Integrated bioinformatics application for automated target discovery

Journal of the American Society for Information Science and Technology

Volumn 56, Issue 5, 2005, Pages 483-492

  Toldo, Luca ^a   Rippmann, Friedrich ^a  

^a MERCK KGAA   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DATA ACQUISITION; DATABASE SYSTEMS; DNA; GENES; KNOWLEDGE ACQUISITION; PROJECT MANAGEMENT; PROTEINS;

BIOINFORMATICS; EXPRESSED SEQUENCE TAGS (EST); KNOWLEDGE-DISCOVERY APPLICATION;

BIOMEDICAL ENGINEERING;

EID: 15944419901     PISSN: 15322882     EISSN: None     Source Type: Journal    
DOI: 10.1002/asi.20137     Document Type: Article

References (54)

1. Ahonen, H., Heikkinen, B., Heinoen, O., Jaakkola, J., Kilpeläinen, P., & Linden, G. (1998). Design and implementation of a document assembly workbench. In R.D. Hersch, J. André, & H. Brown (Eds.), Proceedings of the 7th International Conference on Electronic Publishing (EP'98) (pp. 476-486), Lecture Notes in Computer Science 1375. New York/Berlin/Heidelberg: Springer-Verlag.
2. Andrade, M.A., Brown, N.P., Leroy, C., Hoersch, S., de Daruvar, A., Reich, C., et al. (1999). Automated genome sequence analysis and annotation. Bioinformatics, 15, 391-412.
3. Ashburner, M. (2000). A biologists view of the drosophila genome annotation assessment program [Special issue - Genome annotation problems in eukaryotes]. Genome Research, 10, 391-393.
4. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., et al. (2000). Gene ontology: Tool for the unification of biology. Nature Genetics, 25, 25-28. Retrieved November 25, 2004, from http://www.geneontology. org/
5. Bateman, A., Birney, E., Cerruti, L., Durbin, R., Etwiller, L., Eddy, S.R., et al. (2002). The Pfam Protein Families Database. Nucleic Acids Research, 30, 276-280. Retrieved November 25, 2004, from http://www.sanger.ac.uk/ Software/Pfam/
6. Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., & Wheeler, D.L. (2003). GenBank. Nucleic Acids Research, 31, 23-27. Retrieved November 25, 2004, from http://www.ncbi.nlm.nih.gov/Genbank/
7. Biojava. (2003). Retrieved November 25, 2004, from http://www.biojava. org/
8. Birney, E., & Durbin, R. (2000). Using GeneWise in the Drosophila annotation experiment. Genome Research, 10, 547-548.
9. Boeckmann, B., Bairoch, A., Apweiler, R., Blatter, M.-C., Estreicher, A., Gasteiger, E., et al. (2003). The SWISS-PROT protein knowledgebase and its supplement TrEMBL. Nucleic Acids Research, 31, 365-370. Retrieved November 25, 2004, from http://www.expasy.org/sprot/
10. Boguski, M.S., & Schuler, G.D. (1995). ESTablishing a human transcript map. Nature Genetics, 10, 369-371. Retrieved November 25, 2004, from http://www.ncbi.nlm.nih.gov/UniGene/
11. Bucher, P., Karplus, K., Moeri, N., & Hofmann, K. (1996). A flexible motif search technique based on generalized profiles. Computational Chemistry, 20, 3-24.
12. Bunce, T. (2003). DBI - The Perl database interface. Retrieved November 25, 2004, from http://www.cpan.org/
13. Celera Discovery System. (2003). Retrieved November 25, 2004, from http://www.celeradiscoverysystem.com/
14. Chin, J.P., Diehl, V.A., & Normaln, K. (1988). Development of an instrument measuring user satisfaction of the human-computer interface. In J.J. O'Hare (Ed.), Proceedings of the SIGCHI conference on Human factors in computing systems (ACM CHI '88) (pp. 213-218), Washington, DC: ACM.
15. Clamp, M., Andrews, D., Barker, D., Bevan, P., Cameron, G., Chen, Y., et al. (2002). Ensembl 2002: Accommodating comparative genomics. Nucleic Acids Research, 31, 38-42. Retrieved November 25, 2004, from http://www.ensembl.org/
16. Deerwester, S., Dumais, S.T., Fumas, G.W., Landauer, T.K., & Harshman, R. (1990). Indexing by latent semantic analysis. Journal of American Society for Information Science, 41, 391-407.
17. Eckman, B.A., Kosky, A.S., & Laroco, L.A. (2001). Extending traditional query-based integration approaches for functional characterization of post-genomic data. Bioinformatics, 17, 587-601.
18. Eddy, S.R. (1998). Profile hidden Markov models. Bioinformatics, 14, 755-763.
19. Frishman, D., & Mewes, H.-W. (1997). PEDANTic genome analysis. Trends in Genetics, 13, 415-416.
20. Gaasterland, T., & Sensen, C.W. (1996). MAGPIE: Automated genome interpretation. Trends in Genetics, 12, 76-78.
21. Gansner, E.R., & North, S.C. (2000). An open graph visualization system and its applications to software engineering. Software Practice and Experience, 30, 1203-1233.
22. Garey, M.R., & Johnson, D.S. (1983). Crossing number is NP-complete. SIAM Journal on Algebraic and Discrete Methods, 4, 312-316.
23. Halperin, E., Faigler, S., & Gill-More, R. (1999). FramePlus: Aligning DNA to protein sequences. Bioinformatics, 15, 867-873.
24. Hegyi, H, & Gerstein, M. (2001). Annotation transfer for genomics: Measuring functional divergence in multi-domain proteins. Genome Research, 11, 1632-1640.
25. Hersh, W.R. (1995). Information retrieval: A health care perspective. New York/Berlin/Heidelberg: Springer-Verlag.
26. Iseli, C., Jongeneel, C.V., & Bucher, P. (1999). ESTScan: A program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. In T. Lengauer, R. Schneider, P. Bork, D. Brutlag, J. Glasgow, H.W. Mewes, et al. (Eds.), Proceedings 7th International Conference on Intelligent Systems in Molecular Biology (pp. 138-148). Menlo Park, CA: AAAI Press.
27. Jenssen, T.-K., Lægreid, A., Komorowski, J., & Hovig, E. (2001). A literature network of human genes for high-throughput analysis of gene expression. Nature Genetics, 28, 21-28.
28. Kanehisa, M., Goto, S., Kawashima, S., & Nakaya, A. (2002). The KEGG databases at GenomeNet. Nucleic Acids Research, 30, 42-46. Retrieved November 25, 2004, from http://www.kegg.com/.
29. Kargul, G.J., Dudekula, D.B., Qian, Y., Lim, M.K., Jaradat, S.A., Tanaka, T.S., et al. (2001). Verification and initial annotation of the NIA mouse 15K cDNA clone set. Nature Genetics, 28, 17-18.
30. Lion Bioscience AG (2003). BioScout. Retrieved November 25, 2004, from http://www.lionbioscience.com/
31. McKusick (2002). Online Mendelian Inheritance in Man, OMIM. Retrieved November 25, 2004, from http://www.ncbi.nlm.nih.gov/omim/
32. NIST. (2003). Text retrieval conference. Retrieved November 25, 2004, from: http://trec.nist.gov/
33. National Library of Medicine. (2003a). MEDLINE. Retrieved November 25, 2004, from National Library of Medicine Web site: http://www.nlm.nih.gov/
34. National Library of Medicine. (2003b). Unified medical language system. Retrieved November 25, 2004, from National Library of Medicine Web site: http://www.nlm.nih.gov/
35. National Library of Medicine. (2003c). MeSH tree structures. Retrieved November 25, 2004, from National Library of Medicine Web site: http://www.nlm.nih.gov/
36. Novak, J.D. (1998). Learning, creating, and using knowledge. Mahwah, NJ: Erlbaum. Retrieved November 25, 2004, from http://cmap.coginst.uwf.edu/refs.html
37. Orwant, J., Hietaniemi, J., & Macdonald, J. (1999). Mastering algorithms with Perl. Sebastopol, CA: O'Reilly & Associates.
38. Pruitt, K.D., Katz, K.S., Sicotte, H., & Maglott, D.R. (2000). Introducing RefSeq and LocusLink: Curated human genome resources at the NCBI. Trends in Genetics, 16, 44-47. Retrieved November 25, 2004, from http://www.ncbi.nlm.nih.gov/LocusLink/
39. Rebhan, M., Chalifa-Caspi, V., Prilusky, J., & Lancet, D. (1998). GeneCards: A novel functional genomics compendium with automated data mining and query reformulation support. Bioinformatics, 14, 656-664.
40. Salton, G. (1989). Automatic text processing. Reading, MA: Addison-Wesley.
41. Siedow, J.N. (2001). Making sense of microarrays. Genome Biology, 2, 4003.
42. Stein, L. (2001). Genome annotation: From sequence to biology. Nature Reviews Genetics, 2, 493-503.
43. Stein, L. (2003). BoulderIO. Retrieved November 25, 2004, from http://www.cpan.org/
44. Stodola, R.K., Tobin, F.L., & Williams, A.L. (1997). Method for analyzing partial gene sequences. US Patent 5618672, SmithKline Beecham Corporation.
45. Swanson, D.R., & Smalheiser, N.R. (1997). An interactive system for finding complementary literatures: A stimulus to scientific discovery. Artificial Intelligence, 91, 183-203.
46. Toldo, L. (1997). JaMBW 1.1: Java-based molecular biologists work-bench. Computer Applications in Biological Sciences, 13, 475-176. Retrieved November 25, 2004, from http://www.bioinformatics.org/JaMBW/
47. Toldo, L., & Rippmann, F. (1999). Verfahren zum Ermitteln von Nukleinund/oder Aminosäuresequenzen. DE19941606. [Method for determining nucleic and/or amino acid sequences. Patent Application No. DE19941606, Merck Patent GmbH.]
48. Toldo, L. (2001, May). Interoperability of bioinformatics databases and software systems in the (post) Internet/Genome era. Paper presented at the Meeting on Networked Applications in Bioinformatics, Genova, Italy. Retrieved November 25, 2004, from http://www.nettab.org/2001/
49. Wall, L., & Schwartz, R.L. (1991). Programming Perl. Sebastopol, CA: O'Reilly & Associates.
50. Wilbur, W.J. (1996). Human subjectivity and performance limits in document retrieval. Information Processing & Management, 32, 515-527.
51. Wilbur, W.J. (1998). A comparison of group and individual performance among subject experts and untrained workers at the document retrieval task. Journal of the American Society for Information Science, 49, 517-529.
52. Worley, K.C., Wiese, B.A., & Smith, R.F. (1995). BEAUTY: An enhanced BLAST-based search tool that integrates multiple biological information resources into sequence similarity search results. Genome Research, 5, 173-184.
53. Wu, C.H., Yeh, L.-S.L., Huang, H., Arminski, L., Castro-Alvear, J., Chen, Y., et al. (2003). The protein information resource. Nucleic Acids Research, 31, 345-347. Retrieved November 25, 2004, from http://pir.georgetown.edu/
54. Zemla, A., Venclovas, C., Moult, J., & Fidelis, K. (2001). Processing and evaluation of predictions in CASP4. Proteins, 45, 13-21.