proBed in DocProc [handling editor: Martin Eisenacher]

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:

Comments have been received from two external invited reviewers, and one public commenter. Suggestion to steering group: implementation of minor comments and validator tool for commonly expected errors, 14-days public and external review.

 1.) Original submission (after steering group review):

The attached documents are a new submission of the Recommendation Document for the file format "proBed".

"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)

The format is based on the BED format (Browser Extensive Data, https://genome.ucsc.edu/FAQ/FAQformat.html#format1), developed by the UCSC (University of California, Santa Cruz) team.

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 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.

Attached are the proBed submission cover letter and the specification document in Word and PDF format. Example files are linked here (due to the size of some of them). 3 different example files are provided as requested by the PSI document process, all of them are produced by the same software pipeline (using mzIdentML as the input file format). The authors highlight: "that they are not handcrafted examples, so the software is quite mature already. However, at present, there is no other software that can output the format."

Please add comments (or send them directly to martin.eisenacher: at : rub.de) for example regarding the following criteria:

  1. That it is well formed – that is, it is presented in accordance with the templates and is clearly written.
  2. That it is sufficiently detailed and clearly contains and comprehensively describes the necessary and sufficient explanation of the format.
  3. 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.

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