PSI Editors

mzIdentML 1.2 in DocProc [handling editor: Sylvie Ricard-Blum]

The consultation process is now complete. To see the final specifications, see the mzIdentML page

 

************** Document Process completed in March 2017 ******************

A modififed specification of the mzIdentML recommendation document was submitted to the PSI document process. It contains significant adjustments and is therefore version 1.2.

Please review the updated specification document below 30 days and send any corrections or comments to the handling editor sylvie.ricard-blum:A T:univ-lyon1.fr.

mzQuantML 1.0.1 in DocProc [handling editor: Martin Eisenacher]

A modififed specification of the mzQuantML recommendation document was submitted to the PSI document process including the encoding of SRM quantification results. After careful consideration and discussion with the submitters I think it is minor and therefore version 1.0.1 (if you disagree, especially if existing software is made incompatible, please give me a note).

Please review the updated specification document below WITHIN TWO WEEKS and send any corrections or comments until April 12th to the handling editor martin.eisenacher<AT>rub.de.

PSI-MI XML 3.0.0 in DocProc [handling editor: Martin Eisenacher]

 1.) Original submission (after steering group review)

There has been a submission to the PSI Document Process by the Molecular Interactions workgroup updating the PSI-MI format to version 3.0.0 (from long-time stable XML 2.5, released 2005).

After having passed a review of the PSI steering group with minor changes, the proposed document version 3.0.0 DRAFT now goes through 60-days public comments and external review phase (end: 29th September 2017).

proBed in DocProc [handling editor: Martin Eisenacher]

acceptance: final version 1.0.0 as of March 13th, 2017 (was announced April 13th, 2017)

3.) R1 submission

The attached documents are a revised submission of the Recommendation Document for the file format "proBed". A "responses to reviewers" document is also included. This now goes through a 14-days review phase (public and already invited reviewers, end: 13th March 2017) .

2.) Suggestion after receiving invited and public reviews:

mzQuantml in DocProc (revised version 1.0.0_rc3) [acting handling editor: Pierre-Alain Binz]

The initial mzQuantML specifications were submitted to the PSI process in Nov 2011, as a version 1.0-rc1 release. External reviews were received and acted upon. An internal rc2 release was made, and a manuscript describing the rc2 release, submitted in parallel for (potential) journal publication. Here we report the re-submission of the mzQuantML version1.0-rc3 release, which, it is hoped, will be accepted as a stable standard, and moved to version 1.0 final status shortly.

History of PSI DocProc submissions

(report missings or errors to martin.eisenacher:at:rub.de)

mzML [handling editors: Norman Paton / Christian Stephan]
final (ver 1.0.0): June 1st, 2008
update, begin of public and external review phase: April 17th, 2009
update, final (ver 1.1.0): June 1st, 2009
without DocProc?: update of index wrapper schema (ver 1.1.1.): June 1st, 2010

MIAPE Column Chromatography [handling editor: Norman Paton]

PEFF community practice document [handling editor: Norman Paton]
submission (v1.0-1): August 14th, 2008

MIAPE Gel Informatics [handling editor: Norman Paton]

AnalysisXML / mzIdentML [handling editors: Norman Paton / Christian Stephan]
begin of external and public review (AnalysisXML): February 27th, 2009
final (mzIdentML ver 1.0.0): < August 13th, 2009
update, final (mzIdentML ver 1.1.0): September 12th, 2011

mzIdentML 1.2 [handling editor: Sylvie Ricard-Blum]
submission: July 27th, 2016


PSI-PAR [handling editor: Christian Stephan]
begin of external and public review: April 7th, 2009
final: < August 13th, 2009

TraML [handling editor: Christian Stephan]

mzQuantML [first handling editor: Christian Stephan]
submitted (ver 1.0.0-rc1): August 2011
begin of external and public review: December 12th, 2011
end of external and public review: Feb / March 2012?
[acting handling editor from Nov 2012 onwards, Pierre-Alain Binz]
resubmission (ver 1.0.0-rc2): June 2012
resubmission (ver 1.0.0-rc3) in response to minor corrections
final release (ver 1.0.0): February 2nd, 2013

mzQuantML 1.0.1 [handling editor: Martin Eisenacher]
submission: March 19th, 2015
consideration of changes, decision: minor update from 1.0.0 to 1.0.1
begin of 14-days public comment phase: March 27th, 2015
deadline for corrections and comments: April 12th, 2015
incorporation of minor comments: April 2015
finalization of specification document / migration of files to github / specification document available: October 2015
final announcement via mailing list: January 2016

MIAPE-MS update type b [handling editor: Martin Eisenacher]
submission (ver 2.97.8): before April 2012
begin of external and public review: June 4th, 2012
(comments received from two invited reviewers and two journal editors as public reviewers)
end of external and public review: July 16th, 2012
revision (version 2.98): July 24th, 2012
final (version 2.98): August 15th, 2012

MIAPE-Quant [handling editors: Christian Stephan / Martin Eisenacher]
submission of version 0.9.1
begin of external and public review: February 22nd, 2012
(July 2012: prolongation of public and external review due to web page problems and lack of reviews)
(comments received from two invited and one public reviewer => major revisions)
end of external and public review: August, 14th, 2012
major revision (version 0.9.2_RC) sent into shortend "14 day public review": September 17th, 2012
accepted: October 18th, 2012; final version 1.0 released on October 24th, 2012)

mzTab [handling editor: Martin Eisenacher]
submission: June 7th, 2012
end steering commitee review: August 1st, 2012
begin of external and public review: August 13th, 2012
(comments received from two invited reviewers, one steering committee member, and two public commenters  => major revision)
end of external and public review: November 5th, 2012 (was prolonged, first deadline: October 12th, 2012)

begin of 14-days-resubmission R2 external and public review: March 10th, 2013
end of 14-days-resubmission R2 external and public review: March 24th, 2013
(comments received from two invited reviewers, one steering committee member, and four public commenters  => minor revision, then Final after Editor approval)

re-submission of R3: December 2013 (unexpected restructuring => previous decision changed to major revision and 30-days public and external review)
begin of 30-days-resubmission R3 external and public review: after Christmas break 2014
end of 30-days-resubmission R3 external and public review: April 4th, 2014 (prolonged twice, first deadline: February 14th, 2014)
(comments received from one invited reviewers and three of the previous commenters  => minor revision, wait for changes due to journal reviewers, then Final after Editor Approval)

re-submission of R4: June 20th, 2014 (minor changes after DocProc review and journal review)
After inspection of changes by PSI editor recommendation to the steering committee on August 20th, 2014: accept the mzTab specification R4 without further changes.
acceptance: September 2nd, 2014 (final version 1.0.0 as of June 20th, 2014 was announced September 15th, 2014)

proBED [handling editor: Martin Eisenacher]
original submission: July 7th, 2016
end of steering commitee review: August 22nd, 2016 (minor changes requested)
begin of 60-days public and invited review phase: October 20th, 2016
end of 60-days public and invited review: December 19th, 2016
(comments received from two invited reviewers and one public commenter => request: implementation of minor comments and validator tool for commonly expected errors, then 14-days public and invited review)
begin of 14-days-resubmission R1 public and invited review: February 27th, 2017
deadline for 14-days-resubmission R1 public and invited review: March 13th, 2017
acceptance: final version 1.0.0 as of March 13th, 2017 (was announced April 13th, 2017)

proBAM [handling editor: Martin Eisenacher]
original submission: December 21th, 2016
end of steering commitee review: February 13th, 2017 (minor changes requested, to be implemented before public review phase)
begin of 60-days public and invited review: March 30th, 2017
end of 60-days public and invited review: May 31st, 2017
(comments received from three invited reviewers and one public commenter, suggestion to steering group: implementation of major changes, then 3-weeks public and re-invitation of reviewers for revised version)
begin of 3-weeks-resubmission R1 public and invited review: October 25th, 2017
end of 3-weeks-resubmission R1 public and invited review: November 15th, 2017

PSI-MI XML 3.0 [handling editor: Martin Eisenacher]
original submission: June 7th, 2017
end of steering commitee review: July 19th, 2017 (shortened SG review) (minor changes requested, to be implemented before public review phase)
begin of 60-days public and invited review: July 28th, 2017
end of 60-days public and invited review: October 17th, 2017
(comments received from three invited reviewers =>
request: “minor changes” from the authors which the editor will review after resubmission - no further review by invited reviewers and the public)

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MIAPE Quant in DocProc [handling editors: Christian Stephan / Martin Eisenacher]

Submission of Major Revision :

After considering the comments of one public and two invited reviewers attached is a revised version 0.9.2_RC of MIAPE-Quant (plus answers to reviewers and updated examples). 

It goes through two weeks of further review, which will be viewed and editored after 8th October 2012. Please send any comments about the changes to martin.eisenacher:at:rub.de or add comments to this page.

Major Revision accepted on 18th October 2012; Final version 1.0 published on 24th October 2012).

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