Re: [Psidev-ms-dev] PSI controlled vocabularies maintenance

[Matthew C. <mat...@gm...>]

1. I agree there are a lot of ProteomeDiscoverer terms that never should have been added. We already 
discussed it on a conference call. I don't really understand what you're saying after "In my 
opinion" though. The point of the "search engine specific input parameter" hierarchy is to support 
parameters that are unique to a subset of search engines.
3. Glad to hear it.
4. I assume you'll expand the "source descendents" row into one row for each new term? It'll be good 
to review it that way.

We have a psidev-ms-vocab list which is intended for discussing the CV - especially since MS and PI 
CVs merged. This would be easy to enforce on a forum (moderators simply move CV discussions to the 
appropriate subforum), but very easy to get mixed up between 3 mailing lists.

Thanks,
-Matt


On 5/23/2011 12:08 PM, David Ovelleiro wrote:
> Dear all,
>
> As promised in Heidelberg, we're going to start maintaining the addition
> of new terms to the PSI controlled vocabulary.
>
> 1. At this point, and before starting with a new version, or add/change
> anything, I'd like to have clear something: What are we going to do with
> MS:1001302 (“search engine specific input parameter”). This single term
> has 216 direct sons (or descendants, or whatever). More than 70% of them
> are “ProteomeDiscoverer:”. In my opinion, a general “Search engine
> input” makes sense (input parameters used by many search engines, like
> “Precursor tolerance”,...). Not this huge (more than huge, huger...)
> list. But I'd like to hear more opinions about this.
> 2. The last 3 revisions of psi-ms.obo have the same version (2.51.0) and
> release date (2011-04-07). The three have been published between 7th and
> 21st April.
> 3. Today, I've contacted again (second time) the people from UNIT
> ontology. The repository of PATO had changed (and not reflected in the
> UNIT ontology), and made impossible to open the PSI-MS ontology using
> OBO-Edit. Now is fixed.
> 4. When the point 1 is clear and fixed, I'll start to compile the
> changes, publish them in the mail list and, when accepted by everybody,
> I'll generate a new release of the CV. I've generated a non-editable
> list of the changes I'm working with, with three possible estates:
> “Published in mail list”, “Accepted in mail list”, “Rejected in mail
> list” and “Done”. There's a link in the 10th column directing to the
> thread that suggested the CV param. The link to the list (it will be
> bigger in the next days) is (I know... too long):
> https://spreadsheets.google.com/pub?hl=en_US&hl=en_US&key=0Av19CsTVDoOQdENWSmJDS3ZfN2tPdEhaaldzcWVNY3c&output=html
>
> I'd like to have some answer to the first point before starting with a
> new release: is everything OK in the present version?
> And I'd also appreciate that the new CV proposals (at least those I'm
> going to take care) would be sent to the
> psi...@li... and
> psi...@li... lists... why both??? We could use
> only one list (that's the perfect solution for me), but using
> alternatively one or the other is a pain when you try to compile a list
> of new terms.
>
> Best,
>