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

[Gwinn Giglio, Michelle]

Yes, that¹s what we did before the new documentation came out.  That¹s what
we did at TIGR for years.
But I think under the new ISS guidelines the CBS tools would fall under the
set of things that don¹t get ³with².  That is because the CBS tools are not
always as straightforward as being a single HMM. TMHMM is a single HMM and
therefore I think using CBS:TMHMM is perfectly appropriate, however SignalP
is a combination of a neural network and an HMM, so it is less clear there.

But lets say you are doing tRNAscan automatically or the snoRNA predictor,
just like in ISS, they would not have a ³with².

Michelle




On 6/12/08 2:21 PM, "Pascale Gaudet" <pgaudet at northwestern.edu> 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>
>> <mailto: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>
>>>> <mailto: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
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>>>>>         
>>>>>  
>>>>  
>>>> 
>>>>       
>>>>  
>>>  
>>  
>> 
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>>   
> 


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