[Go] generic GO slim question

[Valerie Wood]

Can we have a Wiki page dedicated to GO slim and put all of these 
suggestions in a list.
I will do it but I don't know the best place for it to live.
Val

Midori Harris wrote:

> On a tangentially related note, we shoud consider making the generic 
> slim(s) is_a-complete. (I brought this up on the ontology editors' 
> list a few month ago, but it fell off the radar.)
>
> m
>
> On Mon, 15 Jun 2009, Sue Rhee wrote:
>
>> It would also be awesome to figure out a way to eliminate 'Other XXX' 
>> from the GO slim terms. I've heard many confusions and complaints 
>> about these from users.
>>
>> Cheers,
>> Sue
>>
>> Judith Blake wrote:
>>
>>> Val,
>>>
>>> I agree with Jane.  It would be excellent if we could provide 
>>> updated slims for 'all' and then a very few subsets.  The question 
>>> would be...
>>>
>>> Eucaryotic/prokaryotic?
>>>
>>> Multi-cellular/single-celled?
>>>
>>> Both? One or the other?
>>>
>>>
>>>
>>> Judy
>>>
>>>
>>> On 6/15/09 11:13 AM, "Jane Lomax" <jane at ebi.ac.uk> wrote:
>>>
>>>     Hi Val - I totally agree with you about the generic GO slim - it's
>>>     embarrassingly out-of-date. I think the problem is partly that
>>>     no-one has
>>>     committed to work on it.
>>>
>>>     Do you have time in the next couple of weeks so you and I can sit
>>>     down and
>>>     at least improve it a bit?
>>>
>>>     I think in the long term seprate multi-cellular 
>>> organism/single-celled
>>>     organism etc slims are the way to go. But think there will 
>>> always be a
>>>     place for a generic slim too.
>>>
>>>     Jane
>>>
>>>
>>>     On Sun, 14 Jun 2009, 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
>>>     f: +44 1223 494468
>>>     _______________________________________________
>>>     Go mailing list
>>>     Go at geneontology.org
>>>     http://fafner.stanford.edu/mailman/listinfo/go
>>>
>>> ------------------------------------------------------------------------ 
>>>
>>>
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>>>
>>
>>
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