Re: [Obo-phenotype] GO vs Phenotype curation

[Pankaj J. <pj...@co...>]

Doug howe wrote:
> To be clear:  I view this largely as a redundancy of doing curatorial 
> work.  Not a redundancy of biological knowledge space per se.  
!

> GO 
> annotation applies to the normal functions, processes, components of 
> wild type gene products.  
This is a tricky situation. The moment we say 'wild type normal ' means 
we are referring to the so called wild type allele or the allele that 
was sequenced (from sequenced stock / accession) as part of the genome 
sequencing effort. Often we have found that major phenotype genes/loci 
are missing from these sequenced genomes. Lets say in case of rice the 
genome was sequenced from Nipponbare variety, but it lacks the 
functional genes (loci) to provide many types of disease resistance. So 
in that case if one has to curate these loci (CDSs) in the genome to 
'response to pathogen' a biological process term, we cannot because its 
not true for the loci from sequenced genome. However, we do want to 
associate these loci to the disease resistance. that can be done if I 
have read the functional allele paper that will tell me the real 
functional loci is the resistant form that comes from a different variety.

I may be overstating but, its very superficial to call what is a wild 
type. It is driven by the experiment. In the example I gave above its 
not clear that's why a use of a reference set is recommended. Also a 
gene in true sense  is just a place holder for all the phenotypes (at 
macro / micro levels) that includes GO annotations at a particular locus 
of a genome. Whether a gene product has a function or not is genotype 
dependent i.e. allele or the genetic background.

> Phenotype describes the characteristics of a 
> specific mutant condition.  When a mutant characteristic is used to 
> imply a GO annotation by IMP there is some overlap between making the 
> phenotype annotations and making the GO annotations.
>   
Agreed. in order to associate many GO-Biological_process term entities 
based on the abnormal eye development example, I am sure one won't be 
able to ascertain the function of the so called wild type (the reference 
allele) unless one has looked at the non-functional/variant form/allele. 
That's why my suggestion (in agreement with you) was, in order to reduce 
the curational load and avoid redundancy we need a curation strategy 
that is driven by gene products with reference to their 
variant/mutant/allele forms and their source stock/germplasm accession 
and not by their generic counterpart 'gene'.

-Pankaj

> -Doug
>
> Pankaj Jaiswal wrote:
>   
>> Sorry for jumping in. The GO and phenotype annotations are essentially 
>> the same thing. Only difference is that the way annotations are 
>> associated/assembled in the current GO association tables, except for 
>> the quality aspect that is new and comes from PATO. In the following 
>> example entity is the 'GO_process: eye development'.
>>
>> e.g.
>> object: allele-A | GO_process: eye development | Quality: abnormal 
>> |Code: IMP | Evidence: PMID-xxxxx
>> The same annotation gets percolated to the gene as well because of its 
>> lineage.
>>
>> -Pankaj
>>
>> Doug howe wrote:
>>     
>>> Michael,
>>>     Consider an alternate example that uses a GO term as the entity in 
>>> the phenotype annotation:
>>>
>>> A mutation in gene A results in cyclopia.
>>> One could annotate gene A with the GO term 'eye development' by IMP
>>> and the allele of gene A with a phenotype annotation like entity: eye 
>>> development + quality:abnormal
>>>
>>> No?
>>>
>>> -Doug
>>>
>>> Michael Ashburner (Genetics) wrote:
>>>   
>>>       
>>>> Doug
>>>>
>>>> I am not sure I see this as a major problem.
>>>>
>>>> Let us imagine you have a mutation in gene A which lacks the dorsal fin.
>>>> You _might_ deduce from this (or an author might) that it is appropriate to
>>>> annotate the corresponding gene as having the GO process
>>>>
>>>> fin morphogenesis
>>>>
>>>> with an IMP evidence code.
>>>>
>>>> That annotation is to the protein (the gene being a proxy for this).
>>>>
>>>> But then the particular _allele_ studied would have a PATO annotation
>>>>
>>>> entity: fin; quality: absent [or whatever, I am just giving the general idea]
>>>>
>>>> These annotations do not seem to be redundant to me
>>>>
>>>> Michael
>>>>
>>>>   
>>>>     
>>>>         
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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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-- 
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