<HTML>
<HEAD>
<TITLE>Re: [Go] generic GO slim question</TITLE>
</HEAD>
<BODY>
<FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN STYLE='font-size:11pt'>Val,<BR>
<BR>
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...<BR>
<BR>
Eucaryotic/prokaryotic?<BR>
<BR>
Multi-cellular/single-celled?<BR>
<BR>
Both? One or the other?<BR>
<BR>
<BR>
<BR>
Judy<BR>
<BR>
<BR>
On 6/15/09 11:13 AM, "Jane Lomax" <<a href="jane@ebi.ac.uk">jane@ebi.ac.uk</a>> wrote:<BR>
<BR>
</SPAN></FONT><BLOCKQUOTE><FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN STYLE='font-size:11pt'>Hi Val - I totally agree with you about the generic GO slim - it's<BR>
embarrassingly out-of-date. I think the problem is partly that no-one has<BR>
committed to work on it.<BR>
<BR>
Do you have time in the next couple of weeks so you and I can sit down and<BR>
at least improve it a bit?<BR>
<BR>
I think in the long term seprate multi-cellular organism/single-celled<BR>
organism etc slims are the way to go. But think there will always be a<BR>
place for a generic slim too.<BR>
<BR>
Jane<BR>
<BR>
<BR>
On Sun, 14 Jun 2009, Valerie Wood wrote:<BR>
<BR>
><BR>
> How was it decided which terms to include in the generic GO slim?<BR>
><BR>
> There have been discussions previously about what makes a useful and relevent<BR>
> generic GO slim (but no agreement). However, it seems that at the very least<BR>
> the terms should be i) general, and ii) high level terms which constitute<BR>
> major cellular processes (and therefore areas of research) should be<BR>
> included.<BR>
><BR>
> So, I was wondering why the following terms are in the slim (I have included<BR>
> the TOTAL number of annotations for all organisms in parenthases)<BR>
><BR>
> i) plastid translation [1]<BR>
> ii) lead ion binding [2]<BR>
> iii) cytoplasmic chromosome [28]<BR>
> iv) neurotransmitter transporter [55]<BR>
><BR>
> Conversely the following biologically important "general" terms (at least<BR>
> from a single celled organism perprective) , are absent from the generic GO<BR>
> slim<BR>
><BR>
> i) DNA replication [1685]<BR>
> ii) DNA repair [1934]<BR>
> iii) transmembrane transport [814]<BR>
> iv) ribosome biogenesis [1849]<BR>
> v) cytokinesis [1049]<BR>
> vi) cytoskeletal organization [2311]<BR>
> and others.<BR>
><BR>
> In addition, there is an obsolete molecular function term in the slim<BR>
> (chaperone regulator activity)<BR>
><BR>
> I wondered whether the contents of the slim need to be to make it more<BR>
> useful. I realise it isn't easy to make a slim which is good for all<BR>
> organisms. If this is the case perhaps we should consider abandoning the<BR>
> "generic generic" slim and define more useful individual generic slims for<BR>
> prokaryotes, eukaryotic unicellular, and multicellular orgs?<BR>
><BR>
> We might not agree about the utility of a "generic slim" but these are used<BR>
> a lot as they are the default slims used by AmiGO, and the Princeton generic<BR>
> GO term mapper.......They should provide a good overview of the known biology<BR>
> of any organism. They should probably provide a starting point for people<BR>
> who wish to refine to make their own slim and include more specific terms<BR>
> for their area of interest, and remove terms which are not useful. I am<BR>
> trying to write a tutorial which includes how to select terms for a slim to<BR>
> give complete coverage for their organism, and refine to make a more specific<BR>
> slim, but the the generic slim doesn't seem to provide very good example for<BR>
> a starting point.<BR>
><BR>
> Val<BR>
><BR>
><BR>
><BR>
><BR>
><BR>
><BR>
><BR>
><BR>
<BR>
--<BR>
Dr Jane Lomax<BR>
GO Editorial Office<BR>
EMBL-EBI<BR>
Wellcome Trust Genome Campus<BR>
Hinxton<BR>
Cambridgeshire, UK<BR>
CB10 1SD<BR>
<BR>
p: +44 1223 492516<BR>
f: +44 1223 494468<BR>
_______________________________________________<BR>
Go mailing list<BR>
<a href="Go@geneontology.org">Go@geneontology.org</a><BR>
<a href="http://fafner.stanford.edu/mailman/listinfo/go">http://fafner.stanford.edu/mailman/listinfo/go</a><BR>
<BR>
</SPAN></FONT></BLOCKQUOTE>
</BODY>
</HTML>