[Go] generic GO slim question "other XXX"

[Valerie Wood]

At present the AmiGO or Princeton slimmer do not provide a way to 
distinguish between unslimmed but annotated and root node (unannotated) 
gene products. You need this information to evaluate how good the 
coverage of your slim is.

At present I don't think any of the available slims give complete 
coverage of annotated process terms (I havn't looked at other aspects)

I will continue anything else to the Wiki.

Val


Sue Rhee wrote:

> 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.
>
> Cheers,
> Sue
>
> 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     embarrassingly out-of-date.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
>>     _______________________________________________
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>>
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>>
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>>
>
>-- 
>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
>



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