[Annotation] evidence code advice

Tue Apr 1 17:55:19 PDT 2008

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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