[Go] generic GO slim question

[David Hill]

It would make sense to have them for at least cellular and multicellular 
organismal, two of the top disjoint categories.


David

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 embarrassingly out-of-date.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
>
>
>   
> ------------------------------------------------------------------------
>
> _______________________________________________
> Go mailing list
> Go at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/go
>   

-- 
David P. Hill, Ph.D.
Bioinformatics Scientist: Ontology Development
Gene Ontology Consortium
The Jackson Laboratory
www.geneontology.org
www.informatics.jax.org
tel:207-288-6430