[Go] generic GO slim question

[Jim Hu]

Including interleaved terms - I am guessing this means parents of the  
terms used for the annotations - would it be correct to think of  
Slices/Subsets as unions and Slims as intersections?  If yes, then I  
think it could be automated, at least as a test to see if the result  
is something that matches expectations.  Was this not formalized when  
the slims were first created?

Jim

On Jun 17, 2009, at 8:56 AM, Judith Blake wrote:

> Maybe we should distinguish ‘slim’ from ‘slice’
>
> Slim:  High level grouping terms
>
> Slice:  Set of all terms (and interleaved terms?) that have been  
> used in annotation for some subset of organisms.
>
> ????
>
> Judy
>
>
> On 6/17/09 6:43 AM, "Jane Lomax" <jane at ebi.ac.uk> wrote:
>
> That's right - case 2 is more like the the prokaryotic 'subset' we
> currently have. It has over 9000 terms so not really a slim, more  
> like a
> slice. There's probably demand for both, but there is a maintenance
> overhead - more so for the second category.
>
> Jane
>
> Valerie Wood wrote:
> > As an example of (1.) fission yeast uses 3361 different terms in
> > total, 3127 of these are used for manual annotation (I was looking  
> at
> > this today) so the 'slim' would be quite 'fat' in this case.
> > Val
> >
> >
> > Judith Blake wrote:
> >
> >> Hi Jim,
> >>
> >> I think you bring forward the two different approaches to slims....
> >>
> >>    1. High level terms, typically fewer than 20, that can be used  
> to
> >>       look at overall distribution of gene attributes of a genome  
> set.
> >>
> >>
> >> 2. Set of terms that have been used in a particular context... Used
> >> to annotate a prokaryotic protein...as in your example.
> >>
> >> Something to keep in mind.
> >>
> >> For me, the first case, with a few high level terms, is a  
> ‘slimming’
> >> more apparently than the 2nd.
> >>
> >> Judy
> >>
> >>
> >> On 6/16/09 12:59 PM, "Jim Hu" <jimhu at tamu.edu> wrote:
> >>
> >>     From what I can tell about the discussions of slims I've  
> heard at
> >>     GOC meetings, part of the problem is that maintaining them is  
> an
> >>     extra task that no one really has time to do. Which makes me
> >>     wonder if slimming can be automated in some way. For example,
> >>     anything that is used for a manual annotation of a prokaryote
> >>     would go in the prokaryotic slim.
> >>
> >>     Jim
> >>
> >>
> >>     On Jun 14, 2009, at 4:54 AM, 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
>
>

=====================================
Jim Hu
Associate Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054


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