Process-driven information management system at a biotech company: Concept and implementation

Journal of Chemical Information and Computer Sciences

Volumn 44, Issue 3, 2004, Pages 964-975

  Gobbi, Alberto ^a   Funeriu, Sandra ^a   Ioannou, John ^a   Wang, Jinyi ^a   Lee, Man Ling ^a   Palmer, Chris ^b   Bamford, Bob ^b   Hewitt, Robin ^c  

^a F HOFFMANN LA ROCHE LTD   (Switzerland)

^b Managed Ventures LLC   (United States)

^c Hewitt Consulting   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL INFORMATION SYSTEMS; HIGH-THROUGHPUT (HT) OPERATIONS; PHARMACEUTICAL COMPANIES;

BIOTECHNOLOGY; BOOLEAN ALGEBRA; DATA PROCESSING; DECISION MAKING; INVENTORY CONTROL; KNOWLEDGE ACQUISITION; MAINTENANCE; MANAGEMENT INFORMATION SYSTEMS; NONBIBLIOGRAPHIC RETRIEVAL SYSTEMS; PROJECT MANAGEMENT; QUALITY CONTROL;

DRUG PRODUCTS;

EID: 2942702318     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci034269o     Document Type: Article

References (47)

1. Ahlberg, C. Visual exploration of HTS databases: bridging the gap between chemistry and biology. Drug Discov. Today 1999, 4, 370-376.
2. Fay, N.; Ullmann, D. Leveraging process integration in early drug discovery. Drug Discov. Today (information biotechnology suppl.) 2002, 7, S181-S186.
3. Claus, B. L.; Underwood, D. J. Discovery informatics: its evolving role in drug discovery. Drug Discov. Today 2002, 7, 957-966.
4. Peakman, T.; Franks, S.; White, C.; Beggs, M. Delivering the power of discovery in large pharmaceutical organizations. Drug Discov. Today 2003, 8, 203-211.
5. Trepalin, S. V.; Yarkov, A. V. CheD: Chemical Database Compilation Tool, Internet Server, and Client for SQL Servers. J. Chem. Inf. Comput. Sci. 2001, 41, 100-107.
6. Ihlenfeldt, W.-D.; Voigt, J. H.; Bienfait, B.; Oellien, F.; Nicklaus, M. C. Enhanced CACTVS Browser of the Open NCI Database. J. Chem. Inf. Comput. Sci. 2002, 42, 46-57.
7. Adams, N.; Schubert, U.S. From Data to Knowledge: Chemical Data Management, Data Mining, and Modeling in Polymer Science. J. Comb. Chem. 2004, 6, 12-23.
8. Vendors of "off-the-shelf chemical, analytical or assay data management system or components include: Advanced Chemistry Development Inc, Toronto, Ontario, Canada; CambridgeSoft, Cambridge, MA, U.S.A.; ID Business Solution Guildford, Surrey, UK.; MDL Information System Inc. San Leandro, CA, U.S.A.; NuGenesis Technologies Corporation, Westborough, MA.
9. Examples of proprietary developments: Celltech's Registration System, http://www.daylight.com/products/casestudies/f_casestudy.html; Senomyx' HT Discovery Platform, http://www.daylight.com/meetings/mug03/Cohen/index.html; Actelion's OSIRIS System http://www.actelion.com/Apps/WebObjects/Actelion.woa/ wa/dp?name=research_informatics.
10. Miled, Z. B.; Liu, Y.; Powers D.; Bukhres O.; Bem M.; Jones R.; Oppelt R. J. An Efficient Implementation of a Drug Candidate Database. J. Chem. Inf. Comput. Sci. 2003, 43, 25-35.
11. The Apache Jakarta Project, Apache Tomcat, http://jakarta.apache.org/ tomcat/index.html.
12. The Apache Jakarta Project, http://jakarta.apache.org.
13. The Apache Software License, http://www.apache.org/licenses/LICENSE.
14. The Apache Jakarta Project, Mailing Lists, http://jakarta.apache.org/ site/mail.html.
15. java.sun.com, Java Servlet Technology, http://java.sun.com/products/ servlets.
16. java.sun.com, JavaServer Pages, http://java.sun.com/products/jsp.
17. Heterogeneous Modeling and Design UC Berkley, EECS, Ptolemy Project, Ptplot http://ptolemy.eecs.berkeley.edu/java/ptplot/.
18. The Apache XML Project, Batik SVG Toolkit, http://xml.apache.org/batik/.
19. The FreeHep Java Library, http://java.freehep.org/index.html.
20. The Apache XML Project, http://xml.apache.org/.
21. The Apache XML Project, Xalan-Java, http://xml.apache.org/xalanj/index. html.
22. JDOM, http://www.jdom.org/.
23. The Apache Jakarta Project, Struts, http://jakarta.apache.org/struts/.
24. Rohde B. private communication.
25. Daylight Theory Manual, http://www.daylight.com/dayhtml/doc/theory/ theory.smiles.html.
26. James, C. A.; Weininger, D. Daylight Software Manual Version 4.42. Daylight Chemical Information Systems Inc., Irvine 1996. http://www.daylight. com.
27. ChemDraw is a product of CambridgeSoft Corporation Cambridge, MA, http://www.camsoft.com/.
28. Rohde B., private communication.
29. NUTS NMR Data Procession Software is a product of AcomNMR, Inc. Livemore, CA, http://www.acomnmr.com/.
30. PostgreSQL, http://www.postgresql.org/.
31. MySQL is developed, supported and distributed by MySQL AB, Uppsala, Sweeden, http://www.mysql.com/.
32. Oracle Corporation, Redwood Shores, CA, http://www.oracle.com/.
33. Raphaely, D.; Rawles, J.; Murray, C.; Agarwal, N.; Al-Shaikh, R.; Banerjee, S.; Das, D.; Murthy, R.; Trezza-Miller, C. Oracle8i: Data Cartridge Developer's Guide, Oracle Corporation: Redwood Shores 1999.
34. Gobbi, A.; Rohde B. unpublished work.
35. Groff, J. R.; Weinberg, P. N. SQL: The Complete Reference, 2nd ed.; McGraw-Hill: U.S.A., 2002.
36. Amanda, University of Maryland at College Park, 1997, http://www.amanda.org/. Further information may be found in the following: Preston, W. C. Unix Backup & Recovery; O'Reilly 1999.
37. ACD Finder is a product from MDL Information System Inc. San Leandro, CA 94577, U.S.A., http://www.mdli.com/.
38. SMIRKS is a language defined for generic reactions developed by Daylight Inc. (cf. ref 26), http://www.daylight.com/dayhtml/doc/theory/theory.rxn.html.
39. The IRORI synthesizer is a product of Discovery Partners International, San Diego, CA, http://www.discoverypartners.com/.
40. The largest number of compounds registered with the batch registration program to date is around 41 500 compounds on plates. This took about 2 h.
41. Gobbi, A.; Lee, M. DISE: Directed Sphere Exclusion. J. Chem. Inf. Comput. Sci. 2003, 43, 317-323.
42. SMS500 Autosampler is available from Varian, Inc., Palo Alto, CA 94304, U.S.A., http://www.varianinc.com/.
43. Chempack is an add-on to the Varian VNMR software.
44. ATHENA was implemented together with of Managed Ventures LLC, Irvine, USA. OpenHTS a follow-up implementation of a very similar system is available from Managed Ventures.
45. Zhang, J. H.; Chung, T. D.; Oldenburg, K. R. A Simple Statistical Parameter for Use in Evaluation and Validation of High Throughput Screening Assays. J. Biomol. Screen. 1999, 4, 67-73
46. Press, W. H.; Teukolsky, S. A.; Vetterling, W. T.; Flannery, B. P. Numerical Recipies in C; Cambridge University Press: UK, 1992.
47. QueryBuilder and the ListHandling module were designed and implemented together with Hewitt Consulting, San Diego, U.S.A.