[Go] generic GO slim question

[Midori Harris]

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     embarrassingly out-of-date.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
>>     _______________________________________________
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