[Psidev-pi-dev] PSI recommendation document (file format proBed), 60-days public review

[Martin E. <mar...@ru...>]

Dear colleague,

dear member of the Proteomics community,

 

this is a short reminder about the ongoing public 

review of the newly suggested PSI format ‘proBed’.

 

PLEASE ADD COMMENTS to the submission page

( <http://www.psidev.info/proBed-in-docproc>
http://www.psidev.info/proBed-in-docproc) 

(or send them directly to martin.eisenacher: at : rub.de).

 

For further details see below.

 

   Many thanks for your valuable time and participation

      Martin Eisenacher (PSI Editor)

 

--

PD DR. MARTIN EISENACHER

Department Leader

DEPARTMENT Medical Bioinformatics

Medizinisches Proteom-Center

Ruhr-University Bochum

Building ZKF E.141 | Universitätsstraße 150 | D-44801 Bochum

Fon +49 (0)234 32-29288 | Fax +49 (0)234 32-14554

E-mail  <mailto:mar...@ru...> mar...@ru...

 <http://www.medizinisches-proteom-center.de/>
www.medizinisches-proteom-center.de

 



 

 

 

Von: psi...@eb... [mailto:psi...@eb...]
Im Auftrag von Martin Eisenacher
Gesendet: Donnerstag, 20. Oktober 2016 11:11
An: psi...@li...;
psi...@li...; psi...@li...;
ps...@eb...; psi...@eb...
Betreff: [Psi-announce] PSI recommendation document (file format proBed),
60-days public review

 

Dear colleague,

dear member of the Proteomics community,

 

please forward this message to potentially interested colleagues!

 

The HUPO Proteomics Standards Initiative (PSI) develops standards 

for documentation and storage of Proteomics data (see 

 <http://www.psidev.info> http://www.psidev.info for an overview of
activities).

 

A recommendation document specifying the proBed file format

has been submitted to the PSI document process.

The submission can be found here:

http://www.psidev.info/proBed-in-docproc

 

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 (end: 19th December 2016).

 

"The format represents systematically the output of proteogenomics

analyses, by mapping peptide identification data retrieved from 

mass spectrometry (MS)-based experiments to the genome."

(see also Cover Letter attached to the submission page)

 

The format is based on the BED format (Browser Extensive Data,

 <https://genome.ucsc.edu/FAQ/FAQformat.html#format1>
https://genome.ucsc.edu/FAQ/FAQformat.html#format1),

developed by the UCSC (University of California, Santa Cruz) team.

 

The public comment period enables the wider community to provide 

feedback on a proposed standard before it is formally accepted, and 

thus is an important step in the standardisation process.

 

PLEASE ADD COMMENTS to the submission page

(http://www.psidev.info/proBed-in-docproc) 

(or send them directly to martin.eisenacher: at : rub.de) for 

 example regarding the following criteria:

 

- That it is well formed – that is, it is presented in accordance with the
templates and is clearly written.

- That it is sufficiently detailed and clearly contains and comprehensively
describes the necessary and sufficient explanation of the format.

- That the examples are in accordance with the specification.> >

 

This message is to encourage you to contribute to the standards

development activity by commenting on the material that is 

available online. We invite both positive and negative comments.

If negative comments are being made, these could be on the relevance, 

clarity, correctness, appropriateness, etc, of the proposal as 

a whole or of specific parts of the proposal.

 

If you do not feel well placed to comment on this document, but 

know someone who may be, please consider forwarding this request. 

There is no requirement that people commenting should have had any 

prior contact with the PSI.

 

    Many thanks for your valuable time and participation

      Martin Eisenacher (PSI Editor)

 

--

PD DR. MARTIN EISENACHER

Department Leader

DEPARTMENT Medical Bioinformatics

Medizinisches Proteom-Center

Ruhr-University Bochum

Building ZKF E.141 | Universitätsstraße 150 | D-44801 Bochum

Fon +49 (0)234 32-29288 | Fax +49 (0)234 32-14554

E-mail  <mailto:mar...@ru...> mar...@ru...

 <http://www.medizinisches-proteom-center.de/>
www.medizinisches-proteom-center.de