[Go] generic GO slim question

[Valerie Wood]

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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