Re: [Obo-phenotype] zonular cataract

[Chris M. <CJM...@lb...>]

We do indeed have a pathological physical entity ontology, but the proposed definition below doesn't reference it, which would make integrated queries and inferences involving both HP and MPATH more difficult.

Put the logical definition of cataracts in MPATH and make the HP definitions simple presence-of type definitions. Avoids redundancy, increases reuse and integration, keeps things simple and intuitive.

On Dec 14, 2010, at 3:58 AM, Paul Schofield wrote:

> 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
>>>>>> 
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>>> 
>>> ---------------------------------------------------
>>> 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
>>> 
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