[Annotation] evidence code advice

[Judith Blake]

Hi Kara.

I like having a new view on this.  something to think about

judy

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 
>> <mailto: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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