Design and use of relational databases in chemistry

Design and Use of Relational Databases in Chemistry

Volumn , Issue , 2008, Pages 1-231

  O'Donnell T J ^a  

^a NONE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

STRUCTURE (COMPOSITION);

CHEMICAL DATABASE; CHEMICAL INFORMATION; DATA INTEGRITY; DATABASE DESIGN; OPEN SOURCES; POSTGRESQL; RELATIONAL DATABASE;

PROJECTILES;

EID: 85055209381     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Book

References (97)

1. Codd, E.F. 1970. A relational model of data for large shared data banks. Communications of the ACM, 13(6):377–387.
2. U.S. Environmental Protection Agency. 2007. Estimation Program Interface (EPI) suite. http://www.epa.gov/oppt/exposure/pubs/episuite.htm (accessed April 21, 2008).
3. Dar, S., Hecht, G., and Shochat, E. 2004. Industrial sessions: Database applications: dbSwitch™: Towards a database utility. In Proceedings of the 2004 ACM SIGMOD International Conference on Management of Data SIGMOD, ed. Weikum, E., König, A.C., and Deßloch, S. Association for Computing Machinery, pp. 892–896.
4. PostgreSQL 8.2 documentation. 2008. Dblink. http://www.postgresql.org/docs/current/static/dblink.html (accessed April 21, 2008).
5. Fermilab Computing Division. 2005. Comparison of Oracle, MySQL and PostgreSQL DBMS. http://www-css.fnal.gov/dsg/external/freeware/mysql-vs-pgsql.html (accessed April 21, 2008).
6. O’Donnell, T.J. 2005. CHORD extension to PostgreSQL. http://www.gnova. com (accessed April 21, 2008).
7. Schmid, E. 2004. Pgchem::tigress extension to PostgreSQL. http://pgfoundry. org/projects/pgchem/(accessed April 21, 2008).
8. Landrum, G. 2006. RDKit: Cheminformatics and Machine Learning Software. http://rdkit.sourceforge.net/(accessed April 22, 2008).
9. Daycart. 2008. http://www.daylight.com (accessed April 21, 2008);
10. Jchem cartridge. http://www.chemaxon.com (accessed April 21, 2008);
11. CambridgeSoft Oracle cartridge. http://www.cambridgesoft.com (accessed April 21, 2008);
12. MDL Isentris. http://www.symyx.com (accessed April 21, 2008)
13. Kumar, T. 2005. Small molecules database cartridge. http://www.unm. edu/~tharun/smdb.html (accessed April 21, 2008).
14. Kline, K. 2004. SQL in a Nutshell, 2nd Edition, Sebastopol, CA: O’Reilly.
15. PostgreSQL 8.2 documentation. 2008. C-language functions. http://www.postgresql.org/docs/8.2/static/xfunc-c.html (accessed April 21, 2008).
16. PhpPgAdmin. 2008. http://www.phppgadmin.com (accessed April 18, 2008).
17. PhpMyAdmin. 2008. http://www.phpmyadmin.net/(accessed April 18, 2008).
18. PgAdminIII. 2008. http://www.pgadmin.org (accessed April 18, 2008).
19. Oracle SQL Developer. 2008. http://www.oracle.com/technology/prod-ucts/database/sql_developer/index.html
20. Toad DBA Suite for Oracle. http://www.quest.com/toad-dba-suite-for-oracle/(accessed April 18, 2008).
21. The R Project for statistical computing. 2008. http://www.r-project.org/(accessed April 18, 2008).
22. RODBC database interface module. 2008. http://cran.r-project.org/web/packages/RODBC/index.html (accessed April 18, 2008).
23. Spotfire. 2008. http://spotfire.tibco.com/(accessed April 18, 2008).
24. SciTegic platform. 2008. http://www.accelrys.com/products/scitegic/(accessed April 18, 2008).
25. Perl DBI module. http://search.cpan.org/~timb/DBI/DBI.pm (accessed April 18, 2008).
26. Matthew, N., and Stones, R. 2005. Beginning databases with PostgreSQL: From novice to professional. 2nd ed. New York: Apress.
27. PyGreSQL – PostgreSQL module for Python. 2006. http://www.pygresql. org/(accessed April 18, 2008).
28. PyGreSQL programming information. http://www.pygresql.org/pg.html (accessed April 18, 2008).
29. Oracle OCI8 functions. 2008. http://us2.php.net/oci (accessed April 18, 2008).
30. PostgreSQL functions. 2008. http://us3.php.net/pgsql (accessed April 18, 2008).
31. Pg_fetch_result function. 2008. http://us.php.net/manual/function.pg-fetch-result.php (accessed April 18, 2008).
32. Package java.sql. 2003. http://java.sun.com/j2se/1.4.2/docs/api/java/sql/package-summary.html (accessed April 18, 2008).
33. PostgreSQL JDBC driver. 2008. http://jdbc.postgresql.org/(accessed April 18, 2008).
34. Creating complete JDBC applications. 2008. http://java.sun.com/docs/books/tutorial/jdbc/basics/complete.html (accessed April 18, 2008).
35. Bales, D.K. 2001. Java programming with Oracle JDBC. Sebastopol, CA: O’Reilly.
36. Melton, J. and Eisenberg, A. 2000. Understanding SQL and Java together: A guide to SQLJ, JDBC, and related technologies, San Francisco: Morgan Kaufmann.
37. PubChem Compound. http://www.ncbi.nlm.nih.gov/sites/entrez?db= pccompound (accessed April 18, 2008).
38. PubChem Text Search. http://pubchem.ncbi.nlm.nih.gov/(accessed April 18, 2008).
39. PubChem BioAssay. http://www.ncbi.nlm.nih.gov/sites/entrez?db= pcassay (accessed April 18, 2008).
40. What is phpPgAdmin. 2008. http://phppgadmin.sourceforge.net/(accessed April 18, 2008).
41. O’Boyle, N., 2007. Pybel—Hack that SD file. http://baoilleach.blogspot. com/2007/07/pybel-hack-that-sd-file.html (accessed April 18, 2008).
42. O’Donnell, T.J., 2008. Sdf2sql program. http://www.gnova.com/software. html (accessed April 18, 2008).
43. Materialized views. http://snapshot.projects.postgresql.org/(accessed April 18, 2008).
44. Pauling, L. 1939. The nature of the chemical bond and the structure of molecules and crystals, 3rd ed. Ithaca, NY: Cornell University Press.
45. Sainsbury, M. 1992. Aromaticity. New York, Oxford University Press, Inc.
46. Molfiles. 2008. http://en.wikipedia.org/wiki/MDL_Molfile (accessed April 18, 2008).
47. PDB Documentation. 2008. http://www.wwpdb.org/docs.html (accessed April 18, 2008).
48. Weininger D. 1988. SMILES, a chemical language and information system, 1. Introduction to methodology and encoding rules. J. Chem. Inf. Comput. Sci. 28:31–36.
49. Weininger, D., Weininger, A., and Weininger, J.L. 1989. SMILES 2. Algorithm for generation of unique SMILES notation. J. Chem. Inf. Comput. Sci. 29:97–101.
50. O’Donnell, T.J. 2008. CHORD. http://www.gnova.com/(accessed April 18, 2008).
51. DayCart®: Chemical intelligence for an Oracle environment. 2007. http://daylight.com/products/daycart.html (accessed April 18, 2008).
52. O’Shea, M.D. 2008. Chemoinformatics chemistry data cartridges. http://www.strychnine.co.uk/oracledatacartridges.html (accessed April 18, 2008).
53. SMARTS tutorial. 2008. http://www.daylight.com/dayhtml/doc/theory/index.html (accessed April 18, 2008).
54. Lipinski, C.A., Lombardo, F., Dominy, B.W., and Feeney, P.J. 2001. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Del. Rev. 46:3–26.
55. Sayle, R. and Skillman, G. 2002. Hooked on protonics. http://www.eyesopen. com/about/events/presentations/acs02/tsld018.htm (accessed April 18, 2008).
56. Sayle, R. and Delany, J. 1999. Canonicalization and enumeration of tau-tomers. http://www.daylight.com/meetings/emug99/Delany/taut_html/index.htm (accessed April 18, 2008).
57. ChemAxon. Calculator plugins. 2008. http://www.chemaxon.com/mar-vin/help/calculations/calculator-plugins.html#tautomer (accessed April 18, 2008).
58. ScienceServe. 2008. Tautomer. http://www.scienceserve.com/Software/molnet/tautomer/index.htm (accessed April 18, 2008).
59. Oellien F., Cramer, J., Beyer, C., Ihlenfeldt, W., and Selzer, P.M. 2006. The impact of tautomer forms on pharmacophore-based virtual screening, J. Chem. Inf. Model. 46(6):2342–2354.
60. Stein, S.E., Heller, S.R., and Tchekhovski, D. 2003. An open standard for chemical structure representation: The IUPAC chemical identifier. In Proceedings of the 2003 International Chemical Information Conference, ed. H. Collier, 131–143. Nimes, France: Infonortics.
61. Durant, J.L., Leland, B.A., Henry, D.R., and Nourse, J.G., 2002. Reoptimization of MDL keys for use in drug discovery, J. Chem. Inf. Comput. Sci., 42(6): 1273–1280.
62. Hash function. 2008. http://en.wikipedia.org/wiki/Hash_function (accessed April 18, 2008).
63. Fingerprints—Screening and Similarity. 2007. http://daylight.com/dayhtml/doc/theory.finger.html (accessed April 18, 2008).
64. Bender, A., Mussa, H.Y., Glen, R.C., and Reiling, S. 2004. Molecular similarity searching using atom environments, information-based feature selection, and a naive Bayesian classifier. J. Chem. Inf. Comput. Sci. 44(1):170–178.
65. Tanimoto, T.T. 1957. IBM Internal Report, November 17.
66. Hert, J., Willett, P., Wilton, D.J., Acklin, P., Azzaoui, K., Jacoby, E., and Schuffenhauer, A. 2004. Comparison of fingerprint-based methods for virtual screening using multiple bioactive reference structures. J. Chem. Inf. Comput. Sci. 44(3):1177–1185.
67. Ertl, P., Rohde, B., and Selzer, P. 2000. Fast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of drug transport properties. J. Med. Chem. 43:3714–3717.
68. Wildman, S.A. and Crippen, G.M. 1999. Prediction of physicochemical parameters by atomic contributions. J. Chem. Inf. Comput. Sci. 39: 868–873.
69. Andrews R., Craik, D.J., and Martin, J.L. 1984. Functional group contributions to drug-receptor interactions. J. Med. Chem. 27(12): 1648–1657.
70. SMIRKS tutorial. 2007. http://www.daylight.com/dayhtml_tutorials/lan-guages/smirks/index.html (accessed April 18, 2008).
71. Yadav M., Kelley, B.P. and Silverman, S.M. 2004. The potential of a chemical graph transformation system. In Graph Transformations: ICGT 2004 Proceedings, ed. H., Ehrig, G., Engels, F., Parisi-Presicce and G., Rozenberg, 83–95. Berlin: Springer Verlag.
72. Ugi, I., 1962. The α-addition of immonium ions and anions to isonitriles accompanied by secondary reactions. Angewandte Chemie International Edition in English 1(1):8–21.
73. Plpgsql. 2008. http://www.postgresql.org/docs/8.2/static/plpgsql.html (accessed April 18, 2008).
74. Stones R. and Matthew, N. 2005. Beginning databases with PostgreSQL. Berkeley: Apress.
75. Tubert-Brohman, I. PerlMol—Perl Modules for Molecular Chemistry. 2006. http://www.perlmol.org/(accessed April 18, 2008).
76. Kelley, B. FROWNS. 2002. http://frowns.sourceforge.net/(accessed April 18, 2008).
77. Open Babel: The Open Source Chemistry Toolbox. 2008. http://openbabel. sourceforge.net/(accessed April 18, 2008).
78. O’Donnell, T.J. CHORD. 2008. http://www.gnova.com/(accessed April 18, 2008).
79. Schmid, E.-G. 2004. Pgchem::tigress extension to PostgreSQL. http://pgfoundry.org/projects/pgchem/(accessed April 18, 2008).
80. Grimes, S. 1998. Modeling object/relational databases. http://www.dbmsmag. com/9804d13.html (accessed April 18, 2008).
81. Object-relational database. 2008. http://en.wikipedia.org/wiki/Object-relational_database (accessed April 18, 2008).
82. Devarakonda, R. S. 2001. Object-relational database systems—The road ahead. http://www.acm.org/crossroads/xrds7-3/ordbms.html (accessed April 18, 2008).
83. O’Donnell, T.J., Rao, S.N., Koehler, K., Martin, Y.C., and Eccles, B. 1990. A general approach for atom-type assignment and the interconversion of molecular structure files. J. Comp. Chem. 12(2):209–214.
84. OpenBabel. http://openbabel.sourceforge.net/(accessed April 18, 2008).
85. QSAR World. http://www.qsarworld.com/(accessed April 18, 2008).
86. Porter, J.R., Archibald, S.C., Brown, J.A. et. al. 2003. Dehydrophenylalanine derivatives as VLA-4 integrin antagonists. Bioorg. Med. Chem. Lett. 13(5): 805–808.
87. VLA4 dataset. http://www.qsarworld.com/qsar-datasets-porter.php (accessed April 18, 2008).
88. Perl DBI fetchall_array. http://search.cpan.org/~timb/DBI/DBI. pm#fetchall_arrayref (accessed April 18, 2008).
89. The R Manuals. 2008. http://cran.r-project.org/manuals.html (accessed April 18, 2008).
90. Venables, W. N. and Ripley, B.D. 2002. Modern Applied Statistics with S. 4th ed. New York: Springer.
91. O’Donnell, T.J. 2006. Using relational databases for physical property prediction. The 232nd ACS National Meeting, San Francisco, CA, September 10–14, 2006.
92. Renxiao Wang, R., Fu, Y., and Lai, L. 1997. A new atom-additive method for calculating partition coefficients. J. Chem. Inf. Comput. Sci. 37:615–621.
93. Kündig, E.P., García, A.E., Lomberget, T., and Bernardinelli, G. 2006. Rediscovery, isolation, and asymmetric reduction of 1,2,3,4-tetrahydronaph-thalene-1,4-dione and studies of its [Cr(CO)3] complex. Angew. Chem. Internat. Ed. 45(1):98–101.
94. Pubchem at http://ncbi.nih.gov/pubchem/(accessed April 18, 2008).
95. Porter, J.R., Archibald, S.C., and Brown, J.A. 2003. Dehydrophenylalanine derivatives as VLA-4 integrin antagonists. Bioorg. Med. Chem. Lett. 13(5):805–808.
96. Marvin. http://www.chemaxon.com/(accessed April 18, 2008).
97. FTP directory /pubchem at ftp.ncbi.nih.gov. 2008: pubchem. ftp://ftp.ncbi. nih.gov/pubchem/ (accessed April 18, 2008).