[Psidev-ms-dev] HUPO PSI recommendation document, PSI Extended FASTA Format (PEFF) 60-days public review

[Sylvie Ricard-B. <syl...@un...>]

Dear colleague, dear member of the Proteomics community,

The HUPO Proteomics Standards Initiative (PSI) develops standards for 
documentation and storage of Proteomics data (see http://www.psidev.info 
for an overview of activities).

The PSI Mass Spectrometry Standards Working Group has submitted to the 
PSI document process a proposal for a PSI standard, the PSI Extended 
FASTA Format (PEFF). With the growing interest in proteogenomics, PEFF 
neatly addresses in a standardized manner the growing problem challenge 
of how to encode and use not just the protein sequences, but also the 
many known annotations on those protein sequences.
After having passed a 30-day review of the PSI steering group with minor 
changes, the proposed document version 1.0.0 DRAFT now goes through 
*60-days public comments and external review phase until* *March 25th, 
2019*).

The specification document and three example files 
(PEFF_Tiny_Valid.peff, SmallTestDB-PEFF1.0.peff and 
PEFF_AnnotID_Insulin_Valid.peff) are attached to this e-mail and are 
available in the PEFF GitHub repository https://github.com/HUPO-PSI/PEFF
Athough not included in this submission bundle, PEFF 1.0 files 
(according to the current draft specification) can already be downloaded 
from the neXtProt knowledge base, 
e.g.ftp://ftp.nextprot.org/pub/current_release/peff/
or through the web interface
https://www.nextprot.org/entry/NX_P00738/ (then select download link in 
upper right and choose PEFF)
https://api.nextprot.org/export/entry/NX_P00738.peff

Furthermore, software supporting PEFF is already being developed. The 
widely used Comet search engine supports the current draft of PEFF as 
described here http://comet-ms.sourceforge.net/release/release_201701/ 
(search on page for PEFF)

We invite both positive and negative comments on the relevance, 
correctness and clarity of the proposal (e.g. is the standard 
comprehensively described and are the examples in agreement with the 
specification?) as a whole or of specific parts of it.

Please feel free to forward this message to potentially interested 
colleagues. There is no requirement that people commenting should have 
had any prior contact with the PSI.

Please send comments by e-mail to syl...@un....

I thank you very much in advance for your valuable time and contribution.

Best regards.

Professor Sylvie RICARD-BLUM - PSI Editor
Pericellular and Extracellular Supramolecular Assemblies
UMR 5246 CNRS - University Lyon 1
Institute of Molecular and Supramolecular Chemistry and Biochemistry
University Claude Bernard Lyon 1, 43 Boulevard du 11 novembre 1918
69622 Villeurbanne Cedex, France
Phone: +33(0)4 72 44 82 32
E-mail: syl...@un...
http://www.icbms.fr
The French Society for Matrix Biology http://www.sfbmec.fr
The International Society for Matrix Biology http://ismb.org