A searching and reporting system for relational databases using a graph-based metadata representation

Journal of Chemical Information and Modeling

Volumn 45, Issue 4, 2005, Pages 863-869

  Hewitt, Robin ^a   Gobbi, Alberto ^b   Lee, Man Ling ^b  

^a Hewitt Consulting   (United States)

^b F HOFFMANN LA ROCHE LTD   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

BIOASSAY; BIOTECHNOLOGY; DATA STORAGE EQUIPMENT; DRUG PRODUCTS; METADATA; PROJECT MANAGEMENT; QUERY LANGUAGES;

DATASETS; DRUG DISCOVERY; METADATA REPRESENTATION; PROJECT TEAMS;

RELATIONAL DATABASE SYSTEMS;

ARTICLE; COMPUTER PROGRAM; COMPUTER SIMULATION; DRUG DESIGN; FACTUAL DATABASE; METHODOLOGY; STANDARD;

COMPUTER SIMULATION; DATABASES, FACTUAL; DRUG DESIGN; RESEARCH DESIGN; SOFTWARE DESIGN;

EID: 23844499225     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci050062e     Document Type: Article

References (35)

1. Gobbi, A.; Funeriu, S.; Ioannou, J.; Wang, J.; Lee, M.; Palmer, C.; Bamford, B.; Hewitt, R. Process-Driven Information Management System at a Biotech Company: Concept and Implementation. J. Chem. Inf. Comput. Sci. 2004, 44, 964-975.
2. Companies providing structure search cartridges include Daylight Inc., Mission Viejo, CA, U. S. A.; Elsevier MDL, San Leandro, CA, U. S. A.; Accelrys, San Diego, CA, U. S. A.; IDBS, Guildford, UK.; ChemAxon, Budapest, Hungary; CambridgeSoft, Cambridge, MA, U. S. A.
3. See, for example, refs 4-8.
4. Object Management Group; Common Warehouse Metamodel (CWM) Specification, version 1.0; 2001. http://www.omg.org/cwm.
5. Poole, J.; Chang, D.; Tolbert, D.; Mellor, D. Common Warehouse Metamodel: An Introduction to the Standard for Data Warehouse Integration; Wiley: New York, 2001.
6. Tannenbaum, A. Metadata Solutions: Using Metamodels, Repositories, XML, and Enterprise Portals to Generate Information on Demand; Addison-Wesley Professional: Reading, MA, 2001.
7. Metadata in Practice; Hillmann, D. I., Westbrooks, E. L., Eds.; American Library Association: Chicago, IL, 2004.
8. Marco, D.; Jennings, M. Universal Meta Data Models; Wiley: New York, 2004.
9. Nadkarni, P. M.; Brandt, C. Data Extraction and Ad Hoc Query of an Entity-Attribute-Value Database. J. Am. Med. Inf. Assoc. 1998, 5, 511-527.
10. Hara, K.; Miyazaki, T.; Nishi, T.; Iwamoto, K.; Ideshita, T. Relational database system RIQS (relational information query system). Basic Software Dev. Div., Jpn. 1985, 77, 55-62.
11. Hripcsak, G. IAIMS Architecture. J. Am. Inf. Assoc. 1997, 4, Suppl. S20-20.
12. Ihnenfeldt, W.-D.; Vogt, J. H.; Bienfait, F.; Oellien, F.; Nicklaus, M. C. Enhanced CACTVS Browser of the Open NCI Database. J. Chem. Inf. Comput. Sci. 2002, 42, 46-57.
13. Walker, M. J.; Hull, R. D.; Singh, S. B. CKB-The Compound Knowledge Base: A Text Based Chemical Search System. J. Chem. Inf. Comput. Sci. 2002, 42, 1293-1295.
14. Cohen, J. Informatics challenges in HTS data retrieval and mining. PharmaChem 2002, 1, 22-24.
15. Smith, P. M. Federated databases: The next level. Abstracts of Papers, 224th ACS National Meeting, Boston, MA, 2002; CINF-086.
16. Fisk, J. M.; Mutalik, P.; Levin, F. W.; Erdos, J.; Taylor, C.; Nadkarni, P. Integrating Query of Relational and Textual Data in Clinical Databases: A Case Study. J. Am. Med. Inf. Assoc. 2003, 10, 21-38.
17. Kasprzyk, A.; Keefe, D.; Smedley, D.; London, D.; Spooner, W.; Melsopp, C.; Hammond, M.; Rocca-Sierra, P.; Cox, T.; Birney, E. EnsMart: A generic system for fast and flexible access to biological data. Genome Res. 2004, 14, 160-169.
18. Atipat, R.; Rotstein, S. H. AQUIRE: ARQULE's United Repository and Information Exchange System. Abstracts of Papers, 228th ACS National Meeting, Philadelphia, PA, 2004; CINF-041.
19. Rojnuckarin, A.; Gschwend, D. A.; Rotstein, S. H.; Hartsough, D. S. ArQiologist: An Integrated Decision Support Tool for Lead Optimization. J. Chem. Inf. Model. 2005, 45, 2-9.
20. The data type definitions are stored in the Thor data type database. James, C. A.; Weininger, D.; Delany, J. Daylight Installation and Administration Guide; Daylight CIS Inc.: Mission Viejo, CA, 2004. http://www.daylight.com/ dayhtml/doc/admin/admin.thoreon.html#RTFToC101 (accessed: November 20, 2004).
21. ISIS/Host, Hview Developer's Guide; Elsevier MDL: San Leandro, CA.
22. CambridgeSoft, Cambridge, MA.
23. Ertl, P. JME Molecular Editor, http://www.molinspiration.com/jme/.
24. Denormalization can result in inconsistencies in the database. However, an API used for any changes on the Substance and Batch tables prevents this from happening.
25. Bohannon, P.; Freire, J.; Roy, P. Siméon, J. From XML Schema to Relations: A Cost-Based Approach to XML Storage. Proceedings of the 18th International Conference on Data Engineering, San Jose, CA, February 26-March 1, 2002, 64.
26. Krishnamurthy, R.; Kaushik, R.; Naughton, J. XML-to-SQL Query Translation Literature: The State of the Art and Open Problems. XML Symposium (XSym) 2003, 1-18.
27. It is not possible to include subqueries of two DRNodes with the same parent in one SQL statement. If the two child nodes were joined by an outer join to the parent node, the result would be a duplication of rows due to the Cartesian product of the child rows. If the two child nodes are joined by an equijoin, some rows are missed if either of the child subqueries does not return any rows, Therefore, the number of SQL statements cannot be further reduced.
28. The Apache Jakarta Project, Apache Tomcat, http://jakarta.apache.org/ tomcat/index,html.
29. The Apache Jakarta Project, http://jakarta.apache.org.
30. Heterogeneous Modeling and Design, UC Berkley, EECS, Ptolemy Project, Ptplot. http://ptolemy.eecs.berkeley.edu/java/ptplot/.
31. The Apache XML Project, Batik SVG Toolkit, http://xml.apache.org/batik/.
32. The FreeHep Java Library, http://java.freehep.org/index.html.
33. The Apache XML Project, http://xml.apache.org/.
34. The Apache XML Project, Xalan-Java. http://xml.apache.org/xalan-j/index. html.
35. JDOM. http://www.jdom.org/.