The NCI's Office of Cancer Clinical Proteomics Research (OCCPR) is leading international efforts to address a considerable obstacle to the field: the lack of widely followed policies governing the rapid release of large-scale proteomic data into the public domain. By emulating the power of the Human Genome Project (HGP) of having community resources of high-quality data, the office has been pushing efforts to accelerate similar efforts in proteomics. As a result, on August 14, 2008, the NCI sponsored an international summit in The Netherlands that included members from the research community, funding agencies (e.g. NIH), policy makers, and industry to define what it will take to have proteomics data released into the public domain as soon as they are produced.
The outcome of this summit, the Amsterdam Principles, provides recommendations for rapid proteomics data release and sharing policies that are similar to the Bermuda Principles, a series of standardized data sharing policies that served as a catalyst in the world of genomics. It was agreed that, at a minimum, what the community both wants and needs is high quality, well-annotated raw data. Access to these data will require the proper infrastructure: community-supported standardized formats, controlled vocabularies and ontologies, minimal reporting requirements, and publicly available online repositories. The release of such data would put the pace of proteomic research on a trajectory similar to that seen in genomics research.
The Amsterdam Principles include guidelines for the following:
The Amsterdam Principles White Paper: Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: The Amsterdam Principles. Journal of Proteome Research 2009; 8: 3689-3692.
To further the advance made in the initial meeting a follow-up meeting was held in Sydney, Australia in September 2010. The meeting addressed questions about establishing standards to ensure the quality of the data, particularly those developed with a technique known as mass spectrometry.
The international workshop included extramural researchers who produce and use proteomics data, managers of database repositories, editors of scientific journals, and representatives of funding agencies. Participants were asked: “How good is good enough, when it comes to the quality of mass spectrometry-based proteomic data?”
The answers to this question would form “the quality criteria for shared data” and would benefit both producers and users of proteomic data, wrote the authors of a meeting report that has were published simultaneously in four peer-reviewed journals. To read this article and find out more about the recommendations click here.
Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles). Molecular Cellular Proteomics 2011;10.12.
Share the Data: Making Large-Scale Proteomics Data Widely Available. Bio-IT World. Published online Aug 25, 2010.
Prepublication data sharing. Nature. 2009 Sep 10;461(7261):168-70.
Sharing The Wealth Of Data. Scientific American worldVIEW. 2008 May.
Opening up Rosetta. SciBX; 2(14); doi:10.1038/scibx.2009.561. Published online April 9 2009.
International Summit on Proteomics Data Release and Sharing Policy. J. Proteome Res.; 2008 Nov; 7(11) pp 4609 - 4609; (Editorial) [Epub 2008 Oct 7]