[Go] generic GO slim question

[Judith Blake]

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embarrassingly out-of-date.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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