[Psidev-ms-dev] revised version R1 of HUPO PSI recommendation document (file format proBAM), 3-weeks public review

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

Dear colleague,

dear member of the Proteomics community,

 

meanwhile the authors of the proBAM specification have submitted a revised
version, 

also reacting on the reviewers’ comments.

Attached are the revised specification document and a file with responses to
all

reviewers’ comments.

 

Also, all necessary information can be found on
http://www.psidev.info/proBAM, 

including links to the documents and example files (accommodating all the 

implemented changes suggested by the reviewers).

 

If you want to comment on the revised version, leave a comment on the web
page

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

or e-mail me until November 15th.

 

  Many thanks for your work

     Martin

 

--

PD DR. MARTIN EISENACHER

Department Leader

DEPARTMENT Medical Bioinformatics

Medizinisches Proteom-Center

Ruhr-University Bochum

Building ZKF 0.056 | 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: Martin Eisenacher [mailto:mar...@ru...] 
Gesendet: Donnerstag, 30. März 2017 09:50
An: 'psi...@li...'
<psi...@li...>; 'psi...@li...'
<psi...@li...>; 'psi...@li...'
<psi...@li...>; 'ps...@eb...'
<ps...@eb...>; 'psi...@eb...' <psi...@eb...>
Betreff: HUPO PSI recommendation document (file format proBAM), 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 for an overview of activities).

 

A recommendation document specifying the proBAM file format

has been submitted to the PSI document process.

The submission can be found here:

http://www.psidev.info/proBAM-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: 31st May 2017).

 

The format represents output from proteogenomic studies,

mapping the MS-based proteomics PSM information to 

the genome. Background: The proBAM format builds upon the structure of the

original SAM/BAM format (http://samtools.github.io/hts-specs/SAMv1.pdf)

by extending it with other mandatory fields to accommodate unique features

on MS-based proteomics peptide-spectrum matches (PSMs) information.

 

PLEASE ADD COMMENTS to the submission page

(http://www.psidev.info/proBAM-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