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Perspective
Nature Biotechnology  22, 177 - 183 (2004)
Published online: 30 January 2004; | doi:10.1038/nbt926

The HUPO PSI's Molecular Interaction format—a community standard for the representation of protein interaction data

Henning Hermjakob1, 22, Luisa Montecchi-Palazzi1, 2, 22, Gary Bader3, Jérôme Wojcik4, Lukasz Salwinski5, Arnaud Ceol2, Susan Moore6, Sandra Orchard1, Ugis Sarkans1, Christian von Mering7, Bernd Roechert8, Sylvain Poux8, Eva Jung9, Henning Mersch1, 10, Paul Kersey1, Michael Lappe1, Yixue Li11, Rong Zeng12, Debashis Rana13, Macha Nikolski19, Holger Husi15, Christine Brun14, K Shanker17, Seth G N Grant15, Chris Sander3, Peer Bork7, Weimin Zhu1, Akhilesh Pandey17, Alvis Brazma1, Bernard Jacq14, Marc Vidal18, David Sherman19, Pierre Legrain4, Gianni Cesareni2, Ioannis Xenarios20, David Eisenberg5, Boris Steipe21, Chris Hogue6, 21 & Rolf Apweiler1

1  European Bioinformatics Institute, EBI-Hinxton, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

2  Department of Biology, University of Rome 'Tor Vergata', Via della Ricerca Scientifica, 00133 Rome, Italy.

3  Computational Biology Center, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, Box 460, New York, New York 10021, USA.

4  Hybrigenics SA, 180 avenue Daumesnil, 75012 Paris, France.

5  Howard Hughes Medical Institute, UCLA-DOE Institute for Genomics and Proteomics, 611 Young Drive East, Los Angeles, California 90095, USA.

6  Samuel Lunenfeld Research Institute, 1060-600 University Avenue, Toronto, Ontario M5G 1X5, Canada.

7  European Molecular Biology Laboratory, Structural and Computational Biology Program, Meyerhofstrasse 1, D−69117, Heidelberg, Germany, and Max Delbrück Center for Molecular Medicine, Department of Bioinformatics, PO Box 740238, 13092 Berlin-Buch, Germany.

8  Swiss Institute for Bioinformatics, CMU-Rue Michel-Servet 1, 1211 Geneva, Switzerland.

9  LG Informatics, Aventis Pharma Deutschland, Königsteiner Strasse 10, 65812 Bad Soden, Germany.

10  Faculty of Technology, University of Bielefeld, Universitätsstrasse 25, D-33615 Bielefeld, Germany.

11  Bioinformation Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 319 Yueyang Road, Shanghai, Peoples Republic of China 200031.

12  Proteomics Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, Peoples Republic of China 200031.

13  Department of Genetics, Cambridge University, Downing Street, Cambridge, CB2 3EH, UK.

14  CNRS Laboratoire de Génétique et Physiologie du Développement−IBDM, 31, chemin Joseph Aiguier, 13402 Marseille, Cedex 9, France.

15  Division of Neuroscience, University of Edinburgh, 1 George Square, Edinburgh EH8 9JZ, UK.

16  Institute of Bioinformatics, International Tech Park, Whitefield Road, 560 066 Bangalore, India.

17  McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University, 600 N. Wolfe Street, Baltimore, Maryland 21287, USA.

18  Dana-Farber Cancer Institute and Department of Genetics, Harvard Medical School, Smith 858, 44 Binney Street, Boston, Massachusetts 02115, USA.

19  Laboratoire Bordelais de Recherche en Informatique CNRS UMR 5800, Domaine Universitaire, 351, cours de la Libération, 33405 Talence Cedex, France.

20  Serono International SA, Chemin des Aulx 14, CH-1228 Plan-les Ouates, Geneva, Switzerland.

21  Departments of Biochemistry and Molecular and Medical Genetics, University of Toronto, Medical Sciences Building, 1 King's College Circle, Toronto M5S 1A8, Canada.

22  These authors have contributed equally to this work.

Correspondence should be addressed to Henning Hermjakob hhe@ebi.ac.uk
A major goal of proteomics is the complete description of the protein interaction network underlying cell physiology. A large number of small scale and, more recently, large-scale experiments have contributed to expanding our understanding of the nature of the interaction network. However, the necessary data integration across experiments is currently hampered by the fragmentation of publicly available protein interaction data, which exists in different formats in databases, on authors' websites or sometimes only in print publications. Here, we propose a community standard data model for the representation and exchange of protein interaction data. This data model has been jointly developed by members of the Proteomics Standards Initiative (PSI), a work group of the Human Proteome Organization (HUPO), and is supported by major protein interaction data providers, in particular the Biomolecular Interaction Network Database (BIND), Cellzome (Heidelberg, Germany), the Database of Interacting Proteins (DIP), Dana Farber Cancer Institute (Boston, MA, USA), the Human Protein Reference Database (HPRD), Hybrigenics (Paris, France), the European Bioinformatics Institute's (EMBL-EBI, Hinxton, UK) IntAct, the Molecular Interactions (MINT, Rome, Italy) database, the Protein-Protein Interaction Database (PPID, Edinburgh, UK) and the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING, EMBL, Heidelberg, Germany).

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