Chapter 15: Search computing and the life sciences

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 5950 LNCS, Issue , 2010, Pages 291-306

  Masseroli, Marco ^a   Paton, Norman W ^b   Spasić, Irena ^b  

^a POLITECNICO DI MILANO   (Italy)

^b UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

Bioinformatics; Data integration; Ranked data; Search computing

Indexed keywords

BIOINFORMATICS DATA; COMPUTATIONAL RESOURCES; DATA INTEGRATION; DATA SEARCHES; EXPRESSION LEVELS; INTEGRATION PLATFORM; KEY FEATURE; LIFE-SCIENCES; MULTI DOMAINS; ORDERED DATA; SEARCH ENGINE RESULTS; SEQUENCE SIMILARITY;

BIOINFORMATICS; DATA HANDLING; INFORMATION RETRIEVAL; SEARCH ENGINES; TECHNICAL PRESENTATIONS; WORLD WIDE WEB;

INTEGRATION;

EID: 77951601284     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-12310-8_15     Document Type: Conference Paper

References (38)

1. Stead, D., Paton, N.W., Missier, P., Embury, S.M., Hedeler, C., Jin, B., Brown, A.J.P., Preece, A.D.: Information quality in proteomics. Brief. Bioinform. 9(2), 174-188 (2008)
2. Parkinson, H., Sarkans, U., Shojatalab, M., Abeygunawardena, N., Contrino, S., Coulson, R., Farne, A., Lara, G.G., Holloway, E., Kapushesky, M., Lilja, P., Mukherjee, G., Oezcimen, A., Rayner, T., Rocca-Serra, P., Sharma, A., Sansone, S., Brazma, A.: ArrayExpress-a public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 33(Database issue), D553-D555 (2005) (Pubitemid 40207935)
3. Galperin, M.Y., Cochrane, G.R.: Nucleic Acids Research annual database issue and the NAR online molecular biology database collection in 2009. Nucleic Acids Res. 37(Database issue), D1-D4 (2009)
4. Krallinger, M., Valencia, A., Hirschman, L.: Linking genes to literature: text mining, information extraction, and retrieval applications for biology. Genome Biol. 9(suppl. 2), S8 (2008)
5. Spasic, I., Ananiadou, S., McNaught, J., Kumar, A.: Text mining and ontologies in biomedicine: making sense of raw text. Brief. Bioinform. 6(3), 239-251 (2005)
6. Braga, D., Ceri, S., Daniel, F., Martinenghi, D.: Mashing up search services. IEEE Internet Comput. 12(5), 16-23 (2008)
7. Hernandez, T., Kambhampati, S.: Integration of biological sources: current systems and challenges ahead. SIGMOD Record 33(3), 51-60 (2004)
8. Masseroli, M., Ceri, S., Campi, A.: Integration and mining of genomic annotations: experiences and perspectives in GFINDer data warehousing. In: Paton, N.W., Missier, P., Hedeler, C. (eds.) DILS 2009. LNCS (LNBI), vol. 5647, pp. 88-95. Springer, Heidelberg (2009)
9. Hull, D., Wolstencroft, K., Stevens, R., Goble, C.A., Pocock, M.R., Li, P., Oinn, T.: Taverna: a tool for building and running workflows of services. Nucleic Acids Res. 34, 729-732 (2006) (Pubitemid 44529867)
10. Goble, C.A., Stevens, R., Ng, G., Bechhofer, S., Paton, N.W., Baker, P.G., Peim, M., Brass, A.: Transparent access to multiple bioinformatics information sources. IBM Systems Journal 40(2), 534-551 (2001) (Pubitemid 32611101)
11. Dwork, C., Kumar, R., Naor, M., Sivakumar, D.: Rank aggregation methods for the web. In: Proceedings of the 10th International World Wide Web Conference, WWW 2001, pp. 613-622. ACM Press, New York (2001)
12. Edgar, R., Domravech, M., Lash, A.E.: Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 30(1), 207-210 (2002) (Pubitemid 34679544)
13. Jones, P., Côté, R.G., Martens, L., Quinn, A.F., Taylor, C.F., Derache, W., Hermjakob, H., Apweiler, R.: PRIDE: a public repository of protein and peptide identifications for the proteomics community. Nucleic Acids Res. 34(Database Issue), D659-D663 (2006)
14. Olken, F.: Graph data management for molecular biology. OMICS: A Journal of Integr. Biol. 7(1), 75-78 (2003)
15. Castrillo, J.I., Zeef, L.A., Hoyle, D.C., Zhang, N., Hayes, A., Gardner, D.C., Cornell, M.J., Petty, J., Hakes, L., Wardleworth, L., Rash, B., Brown, M., Dunn, W.B., Broadhurst, D., O'Donoghue, K., Hester, S.S., Dunkley, T.P., Hart, S.R., Swainston, N., Li, P., Gaskell, S.J., Paton, N.W., Lilley, K.S., Kell, D.B., Oliver, S.G.: Growth control of the eukaryote cell: a systems biology study in yeast. J. Biol. 6(2), 4 (2007)
16. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J.: Basic Local Alignment Search Tool. J. Mol. Biol. 215(3), 403-410 (1990)
17. Salton, G., Buckley, C.: Term-weighting approaches in automatic text retrieval. Inf. Process Manag. 24(5), 513-523 (1988)
18. Leitner, F., Krallinger, M., Rodriguez-Penagos, C., Hakenberg, J., Plake, C., Kuo, C.J., Hsu, C.N., Tsai, R.T., Hung, H.C., Lau, W.W., Johnson, C.A., Saetre, R., Yoshida, K., Chen, Y.H., Kim, S., Shin, S.Y., Zhang, B.T., Baumgartner Jr., W.A., Hunter, L., Haddow, B., Matthews, M., Wang, X., Ruch, P., Ehrler, F., Ozgür, A., Erkan, G., Radev, D.R., Krauthammer, M., Luong, T., Hoffmann, R., Sander, C., Valencia, A.: Introducing metaservices for biomedical information extraction. Genome Biol. 9(suppl. 2), S6 (2008)
19. Goble, C.A., Belhajjame, K., Tanoh, F., Bhagat, J., Wolstencroft, K., Stevens, R., Pettifer, S., Nzuobontane, E., McWilliam, H., Laurent, T., Lopez, R.: BioCatalogue: a curated Web Service registry for the Life Science community. In: ISMB/ECCB 2009. Technology Track: TT40 (2009)
20. Louie, B., Mork, P., Martin-Sanchez, F., Halevy, A., Tarczy-Hornoch, P.: Data integration and genomic medicine. J. Biomed. Inform. 40(1), 5-16 (2007)
21. Pihur, V., Datta, S., Datta, S.: Weighted rank aggregation of cluster validation measures: a Monte Carlo cross-entropy approach. Bioinformatics 23(13), 1607-1615 (2007) (Pubitemid 47244450)
22. DeConde, R., Hawley, S., Falcon, S., Clegg, N., Knudsen, B., Etzioni, R.: Combining results of microarray experiments: a rank aggregation approach. Stat. Appl. Genet. Mol. Biol. 5, Article 15 (2006)
23. Pihur, V., Datta, S., Datta, S.: RankAggreg, an R package for weighted rank aggregation. BMC Bioinformatics 10, 62 (2009)
24. Fagin, R., Kumar, R., Sivakumar, D.: Comparing top k lists. SIAM J. Discrete Math. 17(1), 134-160 (2003)
25. Börzsönyi, S., Kossmann, D., Stocker, K.: The Skyline operator. In: Proceedings 17th International Conference on Data Engineering, ICDE 2001, pp. 421-430. IEEE Press, New York (2001)
26. Hue, C., Boullé, M.: A new probabilistic approach in rank regression with optimal bayesian partitioning. J. Mach. Learn. Res. 8, 2727-2754 (2007)
27. Cheung, C.W.: Probabilistic rank aggregation for multiple SVM ranking. MPhil Thesis. Department of Computer Science and Engineering, The Hong Kong University of Science and Technology. Hong Kong (2009)
28. Sawaragi, Y., Nakayama, H., Tanino, T.: Theory of multiobjective optimization. Mathematics in Science and Engineering, vol. 176. Academic Press Inc., Orlando (1985)
29. Steuer, R.E.: Multiple criteria optimization: theory, computations, and application. John Wiley & Sons, Inc., New York (1986)
30. Deb, K.: Multi-objective optimization using evolutionary algorithms. John Wiley & Sons, Inc., New York (2002)
31. Deb, K., Agrawal, S., Pratap, A., Meyarivan, T.: A fast elitist non-dominated sorting genetic algorithm for multi-objective optimization: NSGA-II. KanGAL Report no.200001 (2000)
32. Zitzler, E., Thiele, L.: An evolutionary algorithm for multiobjective optimization: the strength Pareto approach. TIK-Report no.43 (1998)
33. Handl, F., Kell, D.B., Knowles, J.D.: Multiobjective optimization in bioinformatics and computational biology. IEEE/ACM Trans. Comput. Biol. Bioinform. 4(2), 279-292 (2007)
34. Perez-Iratxeta, C., Bork, P., Andrade, M.A.: Association of genes to genetically inherited diseases using data mining. Nat. Genet. 31(3), 316-319 (2002)
35. Jelier, R., Jenster, G., Dorssers, L.C., van der Eijk, C.C., van Mulligen, E.M., Mons, B., Kors, J.A.: Co-occurrence based meta-analysis of scientific texts: retrieving biological relationships between genes. Bioinformatics 21(9), 2049-2058 (2005) (Pubitemid 40668044)
36. Kerr, G., Ruskin, H.J., Crane, M., Doolan, P.: Techniques for clustering gene expression data. Comput. Biol. Med. 38(3), 283-293 (2008)
37. Kearsey, M.J.: The principles of QTL analysis (a minimal mathematics approach). J. Exp. Bot. 49(327), 1619-1623 (1998)
38. Datta, R., de Schoolmeester, M.L., Hedeler, C., Paton, N.W., Brass, A.M., Else, K.J.: Identification of novel genes in intestinal tissue that are regulated after infection with an intestinal nematode parasite. Infect. Immun. 73(7), 4025-4033 (2005)