Re: [Psidev-ms-dev] Reworking the MS vocab

[Randy J. <rkj...@in...>]

All,

I agree with the idea here - while the terms themselves are established 
by an external standards group - there is little or no organization or 
grouping to them.  I thought of doing this in terms of adding 
'connecting' terms - which presumably would be the same as names of the 
bins - or perhaps subdivisions.

In editing names we need to be aware of both practical use as well as 
standardization efforts by other groups.  I think we can decide on 
separator characters, and if there are other editorial ideas we should 
discuss them.

We have gone back and forth between Excel and OBO (and there are many 
who want RDF or OWL).  If putting things back into a spreadsheet helps 
arrive at a better CV then we should do it, as long as the final result 
ends up in some better format than excel.  I got flak for the CV only 
being available as a spreadsheet - or a 'list of terms' when it was 
first posted.

The general action #1 listed below can also be done directly off the OBO 
file using OBO-Edit (from sourceforge), but again whatever works let's 
do it.

As far as #2 is concerned, is there a formal body (like the ASMS or IMS 
or IUPAC) working on FUGO as was done on the MS terms?  I don't think we 
should change central terms of the CV for mzData if they are not drawn 
from an equivalent authority or community.

Unless there are other suggestions, I would recommend having Chris 
proceed and then look at the spreadsheet.

Thanks,
Randy

Chris Taylor wrote:
> 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.
>
> ~~~~~~~~~~~~~~~~~~~~~~~~
>  chr...@eb...
>  http://psidev.sf.net/
> ~~~~~~~~~~~~~~~~~~~~~~~~
>
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