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CPTAC requests that data users abide by the same principles that were previously established in the Fort Lauderdale and Amsterdam meetings. The recommendations from the Fort Lauderdale meeting (2003) on best practices and principles for sharing large-scale genomic data address the roles and responsibilities of data producers, data users and funders of community resource projects. The aim of the recommendations is to establish and maintain an appropriate balance between the interests that data users have in rapid access to data and the needs that data producers have to publish and receive recognition for their work. The conclusion of the attendees at the Fort Lauderdale meeting was that a “responsible use” approach for secondary data users would be sufficient to ensure that the efforts of data producers will be recognized. “Responsible use” was defined as allowing the data producers to have the opportunity to publish the initial global analyses of the data within a reasonable period of time.
In 2008, the National Cancer Institute organized a workshop to discuss how and when proteomics data should be released. The result was the Amsterdam Principles, that established guidelines for the timing of data release, comprehensiveness of a dataset, data format, deposition to repositories, quality metrics, and responsibility for proteomic data release. Participants agreed that mass spectrometry output data files should be available to support the claims of proteomics publications. In 2010, the National Cancer Institute convened a follow-on workshop to address quality metrics for proteomics, with an emphasis on mass spectrometry. As a sign of solidarity for these principles, four peer-reviewed journals simultaneously published the results.
Agreeing to abide by these principles and the CPTAC Publication Guidelines is required to gain access to CPTAC data.
CPTAC is a community resource project and data are made available rapidly after generation for community research use. To act in accord with the Fort Lauderdale principles and support the continued prompt public release of large-scale proteomic data prior to publication, researchers who plan to prepare manuscripts or presentations involving CPTAC data and journal editors who receive such manuscripts, are encouraged to coordinate their independent reports with CPTAC’s publication schedule. This may be done by contacting the CPTAC network at firstname.lastname@example.org.
CPTAC defines a global analysis publication as the first paper, authored by one or more members of the Clinical Proteomic Tumor Analysis Consortium, which includes analysis of much of the existing CPTAC data on the tumor type or sample set at the time of a data freeze. Specifically, these manuscripts report on the comprehensive, integrated analysis of multiple CPTAC datasets available which may include: global proteome profiling, reverse-phase protein analysis, and profiling on any of the following PTMs: phosphorylation, acetylation, glycosylation, and ubiquitination. Prior to a global analysis publication on a specific tumor type, available data sets should be considered pre-publication data subject to the standard principles of scientific etiquette regarding publication of findings using data obtained from other sources.
The CPTAC program has established the following policy to clarify freedom of CPTAC and non-CPTAC users to publish findings using CPTAC data. There are no limitations on submitting manuscripts to a journal and subsequent publications containing analyses using any CPTAC data set if the data set meets one of the following three freedom-to-publish criteria:
The specific status of each tumor dataset is displayed on the study page.
The CPTAC program requests that publications using data from this program, include the following statement:
“Data used in this publication were generated by the Clinical Proteomic Tumor Analysis Consortium (NCI/NIH).”
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