[Annotation] [Go] Usage of the With/From Column for IEA ?

[Pankaj Jaiswal]

I see your suggestion a mix and match situation. We always use 
'entities' such as accession IDs of genes/proteins in the WITH column, 
because we are trying to assert an association against reference. Now 
with this suggestion of using the resource site and method, it consists 
of a mixed BAG. Ideally there is a need for separate column where even 
for ISS/any_other_code you can say what method was used e.g. 
BLAST/BLATN/BLATP/SignalP/TargetP/TMHMM. I don't think we should 
populate the WITH column with method.

Thisi way method column can be asserted for 'mandatory' status, but not 
'with'.

Pankaj


Pascale Gaudet wrote:
> I wonder why we can't write CBS: TMHMM and CBS: SignalP
> Seems accepted by our guidelines
> http://geneontology.org/cgi-bin/xrefs.cgi#ref-C
> 
> Pascale
> 
> Gwinn Giglio, Michelle wrote:
>> I think we do need some kind of consensus - anyone else want to voice an
>> opinion?
>>
>> Michelel
>>
>>
>>
>> On 6/12/08 11:48 AM, "Pankaj Jaiswal" <pj37 at cornell.edu> wrote:
>>
>>   
>>> Great. Do we need a formal word or voting on this request. We are
>>> waiting to submit some of our annotations that didn't make it through
>>> due to the mandatory 'with' rule.
>>>
>>> Pankaj
>>>
>>> Gwinn Giglio, Michelle wrote:
>>>     
>>>> Hi,
>>>>
>>>> Well, considering our new policy for ISS not requiring "with" for the very
>>>> types of evidence you mention, it seems IEA should not require "with" as
>>>> well......
>>>>
>>>> Michelle
>>>>
>>>>
>>>>
>>>>
>>>> On 6/11/08 1:12 PM, "Pankaj Jaiswal" <pj37 at cornell.edu> wrote:
>>>>
>>>>       
>>>>> I didn't hear from the group on this. Could you please help.
>>>>>
>>>>> Pankaj
>>>>>
>>>>> Pankaj Jaiswal wrote:
>>>>>         
>>>>>> http://www.geneontology.org/GO.evidence.shtml#iea
>>>>>>
>>>>>> Ref: From the above site
>>>>>>
>>>>>> Usage of the With/From Column for IEA
>>>>>>
>>>>>> At the January 2007 GOC meeting, it was agreed that it will be required
>>>>>> to make an entry in the with/from column for all annotations made after
>>>>>> May 1, 2007 when using this evidence code to indicate what individual
>>>>>> sequences, sequence objects, methods, keyword mapping files, etc. are
>>>>>> the basis of the annotation. When multiple entries are placed in the
>>>>>> with/from field, they are separated by pipes.
>>>>>>
>>>>>> ------------
>>>>>> Based on this rule, would you please suggest, what would be the value
>>>>>> for the 'WITH' column.
>>>>>>
>>>>>> - if we are making a TMHMM prediction for a 'putative tansmembrane'
>>>>>> annotation
>>>>>> - if we have used TargetP/SignalP/Predotar/Psort to predict a putative
>>>>>> cellular localization
>>>>>>
>>>>>> None of the above prediction softwares give appropriate value to be
>>>>>> filled in the 'WITH' column.
>>>>>>
>>>>>> If you agree our suggestion is to relax this rule for IEA's.
>>>>>>
>>>>>> Pankaj
>>>>>>
>>>>>>           
>>>>> _______________________________________________
>>>>> Go mailing list
>>>>> Go at geneontology.org
>>>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>>>         
>>>>       
>>
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>>
>>   

-- 
Pankaj Jaiswal
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Dept. of Plant Breeding and Genetics
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