Abstract
Reactome (www.reactome.org) is a curated database describing very diverse biological processes in a computationally accessible format. The data is provided by experts in the field and subject to a peer review process. The core unit of the Reactome data model is the reaction. The entities participating in reactions form a network of biological interactions. Reactions are grouped into pathways. Reactome data are cross-referenced to a wide selection of publically available databases (such as UniProt, Ensembl, GO, PubMed), facilitating overall integration of biological data. In addition to the manually curated, mainly human reactions, electronically inferred reactions to a wide range of other species, are presented on the website. All Reactome reactions are displayed as arrows on a Reactionmap. The Skypainter tool allows visualisation of user-supplied data by colouring the Reactionmap. Reactome data are freely available and can be downloaded in a number of formats.
An erratum to this chapter can be found at http://dx.doi.org/10.1007/11915034_125.
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References
Human Genome Program, U.S. Department of Energy, Genomics and Its Impact on Science and Society: A 2003 Primer (2003)
Wu, C.H., Apweiler, R., Bairoch, A., Natale, D.A., Barker, W.C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M., Martin, M.J., Mazumder, R., O’Donovan, C., Redaschi, N., Suzek, B.: The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucl. Acids Res. 34, D187–D191 (2006); Reactome – A Knowledgebase of Biological Pathways 719
Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., Harris, M.A., Hill, D.P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J.C., Richardson, J.E., Ringwald, M., Rubin, G.M., Sherlock, G.: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25–29 (2000)
Birney, E., Andrews, D., Caccamo, M., Chen, Y., Clarke, L., Coates, G., Cox, T., Cunningham, F., Curwen, V., Cutts, T., Down, T., Durbin, R., Fernandez-Suarez, X.M., Flicek, P., Graf, S., Hammond, M., Herrero, J., Howe, K., Iyer, V., Jekosch, K., Kahari, A., Kasprzyk, A., Keefe, D., Kokocinski, F., Kulesha, E., London, D., Longden, I., Melsopp, C., Meidl, P., Overduin, B., Parker, A., Proctor, G., Prlic, A., Rae, M., Rios, D., Redmond, S., Schuster, M., Sealy, I., Searle, S., Severin, J., Slater, G., Smedley, D., Smith, J., Stabenau, A., Stalker, J., Trevanion, S., Ureta-Vidal, A., Vogel, J., White, S., Woodwark, C., Hubbard, T.J.: Ensembl. Nucl. Acids Res. 34, D556–561 (2006)
Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y., Hattori, M.: The KEGG resource for deciphering the genome. Nucl. Acids Res. 32, D277–280 (2004)
Chen, F., Mackey, A.J., Stoeckert Jr., C.J., Roos, D.S.: OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucl. Acids Res. 34, D363–368 (2006)
Li, L., Stoeckert Jr., C.J., Roos, D.S.: OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13, 2178–2189 (2003)
Hucka, M., Finney, A., Sauro, H.M., Bolouri, H., Doyle, J.C., Kitano, H., Arkin, A.P., Bornstein, B.J., Bray, D., Cornish-Bowden, A., Cuellar, A.A., Dronov, S., Gilles, E.D., Ginkel, M., Gor, V., Goryanin, I.I., Hedley, W.J., Hodgman, T.C., Hofmeyr, J.H., Hunter, P.J., Juty, N.S., Kasberger, J.L., Kremling, A., Kummer, U., Le Novere, N., Loew, L.M., Lucio, D., Mendes, P., Minch, E., Mjolsness, E.D., Nakayama, Y., Nelson, M.R., Nielsen, P.F., Sakurada, T., Schaff, J.C., Shapiro, B.E., Shimizu, T.S., Spence, H.D., Stelling, J., Takahashi, K., Tomita, M., Wagner, J., Wang, J.: The Systems Biology Markup Language (SBML): A Medium for Representation and Exchange of Biochemical Network Models. Bioinformatics 19, 524–531 (2003)
Caspi, R., Foerster, H., Fulcher, C.A., Hopkinson, R., Ingraham, J., Kaipa, P., Krummenacker, M., Paley, S., Pick, J., Rhee, S.Y., Tissier, C., Zhang, P., Karp, P.: MetaCyc: A multiorganism database of metabolic pathways and enzymes. Nucl. Acids Res. 34, D511–D516 (2006)
Romero, P., Wagg, J., Green, M.L., Kaiser, D., Krummenacker, M., Karp, P.D.: Computational prediction of human metabolic pathways from the complete human genome. Genome Biol. 6, R2 (2005)
Karp, P.D., Riley, M., Paley, S.M., Pelligrini-Toole, A.: EcoCyc: an encyclopedia of Escherichia coli genes and metabolism. Nucl. Acids Res. 24, 32–39 (1996)
Mi, H., Lazareva-Ulitsky, B., Loo, R., Kejariwal, A., Vandergriff, J., Rabkin, S., Guo, N., Muruganujan, A., Doremieux, O., Campbell, M.J., Kitano, H., Thomas, P.D.: The PANTHER database of protein families, subfamilies, functions and pathways. Nucl. Acids Res. 33, D284–D288 (2005)
Dahlquist, K.D., Salomonis, N., Vranizan, K., Lawlor, S.C., Conklin, B.R.: GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nat. Genet. 31, 19–20 (2002)
Bader, G.D., Betel, D., Hogue, C.W.: BIND: the Biomolecular Interaction Network Database. Nucl. Acids Res. 31, 248–250 (2003)
Zanzoni, A., Montecchi-Palazzi, L., Quondam, M., Ausiello, G., Helmer-Citterich, M., Cesareni, G.: MINT: a Molecular INTeraction database. FEBS Lett. 513, 135–140 (2002)
Hermjakob, H., Montecchi-Palazzi, L., Lewington, C., Mudali, S., Kerrien, S., Orchard, S., Vingron, M., Roechert, B., Roepstorff, P., Valencia, A., Margalit, H., Armstrong, J., Bairoch, A., Cesareni, G., Sherman, D., Apweiler, R.: IntAct: an open source molecular interaction database. Nucl. Acids Res. 32, D452–455 (2004)
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Schmidt, E. et al. (2006). Reactome – A Knowledgebase of Biological Pathways. In: Meersman, R., Tari, Z., Herrero, P. (eds) On the Move to Meaningful Internet Systems 2006: OTM 2006 Workshops. OTM 2006. Lecture Notes in Computer Science, vol 4277. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11915034_95
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DOI: https://doi.org/10.1007/11915034_95
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