From: Paul S. <ps...@mo...> - 2010-12-14 11:58:27
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Chris, we have a pathological physical entity ontology already and this is how it works now.... On 14 Dec 2010, at 00:46, Chris Mungall wrote: > > You're making this more complicated than it needs to be. My > intuition tells me that "zonular cataract" is a kind of "cataract", > and that a "cataract" is a physical entity, not a quality. A > cataract can have qualities such as size, mass, opacity, position. > > We can *in theory* have a parallel PATO hierarchy with definitions > like the ones below, but these would not be called "cataract" or > "zonular cataract", as these names are highly misleading when you > look at the definition. They would have to be called something like > "zonular cataracticity". The fact that this is beyond awkward is a > red flag that this *isn't* something that's naturally defined as a > quality. > > Let's keep it simple. We should have a pathological physical entity > hierarchy: > > cataract > zonular cataract > ... > > In HP and MP we would have classes such as "having cataract", > "having cataract in one eye", "having cataract in both eyes" etc, > these would be defined using the pattern presented in Rob's paper > and referencing the pathological anatomical entities. > > We should just bite the bullet and make this pathological anatomical > entity ontology. This pattern has worked well for us in defining > neurodegenerative phenotypes - the NIFSTD ontologies can be seen as > a parallel obo foundry dealing with the neurodegenerative domain, > and there are some extremely useful classes there for entities such > as cellular inclusions. This avoids getting into all kinds of PATO > contrusions. > > I'm neutral as to whether this should be MPATH generalized to > mammals. My own choice would be make this as general as possible - > pathological cell component classes can be generalized across a wide > taxonomic range, and this may be true of tissue level pathogenic > entities too. I think we should just go ahead and do it. > > On Dec 12, 2010, at 7:32 AM, George Gkoutos wrote: > >> >> On 12 Dec 2010, at 14:29, Paul Schofield wrote: >> >>> "cataractic" is not really appropriate for PATO. Its a disease >>> concept referring to lenticular opacity of different patterns and >>> etiology. >> >> sure - look at the def I sent to Peter earlier: >> >> Zonular cataract =def >> Quality and inheres-in some (Lens and >> has-part some (has-quality some opaque) and >> has-part some (has-quality some transparent)) >> >>> >>> >>> >>> >>> On 12 Dec 2010, at 12:58, George Gkoutos wrote: >>> >>>> >>>> On 12 Dec 2010, at 11:21, Robert Hoehndorf wrote: >>>> >>>>>>>>>> "PR" == Peter Robinson <pet...@ch...> writes: >>>>> >>>>> Greetings, >>>>> >>>>> PR> I am looking for a PATO term to describe zonular cataract. >>>>> This >>>>> PR> is a type of cataract classification that basically means that >>>>> PR> not the entire lens is affected. Some zones are affected, some >>>>> PR> zones are not. This is not a very ontological way of defining >>>>> PR> things, but would correspond roughly to >>>>> PR> affects_some_but_not_all_parts_of >>>>> >>>>> Ok, I do not know which PATO quality to use for "cataractic", >>>>> but if >>>>> there was such a quality, I guess a way to represent that only >>>>> some >>>>> parts of the lens are affected would be to use part-of twice: >>>>> >>>>> Zonular cataract =def >>>>> Quality and inheres-in some (Lens and >>>>> has-part some (has-quality some cataractic) and >>>>> has-part some (has-quality some non-cataractic/normal)) >>>>> >>>>> And to make it a quality of an organism: >>>>> Having zonular cataract =def >>>>> Quality and inheres-in some (has-part some (has-quality some >>>>> Zonular >>>>> cataract)) >>>> >>>> I think this is a nice pattern and captures the semantics - I think >>>> we >>>> should follow this. >>>> >>>> George >>>> >>>>> >>>>> R >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Oracle to DB2 Conversion Guide: Learn learn about native support >>>>> for >>>>> PL/SQL, >>>>> new data types, scalar functions, improved concurrency, built-in >>>>> packages, >>>>> OCI, SQL*Plus, data movement tools, best practices and more. >>>>> http://p.sf.net/sfu/oracle-sfdev2dev >>>>> _______________________________________________ >>>>> Obo-phenotype mailing list >>>>> Obo...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/obo-phenotype >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Oracle to DB2 Conversion Guide: Learn learn about native support >>>> for PL/SQL, >>>> new data types, scalar functions, improved concurrency, built-in >>>> packages, >>>> OCI, SQL*Plus, data movement tools, best practices and more. >>>> http://p.sf.net/sfu/oracle-sfdev2dev >>>> _______________________________________________ >>>> Obo-phenotype mailing list >>>> Obo...@li... >>>> https://lists.sourceforge.net/lists/listinfo/obo-phenotype >>> >> >> --------------------------------------------------- >> Dr. G.V.Gkoutos >> >> University of Cambridge >> Department of Genetics >> Downing Site, Downing Street >> Cambridge, CB2 3EH >> >> Tel: +44 [0] 01223 766336 >> >> email: gg...@ca... >> url: http://www.gen.cam.ac.uk >> >> ------------------------------------------------------ >> >> >> >> >> >> >> ------------------------------------------------------------------------------ >> Oracle to DB2 Conversion Guide: Learn learn about native support >> for PL/SQL, >> new data types, scalar functions, improved concurrency, built-in >> packages, >> OCI, SQL*Plus, data movement tools, best practices and more. >> http://p.sf.net/sfu/oracle-sfdev2dev >> _______________________________________________ >> Obo-phenotype mailing list >> Obo...@li... >> https://lists.sourceforge.net/lists/listinfo/obo-phenotype > |