Hi all,
So what is needed is to define some relationship between a genotype and
a phenotype.
A common definition of phenotype is the collection of observable
qualities of an organism due to its genotype + environment at any point
in time. In our methodology, we'd like to use the PATO ontology to
describe the qualities, these inhere in an anatomical entity or
biological process and are the direct observables (we'd call it an EQ
description or annotation, or phenotypic character, or see nicole's
other suggestions). A collection of these EQs would be what most
biologists would refer to as the "phenotype". But this phenotype has
context, that of genotype +environment +time.
So we need to define what is an EQ, and what is the collection of EQs,
based on good ontological principles. We were thinking that
BFO:dispositon fit the bill, because it seemed that a phenotypic
character was a disposition.
disposition: A realizable entity that essentially causes a specific
process or transformation in the object in which it inheres, under
specific circumstances and in conjunction with the laws of nature. A
general formula for dispositions is: X (object) has the disposition D to
(transform, initiate a process) R under conditions C." []
-melissa
Judith Blake wrote:
> Nicole, Jim
>
> I quite agree that phenotype descriptions are best defined independent
> of the 'generative process' as Jim says. A phenotype measurement, or
> range of measurements, is what it is, whether the result of one or more
> specific genotypes, with or without an environmental component now or at
> some previous time in the life of the specimen. What we want to get to
> is the ability to describe phenotypes such at we understand that traits
> that compose the phenotype. Then we can experimentally explore the
> genotypes and environment interactions that generate a certain phenotype.
>
> Judy
>
>
> Jim Balhoff wrote:
>
>> Hi Nicole,
>>
>> Is there a reason for including genotype in the definition for
>> phenotype? I think it could be left out entirely - I see a phenotype
>> as stating the qualities of, for example, an anatomical entity. The
>> generative process for the phenotype seems irrelevant (especially
>> since there may be other types of causes).
>>
>> Thanks,
>> Jim
>>
>>
>> On Jul 31, 2008, at 4:22 PM, Nicole Washington wrote:
>>
>>
>>
>>> From our work with describing phenotypes, we need a hook into BFO...
>>> we need to be able to link all phenotypes together in a higher-order
>>> "phenotype" class. so, i'm proposing some new additions to BFO...
>>> this may require some conversation, and possibly new relations. here
>>> goes...
>>>
>>> Term: Phenotypic character
>>> Def: A phenotypic attribute is a disposition wherein a genotype causes
>>> a manifestation of a quality in a bearer entity in a specific
>>> environment
>>> is_a: Disposition
>>>
>>> This would reflect a single EQ pair.
>>>
>>> As the term name could be controversial, here's some other options:
>>> Phenotypic attribute, Phenotypic description, Phenotypic element,
>>> Phenotypic component.
>>>
>>> Then, we'd need to hook some of the terms (and/or the root) in the
>>> genetic context ontology into this BFO term, or at least into
>>> Disposition.
>>>
>>> Then, possibly controversally, there's a desire for another term which
>>> would reflect a collection of EQs... in a similar vain to
>>> "object_aggregate",
>>>
>>> Term: Phenotype_aggregate
>>> Def: A disposition that is the mereological sum of separate
>>> dispositions caused by a single genotype
>>>
>>>
>>> discuss...
>>>
>>> Nicole
>>>
>>> -------------------------------------------------------------------------
>>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>>> challenge
>>> Build the coolest Linux based applications with Moblin SDK & win
>>> great prizes
>>> Grand prize is a trip for two to an Open Source event anywhere in
>>> the world
>>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>>> _______________________________________________
>>> Obo-phenotype mailing list
>>> Obo-phenotype@...
>>> https://lists.sourceforge.net/lists/listinfo/obo-phenotype
>>>
>>>
>> -------------------------------------------------------------------------
>> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
>> Build the coolest Linux based applications with Moblin SDK & win great prizes
>> Grand prize is a trip for two to an Open Source event anywhere in the world
>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> _______________________________________________
>> Obo-phenotype mailing list
>> Obo-phenotype@...
>> https://lists.sourceforge.net/lists/listinfo/obo-phenotype
>>
>>
>
>
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> Obo-relations mailing list
> Obo-relations@...
> https://lists.sourceforge.net/lists/listinfo/obo-relations
>
|