[Psidev-ms-dev] psi-ms controlled vocabulary: Changes to be made related to mzIdentML if everybody is happy (with the changes)

[David O. <do...@eb...>]

Dear community,

I've done all the changes summarized in the last email about this (sept 
16th). I attach the resultant "obo" (compressed as psi-ms.zip), to give 
the community the opportunity to check things. Please, any feedback will 
be really appreciated. If everybody is fine with this, I'll submit it on 
Thursday.

Summary of changes proposed in the previous mail (see attachment 
"changes.zip"):
- Addition of 9 terms, MS:1001868 to MS:1001876 (q/p/E values to protein 
and peptides -6 first terms-, FDRScore, modification motif and 
modification probability)
- 1 term obsolete (MS:1001191, p-value)
- changed terms: 10 direct changes and 11 "is_a" related changes (5 
terms where "is_a: MS:1001092 ! peptide identification confidence 
metric" and 6 terms where "is_a: MS:1001198 ! protein identification 
confidence metric").

In addition to the changes proposed in the last email, I've taken into 
account in the psi-ms update all the proposal made by Sean Seymour in 
his last email (Sept 24th). Because all the changes are quite 
straightforward and related to Applied Biosystems hardware, and he's 
working in that company, I found no need to postpone more the update of 
the controlled vocabulary. Please, as these changes are included in the 
attached obo file (not in the "changes" log, only related to my last 
email), feel free to check if everything is correct.
Summary of the changes made after proposal by Sean Seymour:
- MS:10006452 -> "-" changed by "/", and "Analyzer" removed
- "AB SCIEX2 removed from MS:1000931, MS:1000932 and MS:1001482 definitions
- MS:1000870 is now obsolete (because was redundant to MS:1000139)
- the "?" has been removed from MS:1000672

Please, comment at discretion.

David

-- 
David Ovelleiro
Bioinformatician
PRIDE Group
Proteomics Services Team, PANDA Group
EMBL European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge, UK
CB10 1SD