molecular interaction database: 2009 update. Nucleic Acids Res., 38, D532–D539. 18. Jensen,L.J., Kuhn,M., Stark,M., Chaffron,S., Creevey,C., Muller,J., Doerks,T., Julien,P., Roth,A., Simonovic,M. et al. (2009) STRING 8–a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res., 37, D412–D416. 19. Overington,J. (2009) ChEMBL. An interview with John Overington, team leader, chemogenomics at the European Bioinformatics Institute Outstation of the European Molecular Biology Laboratory (EMBL-EBI). Interview by Wendy A. Warr. J. Comput. Aided Mol. Des., 23, 195–198. 20. Razick,S., Magklaras,G. and Donaldson,I.M. (2008) iRefIndex: a consolidated protein interaction database with provenance. BMC Bioinformatics, 9, 405. 21. Caspi,R., Altman,T., Dale,J.M., Dreher,K., Fulcher,C.A., Gilham,F., Kaipa,P., Karthikeyan,A.S., Kothari,A., Krummenacker,M. et al. (2010) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res., 38, D473–D479. 22. Mi,H., Dong,Q., Muruganujan,A., Gaudet,P., Lewis,S. and Thomas,P.D. (2010) PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucleic Acids Res., 38, D204–D210. 23. Schaefer,C.F., Anthony,K., Krupa,S., Buchoff,J., Day,M., Hannay,T. and Buetow,K.H. (2009) PID: the Pathway Interaction Database. Nucleic Acids Res., 37, D674–D679. 24. Wu,G., Feng,X. and Stein,L. (2010) A human functional protein interaction network and its application to cancer data analysis. Genome Biol., 11, R53. 25. Chen,F., Mackey,A.J., Stoeckert,C.J. Jr and Roos,D.S. (2006) OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res., 34, D363–D368. 26. Vilella,A.J., Severin,J., Ureta-Vidal,A., Heng,L., Durbin,R. and Birney,E. (2009) EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Res., 19, 327–335. 27. Reference Genome Group of the Gene Ontology Consortium. (2009) The Gene Ontology’s Reference Genome Project: a uniﬁed framework for functional annotation across species. PLoS Comput. Biol., 5, e1000431. Nucleic Acids Research, 2011, Vol. 39, Database issue D697 28. Geer,L.Y., Marchler-Bauer,A., Geer,R.C., Han,L., He,J., He,S., Liu,C., Shi,W. and Bryant,S.H. (2010) The NCBI BioSystems database. Nucleic Acids Res., 38, D492–D496. 29. Demir,E., Cary,M.P., Paley,S., Fukuda,K., Lemer,C., Vastrik,I., Wu,G., D’Eustachio,P., Schaefer,C., Luciano,J. et al. (2010) The BioPAX community standard for pathway data sharing. Nat. Biotechnol., 28, 935–942. 30. Subramanian,A., Kuehn,H., Gould,J., Tamayo,P. and Mesirov,J.P. (2007) GSEA-P: a desktop application for gene set enrichment analysis. Bioinformatics, 23, 3251–3253. 31. Pico,A.R., Kelder,T., van Iersel,M.P., Hanspers,K., Conklin,B.R. and Evelo,C. (2008) WikiPathways: pathway editing for the people. PLoS Biol., 6, e184. 32. Kerrien,S., Orchard,S., Montecchi-Palazzi,L., Aranda,B., Quinn,A.F., Vinod,N., Bader,G.D., Xenarios,I., Wojcik,J., Sherman,D. et al. (2007) Broadening the horizon–level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol., 5, 44. 33. Montecchi-Palazzi,L., Beavis,R., Binz,P.A., Chalkley,R.J., Cottrell,J., Creasy,D., Shofstahl,J., Seymour,S.L. and Garavelli,J.S. (2008) The PSI-MOD community standard for representation of protein modiﬁcation data. Nat. Biotechnol., 26, 864–866. 34. Dutta,S., Burkhardt,K., Young,J., Swaminathan,G.J., Matsuura,T., Henrick,K., Nakamura,H. and Berman,H.M. (2009) Data deposition and annotation at the worldwide protein data bank. Mol. Biotechnol., 42, 1–13. 35. Wiegers,T.C., Davis,A.P., Cohen,K.B., Hirschman,L. and Mattingly,C.J. (2009) Text mining and manual curation of chemical-gene-disease networks for the comparative toxicogenomics database (CTD). BMC Bioinformatics, 10, 326. 36. Irwin,J.J., Shoichet,B.K., Mysinger,M.M., Huang,N., Colizzi,F., Wassam,P. and Cao,Y. (2009) Automated docking screens: a feasibility study. J. Med. Chem., 52, 5712–5720. 37. Wu,C., Orozco,C., Boyer,J., Leglise,M., Goodale,J., Batalov,S., Hodge,C.L., Haase,J., Janes,J., Huss,J.W. 3rd et al. (2009) BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. Genome Biol., 10, R130. 38. Sherry,S.T., Ward,M.H., Kholodov,M., Baker,J., Phan,L., Smigielski,E.M. and Sirotkin,K. (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Res., 29, 308–311.