Database of Interacting Proteins

Database of Interacting Proteins (DIP)
Content
Description protein interaction database
Contact
Research center University of California, Los Angeles
Authors David Eisenberg
Primary citation Xenarios, & al. (2002)[1]
Release date 2002
Access
Website http://dip.doe-mbi.ucla.edu
Miscellaneous
License CC BY-ND 3.0

The Database of Interacting Proteins (DIP) is a biological database which catalogs experimentally determined interactions between proteins.[2][3] It combines information from a variety of sources to create a single, consistent set of protein–protein interactions. The data stored within DIP have been curated, both manually, by expert curators, and automatically, using computational approaches that utilize the knowledge about the protein–protein interaction networks extracted from the most reliable, core subset of the DIP data. The database was initially released in 2002. As of 2014, DIP is curated by the research group of David Eisenberg at UCLA.

DIP can be searched through its web interface; searches may be based on the interactions described in a selected journal article, or interactions supported by experimental evidence, amongst others.[4]

DIP is a member of the International Molecular Exchange Consortium (IMEx),[5] a group of the major public providers of interaction data. Other participating databases include the Biomolecular Interaction Network Database (BIND),[6] IntAct,[7] the Molecular Interaction Database (MINT),[8] MIPS,[9] MPact, and BioGRID.[5] The databases of IMEx work together to prevent duplications of effort, collecting data from non-overlapping sources and sharing the curated interaction data. The IMEx consortium also worked to develop the HUPO-PSI-MI XML format, which is now widely implemented.[5][10]

All of the information within DIP is freely available under a Creative Commons BY-ND 3.0 license.[2]

References

  1. ↑ Xenarios, I; Salwínski, L; Duan, XJ; Higney, P; Kim, SM; Eisenberg, D (Jan 1, 2002). "DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions.". Nucleic Acids Research. 30 (1): 303–5. doi:10.1093/nar/30.1.303. PMC 99070Freely accessible. PMID 11752321.
  2. 1 2 "DIP:Home". http://dip.doe-mbi.ucla.edu. Retrieved 8 September 2014. External link in |website= (help)
  3. ↑ Salwinski, L.; Miller, C. S.; Smith, A. J.; Pettit, F. K.; Bowie, J. U.; Eisenberg, D. (2004). "The Database of Interacting Proteins: 2004 update". Nucleic Acids Research. 32 (90001): D449–D451. doi:10.1093/nar/gkh086. PMC 308820Freely accessible. PMID 14681454.
  4. ↑ "DIP:Search". http://dip.doe-mbi.ucla.edu. Retrieved 8 September 2014. External link in |website= (help)
  5. 1 2 3 Orchard, S.; Kerrien, S.; Abbani, S.; Aranda, B.; Bhate, J.; Bidwell, S.; Bridge, A.; Briganti, L.; Brinkman, F.; Cesareni, G.; Chatr-Aryamontri, A.; Chautard, E.; Chen, C.; Dumousseau, M.; Goll, J.; Hancock, R.; Hannick, L. I.; Jurisica, I.; Khadake, J.; Lynn, D. J.; Mahadevan, U.; Perfetto, L.; Raghunath, A.; Ricard-Blum, S.; Roechert, B.; Salwinski, L.; Stümpflen, V.; Tyers, M.; Uetz, P.; Xenarios, I. (2012). "Protein interaction data curation: The International Molecular Exchange (IMEx) consortium". Nature Methods. 9 (4): 345–350. doi:10.1038/nmeth.1931. PMC 3703241Freely accessible. PMID 22453911.
  6. ↑ Alfarano, C. (17 December 2004). "The Biomolecular Interaction Network Database and related tools 2005 update". Nucleic Acids Research. 33 (Database issue): D418–D424. doi:10.1093/nar/gki051.
  7. ↑ Kerrien, S.; Aranda, B.; Breuza, L.; Bridge, A.; Broackes-Carter, F.; Chen, C.; Duesbury, M.; Dumousseau, M.; Feuermann, M.; Hinz, U.; Jandrasits, C.; Jimenez, R. C.; Khadake, J.; Mahadevan, U.; Masson, P.; Pedruzzi, I.; Pfeiffenberger, E.; Porras, P.; Raghunath, A.; Roechert, B.; Orchard, S.; Hermjakob, H. (24 November 2011). "The IntAct molecular interaction database in 2012". Nucleic Acids Research. 40 (D1): D841–D846. doi:10.1093/nar/gkr1088. PMC 3245075Freely accessible. PMID 22121220.
  8. ↑ Zanzoni, A; Montecchi-Palazzi, L; Quondam, M; Ausiello, G; Helmer-Citterich, M; Cesareni, G (Feb 20, 2002). "MINT: a Molecular INTeraction database.". FEBS Letters. 513 (1): 135–40. doi:10.1016/s0014-5793(01)03293-8. PMID 11911893.
  9. ↑ Guldener, U. (1 January 2006). "MPact: the MIPS protein interaction resource on yeast". Nucleic Acids Research. 34 (90001): D436–D441. doi:10.1093/nar/gkj003. PMC 1347366Freely accessible. PMID 16381906.
  10. ↑ Hermjakob, Henning; Montecchi-Palazzi, Luisa; Bader, Gary; Wojcik, Jérôme; Salwinski, Lukasz; Ceol, Arnaud; Moore, Susan; Orchard, Sandra; Sarkans, Ugis; von Mering, Christian; Roechert, Bernd; Poux, Sylvain; Jung, Eva; Mersch, Henning; Kersey, Paul; Lappe, Michael; Li, Yixue; Zeng, Rong; Rana, Debashis; Nikolski, Macha; Husi, Holger; Brun, Christine; Shanker, K; Grant, Seth G N; Sander, Chris; Bork, Peer; Zhu, Weimin; Pandey, Akhilesh; Brazma, Alvis; Jacq, Bernard; Vidal, Marc; Sherman, David; Legrain, Pierre; Cesareni, Gianni; Xenarios, Ioannis; Eisenberg, David; Steipe, Boris; Hogue, Chris; Apweiler, Rolf. "The HUPO PSI's Molecular Interaction format—a community standard for the representation of protein interaction data". Nature Biotechnology. 22 (2): 177–183. doi:10.1038/nbt926.

External links

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