GenoQuery: A new querying module for functional annotation in a genomic warehouse

Bioinformatics

Volumn 24, Issue 13, 2008, Pages

  Lemoine, Frédéric ^a,b   Labedan, Bernard ^a   Froidevaux, Christine ^b  

^a INSTITUTE FOR INTEGRATIVE BIOLOGY OF THE CELL I2BC   (France)

^b UFR 919 Laboratoire d'Informatique Pour la Mécanique et les Sciences de l'Ingénieur   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER AIDED DESIGN; FUNCTIONAL GENOMICS; GENETIC DATABASE; GENOQUERY; INFORMATION PROCESSING; INFORMATION RETRIEVAL; MATHEMATICAL COMPUTING; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PRIORITY JOURNAL; PROCESS DESIGN; PROCESS DEVELOPMENT; SYSTEM ANALYSIS; SYSTEMS BIOLOGY;

GENES; INTELLIGENT SYSTEMS; MOLECULAR BIOLOGY; QUERY LANGUAGES; WAREHOUSES;

ALTERNATIVE QUERIES; BIOLOGICAL ENTITIES; FUNCTIONAL ANNOTATION; GENOME SEQUENCES; HIGH-THROUGHPUT APPROACHES; INTEGRATED DATABASE; INTEGRATION SYSTEMS; MULTI-LAYER ARCHITECTURES;

QUERY PROCESSING;

EID: 46249114584     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn159     Document Type: Article

References (33)

1. Altschul,S.F. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
2. Bairoch,A. et al. (2005) The universal protein resource (UniProt). Nucleic Acids Res., 33, D154-D159.
3. Birkland,A. and Yona,G. (2006) BIOZON: A system for unification, management and analysis of heterogeneous biological data. BMC Bioinformatics, 7, 70.
4. Bryson,K. et al. (2006) AGMIAL: Implementing an annotation strategy for prokaryote genomes as a distributed system. Nucleic Acids Res., 34, 3533-3545.
5. Cadag,E. et al. (2007) Biomediator data integration and inference for functional annotation of anonymous sequences. In Pacific Symposium on Biocomputing, pp. 343-354.
6. Cohen-Boulakia,S. et al. (2002) Genopage: A database of all protein modules encoded by completely sequenced gcnomes. In Actes de JOBIM2002, Journées Ouvertes, Biologie, Informatique et Mathématiques, pp. 187-193.
7. Cohen-Boulakia,S. et al. (2006) Path-based systems to guide scientists in the maze of biological data sources. J. Bioinform. Comput. Biol., 4, 1069-1095.
8. Cohen-Boulalia,S., et al. (2007) BioGuideSRS: Querying multiple sources with a user-centric perspective. Bioinformatics, 23, 1301-133.
9. Davidson,S.B. et al. (2001) K2/kleisli and gus: Experiments in integrated access to genomic data sources. IBM Syst. J., 40, 512-531.
10. Durinck,S. et al. (2005) Biomart and bioconductor: A powerful link between biological databases and microarray data analysis. Bioinformatics, 21, 3439-3440.
11. Etzold,T. et al. (1996) SRS: Information retrieval system for molecular biology data banks. Methods Enzymol., 266, 114-128.
12. Gasteiger,E. et al. (2003) Expasy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res., 31 3784-3788.
13. Gonnet,G. et al. (2000) Darwin v. 2.0: An interpreted computer language for the biosciences. Bioinformatics, 16, 101-103.
14. Green,T.J. et al. (2007) Orchestra: Facilitating collaborative data sharing. In SIGMOD '07: Proceedings of the 2007 ACM SIGMOD international conference on Management of data (SIGMOD'07). ACM, New York, USA, pp. 1131-1133.
15. Guérin,E. et al. (2005) Integrating and warehousing liver gene expression data and related biomedical resources in GEDAW. In Second International Workshop on Data Integration in the Life Sciences (DILS) Vol. 3615/2005 of LNCS, San Diego, CA, US, pp. 158-174.
16. Halevy,A.Y. et al. (2003) Schema mediation in pecr data management systems. In Dayal,U. Ramamritham,K. and Vijayaraman,T.M. editiors, Proceedings of the 19th International Conference on Data Engineering, IEEE Computer Society, pp. 505-.
17. Kanehisa,M. et al. (2006) From genomics to chemical genomics: New developments in KEGG. Nucleic Acids Res., 34, D354-D357.
18. Karp,PD. et al. (2005) Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res., 33 6083-6089.
19. Kasprzyk,A. et al. (2004) Ensmart: A generic system for fast and flexible access to biological data. Genome Res., 14, 160-169.
20. Klyne,J. (2004) Resource description framework (RDF): Concepts and Abstract Syntax, recommendation. W3C: http://www.w3.org/TR/ rdf-concepts/.
21. Le Bouder-Langevin,S. et al. (2002) A strategy to retrieve the whole set of protein modules in microbial proteomes. Genome Res., 12, 1961-1973.
22. Lee,T. et al. (2006) BioWarehouse: A bioinformatics database warehouse toolkit. BMC Bioinformatics, 7, 170.
23. Lemoine,F. et al. (2007) Assessing the evolutionary rate of positional orthologous genes in prokaryotes using synteny data. BMC Evol. Biol., 7, 237.
24. Lespinet,O. and Labedan,B. (2006) ORENZA: A web resource for studying ORphan ENZyme activities. BMC Bioinformatics, 7, 436.
25. Lowden,B.G.T. and Robinson,J. (2004) Improved data retrieval using semantic transformation. In Galindo,F. and Takizawa,M. (eds) DEXA, Lecture Notes in Computer Science, Vol. 3180. Springer, Zaragoza, Spain, pp. 391-400.
26. Necib C.B. and Freytag,J.C. (2004) Using ontologies for database query reformulation. In ADBIS (Local Proceedings).
27. Ouzounis,C.A. and Karp,P.D. (2002) The past, present and future of genome-wide re-annotation. Genome Biol., 3, c2001.1-c2001.6.
28. Pennisi,E. (2008) DNA data. Proposal to Wikify' GenBank meets stiff resistance. Science, 319, 1598-1599.
29. Prud'hommeaux,E. and Seaborne,A. (2007) SPARQL Query Language for RDF. W3C: http://www.w3.org/TR/rdf-sparql-query/.
30. Pruitt,K. D. et al. (2007) NCBI Reference Sequences (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res., 35, D61-D65.
31. Sterk,P. et al. (2006) Genome reviews: Standardizing content and representation of information about complete genomes. OMICS, 10 114-118.
32. Stevens,R. et al. (2000) TAMBIS: Transparent access to multiple bioinformatics information sources. Bioinformatics, 16, 184-185.
33. Trissl,S. et al. (2005) Columba: An integrated database of proteins, structures, and annotations. BMC Bioinformatics, 6 81.