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

[Benjamin Hitz]

WITH fields are very important for IEA and "true" ISS where you are  
inferring an annotation based on sequence similarity.
The reason is to prevent circular associations via sequence similarity.

That is why the WITH column was made mandatory for IEAs and (old)  
ISS.  From a database/machine loading perspective, the only way to  
enforce this is to make the with field MANDATORY.

Ben

On Jun 12, 2008, at 10:02 AM, 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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--
Ben Hitz
Senior Scientific Programmer ** Saccharomyces Genome Database ** GO  
Consortium
Stanford University ** hitz at genome.stanford.edu