[go] partitioning gene association files

[E Dimmer]

I feel that we will be inconveniencing the majority of our users (people 
with large datasets to analyse, databases that integrate GO data) who 
will find that they will have to now need to download two files instead 
of one.

For many species (including reference genome species) there simply is 
not enough manual annotation coverage to be able to use just the manual 
annotation file to get a decent result from an carrying out an 
over-representation analysis. And as the GO Consortium has decided that 
electronic annotations are of high-enough quality to be displayed in 
AmiGO for the reference genome species, this action does seem to go in 
the opposite direction.

I imagine that many microarray tool providers will start to load up both 
files as a matter of course - we will continue to have to make sure that 
instead they improve their representation of the range evidence codes to 
users.

(though separate files containing the the 'NOT' qualified annotations 
would be nice as for many users, parsing out such annotations tends to 
be a first step before using the annotations in most THP analyses)

Emily

Jennifer Deegan (nee Clark) wrote:
> Hi Doug,
>
> Thanks, I'm glad you don't mind the realist view. :-)
>
> Jen
>
> Doug Howe wrote:
>
>> Hi Jen,
>>   Points all well taken!
>> -Doug
>>
>> On Wed, 30 Jan 2008, Jennifer Deegan (nee Clark) wrote:
>>
>>> Hi,
>>>
>>> Doug howe wrote:
>>>
>>>> If even advanced users who work with GA files can't get past the
>>>> distinction between IEA and experimental codes, I have to wonder if 
>>>> they
>>>> are serving any purpose worth their hassle?  By splitting the file we
>>>> are just shielding users from the complexity of the evidence codes and
>>>> allowing them to continue to not understand them.
>>>
>>>
>>>
>>> Just for context, this question came up because a group of advanced 
>>> users at a meeting last year specifically asked us to split out 
>>> electronic annotations and NOT annotations into separate files.
>>>
>>> I think that whilst there are advanced users, and we would like to 
>>> think that they understand our system in all its details, we have to 
>>> accept that users have a lot to do, and many tight deadlines. If we 
>>> know that there are difficult things in the files (such as NOT 
>>> annotations) that might trip people up, then it makes sense that 
>>> there should be an extra step in downloading these just so that they 
>>> notice that they are getting something slightly different.
>>>
>>> The users often ask me for separation of electronic annotations, 
>>> because they do not wholely trust these annotations. We may not 
>>> agree with that assessment, but this lack of trust is common amongst 
>>> the users, and having the separate files just allows them to play it 
>>> safe. In some cases it gets them past a barrier to using the GO at 
>>> all. It also encourages groups to start manual annotation, which has 
>>> to be a good thing.
>>>
>>> Jen
>>>
>


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------------------------------------------------------------------ 

    Emily Dimmer
    GOA Coordinator
    EMBL-EBI
    Wellcome Trust Genome Campus
    Hinxton
    Cambridge CB10 1SD, U.K.
    Tel:     +44 1223 494654
    Fax:    +44 1223 494468
    email:  edimmer at ebi.ac.uk
    URL:    http://www.ebi.ac.uk/goa