Bio-Broker: A tool for integration of biological data sources and data analysis tools

Software - Practice and Experience

Volumn 36, Issue 14, 2006, Pages 1585-1604

  Aldana, J F ^a   Roldan Castro M ^a   Navas, I ^a,b   Roldan Garcia M M ^a   Hidalgo Conde, M ^a   Trelles, O ^b  

^a ETSI Informatica   (Spain)

^b UNIVERSITY OF MÁLAGA   (Spain)

Author keywords

Biological dataflow; Biological mediation; Data analysis tools; XML

Indexed keywords

ALGORITHMS; COMPUTER ARCHITECTURE; DATA PROCESSING; DISTRIBUTED COMPUTER SYSTEMS; INFORMATION MANAGEMENT; XML;

BIOLOGICAL DATAFLOW; BIOLOGICAL MEDIATION; DATA ANALYSIS TOOLS; GENE EXPRESSION DATA;

DATA REDUCTION;

EID: 33750715085     PISSN: 00380644     EISSN: 1097024X     Source Type: Journal    
DOI: 10.1002/spe.733     Document Type: Article

References (38)

1. Rechenmann F. From data to knowledge. Bioinformatics 2000; 16:411.
2. Abiteboul S, Buneman P, Suciu D. Data on the Web from Relations to Semistructured Data and XML. Morgan Kaufmann: San Francisco, CA, 2000.
3. Roth MT, Schwarz PM. Don't scrap it, wrap it! A wrapper architecture for legacy data sources. Proceedings of the 23rd International Conference on Very Large Data Bases, Athens, Greece, 25-29 August 1997, Jarke M, Carey MJ, Dittrich KR, Lochovsky FH, Loucopoulos P, Jeusfeld MA (eds.). Morgan Kaufmann: San Francisco, CA, 1997; 266-275.
4. Sahuguet A, Azavant F. Building light-weight wrappers for legacy Web data-sources using W4F. Proceedings of the 25th International Conference on Very Large Data Bases, Edinburgh, Scotland, 7-10 September 1999, Atkinson MP, Orlowska ME, Valduriez P, Zdonik SB, Brodie ML (eds.). Morgan Kaufmann: San Francisco, CA, 1999; 738-741.
5. Fahl G, Risch T, Skold M. AMOS - an architecture for active mediators. Proceedings of the 1993 Workshop on Next Generation Information Technologies and Systems (NGITS'93). The Technian: Haifa, Israel, 1993; 47-53.
6. Garcia-Molina H, Papakonstantinou Y, Quass D, Rajararnan A, Sagiv Y, Ullman J, Vassalos V, Widom J. The TSIMMIS approach to mediation: Data models and languages. Journal of Intelligent Information Systems 1997; 2:117-132.
7. Tomasic A, Raschid L, Valduriez P. Scaling heterogeneous databases and the design of disco. Proceedings of the International IEEE Conference on Parallel and Distributed Information Systems, Hong Kong, 1996. IEEE Computer Society Press: Los Alamitos, CA, 1996; 449-457.
8. Haas L, Kossmann D, Wimmers EL, Yang J. Optimizing queries across diverse data sources. Proceedings of the 23th International Conference on Very Large Databases (VLDB'97). Morgan Kaufmann: San Francisco, CA, 1997; 276-285.
9. Stevens R, Baker P, Bechhofer S, Ng G, Jacoby A, Paton NW, Goble CA, Brass A. TAMBIS: Transparent access to multiple bioinformatics information sources. Bioinformatics 2000; 16:184-186.
10. Lange M, Freier A, Scholz U, Stephanik A. A computational support for access to integrated molecular biology data. German Conference on Bioinformatics, 2001. Available at: http://www.bioinfo.de/isb/gcb01/poster/ lange.htmWimg-l.
11. Gupta A, Ludascher B, Martone ME. Knowledge-based integration of neuroscience data sources. Proceedings of the 12th International Conference on Scientific and Statistical Database Management (SSDBM), Berlin, Germany, July 2000. IEEE Computer Society: Los Alamitos, CA, 2000.
12. Liu L, Buttler D, Critchlow T, Han W, Páques H, Pu C, Rocco D. BioZoom: Exploiting source-capability information for integrated access to multiple bioinformatics data sources. Proceedings of the 3rd IEEE Symposium on BioInformatics and BioEngineering (BIBE 2003), Washington, DC, 10-12 March 2003. IEEE Computer Society Press: Los Alamitos, CA. 2003.
13. Davidson S, Overton C, Tannen V, Wong L. BioKleisli: A digital library for biomedical researchers. International Journal of Digital Libraries 1997; 1:36-53.
14. IBM Corp. 'DiscoveryLink'. http://www.ibm.com/discoverylink [23 August 2004]
15. Baru C, Gupta A, Ludascher B, Marciano R, Papakonstantinou Y, Velikhov P, Chu V. XML-based information mediation with MIX. Proceedings of the Special Interest Group on Management of Data (SIGMOD'98). ACM Press: New York, 1998; 597-599.
16. Rodgriguez-Martinez M, Roussopoulos N. MOCHA: A sell-extensible database middleware system for distributed data sources. Proceedings of the 2000 ACM SIGMOD International Conference on Management of Data. Dallas, TX, May 2000. ACM Press: New York, 2000; 213-224.
17. Buttler D, Coleman M, Critchlow T, Fileto R, Han W, Pu C, Rocco D, Xiong L. Querying multiple bioinformatics information sources: Can semantic Web research help? SIGMOD Record 2002; 31(4):59-64.
18. Bairoch A, Apweiler R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Research 2000; 28(1):45-48.
19. Wang L, Riethoven JJM, Robinson AJ. XEMBL - distributing EMBL data in XML format. Bioinformatics 2002; 18(8): 1147-1148.
20. Biaudet V. Samson F, Bessieres P. Micado - a network oriented database for microbial genomes. Computer Applications in the BioSciences 1997; 13:431-438.
21. The PDB Team (2003). Details the history, function, development, and future goals of the PDB resource. Structural Bioinformatics, Bourne PE, Weissig H (eds.). Wiley: New York, 2003; 181-198.
22. Xenarios I, Salwinski L, Duan XJ, Higney P, Kim S, Eisenberg D. DIP: The Database of Interacting Proteins. A research tool for studying cellular networks of protein interactions. Nucleic Acids Research 2000; 30(1):303-305.
23. Bader GD, Betel D. Hogue CW. BIND: The Biomolecular Interaction Network Database. Nucleic Acids Research 2003: 31(1):248-250.
24. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Gapped BLAST and PSI-PLAST: A new generation of protein DB search programs. Nucleic Acids Research 1997; 25(17):3389-3402.
25. Pérez AJ. Rodríguez A, Trelles O, Thode G. A computational strategy for protein structure-function assignment which approaches the multidomain problem. Comparative and Functional Genomics 2002; 3(5):423-440.
26. Rodríguez A. Carazo JM, Trelles O. Mining association rules from biological databases. Journal of American Society Information Systems and Technologies 2005; 56(5):493-504.
27. Garcia de la Nava J, Santaella DF, Cuenca Alba J, Maria Carazo J, Trelles O, Pascual-Montano A. Engene: The processing and exploratory analysis of gene expression data. Bioinformatics 2003; 19:657-658.
28. Aldana JF, Gomez AC, Roldan MM, Moreno N, Nebro A. Metadata functionality for semantic Web integration. Proceedings of the 7th International Conference of the International Society of Knowledge Organization (ISKO'02). Ergon: Würzburg. Germany, 2002.
29. Aldana JF, Roldán MM, Gómez AC, Yagüe ME. Un framework para la consulta e integración de fuentes de datos heterogéneas y distribuidas sobre la Web. Memorias de las Jornadas Iberoamericanas de Ingeniería de Requisitos de Ambientes y de Software (IDEAS'2001). Institute Technológico de Costa Rica. Centro de Información Tecnológica (CIT): Cartago, Costa Rica, 2001: 65-76.
30. XML. Extensible Markup Language (XML) 1.1. W3C Candidate Recommendation. http://www.w3.org/TR/2002/CR-xml11-20021015 [15 October 2003].
31. XQuery 1.0. W3C Working Draft, 16 August 2002. http://www.w3.org/TR/ xquery [23 August 2004]
32. XML Schema. W3C Recommendation. http://www.w3.org/TR/xmlschema-{0, 1, 2} [2 May 2001].
33. RDF Schema. Resource Description Framework Schema Specification 1.0. W3C Candidate Recommendation. http://www.w3.org/TR/2000/CR-rdf-schema-20000327 [March 2000].
34. Berman HM, Westbrook J, Feng Z, Gilliland G. Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Research 2000; 28(1):235-242.
35. Samson F, Biaudet-Brunaud V, Gas S, Dervyn E, Gallezot G, Duchet S, Batto JM, Ehrlich D, Bessières P. Micado, an Integrative Database Dedicated to the Functional Analysis of Bacillus Subtilis and Microbial Genomics. Functional Analysis of Bacterial Genes. Schumann W, Ehrlich SO, Ogasawara N (eds.). Wiley: New York, 2000.
36. Kobayashi K, Ogura M, Yamaguchi H, Yoshida K, Ogasawara N, Tanaka T, Fujita Y. Comprehensive DNA microarray analysis of Bacillus subtilis two-component regulatory systems. Journal of Bacteriology 2001; 183(24):7365-7370.
37. Tamames J, Casari G, Ouzounis C, Valencia A. Conserved clusters of functionally related genes in two bacterial genomes. Journal of Mollecular Evolution 1997; 44:66-73.
38. Dandekar T et al. Systematic genomic screening and analysis of mRNA in untranslated regions and mRNA precursors: Combining experimental and computational approaches. Bioinformatics 1998; 14:271-278.