Literature DB >> 19344107

Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles.

Henry Rodriguez1, Mike Snyder, Mathias Uhlén, Phil Andrews, Ronald Beavis, Christoph Borchers, Robert J Chalkley, Sang Yun Cho, Katie Cottingham, Michael Dunn, Tomasz Dylag, Ron Edgar, Peter Hare, Albert J R Heck, Roland F Hirsch, Karen Kennedy, Patrik Kolar, Hans-Joachim Kraus, Parag Mallick, Alexey Nesvizhskii, Peipei Ping, Fredrik Pontén, Liming Yang, John R Yates, Stephen E Stein, Henning Hermjakob, Christopher R Kinsinger, Rolf Apweiler.   

Abstract

Policies supporting the rapid and open sharing of genomic data have directly fueled the accelerated pace of discovery in large-scale genomics research. The proteomics community is starting to implement analogous policies and infrastructure for making large-scale proteomics data widely available on a precompetitive basis. On August 14, 2008, the National Cancer Institute (NCI) convened the "International Summit on Proteomics Data Release and Sharing Policy" in Amsterdam, The Netherlands, to identify and address potential roadblocks to rapid and open access to data. The six principles agreed upon by key stakeholders at the summit addressed issues surrounding (1) timing, (2) comprehensiveness, (3) format, (4) deposition to repositories, (5) quality metrics, and (6) responsibility for proteomics data release. This summit report explores various approaches to develop a framework of data release and sharing principles that will most effectively fulfill the needs of the funding agencies and the research community.

Entities:  

Mesh:

Substances:

Year:  2009        PMID: 19344107      PMCID: PMC2742685          DOI: 10.1021/pr900023z

Source DB:  PubMed          Journal:  J Proteome Res        ISSN: 1535-3893            Impact factor:   4.466


  4 in total

1.  The Proteomics Identifications Database (PRIDE) and the ProteomExchange Consortium: making proteomics data accessible.

Authors:  Henning Hermjakob; Rolf Apweiler
Journal:  Expert Rev Proteomics       Date:  2006-02       Impact factor: 3.940

2.  Guidelines for the next 10 years of proteomics.

Authors:  Marc R Wilkins; Ron D Appel; Jennifer E Van Eyk; Maxey C M Chung; Angelika Görg; Michael Hecker; Lukas A Huber; Hanno Langen; Andrew J Link; Young-Ki Paik; Scott D Patterson; Stephen R Pennington; Thierry Rabilloud; Richard J Simpson; Walter Weiss; Michael J Dunn
Journal:  Proteomics       Date:  2006-01       Impact factor: 3.984

3.  mzML: a single, unifying data format for mass spectrometer output.

Authors:  Eric Deutsch
Journal:  Proteomics       Date:  2008-07       Impact factor: 3.984

4.  International summit on proteomics data release and sharing policy.

Authors:  Henry Rodriguez
Journal:  J Proteome Res       Date:  2008-10-07       Impact factor: 4.466

  4 in total
  27 in total

Review 1.  The tension between data sharing and the protection of privacy in genomics research.

Authors:  Jane Kaye
Journal:  Annu Rev Genomics Hum Genet       Date:  2012-03-09       Impact factor: 8.929

2.  Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles).

Authors:  Christopher R Kinsinger; James Apffel; Mark Baker; Xiaopeng Bian; Christoph H Borchers; Ralph Bradshaw; Mi-Youn Brusniak; Daniel W Chan; Eric W Deutsch; Bruno Domon; Jeff Gorman; Rudolf Grimm; William Hancock; Henning Hermjakob; David Horn; Christie Hunter; Patrik Kolar; Hans-Joachim Kraus; Hanno Langen; Rune Linding; Robert L Moritz; Gilbert S Omenn; Ron Orlando; Akhilesh Pandey; Peipei Ping; Amir Rahbar; Robert Rivers; Sean L Seymour; Richard J Simpson; Douglas Slotta; Richard D Smith; Stephen E Stein; David L Tabb; Danilo Tagle; John R Yates; Henry Rodriguez
Journal:  Mol Cell Proteomics       Date:  2011-11-03       Impact factor: 5.911

3.  Mapping plant interactomes using literature curated and predicted protein-protein interaction data sets.

Authors:  KiYoung Lee; David Thorneycroft; Premanand Achuthan; Henning Hermjakob; Trey Ideker
Journal:  Plant Cell       Date:  2010-04-06       Impact factor: 11.277

4.  The Bermuda Triangle: The Pragmatics, Policies, and Principles for Data Sharing in the History of the Human Genome Project.

Authors:  Kathryn Maxson Jones; Rachel A Ankeny; Robert Cook-Deegan
Journal:  J Hist Biol       Date:  2018-12       Impact factor: 1.326

5.  ProteomeCommons.org collaborative annotation and project management resource integrated with the Tranche repository.

Authors:  James A Hill; Bryan E Smith; Panagiotis G Papoulias; Philip C Andrews
Journal:  J Proteome Res       Date:  2010-06-04       Impact factor: 4.466

Review 6.  Minireview: progress and challenges in proteomics data management, sharing, and integration.

Authors:  Lauren B Becnel; Neil J McKenna
Journal:  Mol Endocrinol       Date:  2012-08-17

7.  The International Cancer Genome Consortium's evolving data-protection policies.

Authors:  Djims Milius; Edward S Dove; Donald Chalmers; Stephanie O M Dyke; Kazuto Kato; Pilar Nicolás; B F Francis Ouellette; Brad Ozenberger; Laura L Rodriguez; Nikolajs Zeps; Yann Joly
Journal:  Nat Biotechnol       Date:  2014-06       Impact factor: 54.908

Review 8.  Quality assessment for clinical proteomics.

Authors:  David L Tabb
Journal:  Clin Biochem       Date:  2012-12-12       Impact factor: 3.281

Review 9.  Bioinformatics and molecular modeling in glycobiology.

Authors:  Martin Frank; Siegfried Schloissnig
Journal:  Cell Mol Life Sci       Date:  2010-04-04       Impact factor: 9.261

10.  The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.

Authors:  Gerhard Mayer; Luisa Montecchi-Palazzi; David Ovelleiro; Andrew R Jones; Pierre-Alain Binz; Eric W Deutsch; Matthew Chambers; Marius Kallhardt; Fredrik Levander; James Shofstahl; Sandra Orchard; Juan Antonio Vizcaíno; Henning Hermjakob; Christian Stephan; Helmut E Meyer; Martin Eisenacher
Journal:  Database (Oxford)       Date:  2013-03-12       Impact factor: 3.451

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.