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[Psidev-ms-dev] REVISED VERSION R1: PSI recommendation document (file format proBed), 14-days public review
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From: Martin E. <mar...@ru...> - 2017-02-27 16:43:08
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Dear colleague, dear member of the Proteomics community, please forward this message to potentially interested colleagues! I received a revised version (R1) of the proBed format specification: http://www.psidev.info/proBed-in-docproc A responses to reviewers document is also included. It would be great to receive your comments within two weeks (13th March 2017). 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 Von: Martin Eisenacher [mailto:mar...@ru...] Gesendet: Donnerstag, 20. Oktober 2016 11:11 An: psi...@li...; psi...@li...; psi...@li...; ps...@eb...; psi...@eb... Betreff: [Psidev-qc-dev] 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 |
