[Annotation] evidence code advice

Tue Apr 1 15:24:30 PDT 2008

Hi,

I think Kara's suggestion is a great idea, though more of a long term 
possibility and not an immediate solution to the issue Rama brought up of 
what evidence code to use for annotations that are based on an RCA type of 
method but not reviewed by a curator.

As for the with column and IEA, yes, at the Jan 2007 meeting in Cambridge, 
we agreed to make the with column mandatory for IEA. At the time, we 
considered whether or not to make the with column mandatory based only on 
sequenced based methods and keyword based methods. The need to make IEA 
annotations for non-reviewed RCA methods was not considered. The initial 
documentation for the RCA code allowed the RCA code to be used for both 
curator reviewed and non-curator reviewed annotations. However, at that 
meeting, the RCA code was sent back to committee for further review.

During subsequent review of the RCA code by the evidence code committee, 
it was agreed that the RCA code should be more like the other codes and 
thus it was limited to be a curator-reviewed code, with the thought that 
when annotations were made based on RCA methods but without curator review 
that they would be IEA, similarly to unreviewed annotations based on ISS 
methods. Clearly we'd forgotten about the newly instituted requirement for 
the with column to be filled for IEA.

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.

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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