The pathway tools software

Bioinformatics

Volumn 18, Issue SUPPL. 1, 2002, Pages

  Karp, Peter D ^a   Paley, Suzanne ^a   Romero, Pedro ^a  

^a SRI INTERNATIONAL   (United States)

Author keywords

Bioinformatics; Genome analyses; Metabolic pathways; Model organism database

Indexed keywords

BIOINFORMATICS; BIOLOGICAL MODEL; COMPARATIVE STUDY; COMPUTER INTERFACE; COMPUTER PROGRAM; CONFERENCE PAPER; GENE EXPRESSION REGULATION; GENETIC ANALYSIS; GENETIC DATABASE; GENOMICS; INFORMATION RETRIEVAL; PRIORITY JOURNAL; SIGNAL TRANSDUCTION; ANIMAL; ARTICLE; DATA BASE; DOCUMENTATION; EVALUATION; GENETICS; HUMAN; METABOLISM; METHODOLOGY; PHYSIOLOGY;

LEOPARDUS PARDALIS;

PROTEOME;

ABSTRACTING AND INDEXING; ANIMALS; DATABASE MANAGEMENT SYSTEMS; DATABASES, GENETIC; GENE EXPRESSION REGULATION; HUMANS; INFORMATION STORAGE AND RETRIEVAL; MODELS, BIOLOGICAL; PROTEOME; SIGNAL TRANSDUCTION; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 11244328060     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/18.suppl_1.S225     Document Type: Conference Paper

References (18)

1. Ball, CA., Dolinski, K., Dwight, S.S., Harris, M.A., Issel-Tarver, L., Kasarskis, A., Scafe, C.R., Sherlock, G., Binkley, G., Jin, H., Kaloper, M., Orr, S.D., Schroeder, M., Weng, S., Zhu, Y., Botstein, D. and Cherry, J.M. (2000) Integrating functional genomic information into the Saccharomyces Genome Database. Nucleic Acids Res., 28, 77-80.
2. Blake, J.A., Eppig, J.T., Richardson, J.E., Bult, C.J. and Kadin, J.A. (2001) The Mouse Genome Database (MGD): Integration nexus for the laboratory mouse. Nucleic Acids Res., 29, 91-94.
3. Flybase Consortium (1998) FlyBase: a Drosophila database. Nucleic Acids Res., 26, 85-88.
4. Kanehisa, M., and Goto, S. (2000) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res., 28, 27-30.
5. Karp, P. and Gruber, T. (1995) The Generic Frame Protocol. Available via World Wide Web URL http://www.ai.sri.com/~gfp/ spec/paper/paper.html.
6. Karp, P., Krummenacker, M., Paley, S. and Wagg, J. (1999) Integrated pathway/genome databases and their role in drug discovery. Trends Biotechnol., 17, 275-281.
7. Karp, P.D. (2000) An ontology for biological function based on molecular interactions. Bioinformatics, 16, 269-285.
8. Karp, P.D. (1992) The design space of frame knowledge representation systems. Technical Report 520. SRI International AI Center, URL ftp://www.ai.sri.com/pub/papers/karp-freview.ps.Z
9. Karp, P.D. (2001) Pathway databases: A case study in computational symbolic theories. Science, 293, 2040-2044.
10. Karp, P.D., Chaudhri, V.K. and Paley, S.M. (1999) A collaborative environment for authoring large knowledge bases. J. Intelligent Information Systems, 13, 155-194.
11. Karp, P.D., Riley, M., Paley, S. and Pellegrini-Toole, A. (2002) The MetaCyc database. Nucleic Acids Res., 30, 59-61.
12. Karp, P.D., Riley, M., Saier, M., Paulsen, I.T., Paley, S. and Pellegrini-Toole, A. (2002) The EcoCyc database. Nucleic Acids Res., 30, 56-58.
13. Mural, R.J., Parang, M., Shah, M., Snoddy, J. and Uberbacher, E.C. (1999) The Genome Channel: A browser to a uniform first-pass annotation of genomic dna. Trends Genet., 15, 38-39.
14. Ouzounis, C. and Karp, P.D. (2000) Global properties of the metabolic map of Escherichia coli. Genome Res., 10, 568.
15. Paley, S. and Karp, P.D. (2002) Evaluation of computational metabolic-pathway predictions for H. pylori, in press.
16. Peterson, J.D., Umayam, L.A., Dickinson, T., Hickey, E.K. and White, O. (2001) The Comprehensive Microbial Resource. Nucleic Acids Res., 29, 123-125.
17. Stein, L., Sternberg, P., Durbin, R., Thierry-Mieg, J. and Spieth, J. (2001) WormBase: Network access to the genome and biology of Caenorhabditis elegans. Nucleic Acids Res., 29, 82-86.
18. Thierry-Mieg, J., Thierry-Mieg, D. and Stein, L. (1999) ACEDB: The ACE Database Manager. Bioinformatics Databases and Systems. Kluwer Academic Publishers, Norwell, MA, pp. 265-278.