Visualizing information across multidimensional post-genomic structured and textual databases

Bioinformatics

Volumn 21, Issue 8, 2005, Pages 1659-1667

  Tao, Ying ^a   Friedman, Carol ^a   Lussier, Yves A ^a  

^a Och Spine at New York Presbyterian Hospitals   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; ARTIFICIAL INTELLIGENCE; AUTOMATION; CLUSTER ANALYSIS; COMPUTER INTERFACE; COMPUTER PROGRAM; GENETIC DATABASE; GENOMICS; GENOTYPE PHENOTYPE CORRELATION; HUMAN; HUMAN GENETICS; MEDICAL RESEARCH; PRIORITY JOURNAL;

EID: 17444408180     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti210     Document Type: Article

References (44)

1. Al-Shahrour,F., Diaz-Uriarte,R. and Dopazo,J. (2004) FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics, 20, 578-580.
2. 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. et al. (2000) Gene Ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29.
3. Bairoch,A. and Apweiler,R. (1996) The SWISS-PROT protein sequence data bank and its new supplement TREMBL. Nucleic Acids Res. 24, 21-25.
4. Baker,P.G., Brass,A., Bechhofer,S., Goble,C., Paton,N. and Stevens,R. (1998) TAMBIS - Transparent Access to Multiple Bioinformatics Information Sources. In Proceedings of Sixth International Conference on Intelligent Systems for Molecular Biology, Montréal, Québec, Canada, pp. 25-34.
5. Benson,D.A., Karsch-Mizrachi,I., Lipman,D.J., Ostell,J., Rapp,B.A. and Wheeler,D.L. (2000) GenBank. Nucleic Acids Res., 28, 15-18.
6. Bodenreider,O. and Mitchell,J.A. (2003) Graphical visualization and navigation of genetic disease information. In Proceedings of the AMIA Symposium, Washington DC, 792 p.
7. Bult,C.J., Blake,J.A., Richardson,J.E., Kadin,J.A., Eppig,J.T., Baldarelli,R.M., Barsanti,K., Baya,M., Beal,J.S., Boddy,W.J. et al. (2004) The Mouse Genome Database (MGD): integrating biology with the genome. Nucleic Acids Res., 32 (Database issue), D476-D481.
8. Cantor,M.N. and Lussier,Y.A. (2003) Putting data integration into practice: using biomedical terminologies to add structure to existing data sources. In Proceedings of the AMIA Symposium, Washington, DC, pp. 125-129.
9. Cantor,M.N. and Lussier,Y.A. (2004) Mining OMIM for Insight in Complex Diseases. Medinfo 2004, 735-737.
10. Chen,I.M., Kosky,A.S., Markowitz,V.M., Szeto,E. and Topaloglou,T. (1998) Advanced query mechanisms for biological databases. Proc. Int. Conf. Intell. Syst. Mol. Biol., 6, 43-51.
11. Chen,L. and Friedman,C. (2004) Extracting Phenotypic Information from the Literature via Natural Language Processing. Medinfo 2004, 758-762.
12. Eckman,B.A., Kosky,A.S. and Laroco,L.A.,Jr (2001) Extending traditional query-based integration approaches for functional characterization of post-genomic data. Bioinformatics, 17, 587-601.
13. FlyBase_Consortium (2003) The FlyBase database of the Drosophila genome projects and community literature. Nucleic Acids Res., 31, 172-175.
14. Freimer,N. and Sabatti,C. (2003) The human phenome project. Nat. Genet., 34, 15-21.
15. Friedman,C., Alderson,P.O., Austin,J.H., Cimino,J.J. and Johnson,S.B. (1994) A general natural-language text processor for clinical radiology. J. Am. Med. Inform. Assoc., 1, 161-174.
16. Friedman,C., Kra,P., Yu,H., Krauthammer,M. and Rzhetsky,A. (2001) GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles. Bioinformatics, 17 Suppl. 1), S74-S82.
17. Friedman,C., Liu,H. and Shagina,L. (2003) A vocabulary development and visualization tool based on natural language processing and the mining of textual patient reports. J. Biomed. Inform., 36, 189-201.
18. Graefe, G. et al. (1998) Electronic database operations for perspective transformations on relational tables using pivot and unpivot columns. Microsoft Corporation, Patent number 6298342.
19. Gray,J., Bosworth,A., Layman,A. and Pirahesh,H. (1996) Data cube: a relational aggregation operator generalizing GROUP-BY, CROSS-TAB, and SUB-TOTALS. In Proceedings of the Twelfth International Conference on Data Engineering, New Orleans, LA, pp. 152-159, IEEE Computer Society Press.
20. Hamosh,A., Scott,A.F., Amberger,J., Bocchini,C., Valle,D. and McKusick,V.A. (2002) Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and generic disorders. Nucleic Acids Res. 30, 52-55.
21. Hristovski,D., Peterlin,B., Mitchell,J.A. and Humphrey,S.M. (2003). Improving literature based discovery support by genetic knowledge integration. Stud. Health Technol. Inform., 95, 68-73.
22. Jenssen,T.K., Laegreid,A., Komorowski,J. and Hovig,E. (2001) A literature network of human genes for high-throughput analysis of gene expression. Nat. Genet., 28, 21-28.
23. Karp,P.D. (2001) Pathway databases: a case study in computational symbolic theories. Science, 293, 2040-2044.
24. Kasprzyk,A., Keefe,D., Smedley,D., London,D., Spooner,W., Melsopp,C., Hammond,M., Rocca-Serra,P., Cox,T. and Birney,E. (2004) EnsMart: a generic system for fast and flexible access to biological data. Genome Res., 14, 160-169.
25. Koike,T. and Rzhetsky,A. (2000) A graphic editor for analyzing signal-transduction pathways. Gene, 259, 235-244.
26. Kolpakov,F., Ananko,E., Kolesov,G.B. and Kolchanov,N.A. (1998) GeneNet: a gene network database and its automated visualization. Bioinformatics, 14, 529-537.
27. Krauthammer,M., Kra,P., Iossifov,I., Gomez,S.M., Hripcsak,G., Hatzivassiloglou,V., Friedman,C. and Rzhetsky,A. (2002) Of truth and pathways: chasing bits of information through myriads of articles. Bioinformatics, 18 (Suppl. 1), S249-S257.
28. Lindberg,C. (1990) The Unified Medical Language System (UMLS) of the National Library of Medicine. J. Am. Med. Rec. Assoc., 61 40-42.
29. Liu,H. and Friedman,C. (2000) A method for vocabulary development and visualization based on medical language processing and XML. In Proceedings of the AMIA Symposium, Los Angeles, CA, pp. 502-506.
30. Lussier,Y.A. and Li,J. (2004) Terminological mapping for high throughput comparative biology of phenotypes. Pac. Symp. Biocomput. 202-213.
31. Maglott,D.R., Katz,K.S., Sicotte,H. and Pruitt,K.D. (2000) NCBI's LocusLink and RefSeq. Nucleic Acids Res., 28, 126-128.
32. Mahner,M. and Kary,M. (1997) What exactly are genomes, genotypes and phenotypes? And what about phenomes? J. Theoret. Biol. 186, 55-63.
33. Marchler-Bauer,A., Addess,K.J., Chappey,C., Geer,L., Madej,T., Matsuo,Y., Wang,Y. and Bryant,S.H. (1999) MMDB: Entrez's 3D structure database. Nucleic Acids Res., 27, 240-243.
34. Rebhan,M., Chalifa-Caspi,V., Prilusky,J. and Lancet,D. (1998) GeneCards: a novel functional genomics compendium with automated data mining and query reformulation support. Bioinformatics, 14, 656-664.
35. Rindflesch,T.C., Libbus,B., Hristovski,D., Aronson,A.R. and Kilicoglu,H. (2003) Semantic relations asserting the etiology of genetic diseases. In Proceedings of the AMIA Symposium, Washington, DC, pp. 554-558.
36. Rzhetsky,A., Iossifov,I., Koike,T., Krauthammer,M., Kra,P., Morris,M., Yu,H., Duboué,P.A., Weng,W. and Wilbur,W.J. (2004) GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data. J. Biomed. Inform., 37, 43-53.
37. Rzhetsky,A., Koike,T., Kalachikov,S., Gomez,S.M., Krauthammer,M., Kaplan,S.H., Kra,P., Russo,J.J. and Friedman,C. (2000) A knowledge model for analysis and simulation of regulatory networks. Bioinformatics, 16, 1120-1128.
38. Sarkar,I.N., Cantor,M.N., Gelman,R., Hartel,F. and Lussier,Y.A. (2003) Linking biomedical language information and knowledge resources: GO and UMLS. Pac. Symp. Biocomput., 439-450.
39. Tao,Y., Liu,Y., Friedman,C. and Lussier,Y.A. (2004) The use of information visualization techniques in bioinformatics during the postgenomic era. Drug Discov. Today: BIOSILICO, 2, 237-245.
40. Wheeler,D.L., Chappey,C., Lash,A.E., Leipe,D.D., Madden,T.L., Schuler,G.D., Tatusova,T.A. and Rapp,B.A. (2000) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 28, 10-14.
41. Wong,L. (2000) The functional guts of the Kleisli query system. ACM SIGPLAN Notices, 35, 1-10.
42. Zeeberg,B.R., Feng,W., Wang,G., Wang,M.D., Fojo,A.T., Sunshine,M., Narasimhan,S., Kane,D.W., Reinhold,W.C., Lababidi,S. et al. (2003) GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol., 4, R28.
43. Zhang,B., Schmoyer,D., Kirov,S. and Snoddy,J. (2004) GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies. BMC Bioinformatics, 5, 16.
44. Zhong,S., Li,C. and Wong,W.H. (2003) ChipInfo: software for extracting gene annotation and gene ontology information for microarray analysis. Nucleic Acids Res., 31, 3483-3486.