[Go] generic GO slim question

Tue Jun 16 02:56:33 PDT 2009

Here you go:

http://wiki.geneontology.org/index.php/GO_slim_overhaul

linked to main ontology development page

m

On Tue, 16 Jun 2009, Valerie Wood wrote:

> 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     embarrassingly out-of-date.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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