Re: [Obo-phenotype] attribute & value slims in pato

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Pankaj, I think what you are referring to would be a 
taxonomically-limited PATO slim. This could be useful too, but wouldn't 
necessarily be the only kind of slim you might want to have. What Jim is 
proposing has to do with separating out the values (usually the leaf 
nodes) from the PATO terms which are attributes (necessarily not the 
leaf nodes). The problem is that there can be some values which are not 
leaf nodes. This makes PATO much more useful for the evolutionary community.

melissa

Pankaj Jaiswal wrote:
> I think we are mixing the concepts of ontology slims Vs the database 
> searches. Please correct me, PATO holds just the attribute and the value 
> but not the entity. Whereas we intend to use the PATO in conjunction 
> with the entity (other) ontologies.  If so I think the point should have 
> been, which of the PATO terms are applicable to plants/fishes/other 
> phylas and families by creating a subsets (slims). This will help the 
> curators and even the db searchers to find out the subset of attributes 
> that are applicable to fish or the plant phenotypes for example.
>
> -Pankaj
>
> Melissa Haendel wrote:
>   
>> Hi, I agree that the slim should be included in PATO. Here is why:
>>
>> Lets say that we have two species that we want to compare, one with 
>> red eye color and the other with blue eye color.
>> The EQ statements would be:
>> species a: SAA:eye PATO:red
>> species b: SBA:eye PATO:blue
>>
>> where each species has its own anatomy ontology- SBA and SAA. There is 
>> no way to compare these, they have no E or Q in common (at least until 
>> CARO or some other multi-organism anatomy ontology has a relationship 
>> between the eyes of of species a and b, though a text search would 
>> work in this case).
>>
>> However, if we break out the attributes, then we can use the old EAV 
>> system, in a sense:
>> species a: SAA:eye A:color V:red
>> species b: SBA:eye A: color V:blue
>>
>> Now we can say, give me all the phenotypes that affect the attribute 
>> color, which can then be sorted by which E they affect.
>>
>> I know it sounds strange, but this really facilitates conversion of 
>> evolutionary characters to an EQ format. Characters are usually 
>> written as the entity and the attribute together, with the value being 
>> what varies across species. For example, the character here would be 
>> eye color, and the values blue and red. However, this does assume that 
>> eye means the same thing in the species being compared (and we are 
>> working on better ways to do this :-) ).
>>
>> This also facilitates comparison of entities which are not the same- 
>> perhaps the compound eye of the fly and the camera lens eye of 
>> vertebrates. We might want to find phenotypes that affect size of 
>> these entities, which otherwise not related.
>>
>> Melissa
>>
>> Pankaj Jaiswal wrote:
>>     
>>> Same attribute in different organisms --->  for what?
>>>
>>> May be you want to say that show me all the phenotypes in organisms-X 
>>> and Y and Z that were observed for e.g.
>>>
>>> eye color red
>>> enzyme-X activity increased
>>>
>>> Compared to this the slims you are getting is like
>>>
>>> everything that has  color red
>>>  activity increased
>>>
>>> I am not sure of the objectives of this slim but seems that it is not 
>>> useful without the inclusion of entity
>>>
>>> Pankaj
>>>  
>>>
>>> mark gibson wrote:
>>>       
>>>> On Jan 18, 2007, at 7:46 PM, Jim Balhoff wrote:
>>>>
>>>>  
>>>>         
>>>>> I have created subsets ("slims") in my copy of PATO, labeling each
>>>>> term as either an "attribute" or a "value".  I am trying to figure
>>>>> out the best way to maintain this.  Is this of general enough
>>>>> interest to go into the official PATO?  I think it is quite useful
>>>>> because I don't believe there is another way to group phenotypic
>>>>> statements which describe the same attribute in different organisms.
>>>>>     
>>>>>           
>>>> i agree with jim with putting these slims in the main pato - george  
>>>> what do you think?
>>>>
>>>>
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>>>>         
>>> -- 
>>> Pankaj Jaiswal
>>> G-15, Bradfield Hall
>>> Dept. of Plant Breeding and Genetics
>>> Cornell University
>>> Ithaca, NY-14853, USA
>>>
>>> Ph. +1-607-255-3103 / 4199
>>> fax: +1-607-255-6683
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>
>   

-- 

Melissa Haendel, Ph.D.

ZFIN Scientific Curator

Zebrafish Information Network

5291 University of Oregon

Eugene, OR 97403-5291

Phone: (541) 346-5108