[Go] [Evidence] question about download page

[MICHELLE GIGLIO]

Hi all,

Yes, I have Karen's list as well as a list of my own that I hope to get through in the near future.

Finding the time is the only problem.  Also, I have been hesitant to just make changes as I see fit because perhaps some of these things need broader input.  There is a plan to have an ECO content meeting - but at this point I don't know when that would happen.

My current plan is to put together a proposal of changes that I plan to make and send to the evidence list.  If I don't hear any objections I'll go ahead and make the changes.  If there is disagreement, I'll schedule a skype.

But it will be a few weeks until I get this out - I'm in the middle of moving and barely keeping up with only my most essential work activities.

Sorry for the delays on this.

Michelle




-----Original Message-----
From: evidence-bounces at genome.stanford.edu on behalf of Karen Christie
Sent: Thu 4/16/2009 1:26 PM
To: Midori Harris
Cc: Chris Mungall; go list; Evidence Code Group
Subject: Re: [Evidence] [Go] question about download page
 
I agree that TAS is not placed correctly in the ECO. This is one of the 
things that I commented upon a while ago, when the evidence code 
documentation was under revision. Michelle Gwinn said she's working on the 
ECO now and I recently sent her my whole list of comments/questions on the 
ECO.

-Karen

On Thu, 16 Apr 2009, Midori Harris wrote:

> My guess would be that TAS isn't placed correctly; it's been a last-resort 
> code used in manual annotation, when a curator is inclined to believe 
> something an author says despite being unable to track down an experiment. 
> I'm not aware of it being used for any kind of computational analysis.
>
> m
>
> On Thu, 16 Apr 2009, Chris Mungall wrote:
>
>> We should be using ECO here rather than hardcoding ad-hoc lists of codes in 
>> various pieces of code
>> 
>> There should be some explicitly declared property in ECO that RCA and IEA 
>> share - either via shared is_a parent or via a relationship to some aspect 
>> of the type of evidence.
>> 
>> At the moment we have:
>> 
>> is_a ECO:0000043 ! inferred from in-silico analysis
>>  is_a ECO:00000067 ! inferred from electronic annotation ***  [SYNONYM: 
>> "IEA" (related)]
>>  is_a ECO:0000033 ! traceable author statement [SYNONYM: "TAS" (related)]
>>  is_a ECO:0000053 ! inferred from reviewed computational analysis *** 
>> [SYNONYM: "RCA" (related)]
>> 
>> Which seems dubious. If TAS is placed correctly then we can perhaps use 
>> inferred from in-silico analysis. But I think ECO needs further 
>> re-arrangement or changes such that we have an evidence type "inferred 
>> SOLELY from in-silico analysis"
>> 
>> On Apr 16, 2009, at 8:01 AM, Valerie Wood wrote:
>> 
>>> 
>>> 
>>> On the download page, the number of annotations for each organism are 
>>> reported and the number of these which are IEA are specified.
>>> Should this also specify the number which are non-RCA (as these are 
>>> generally function predictions, with less support than the IEA mappings, 
>>> and users should be made as aware of the 'dangers' of these,  as of the 
>>> IEA data).
>>> 
>>> Val
>>> 
>>> 
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>>> The Wellcome Trust Sanger Institute is operated by Genome Research 
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>>> registered in England with number 2742969, whose registered office is 215 
>>> Euston Road, London, NW1 2BE. 
>>> _______________________________________________
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>> 
>> _______________________________________________
>> Go mailing list
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