[Go] generic GO slim question

[Jane Lomax]

How about we add GO slims to the agenda for September? Be nice to have a 
GOC-wide decision on what slims we want to maintain, and a set of 
recommendations on how we build them. I the meanwhile Val and I can 
improve the generic GO slim.

Jane

Jane Lomax wrote:
> 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

p: +44 1223 492516
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