[Go] generic GO slim question

[Judith Blake]

Hi Jim,

I think you bring forward the two different approaches to slims....


 1.  High level terms, typically fewer than 20, that can be used to look at overall distribution of gene attributes of a genome set.

2.  Set of terms that have been used in a particular context... Used to annotate a prokaryotic protein...as in your example.

Something to keep in mind.

For me, the first case, with a few high level terms, is a 'slimming' more apparently than the 2nd.

Judy


On 6/16/09 12:59 PM, "Jim Hu" <jimhu at tamu.edu> wrote:

>From what I can tell about the discussions of slims I've heard at GOC meetings, part of the problem is that maintaining them is an extra task that no one really has time to do.  Which makes me wonder if slimming can be automated in some way.  For example, anything that is used for a manual annotation of a prokaryote would go in the prokaryotic slim.

Jim


On Jun 14, 2009, at 4:54 AM, 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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