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

[Gwinn Giglio, Michelle]

Ben,

No one is disputing the importance of the "with" fields and I think we all
know why we have them.  However, even making the "with" field always
mandatory will not make people annotate correctly.  It is easy to get around
the spirit of these "rules" if someone wants to.

The bottom line is we have had this debate more than once and have reached
the decision not to require "with" for all ISS annotations - it only  makes
sense that the IEAs using the same kinds of information would be treated the
same way.

Let's think about the people who are trying to do a thoughtful and careful
job of annotating using best GO practices.  They will read the guidelines
and they will try to follow them.
As for those who use bad annotation practices, they will produce bad
annotation whether or not we make them populate "with".

Putting the methods/tools like tRNAscan and snoRNA scan into "with" would be
mixing methods and accessions-of-items-found-with-methods in the "with"
column.  Many GO folks have expressed that they don't want to do this.  As
Pankaj and others have pointed out, there is always the option of yet
another column for this.  Or, others have argued it can be captured in the
reference field.

Anyway, we have a policy in place.  Of course we've changed our minds in the
past before.....

Michelle





On 6/12/08 2:38 PM, "Benjamin Hitz" <hitz at genome.stanford.edu> wrote:

> 
> 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
>>>> 
>>>> 
>> 
>> _______________________________________________
>> Go mailing list
>> Go at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/go
> 
> --
> Ben Hitz
> Senior Scientific Programmer ** Saccharomyces Genome Database ** GO
> Consortium
> Stanford University ** hitz at genome.stanford.edu
> 
> 
> 
> _______________________________________________
> Annotation mailing list
> Annotation at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/annotation