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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.<br>
<br>
Cheers,<br>
Sue<br>
<br>
Judith Blake wrote:
<blockquote cite="mid:C65BEA9D.78EF%25judith.blake@jax.org" type="cite">
<title>Re: [Go] generic GO slim question</title>
<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 moz-do-not-send="true"
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embarrassingly out-of-date.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>
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</span></font></blockquote>
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<br>
<pre class="moz-signature" cols="100">--
Sue Rhee
Staff Scientist
Carnegie Institution, Department of Plant Biology
260 Panama Street, Stanford, CA 94305
Phone: (650) 325-1521 x251
Fax: (650) 325-6857</pre>
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