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


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2004-01-30

AUTHORS

Henning Hermjakob, Luisa Montecchi-Palazzi, Gary Bader, Jérôme Wojcik, Lukasz Salwinski, Arnaud Ceol, Susan Moore, Sandra Orchard, Ugis Sarkans, Christian von Mering, Bernd Roechert, Sylvain Poux, Eva Jung, Henning Mersch, Paul Kersey, Michael Lappe, Yixue Li, Rong Zeng, Debashis Rana, Macha Nikolski, Holger Husi, Christine Brun, K Shanker, Seth G N Grant, Chris Sander, Peer Bork, Weimin Zhu, Akhilesh Pandey, Alvis Brazma, Bernard Jacq, Marc Vidal, David Sherman, Pierre Legrain, Gianni Cesareni, Ioannis Xenarios, David Eisenberg, Boris Steipe, Chris Hogue, Rolf Apweiler

ABSTRACT

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). More... »

PAGES

177-183

Journal

TITLE

Nature Biotechnology

ISSUE

2

VOLUME

22

Author Affiliations

  • European Bioinformatics Institute, EBI-Hinxton, Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK
  • Department of Biology, University of Rome 'Tor Vergata', Via della Ricerca Scientifica, 00133, Rome, Italy
  • Computational Biology Center, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, Box 460, 10021, New York, New York, USA
  • Hybrigenics SA, 180 avenue Daumesnil, 75012, Paris, France
  • Howard Hughes Medical Institute, UCLA-DOE Institute for Genomics and Proteomics, 611 Young Drive East, 90095, Los Angeles, California, USA
  • Samuel Lunenfeld Research Institute, 1060-600 University Avenue, M5G 1X5, Toronto, Ontario, Canada
  • Department of Bioinformatics, Max Delbrück Center for Molecular Medicine, PO Box 740238, 13092, Berlin-Buch, Germany
  • Swiss Institute for Bioinformatics, CMU-Rue Michel-Servet 1, 1211, Geneva, Switzerland
  • LG Informatics, Aventis Pharma Deutschland, Königsteiner Strasse 10, 65812, Bad Soden, Germany
  • Faculty of Technology, University of Bielefeld, Universitätsstrasse 25, D-33615, Bielefeld, Germany
  • Bioinformation Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 319 Yueyang Road, 200031, Shanghai, People's Republic of China
  • Proteomics Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, People's Republic of China
  • Department of Genetics, Cambridge University, Downing Street, CB2 3EH, Cambridge, UK
  • Laboratoire Bordelais de Recherche en Informatique CNRS UMR 5800, Domaine Universitaire, 351, cours de la Libération, 33405, Talence, Cedex, France
  • Division of Neuroscience, University of Edinburgh, 1 George Square, EH8 9JZ, Edinburgh, UK
  • CNRS Laboratoire de Génétique et Physiologie du Développement–IBDM, 31, chemin Joseph Aiguier, 13402 Cedex 9, Marseille, France
  • McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University, 600 N. Wolfe Street, 21287, Baltimore, Maryland, USA
  • Dana-Farber Cancer Institute and Department of Genetics, Harvard Medical School, Smith 858, 44 Binney Street, 02115, Boston, Massachusetts, USA
  • Serono International SA, Chemin des Aulx 14, CH-1228 Plan-les Ouates, Geneva, Switzerland
  • Departments of Biochemistry and Molecular and Medical Genetics, University of Toronto, Medical Sciences Building, 1 King's College Circle, M5S 1A8, Toronto, Canada
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/nbt926

    DOI

    http://dx.doi.org/10.1038/nbt926

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1013367542

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/14755292


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