[Go] generic GO slim question/ and another question

[Valerie Wood]

Hi Jane,

Not in the next few weeks, grant to finish and workshop to write for 
next week (which was why I was faffing with the slims at the weekend!)

Will have time to do this with you afterwards, perhaps in about a month. 
I have already asked SGD some questions about the generic yeast GO slim 
which could possibly  be fed back to the generic slim if they agree with 
the suggestions (when I looked into this more closely the "generic slim" 
appears to be a union of all of the other maintained slims, if this is 
the case I don't know if it sensible....).

On a related note, does anyone know of a  web-based slimming tool which 
shows the number of gene products which are  annotated, but not to any  
term in your slim, and the number which are not annotated to any GO term 
(i.e  root node annotations). I can't distinguish these  with AmiGO or 
Princeton, so I wondered if there was any other tool out there that 
anyone had used.

Val



Jane Lomax 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 embarrassingly out-of-date.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
>>
>>
>>
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>



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