[Go] generic GO slim question

[Sue Rhee]

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     embarrassingly out-of-date.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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-- 
Sue Rhee
Staff Scientist
Carnegie Institution, Department of Plant Biology
260 Panama Street, Stanford, CA 94305
Phone: (650) 325-1521 x251
Fax: (650) 325-6857

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