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

Item Type:Article
Title:The HUPO PSI's Molecular Interaction format - a community standard for the representation of protein interaction data
Creators Name:Hermjakob, H. and Montecchi-Palazzi, L. and Bader, G. and Wojcik, R. and Salwinski, L. and Ceol, A. and Moore, S. and Orchard, S. and Sarkans, U. and von Mering, C. and Roechert, B. and Poux, S. and Jung, E. and Mersch, H. and Kersey, P. and Lappe, M. and Li, Y.X. and Zeng, R. and Rana, D. and Nikolski, M. and Husi, H. and Brun, C. and Shanker, K. and Grant, S.G.N. and Sander, C. and Bork, P. and Zhu, W.M. and Pandey, A. and Brazma, A. and Jacq, B. and Vidal, M. and Sherman, D. and Legrain, P. and Cesareni, G. and Xenarios, L. and Eisenberg, D. and Steipe, B. and Hogue, C. and Apweiler, R.
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).
Keywords:Database Management Systems, Guidelines, Information Storage and Retrieval, Internationality, Natural Language Processing, Protein Binding, Protein Databases, Protein Interaction Mapping, Proteins, Proteomics, Reference Standards, Software, User-Computer Interface
Source:Nature Biotechnology
Publisher:Nature Publishing Group
Page Range:177-183
Date:1 January 2004
Official Publication:https://doi.org/10.1038/nbt926
PubMed:View item in PubMed

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