[Annotation] evidence code advice

[Suzanna Lewis]

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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