Data processing: database and file management or data structures – Database design – Database and data structure management
Reexamination Certificate
2011-01-04
2011-01-04
Pham, Khanh B (Department: 2166)
Data processing: database and file management or data structures
Database design
Database and data structure management
C707S798000, C702S019000, C702S020000, C706S045000
Reexamination Certificate
active
07865534
ABSTRACT:
Method and system for managing and evaluating life science data. Life Science data is placed in a knowledge base, that may be used for a variety of analysis tasks. Creating a knowledge base from the life science data involves generating two or more nodes indicative of life science data, assigning to one or more pairs of nodes a representation descriptor that corresponds to a relationship between the nodes, and assembling the nodes and the relationship descriptor into a database, such that at least one of the nodes is joined to another node by a representation descriptor. In some embodiments, the representation descriptor includes a case frame that describes the relationships between elements of life science data.
REFERENCES:
patent: 4935877 (1990-06-01), Koza
patent: 5136686 (1992-08-01), Koza
patent: 5148513 (1992-09-01), Koza et al.
patent: 5343554 (1994-08-01), Koza et al.
patent: 5390282 (1995-02-01), Koza et al.
patent: 5742738 (1998-04-01), Koza et al.
patent: 5867397 (1999-02-01), Koza et al.
patent: 5914891 (1999-06-01), McAdams et al.
patent: 6058385 (2000-05-01), Koza et al.
patent: 6360191 (2002-03-01), Koza et al.
patent: 6424959 (2002-07-01), Bennett, III et al.
patent: 6532453 (2003-03-01), Koza et al.
patent: 6564194 (2003-05-01), Koza et al.
patent: 6594587 (2003-07-01), Askenazi
patent: 6665669 (2003-12-01), Han et al.
patent: 6741986 (2004-05-01), Cho et al.
patent: 6772160 (2004-08-01), Cho et al.
patent: 2001/0016822 (2001-08-01), Bessette
patent: 2001/0047353 (2001-11-01), Talib et al.
patent: 2002/0002559 (2002-01-01), Busa
patent: 2002/0049782 (2002-04-01), Herzenberg et al.
patent: 2002/0087275 (2002-07-01), Kim et al.
patent: 2002/0123847 (2002-09-01), Askenazi
patent: 2002/0198858 (2002-12-01), Stanley et al.
patent: 2003/0074516 (2003-04-01), Cho et al.
patent: 1248231 (2002-10-01), None
patent: WO 02/11048 (2002-02-01), None
patent: WO 02/093409 (2002-11-01), None
patent: WO 03/067504 (2003-08-01), None
patent: WO 03/082214 (2003-10-01), None
Goldberg, David E., “Genetic and Evolutionary Algorithms Come of Age,” Communications of the ACM, vol. 37, No. 3, Mar. 1994, pp. 113-119.
van Helden, Jacques, etal., “Representing and Analysing Molecular and Cellular Function Using the Computer,” Biol. Chem., vol. 381, pp. 921-935, Sep.-Oct. 2000.
Uetz, Peter, et al., “Visualization and Integration of Protein-Protein Interactions,” in Golemis E (ed.)Protein-Protein Interactions—A Molecular Cloning Manual, Cold Spring Harbor Laboratory Press (available at: http://itgmv1.fzk.de/www/itg/uetz/publications/Visualization.pdf), 2002.
International Search Report for International Application No. PCT/US/2005/00202 mailed from the International Searching Authority on Nov. 24, 2005.
Written Opinion of the International Searching Authority for International Application No. PCT/US/2005/00202 mailed from the International Searching Authority on Nov. 24, 2005.
International Search Report for PCT/US03/36857, mailed Mar. 9, 2005.
International Preliminary Report on Patentability for PCT/US2004/039159 dated May 29, 2006.
Written Opinion of the International Searching Authority for PCT/US2004/039159 dated May 29, 2006.
International Search Report for International Application No. PCT/US/2004/039159 mailed from the International Searching Authority on Aug. 31, 2005.
Written Opinion of the International Searching Authority for International Application No. PCT/US/2004/039159 mailed from the International Searching Authority on Aug. 31, 2005.
Kanehisa, Minoru et al, “The KEGG Databases at GenomeNet,” Nucleic Acids Research, vol. 30, No. 1, pp. 42-46 (2002).
European Search Report for Application No. PCT/US03/30653 dated Sep. 6, 2007 (3 pages).
Center for Development of Advanced Computing, “Workshop on Genetic Algorithms in Bioinformatics,” http://www.cdacindia.com/html/ecents/bioinfo/genetic/genidx.asp, pp. 1-6 (printed Oct. 22, 2002).
Jansen, Ronald, “A Bayesian Networks Approach for Predicting Protein-Protein Interactiojns from Genomic Data,” Science, vol. 302, pp. 449-453 (Oct. 17, 2003).
Karp, Peter D., “The EcoCyc Database,” pp. 1-6 (Jan. 25, 2002).
Karp, Peter D., “Integrated Access to Metabolic and Genomic Data,” pp. 1-32 (Apr. 1, 1996).
Karp, Peter D., “The MetaCyc Database,” pp. 1-7 (Jan. 25, 2002).
Karp, Peter D., “Pathway Databases: A Case Study in Computational Symbolic Theories,” Science, vol. 293, pp. 2040-2044 (Sep. 14, 2001).
Karp, Peter D., “The Pathway Tools Software,” Bioinformatics, vol. 18 Suppl. 1 2002, pp. S1-S8 (2002).
Koza, John R., “Reverse Engineering and Automatic Synthesis of Metabolic Pathways From Observed Data Using Genetic Programming,” pp. 1-53 (2000).
Koza, John R., “Reverse Engineering and Automatic Synthesis of Metabolic Pathways From Observed Data Using Genetic Programming,” Symposium on Computational Discovery of Communicatable Knowledge, pp. 1-63 (Mar. 25, 2001).
Koza, John R., “Reverse Engineering and Automatic Synthesis of Metabolic Pathways From Observed Data Using Genetic Programming,” Biomedical Informatics, pp. 1-12, Aug. 2000.
Rindfleisch, Thomas C., “Extracting Molecular Binding Relationships from Biomedical Text,” pp. 188-195, 2000.
Stevens, Robert “Building a Reason-able Bioinformatics Ontology Using OIL,” Department of Computer Science, University of Manchester, pp. 1-11, Aug. 2001.
Yen, John, “A Hybrid Approach to Modeling Metabolic Systems Using Genetic Algorithm and Siomplex Method,” pp. 1-42, Feb. 1995.
Yen, John, “Using Fuzzy Logic and a Hybrid Genetic Algorithm for Metabolic Modeling,” pp. 1-6, 1996.
International Search Report for PCT/US2003/030653, mailed Feb. 3, 2004.
Chandra D. Navin
Chandra, legal representative Fatima
Elliston Keith O.
Neumann Eric K.
Pratt Dexter R.
Genstruct, Inc.
Judson David H.
Pham Khanh B
LandOfFree
System, method and apparatus for assembling and mining life... does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with System, method and apparatus for assembling and mining life..., we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and System, method and apparatus for assembling and mining life... will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-2625966