The HUPO PSI's Molecular Interaction format - A community standard for the representation of protein interaction data Journal Article
| Authors: | 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.; Nikolski, M.; Husi, H.; Brun, C.; Shanker, K.; Grant, S. G. N.; Sander, C.; Bork, P.; Zhu, W.; Pandey, A.; Brazma, A.; Jacq, B.; Vidal, M.; Sherman, D.; Legrain, P.; Cesareni, G.; Xenarios, I.; Eisenberg, D.; Steipe, B.; Hogue, C.; Apweiler, R. |
| Article Title: | The HUPO PSI's Molecular Interaction format - A community standard for the representation of protein interaction data |
| 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: | protein expression; review; proteins; proteome; cell function; gene expression; protein; protein binding; user-computer interface; protein interaction; data base; biotechnology; computer language; information processing; proteomics; publication; databases, protein; standard; reference standards; human growth hormone; medical literature; molecular structure; dna microarray; molecular interaction; bioinformatics; computer graphics; protein interaction mapping; software; guidelines; growth hormone receptor; internationality; cells; database systems; natural language processing; information storage and retrieval; database management systems; priority journal; mentha |
| Journal Title: | Nature Biotechnology |
| Volume: | 22 |
| Issue: | 2 |
| ISSN: | 1087-0156 |
| Publisher: | Nature Publishing Group |
| Date Published: | 2004-02-01 |
| Start Page: | 177 |
| End Page: | 183 |
| Language: | English |
| DOI: | 10.1038/nbt926 |
| PROVIDER: | scopus |
| PUBMED: | 14755292 |
| DOI/URL: | |
| Notes: | Nat. Biotechnol. -- Cited By (since 1996):334 -- Export Date: 16 June 2014 -- CODEN: NABIF -- Source: Scopus |
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