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

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 NikolskiHolger 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

Research output: Contribution to journalReview article

464 Scopus citations

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).

Original languageEnglish (US)
Pages (from-to)177-183
Number of pages7
JournalNature biotechnology
Volume22
Issue number2
DOIs
StatePublished - Feb 1 2004

ASJC Scopus subject areas

  • Biotechnology
  • Bioengineering
  • Applied Microbiology and Biotechnology
  • Molecular Medicine
  • Biomedical Engineering

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    Hermjakob, H., Montecchi-Palazzi, L., Bader, G., Wojcik, J., Salwinski, L., Ceol, A., Moore, S., Orchard, S., Sarkans, U., Von Mering, C., Roechert, B., Poux, S., Jung, E., Mersch, H., Kersey, P., Lappe, M., Li, Y., Zeng, R., Rana, D., ... Apweiler, R. (2004). The HUPO PSI's Molecular Interaction format - A community standard for the representation of protein interaction data. Nature biotechnology, 22(2), 177-183. https://doi.org/10.1038/nbt926