Skip Navigation

 

International Summit on Proteomics Data Release and Sharing
Hotel Novotel, Amsterdam, the Netherlands

On August 14, 2008, the National Cancer Institute (NCI) of the National Institutes of Health (NIH) sponsored a summit in Amsterdam that included members from the international proteomics community. The purpose of this workshop was to begin defining policies and practices that would govern the release of proteomics data into the public domain.

Taking part in these discussions were representatives from European Union funding agencies, the NCI/NIH, European Bioinformatics Institute (EBI), The Wellcome Trust, Genome Canada, National Center for Biotechnology Information, National Institute of Standards and Technology, proteomics journals, and many international universities.

This international one-day summit was a major step forward for the proteomics community. It is anticipated that after this process and the release of a white paper that the principles developed at this meeting can be readily adopted by the field as guidelines for releasing and sharing proteomics data.

PDF File Agenda (Size: 35 KB)

Agenda

8:30 a.m. - 8:10 a.m.

Welcome and Review of Agenda
• Meeting background and framework
• Defining the stakeholders (i.e., producers, users, funding agencies, others?)

Henry Rodriguez, Ph.D., M.B.A.
National Cancer Institute, NIH

Rolf Apweiler, M.Sc., Ph.D.
European Bioinformatics Institute
Session: History on Data Standards and Challenges
8:10 a.m. - 8:35 a.m.

Lessons Learned from Genomics
• Current Bermuda Policies on pre-publication data access
• History of a successful policy adoption and implementation

Michael Dunn
The Wellcome Trust
 
8:35 a.m. - 9:00 a.m.

Challenges in Release and Sharing of Mass Spectrometry Data
• MS data formats and analysis workflow
• Quantitative proteomics data and processing methods
• Diversity of software tools and data analysis methods
• Dependence of results on evolving data processing methods

Alexey I. Nesvizhskii, Ph.D.
University of Michigan

9:00 a.m. - 9:25 a.m.

Other Forms of Proteomics Data
• Tissues arrays
• Antibodies
• Images

Fredrik Pontén, M.D., Ph.D.
Uppsala University

Session: Current Standards and Requirements
9:25 a.m. - 9:50 a.m.

Molecular and Cellular Proteomics (MCP Journal)
• “Paris Guidelines” (MCP)
• Implementation and Success of the MCP Guidelines

Robert J. Chalkley
University of California, San Francisco

9:50 a.m. - 10:00 a.m.

Break

10:00 a.m. - 10:25 a.m.

Emerging Standards in Proteomics and European Bioinformatics Institute (EBI) Policies on Data Sharing - HUPO-PSI
• PRIDE (PRoteomics IDEntifications database)
• Other EBI guidelines

Rolf Apweiler, M.Sc., Ph.D.
European Bioinformatics Institute

10:25 a.m. - 10:50 a.m. caBIG®: a Federated Strategy for Proteomics Data
• Interoperability
• Compliance standards

Liming Yang, Ph.D.
National Cancer Institute, NIH
10:50 a.m. - 11:15 a.m.

Repositories (including Formats)
• Successful data sharing at National Center for Biotechnology information (NCBI)
• Standards
• Curation
• Automation

Ron Edgar, Ph.D.
National Center for Biotechnology Information, NIH
11:15 a.m. - 11:55 a.m.

What’s Missing and What Can Be Done To Improve Data Sharing?
• Who wants to use the data?
• Processed results vs. raw data?
• How to integrate with existing data sharing efforts?
• What ‘standards’ are needed (formats, annotation, sequence, …)
• How to deal with evolving experiments and data analysis?
• How to minimize risks of pre-publication sharing?
• How to promote and what to avoid?
• Where data should be stored and made available?

Ronald Beavis, B.Sc., Ph.D.
University of British Columbia
  Group Discussion
11:55 a.m. - 12:55 p.m.

Lunch
Session: Breakout Groups
1:00 p.m. - 3:15 p.m.

Breakout Groups

Group 1: Define metrics for data quality in the context of establishing a threshold as to what data is fit to be shared

Chair: Ronald Beavis, B.Sc., Ph.D.
University of British Columbia

Co-Chair: Stephen E. Stein, Ph.D.
National Institute of Standards and Technology

Group 2: Publishers – How should policies be designed and implemented?

Chair: Mike Snyder
Yale University

Co-Chair: Peter Hare
Nature Biotechnology

Group 3: Protein/Affinity Arrays – What data needs to be shared?

Chair: Albert J.R. Heck
Netherlands Proteomics Centre and Utrecht University

Co-Chair: Fredrik Pontén, M.D., Ph.D.
Uppsala University
3:15 p.m. - 4:00 p.m.

Break
(chair and co-chairs write outcomes for presentation)
4:00 p.m. - 5:30 p.m.

Breakout Groups Report to Meeting Attendees
5:30 p.m. - 5:45 p.m.

Closing Questions/Comments, Action Items
5:45 p.m.

Meeting Adjournment