[Psidev-ms-dev] Pending changes in PSI-MS controlled vocabulary (CV terms for mzIdentML)

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

Dear community,

I'm going to try to summarize the pending changes in the controlled 
vocabulary, related to mzIdentML. The final list was sent by Martin 
(Sept 9th) and some suggestions and changes proposals where made:
- Martin sent a list with several terms to be added to the cv: 6 term 
about protein/peptide p/q/e-values, 1 term about FDRScore, 4 terms about 
modification specificity peptide/protein Ct/Nt, 1 term about 
modification motif and 1 term about modification probability
- in Martin proposal we found the obsolescence of the previous terms 
about modification specificity Nt/Ct, and in addition, the obsolescence 
of the term about p-value (now split into peptide and protein terms)
- in Martin proposal, changes in 8 terms where also proposed, mainly 
related, but not limited, to adding some children under  p/q/e-values
- Matt and David (me), showed some concern about obsoleting the previous 
modification specificity terms. No further discussion was maintained 
about this.
- Pierre-Alain proposed some changes in the definitions. First, 
"Peptide/Protein identification confidence metric q,p,e value and 
FDRScore" instead of "Quality measurement" or "Quality estimation" 
(having then something like "q-value for peptides"-> def: 
"Identification confidence metric q-value for peptides." instead of 
"Quality measurement q-value for peptides.", if I've understood 
correctly). This change would also mean changing the definition of the 
parents (e.g. in MS:1001092 we would have "peptide identification 
confidence metric"  instead of "peptide quality estimation measure"). 
Secondly, Pierre-Alain proposed replacing "modification" by "amino acid 
residue modification" (I've changed "amino-acid" by "amino acid" for 
consistency shake in the whole controlled vocabulary). In third place, 
Pierre-Alain also proposed changing "unknown modifications" to "unknown 
amino acid residue modification" in MS:1001460.

Here, what I'm going to do about this, if you agree:
- It seems to me that enough consensus have been reached about the 6 
terms in Martin's proposal about protein/peptide p/q/e-values, 1 term 
about FDRScore, the 1 term about modification motif and the 1 term about 
modification probability. If there's no more comments about this, in a 
couple of days, I'll add these terms to the c.v.
- It also seems that the 8 changes in Martin's proposal are agreed: If 
there's no more comments about this in a couple of days, I'll add these 
terms to the c.v.
- All the changes proposed by Pierre-Alain seem reasonable to me and 
nobody objected: I'll change things in proper places in the coming new 
version (please, check the example of change that I've written before). 
If anybody has something to say about this, please, be quick! (I'm 
planing doing this in a couple of working days).
- About the proposed changes related to modifications specificity, I'll 
wait until we have more comments and consensus. We are talking here 
about 2 obsolescences and 4 new terms.

Best,
david




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