IBM®
Skip to main content
    Country/region [change]    Terms of use
 
 
 
    Home    Products    Services & solutions    Support & downloads    My account    

IBM Journal of Research and Development
Systems Biology   Volume 50, Number 6, 2006
Table of contents: HTMLPDF This article: HTMLPDF   Copyright info

Graph data management for molecular and cell biology - References

 by B. A. Eckman
and P. G. Brown
References

  1. The Institute for Systems Biology; see http://www.systemsbiology.org.
  2. H. Hermjakob, L. Montecchi-Palazzi, C. Lewington, S. Mudali, S. Kerrien, S. Orchard, M. Vingron, B. Roechert, P. Roepstorff, A. Valencia, H. Margalit, J. Armstrong, A. Bairoch, G. Cesareni, D. Sherman, and R. Apweiler, “IntAct: An Open Source Molecular Interaction Database,” Nucl. Acids Res. 32, Database issue, D452–D455 (2004).
  3. L. Salwinski, C. S. Miller, A. J. Smith, F. K. Pettit, J. U. Bowie, and D. Eisenberg, “The Database of Interacting Proteins: 2004 Update,” Nucl. Acids Res. 32, Database issue, D449–D451 (2004).
  4. G. D. Bader, D. Betel, and C. W. V. Hogue, “BIND: The Biomolecular Interaction Network Database,” Nucl. Acids Res. 31, No. 1, 248–250 (2003).
  5. M. Kanehisa, S. Goto, S. Kawashima, Y. Okuno, and M. Hattori, “The KEGG Resource for Deciphering the Genome,” Nucl. Acids Res. 32, Database issue, D277–D280 (2004).
  6. B.-J. Breitkreutz, C. Stark, and M. Tyers, “The GRID: The General Repository for Interaction Datasets,” Genome Biol. 4, No. 3, R23 (2003).
  7. M. Ashburner, C. A. Ball, J. A. Blake, D. Botstein, H. Butler, J. M. Cherry, A. P. Davis, K. Dolinski, S. S. Dwight, J. T. Eppig, M. A. Harris, D. P. Hill, L. Issel-Tarver, A. Kasarskis, S. Lewis, J. C. Matese, J. E. Richardson, M. Ringwald, G. M. Rubin, and G. Sherlock, “Gene Ontology: Tool for the Unification of Biology. The Gene Ontology Consortium,” Nature Genet. 25, No. 1, 25–29 (2000).
  8. D. L. Wheeler, T. Barrett, D. A. Benson, S. H. Bryant, K. Canese, D. M. Church, M. DiCuccio, R. Edgar, S. Federhen, W. Helmberg, D. L. Kenton, O. Khovayko, D. J. Lipman, T. L. Madden, D. R. Maglott, J. Ostell, J. U. Pontius, K. D. Pruitt, G. D. Schuler, L. M. Schriml, E. Sequeira, S. T. Sherry, K. Sirotkin, G. Starchenko, T. O. Suzek, R. Tatusov, T. A. Tatusova, L. Wagner, and E. Yaschenko, “Database Resources of the National Center for Biotechnology Information,” Nucl. Acids Res. 33, Database issue, D39–D45 (2005).
  9. S. J. Nelson, T. Powell, and B. L. Humphreys, “The Unified Medical Language System (UMLS) Project,” Encyclopedia of Library and Information Science, M. J. Bates, M. N. Maack, and M. Drake, Eds., Marcel Dekker, Inc., New York, 2002, pp. 369–378.
  10. A. L. Hopkins and C. R. Groom, “The Druggable Genome,” Nature Rev. Drug Discovery 1, No. 9, 727–730 (2002).
  11. L. Salwinski and D. Eisenberg, “Computational Methods of Analysis of Protein–Protein Interactions,” Curr. Opin. Struct. Biol. 13, No. 3, 377–382 (2003).
  12. E. Ravasz, A. L. Somera, D. A. Mongru, Z. N. Oltvai, and A.-L. Barabasi, “Hierarchical Organization of Modularity in Metabolic Networks,” Science 297, No. 5586, 1551–1555 (2002).
  13. A. Ma'ayan, S. L. Jenkins, S. Neves, A. Hasseldine, E. Grace, B. Dubin-Thaler, N. J. Eungdamrong, G. Weng, P. T. Ram, J. J. Rice, A. Kershenbaum, G. A. Stolovitzky, R. D. Blitzer, and R. Iyengar, “Formation of Regulatory Patterns During Signal Propagation in a Mammalian Cellular Network,” Science 309, No. 5737, 1078–1083 (2005).
  14. A. J. Walhout, R. Sordella, X. Lu, J. L. Hartley, G. F. Temple, M. A. Brasch, N. Thierry-Mieg, and M. Vidal, “Protein Interaction Mapping in C. elegans Using Proteins Involved in Vulval Development,” Science 287, No. 5450, 116–122 (2000).
  15. E. M. Marcotte, M. Pellegrini, M. J. Thompson, T. O. Yeates, and D. Eisenberg, “A Combined Algorithm for Genome-Wide Prediction of Protein Function,” Nature 402, No. 6757, 83–86 (1999).
  16. J. C. Mellor, I. Yanai, K. H. Clodfelter, J. Mintseris, and C. DeLisi, “Predictome: A Database of Putative Functional Links Between Proteins,” Nucl. Acids Res. 30, No. 1, 306–309 (2002).
  17. C. von Mering, L. J. Jensen, B. Snel, S. D. Hooper, M. Krupp, M. Foglierini, N. Jouffre, M. A. Huynen, and P. Bork, “STRING: Known and Predicted Protein–Protein Associations, Integrated and Transferred Across Organisms,” Nucl. Acids Res. 33, Database issue, D433–D437 (2005).
  18. U. Leser, “A Query Language for Biological Networks,” Proceedings of the 3rd European Conference on Computational Biology, Madrid, Spain, 2005, pp. ii33–ii39.
  19. F. Olken and K. D. Keck, Biopathways Graph Data Manager (BGDM) Project; see http://hpcrd.lbl.gov/staff/olken/graphdm/graphdm.htm.
  20. B. A. Eckman, “A Practitioner's Guide to Data Management and Data Integration in Bioinformatics,” Bioinformatics: Managing Scientific Data, Z. Lacroix and T. Critchlow, Eds., Morgan Kaufmann Publishers, San Francisco, 2003, pp. 35–73.
  21. S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, “Basic Local Alignment Search Tool,” J. Molec. Biol. 215, No. 3, 403–410 (1990).
  22. Ingenuity Systems, Ingenuity Pathways Knowledge Base; see http://www.ingenuity.com/products/pathways_knowledge.html.
  23. H. V. Jagadish and F. Olken, “Database Management for Life Science Research: Summary Report of the Workshop on Data Management for Molecular and Cell Biology at the National Library of Medicine, Bethesda, MD, February 2–3, 2003,” OMICS: J. Integrat. Biol. 7, No. 1, 131–137 (2003).
  24. M. Stonebraker and P. G. Brown, with D. Moore, Object-Relational DBMSs: Tracking the Next Great Wave, Morgan Kaufmann Publishers, New York, 1999.
  25. H. Wang and C. Zaniolo, “User-Defined Aggregates in Database Languages,” Proceedings of the 7th International Workshop on Database Programming Languages: Research Issues in Structured and Semistructured Database Programming, Kinloch Rannoch, Scotland, 1999, pp. 43–60.
  26. A. Benson, I. Karsch-Mizrachi, D. J. Lipman, J. Ostell, and D. L. Wheeler, “GenBank,” Nucl. Acids Res. 34, Database issue, D16–D20 (2006).
  27. K. R. Christie, S. Weng, R. Balakrishnan, M. C. Costanzo, K. Dolinski, S. S. Dwight, S. R. Engel, B. Feierbach, D. G. Fisk, J. E. Hirschman, E. L. Hong, L. Issel-Tarver, R. Nash, A. Sethuraman, B. Starr, C. L. Theesfeld, R. Andrada, G. Binkley, Q. Dong, C. Lane, M. Schroeder, D. Botstein, and J. M. Cherry, “Saccharomyces Genome Database (SGD) Provides Tools to Identify and Analyze Sequences from Saccharomyces cerevisiae and Related Sequences from Other Organisms,” Nucl. Acids Res. 32, Database issue, D311–D314 (2004).
  28. P. D. Karp, M. Riley, M. Saier, I. T. Paulsen, J. Collado-Vides, S. M. Paley, A. Pellegrini-Toole, C. Bonavides, and S. Gama-Castro, “The EcoCyc Database,” Nucl. Acids Res. 30, No. 1, 56–58 (2002).
  29. Molecule Pages: A Comprehensive Signaling Database; see http://www.signaling-gateway.org/molecule/.
  30. D. A. Benson, I. Karsch-Mizrachi, D. J. Lipman, J. Ostell, and D. L. Wheeler, “GenBank,” Nucl. Acids Res. 33, Database issue, D34–D38 (2005).
  31. A. Bairoch, R. Apweiler, C. H. Wu, W. C. Barker, B. Boeckmann, S. Ferro, E. Gasteiger, H. Huang, R. Lopez, M. Magrane, M. J. Martin, D. A. Natale, C. O'Donovan, N. Redaschi, and L.-S. L. Yeh, “The Universal Protein Resource (UniProt),” Nucl. Acids Res. 33, Database issue, D154–D159 (2005).
  32. N. Deshpande, K. J. Addess, W. F. Bluhm, J. C. Merino-Ott, W. Townsend-Merino, Q. Zhang, C. Knezevich, L. Xie, L. Chen, Z. Feng, R. K. Green, J. L. Flippen-Anderson, J. Westbrook, H. M. Berman, and P. E. Bourne, “The RCSB Protein Data Bank: A Redesigned Query System and Relational Database Based on the mmCIF Schema,” Nucl. Acids Res. 33, Database issue, D233–D237 (2005).
  33. Daylight Chemical Information Systems, Inc., Daylight Toolkit; see http://www.daylight.com/products/toolkit.html.
  34. MDL Information Systems, Inc., ISIS; see http://www.mdli.com/products/framework/isis/.
  35. F. Horn, J. Weare, M. W. Beukers, S. Horsch, A. Bairoch, W. Chen, O. Edvardsen, F. Campagne, and G. Vriend, “GPCRDB: An Information System for G Protein-Coupled Receptors,” Nucl. Acids Res. 26, No. 1, 275–279 (1998).
  36. A. Bairoch, “The ENZYME Database in 2000,” Nucl. Acids Res. 28, No. 1, 304–305 (2000).
  37. V. Matys, E. Fricke, R. Geffers, E. Gossling, M. Haubrock, R. Hehl, K. Hornischer, D. Karas, A. E. Kel, O. V. Kel-Margoulis, D. U. Kloos, S. Land, B. Lewicki-Potapov, H. Michael, R. Munch, I. Reuter, S. Rotert, H. Saxel, M. Scheer, S. Thiele, and E. Wingender, “TRANSFAC: Transcriptional Regulation, from Patterns to Profiles,” Nucl. Acids Res. 31, No. 1, 374–378 (2003).
  38. J. T. Eppig, C. J. Bult, J. A. Kadin, J. E. Richardson, J. A. Blake, A. Anagnostopoulos, R. M. Baldarelli, M. Baya, J. S. Beal, S. M. Bello, W. J. Boddy, D. W. Bradt, D. L. Burkart, N. E. Butler, J. Campbell, M. A. Cassell, L. E. Corbani, S. L. Cousins, D. J. Dahmen, H. Dene, A. D. Diehl, H. J. Drabkin, K. S. Frazer, P. Frost, L. H. Glass, C. W. Goldsmith, P. L. Grant, M. Lennon-Pierce, J. Lewis, I. Lu, L. J. Maltais, M. McAndrews-Hill, L. McClellan, D. B. Miers, L. A. Miller, L. Ni, J. E. Ormsby, D. Qi, T. B. Reddy, D. J. Reed, B. Richards-Smith, D. R. Shaw, R. Sinclair, C. L. Smith, P. Szauter, M. B. Walker, D. O. Walton, L. L. Washburn, I. T. Witham, and Y. Zhu, “The Mouse Genome Database (MGD): From Genes to Mice—A Community Resource for Mouse Biology,” Nucl. Acids Res. 33, Database issue, D471–D475 (2005).
  39. R. A. Drysdale and M. A. Crosby, “FlyBase: Genes and Gene Models,” Nucl. Acids Res. 33, Database issue, D390–D395 (2005).
  40. Saccharomyces Genome Database; see http://www.yeastgenome.org/.
  41. D. Heimbigner and D. McLeod, “A Federated Architecture for Information Management,” ACM Trans. Info. Syst. 3, No. 3, 253–278 (1985).
  42. L. M. Haas, P. M. Schwarz, P. Kodali, E. Kotlar, J. E. Rice, and W. C. Swope, “DiscoveryLink: A System for Integrated Access to Life Sciences Data Sources,” IBM Syst. J. 40, No. 2, 489–511 (2001).
  43. L. Haas, B. A. Eckman, P. Kodali, E. Lin, J. E. Rice, and P. M. Schwarz, “DiscoveryLink,” Bioinformatics: Managing Scientific Data, Z. Lacroix and T. Critchlow, Eds., Morgan Kaufmann Publishers, San Francisco, 2003, p. 428.
  44. M. S. Boguski and G. D. Schuler, “ESTablishing a Human Transcript Map,” Nature Genet. 10, No. 4, 369–371 (1995).
  45. S. T. Sherry, M. H. Ward, M. Kholodov, J. Baker, L. Phan, E. M. Smigielski, and K. Sirotkin, “dbSNP: The NCBI Database of Genetic Variation,” Nucl. Acids Res. 29, No. 1, 308–311 (2001).
  46. J. F. Allen and P. J. Hayes, “Moments and Points in an Interval-Based Temporal Logic,” Comput. Intell. 5, No. 4, 225–238 (1990).
  47. BioPAX: Biological Pathways Exchange; see http://www.biopax.org/.
  48. H. Hermjakob, L. Montecchi-Palazzi, G. Bader, J. Wojcik, L. Salwinski, A. Ceol, S. Moore, S. Orchard, U. Sarkans, C. von Mering, B. Roechert, S. Poux, E. Jung, H. Mersch, P. Kersey, M. Lappe, Y. Li, R. Zeng, D. Rana, M. Nikolski, H. Husi, C. Brun, K. Shanker, S. G. N. Grant, C. Sander, P. Bork, W. Zhu, A. Pandey, A. Brazma, B. Jacq, M. Vidal, D. Sherman, P. Legrain, G. Cesareni, I. Xenarios, D. Eisenberg, B. Steipe, C. Hogue, and R. Apweiler, “The HUPO PSI's Molecular Interaction Format—A Community Standard for the Representation of Protein Interaction Data,” Nature Biotechnol. 22, No. 2, 177–183 (2004).
  49. Kyoto Encyclopedia of Genes and Genomes (KEGG); see http://www.genome.jp/kegg/.
  50. BioCyc Database Collection; see http://www.biocyc.org/.


    About IBM    Privacy    Contact