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<P><FONT SIZE=2>Hi all,<BR>
<BR>
Yes, I have Karen's list as well as a list of my own that I hope to get through in the near future.<BR>
<BR>
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.<BR>
<BR>
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.<BR>
<BR>
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.<BR>
<BR>
Sorry for the delays on this.<BR>
<BR>
Michelle<BR>
<BR>
<BR>
<BR>
<BR>
-----Original Message-----<BR>
From: evidence-bounces@genome.stanford.edu on behalf of Karen Christie<BR>
Sent: Thu 4/16/2009 1:26 PM<BR>
To: Midori Harris<BR>
Cc: Chris Mungall; go list; Evidence Code Group<BR>
Subject: Re: [Evidence] [Go] question about download page<BR>
<BR>
I agree that TAS is not placed correctly in the ECO. This is one of the<BR>
things that I commented upon a while ago, when the evidence code<BR>
documentation was under revision. Michelle Gwinn said she's working on the<BR>
ECO now and I recently sent her my whole list of comments/questions on the<BR>
ECO.<BR>
<BR>
-Karen<BR>
<BR>
On Thu, 16 Apr 2009, Midori Harris wrote:<BR>
<BR>
> My guess would be that TAS isn't placed correctly; it's been a last-resort<BR>
> code used in manual annotation, when a curator is inclined to believe<BR>
> something an author says despite being unable to track down an experiment.<BR>
> I'm not aware of it being used for any kind of computational analysis.<BR>
><BR>
> m<BR>
><BR>
> On Thu, 16 Apr 2009, Chris Mungall wrote:<BR>
><BR>
>> We should be using ECO here rather than hardcoding ad-hoc lists of codes in<BR>
>> various pieces of code<BR>
>><BR>
>> There should be some explicitly declared property in ECO that RCA and IEA<BR>
>> share - either via shared is_a parent or via a relationship to some aspect<BR>
>> of the type of evidence.<BR>
>><BR>
>> At the moment we have:<BR>
>><BR>
>> is_a ECO:0000043 ! inferred from in-silico analysis<BR>
>> is_a ECO:00000067 ! inferred from electronic annotation *** [SYNONYM:<BR>
>> "IEA" (related)]<BR>
>> is_a ECO:0000033 ! traceable author statement [SYNONYM: "TAS" (related)]<BR>
>> is_a ECO:0000053 ! inferred from reviewed computational analysis ***<BR>
>> [SYNONYM: "RCA" (related)]<BR>
>><BR>
>> Which seems dubious. If TAS is placed correctly then we can perhaps use<BR>
>> inferred from in-silico analysis. But I think ECO needs further<BR>
>> re-arrangement or changes such that we have an evidence type "inferred<BR>
>> SOLELY from in-silico analysis"<BR>
>><BR>
>> On Apr 16, 2009, at 8:01 AM, Valerie Wood wrote:<BR>
>><BR>
>>><BR>
>>><BR>
>>> On the download page, the number of annotations for each organism are<BR>
>>> reported and the number of these which are IEA are specified.<BR>
>>> Should this also specify the number which are non-RCA (as these are<BR>
>>> generally function predictions, with less support than the IEA mappings,<BR>
>>> and users should be made as aware of the 'dangers' of these, as of the<BR>
>>> IEA data).<BR>
>>><BR>
>>> Val<BR>
>>><BR>
>>><BR>
>>> --<BR>
>>> The Wellcome Trust Sanger Institute is operated by Genome Research<BR>
>>> Limited, a charity registered in England with number 1021457 and a company<BR>
>>> registered in England with number 2742969, whose registered office is 215<BR>
>>> Euston Road, London, NW1 2BE.<BR>
>>> _______________________________________________<BR>
>>> Go mailing list<BR>
>>> Go@geneontology.org<BR>
>>> <A HREF="http://fafner.stanford.edu/mailman/listinfo/go">http://fafner.stanford.edu/mailman/listinfo/go</A><BR>
>>><BR>
>><BR>
>> _______________________________________________<BR>
>> Go mailing list<BR>
>> Go@geneontology.org<BR>
>> <A HREF="http://fafner.stanford.edu/mailman/listinfo/go">http://fafner.stanford.edu/mailman/listinfo/go</A><BR>
> _______________________________________________<BR>
> Go mailing list<BR>
> Go@geneontology.org<BR>
> <A HREF="http://fafner.stanford.edu/mailman/listinfo/go">http://fafner.stanford.edu/mailman/listinfo/go</A><BR>
><BR>
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