Broadening the horizon - Level 2.5 of the HUPO-PSI format for molecular interactions

BMC Biology

Volumn 5, Issue , 2007, Pages

  Kerrien, Samuel ^a   Orchard, Sandra ^a   Montecchi Palazzi, Luisa ^a   Aranda, Bruno ^a   Quinn, Antony F ^a   Vinod, Nisha ^a   Bader, Gary D ^b,c   Xenarios, Ioannis ^d   Wojcik, Jérôme ^d   Sherman, David ^e   Tyers, Mike ^c   Salama, John J ^c   Moore, Susan ^c,f   Ceol, Arnaud ^g   Chatr Aryamontri, Andrew ^g   Oesterheld, Matthias ^h   Stümpflen, Volker ^h   Salwinski, Lukasz ⁱ   Nerothin, Jason ⁱ   Cerami, Ethan ^j   Cusick, Michael E ^k   Vidal, Marc ^k   Gilson, Michael ^l   Armstrong, John ^m   Woollard, Peter ^m   Hogue, Christopher ^b   Eisenberg, David ⁱ   Cesareni, Gianni ^g   Apweiler, Rolf ^a   Hermjakob, Henning ^a   more..

^a EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^b UNIVERSITY OF TORONTO   (Canada)

^c MOUNT SINAI HOSPITAL   (Canada)

^d MERCK SERONO S A   (Switzerland)

^e UNIVERSITÉ BORDEAUX 1   (France)

^f NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^g UNIVERSITY OF ROME TOR VERGATA   (Italy)

^h INSTITUTE OF EPIDEMIOLOGY   (Germany)

ⁱ UNIVERSITY OF CALIFORNIA   (United States)

^j MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^k HARVARD MEDICAL SCHOOL   (United States)

^l UNIVERSITY OF MARYLAND BIOTECHNOLOGY INSTITUTE   (United States)

^m GLAXOSMITHKLINE   (United Kingdom)

more..

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL AGENT; CHEMICAL COMPOUND; NUCLEIC ACID; PROTEIN;

ACCESS TO INFORMATION; ARTICLE; AUTOMATION, COMPUTERS AND DATA PROCESSING; BIOLOGICAL ACTIVITY; COMPUTER SYSTEM; DATA ANALYSIS; DATA ANALYSIS SOFTWARE; DATA SYNTHESIS; HEALTH CARE ORGANIZATION; INFORMATION PROCESSING; INFORMATION TECHNOLOGY; MOLECULAR COMPUTER; MOLECULAR INTERACTION; MOLECULAR MECHANICS; PROGRAM DEVELOPMENT; PROTEIN ANALYSIS; PROTEIN PROTEIN INTERACTION; REFERENCE DATABASE; BIOLOGY; COMPUTER GRAPHICS; COMPUTER INTERFACE; DATA BASE; METHODOLOGY; NATURAL LANGUAGE PROCESSING; PROTEIN DATABASE; PROTEOMICS; STANDARD;

COMPUTATIONAL BIOLOGY; COMPUTER GRAPHICS; DATABASE MANAGEMENT SYSTEMS; DATABASES, PROTEIN; NATURAL LANGUAGE PROCESSING; PROTEIN INTERACTION MAPPING; PROTEOMICS; USER-COMPUTER INTERFACE;

EID: 35348976204     PISSN: None     EISSN: 17417007     Source Type: Journal    
DOI: 10.1186/1741-7007-5-44     Document Type: Article

References (26)

1. Hermjakob H Montecchi-Palazzi L Bader G Wojcik J Salwinski L Ceol A Moore S Orchard S Sarkans U von Mering C: The HUPO PSI's molecular interaction format - a community standard for the representation of protein interaction data. Nat Biotechnol 2004, 22:177-183. 10.1038/ nbt926 14755292
2. Alfarano C Andrade CE Anthony K Bahroos N Bajec M Bantoft K Betel D Bobechko B Boutilier K Burgess E; The Biomolecular Interaction Network Database and related tools 2005 update. Nucleic Acids Res 2005, 33:D418-424. 540005 15608229 10.1093/nar/gki051
3. Salwinski L Miller CS Smith AJ Pettit FK Bowie JU Eisenberg D; The Database of Interacting Proteins: 2004 update. Nucleic Acids Res 2004, 32:D449-451. 308820 14681454 10.1093/nar/gkh086
4. Kerrien S Alam-Faruque Y Aranda B Bancarz I Bridge A Derow C Dimmer E Feuermann M Friedrichsen A Huntley R: IntAct - open source resource for molecular interaction data. Nucleic Acids Res 2007, 35:D561-565. 1751531 17145710 10.1093/nar/gkl958
5. Chatr-Aryamontri A Ceol A Palazzi LM Nardelli G Schneider MV Castagnoli L Cesareni G; MINT: The Molecular INTeraction database. Nucleic Acids Res 2007, 35:D572-574. 1751541 17135203 10.1093/nar/gkl950
6. Guldener U Munsterkotter M Oesterheld M Pagel P Ruepp A Mewes HW STumpflen V: MPact: the MIPS protein interaction resource on yeast. Nucleic Acids Res 2006, 34:D436-441. 1347366 16381906 10.1093/nar/gkj003
7. Hybrigenics http://www.hybrigenics.fr
8. The HUPO Proteomics Standards Initiative, Molecular Interaction work group http://www.psidev.info/index.php?q=node/60
9. Bradshaw RA Burlingame AL Carr S Aebersold R; Reporting protein identification data: The next generation of guidelines. Mol Cell Proteomics 2006, 5:787-788. 10.1074/mcp.E600005-MCP200 16670253
10. Wilkins MR Appel RD Van Eyk JE Chung MC Gorg A Hecker M Huber LA Langen H Link AJ Paik YK: Guidelines for the next 10 years of proteomics. Proteomics 2006, 6:4-8. 10.1002/pmic.200500856 16400714
11. Jones AR Pizarro A Spellman P Miller M: FuGE Working Group FuGE: Functional Genomics Experiment Object Model. OMICS 2006, 10:179-184. 10.1089/omi.2006.10.179 16901224
12. Open Biomedical Ontologies http://obo.sf.net
13. The IntAct validator http://www.ebi.ac.uk/intact/validator
14. The HUPO Proteomics Standards Initiative http://www.psidev.info
15. BioPAX http://www.biopax.org
16. BioPAX wiki http://www.biopaxwiki.org/cgi-bin/moin.cgi/PSI-MI_Conversion
17. The UniProt Consortium The Universal Protein Resource (UniProt). Nucleic Acids Res 2007, 35:D193-197. 1669721 17142230 10.1093/nar/gkl929
18. ChEBI - Chemical Entities of Biological Interest http://www.oxfordjournals.org/nar/database/summary/646
19. Liu TALin Y Wen X Jorissen RN Gilson MK: BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities. Nucleic Acids Res 2007, 35:D198-201. 1751547 17145705 10.1093/nar/gkl999
20. Cote RG Jones P Apweiler R Hermjakob H: The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries. BMC Bioinformatics 2006, 7:97. 1420335 16507094 10.1186/1471-2105-7-97
21. Shannon P Markiel A Ozier O Baliga NS Wang JT Ramage D Amin N SchwiAowski B Ideker T: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13:2498-2504. 403769 14597658 10.1101/gr.1239303
22. Stark C Breitkreutz BJ Reguly T Boucher L Breitkreutz A Tyers M: BioGRID: A general repository for interaction datasets. Nucleic Acids Res 2006, 34:D535-539. 1347471 16381927 10.1093/nar/gkj109
23. The International Molecular Exchange Consortium(IMEx) http://imex.sf.net
24. Wheeler DL Barrett T Benson DA Bryant SH Canese K Chetvernin V Church DM DiCuccio M Edgar R Federhen S: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2007, 35:D21-22. 1781245 17202161 10.1093/nar/gkl1031
25. Orchard S Salwinski L Kerrien S Montecchi-Palazzi L Oesterheld M Stümpflen V Ceol A Chatr-aryamontri A Armstrong J Woollard P: The Minimum Information required for reporting a Molecular Interaction Experiment (MIMIx). Nat Biotechnol 2007, 25:894-898. 10.1038/nbt1324 17687370
26. Hobson SD Rosenblum ES Richards OC Richmond K Kirkegaard K Schultz SC: Oligomeric structures of poliovirus polymerase are important for function. EMBO J 2001, 20:1153-1163. 145502 11230138 10.1093/emboj/ 20.5.1153