[Go] generic GO slim question

[Jane Lomax]

That's right - case 2 is more like the the prokaryotic 'subset' we 
currently have. It has over 9000 terms so not really a slim, more like a 
slice. There's probably demand for both, but there is a maintenance 
overhead - more so for the second category.

Jane

Valerie Wood wrote:
> As an example of (1.) fission yeast uses 3361 different terms in 
> total, 3127 of these are used for manual annotation (I was looking at 
> this today) so the 'slim' would be quite 'fat' in this case.
> Val
>
>
> Judith Blake wrote:
>
>> Hi Jim,
>>
>> I think you bring forward the two different approaches to slims....
>>
>>    1. High level terms, typically fewer than 20, that can be used to
>>       look at overall distribution of gene attributes of a genome set.
>>
>>
>> 2. Set of terms that have been used in a particular context... Used 
>> to annotate a prokaryotic protein...as in your example.
>>
>> Something to keep in mind.
>>
>> For me, the first case, with a few high level terms, is a ‘slimming’ 
>> more apparently than the 2nd.
>>
>> Judy
>>
>>
>> On 6/16/09 12:59 PM, "Jim Hu" <jimhu at tamu.edu> wrote:
>>
>>     From what I can tell about the discussions of slims I've heard at
>>     GOC meetings, part of the problem is that maintaining them is an
>>     extra task that no one really has time to do. Which makes me
>>     wonder if slimming can be automated in some way. For example,
>>     anything that is used for a manual annotation of a prokaryote
>>     would go in the prokaryotic slim.
>>
>>     Jim
>>
>>
>>     On Jun 14, 2009, at 4:54 AM, Valerie Wood wrote:
>>
>>
>>         How was it decided which terms to include in the generic GO 
>> slim?
>>
>>         There have been discussions previously about what makes a
>>         useful and relevent generic GO slim (but no agreement).
>>         However, it seems that at the very least the terms should be
>>         i) general, and ii) high level terms which constitute major
>>         cellular processes (and therefore areas of research) should be
>>         included.
>>
>>         So, I was wondering why the following terms are in the slim (I
>>         have included the TOTAL number of annotations for all
>>         organisms in parenthases)
>>
>>         i) plastid translation [1]
>>         ii) lead ion binding [2]
>>         iii) cytoplasmic chromosome [28]
>>         iv) neurotransmitter transporter [55]
>>
>>         Conversely the following biologically important "general"
>>         terms (at least from a single celled organism perprective) ,
>>         are absent from the generic GO slim
>>
>>         i) DNA replication [1685]
>>         ii) DNA repair [1934]
>>         iii) transmembrane transport [814]
>>         iv) ribosome biogenesis [1849]
>>         v) cytokinesis [1049]
>>         vi) cytoskeletal organization [2311]
>>         and others.
>>
>>         In addition, there is an obsolete molecular function term in
>>         the slim (chaperone regulator activity)
>>
>>         I wondered whether the contents of the slim need to be to make
>>         it more useful. I realise it isn't easy to make a slim which
>>         is good for all organisms. If this is the case perhaps we
>>         should consider abandoning the "generic generic" slim and
>>         define more useful individual generic slims for prokaryotes,
>>         eukaryotic unicellular, and multicellular orgs?
>>
>>         We might not agree about the utility of a "generic slim" but
>>         these are used a lot as they are the default slims used by
>>         AmiGO, and the Princeton generic GO term mapper.......They
>>         should provide a good overview of the known biology of any
>>         organism. They should probably provide a starting point for
>>         people who wish to refine to make their own slim and include
>>         more specific terms for their area of interest, and remove
>>         terms which are not useful. I am trying to write a tutorial
>>         which includes how to select terms for a slim to give complete
>>         coverage for their organism, and refine to make a more
>>         specific slim, but the the generic slim doesn't seem to
>>         provide very good example for a starting point.
>>
>>         Val
>>
>>
>>
>>
>>
>>
>
>
>


-- 
Dr Jane Lomax
GO Editorial Office
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire, UK
CB10 1SD

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