[Psidev-ms-dev] Reworking the MS vocab

[Chris T. <chr...@eb...>]

Hi all.

In examining the MS CV (as part of an exercise to evolve the 
Functional Genomics Ontology) I have come across some real 
problems, in terms of naming, use of relationships and overall 
structure. To resolve these issues, and to provide a solid 
working model for gel terms etc. as they come along I'd like to 
propose the following:

[Chris' action #1] I can provide an Excel spreadsheet developed 
by completely flattening the 1.6 OBO and re-binning all the 
terms, editing names etc. as necessary on the fly
[General action #1] People then need to properly scrutinise that 
spreadsheet, to offer opinions on (1) whether the bins 
themselves are sensible and (2) whether the binning is correct.

[Chris' action #2] #1 having been closed as an item, I can then 
provide two things -- a set of terms tightly linked to mzData 
and something approximating a 'proper' ontology (i.e. all 
relationships bulletproof, all terms correct in all senses); 
this ontology will borrow heavily from FuGO's parallel evolution 
(anticipating insertion of those terms there). That having been 
done and signed off on, we can then follow that model for gels etc.

[Chris' action #3, unless someone else wants it...] Ensuring 
that the association between the suggested (assuming all the 
above appeals) 2.0 MS CV and (partial) ontology and all previous 
versions is established and verified, allowing back-propagation 
of terms into old data files (all of which are I think in PRIDE 
only).

I appreciate that some of this is a bit hard to think about 
without examples in hand -- I'm already having a go at my action 
#1 (Excel); the results of this should be available later today 
of anyone wants a look. Whatever though, do please offer an 
opinion on all of the above, so that we can be sure that any 
changes happen sooner rather than later.

Cheers, Chris.

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  chr...@eb...
  http://psidev.sf.net/
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