Haendel, Ph.D. ZFIN Scientific Curator Zebrafish Information Network 5291 University of Oregon Eugene, OR 97403-5291 Phone: (541) 346-5108 |