[Annotation] evidence code advice

Wed Apr 2 14:40:11 PDT 2008

Added to the agenda.

Rama

On Apr 1, 2008, at 5:55 PM, Judith Blake wrote:

> Rama,
> If this hasn't been done, would you please add to the wiki agenda  
> list with a pointer to a page with Kara's (and others?) emails...
>
> Thanks very much
> judy
>
> Rama Balakrishnan wrote:
>>> Anyway, in light of that history, I think it would make most  
>>> sense  if the
>>> absolute requirement for the with column to be filled for IEA was   
>>> dropped
>>> in the short term, so that we can use the IEA code for unreviewed
>>> annotations from RCA methods.
>>>
>>
>> I think it is important to require the 'with' column for IEAs to   
>> prevent circular annotations.
>> The other option is to revert the RCA code to its original version   
>> which required only the computational method to be reviewed and  
>> not  every annotation.
>>
>> I also really like Kara's proposal and hopefully this will be   
>> discussed at the upcoming GO meeting.
>>
>> Rama
>>
>>
>>
>>> In the long term, I think Kara's proposal is a better way to go.
>>>
>>> -Karen
>>>
>>>
>>> On Sun, 30 Mar 2008, Suzanna Lewis wrote:
>>>
>>>
>>>> This is very much along the lines that I've been trying to foster
>>>> (remember the meeting in Cambridge at Jesus College). The bit- 
>>>> code  (or
>>>> bar-code) for evidence codes, with each bit indicating one of these
>>>> flags for a different piece of information. Not only automated/  
>>>> manual,
>>>> but also large-scale/small-scale, and other characteristics of the
>>>> evidence.
>>>>
>>>> As Kara (and many others) have said, there is quite a bit of over-
>>>> loading of multiple pieces of information in the current evidence
>>>> codes. It would be nice one day to see these distinguished into
>>>> different constituent bits of information.
>>>>
>>>> -S
>>>>
>>>> p.s. I thought that IEA did not -require- the with column.
>>>> p.p.s Was the decision tree a step in this direction?
>>>>
>>>> On Mar 26, 2008, at 1:59 PM, Kara Dolinski wrote:
>>>>
>>>>
>>>>> Hi,
>>>>>
>>>>> The root of the problem, as I see it, is that we are mixing apples
>>>>> and oranges with evidence codes.  All but one of the evidence  
>>>>> codes
>>>>> indicate the type of experimental evidence for a GO annotation,  
>>>>> but
>>>>> we have one oddball, IEA, that indicates not what the experiment  
>>>>> is,
>>>>> but rather how the annotation was done.  We keep running into
>>>>> variations of the same problem:  we have some evidence (whether
>>>>> experimental or computational) for a GO annotation, but also  
>>>>> want to
>>>>> indicate whether a curator looked at it or not.
>>>>>
>>>>> My proposed (albeit radical) solution:
>>>>>
>>>>> Remove IEA as an evidence code.
>>>>>
>>>>> Create a new property for GO annotations (or add a new type of
>>>>> qualifier) that captures how the annotation was done:  manual or
>>>>> automated.
>>>>>
>>>>> Everything that is currently IEA would be given the 'automated'
>>>>> property/qualifier, and then would be given a new evidence code as
>>>>> appropriate (mostly a flavor of ISS I would assume).
>>>>> There can be a rule that all 'automated' annotations that are a
>>>>> flavor of ISS must have a 'with' value.
>>>>>
>>>>> This would allow us to use 'RCA' as appropriate, in some cases
>>>>> they'd be 'manual', in others, they'd be 'automated'.  In Rama's
>>>>> case, the annotations would be 'RCA' with an 'automated'  
>>>>> qualifier.
>>>>>
>>>>> I realize the issues involved in making such a drastic change,  
>>>>> so I
>>>>> understand if we don't go there, but I do think that some approach
>>>>> such as the one above is the best representation of the  
>>>>> information
>>>>> that we are trying to capture.
>>>>>
>>>>> Cheers,
>>>>> Kara
>>>>>
>>>>> On Mar 26, 2008, at 4:30 PM, Rama Balakrishnan wrote:
>>>>>
>>>>>
>>>>>> Hi All,
>>>>>>
>>>>>> SGD has come across couple of computationally predicted GO
>>>>>> annotation data sets for S. cerevisiae that we would like to  
>>>>>> add to
>>>>>> our database. The GO annotations from these data sets are
>>>>>> predictions based on multiple high-throughput data sets. RCA
>>>>>> evidence code came to our minds but according to the  
>>>>>> documentation,
>>>>>> the annotations all have to be manually reviewed by a curator to
>>>>>> use this evidence. There are several 100 annotations of this kind
>>>>>> and it is not feasible for us to manually review these  
>>>>>> annotations.
>>>>>>
>>>>>> Hence, we thought these annotations can be bulk loaded with IEA
>>>>>> evidence code. However, in the Jan 2007 (Cambridge) GO meeting,  
>>>>>> it
>>>>>> was decided that the 'with' column information has to be filled  
>>>>>> in
>>>>>> for all IEAs (else Mike's filtering script strips them out). But
>>>>>> these GO annotations being predictions based on multiple high-
>>>>>> throughput data sets, don't have any information for the with
>>>>>> column.  So, we are left with no choice.
>>>>>>
>>>>>> Which evidence code do people think should be used for these  
>>>>>> kinds
>>>>>> of computational datasets when there is not an obvious "with"?
>>>>>>
>>>>>> Thanks for your input.
>>>>>>
>>>>>>
>>>>>> Rama
>>>>>>
>>>>>>
>>>>>> +-----o--o
>>>>>> ---------------------------------------------------------------
>>>>>>       o-o       Rama Balakrishnan Ph.D
>>>>>>       O          Senior Scientific Curator
>>>>>>     o-o         Saccharomyces Genome Database
>>>>>>    o---o       Stanford University
>>>>>>  o----o        Stanford, CA 94305-5120
>>>>>> O-----O       Ph: 650.725.8956 Fax: 650.723.7016
>>>>>>  0--o          email: rama at genome.stanford.edu
>>>>>>    O            Website: http://www.yeastgenome.org
>>>>>>   o-o           SGD Wiki- http://wiki.yeastgenome.org
>>>>>> +- o---o
>>>>>> -----------------------------------------------------------------
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
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