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| The HUPOPSI's Molecular Interaction format - a community standard for the representation of protein interaction data |
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| Author(s): Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik R, 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 YX, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SGN, Sander C, Bork P, Zhu WM, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios L, Eisenberg D, Steipe B, Hogue C, Apweiler R |
| Source: NATURE BIOTECHNOLOGY Volume: 22 Issue: 2 Pages: 177-183 Published: FEB 2004 |
| Times Cited: 187 References: 29 |
| 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). |
| Document Type: Article |
| Language: English |
| Reprint Address: Hermjakob, H (reprint author), European Bioinformat Inst, EBI Hinxton, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England |
Addresses:
1. European Bioinformat Inst, EBI Hinxton, Cambridge CB10 1SD, England
2. Univ Roma Tor Vergata, Dept Biol, I-00133 Rome, Italy
3. Mem Sloan Kettering Canc Ctr, Computat Biol Ctr, New York, NY 10021 USA
4. Hybrigen SA, F-75012 Paris, France
5. Univ Calif Los Angeles, Howard Hughes Med Inst, DOE Inst Gen & Prote, Los Angeles, CA 90095 USA
6. Mt Sinai Hosp, Samuel Lunenfeld Res Inst, Toronto, ON M5G 1X5 Canada
7. European Mol Biol Lab, Struct & Computat Biol Program, D-69117 Heidelberg, Germany
8. Max Delbruck Ctr Mol Med, Dept Bioinformat, D-13092 Berlin, Germany
9. Swiss Inst Bioinformat, CH-1211 Geneva, Switzerland
10. LG Informat, Aventis Pharma Deutschland, D-65812 Bad Soden, Germany
11. Univ Bielefeld, Fac Technol, D-33615 Bielefeld, Germany
12. Chinese Acad Sci, Shanghai Inst Biol Sci, Bioinformat Ctr, Shanghai 200031, Peoples R China
13. Chinese Acad Sci, Shanghai Inst Biol Sci, Prote Ctr, Shanghai 200031, Peoples R China
14. Univ Cambridge, Dept Genet, Cambridge CB2 3EH, England
15. CNRS, Lab Genet & Physiol Dev, IBDM, F-13402 Marseille 9, France
16. Univ Edinburgh, Div Neurosci, Edinburgh EH8 9JZ, Midlothian Scotland
17. Inst Bioinformat, Bangalore 560066, Karnataka India
18. Johns Hopkins Univ, McKusick Nathans Inst Genet Med, Baltimore, MD 21287 USA
19. Johns Hopkins Univ, Dept Biol Chem, Baltimore, MD 21287 USA
20. Harvard Univ, Sch Med, Dana Farber Canc Inst, Boston, MA 02115 USA
21. Harvard Univ, Sch Med, Dept Genet, Boston, MA 02115 USA
22. CNRS, Lab Bordelais Rech Informat, UMR 5800, F-33405 Talence, France
23. Serono Int SA, CH-1228 Geneva, Switzerland
24. Univ Toronto, Dept Biochem, Toronto, ON M5S 1A8 Canada
25. Univ Toronto, Dept Mol & Med Genet, Toronto, ON M5S 1A8 Canada |
| Publisher: NATURE PUBLISHING GROUP, 345 PARK AVE SOUTH, NEW YORK, NY 10010-1707 USA |
| Subject Category: Biotechnology & Applied Microbiology |
| IDS Number: 770KT |
| ISSN: 1087-0156 |
| DOI: 10.1038/nbt926 |
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