The Community for Technology Leaders
RSS Icon
Subscribe
Issue No.05 - September/October (2011 vol.13)
pp: 12-23
Lena Strömbäck , Linköping University
Juliana Freire , University of Utah
ABSTRACT
<p>Scientific exploration has become a data-intensive process, and increasing amounts of data need to be stored, analyzed, and shared. XML can help address these needs. As concrete examples from systems biology show, native XML storage can be combined with traditional relational databases to offer an effective, usable solution for storing scientific data.</p>
INDEX TERMS
Scientific data management, XML standardization, bioinformatics, hybrid XML management
CITATION
Lena Strömbäck, Juliana Freire, "XML Management for Bioinformatics Applications", Computing in Science & Engineering, vol.13, no. 5, pp. 12-23, September/October 2011, doi:10.1109/MCSE.2010.100
REFERENCES
1. F.S. Collins et al., "A Vision for the Future of Genomics Research: A Blueprint for the Genomic Era," Nature, vol. 422, 2003, pp. 835–847.
2. F. Achard, G. Vaysseix, and E. Barillot, "XML, Bio-informatics and Data Integration," Bioinformatics, vol. 17, no. 2, 2001, pp. 115–125.
3. L. Strömbäck and P. Lambrix, "Representations of Molecular Pathways: An Evaluation of SBML, PSI MI and BioPAX," Bioinformatics, vol. 21, no. 24, 2005, pp. 4401–4407.
4. L. Strömbäck, D. Hall, and P. Lambrix, "A Review of Standards for Data Exchange within Systems Bio-logy," Proteomics, vol. 7, no. 6, 2007, pp. 857–867.
5. D. Barbosa et al., XML Storage in Encyclopedia of Database Systems, Springer-Verlag, 2009.
6. D. Florescu and D. Kossmann, "Storing and Querying XML Data Using an RDMBS," IEEE Data Engineering Bulletin, vol. 22, no. 3, 1999, pp. 27–34.
7. J. Shanmugasundaram et al., "Relational Databases for Querying XML Documents: Limitations and Opportunities," Proc. Int'l Conf. Very Large Data Bases (VLDB), Morgan Kauffman, 1999, pp. 302–314.
8. D. Barbosa, J. Freire, and A. Mendelzon, "Designing Information-Preserving Mapping Schemes for XML," Proc. Int'l Conf. Very Large Databases (VLDB), Morgan Kauffman, 2005, pp. 109–120.
9. B. Bohannon et al., "From XML Schema to Relations: A Cost-Based Approach to XML Storage," Proc. IEEE Int'l Conf. Data Engineering, IEEE Press, 2002, pp. 64–75.
10. M. Hucka et al., "The Systems Biology Markup Language (SBML): A Medium for Representation and Exchange of Biochemical Network Models," Bioinformatics, vol. 19, no. 4, 2003, pp. 524–531.
11. J.J. Tyson, "Modeling the Cell Division Cycle: cdc2 and cyclin Interactions," Proc. Nat'l Academic Sciences USA, vol. 88, no. 16, 1991, pp. 7328–7332.
12. M. Rys et al., "XML and Relational Database Management Systems: The Inside Story Tutorial at SIGMOD," Proc. ACM Sigmod Int'l Conf. Management of Data, ACM Press, 2005, doi:10.1145/1066157.1066298.
13. K. Krishnaprasad et al., "Query Rewrite for XML in Oracle XML DB," Proc. Int'l Conf. Very Large Databases (VLDB), Morgan Kauffman, 2005, pp. 1122–1133.
14. S. Amer-Yahia, F. Du, and J. Freire, "A Comprehensive Solution to the XML-to-Relational Mapping Problem," Proc. ACM Int'l Workshop on Web Information and Data Management (WIDM), ACM Press, 2004, pp. 31–38.
15. S. Chaudhuri et al., "Storing XML (with XSD) in SQL Databases: Interplay of Logical and Physical Designs," IEEE Trans. Knowledge and Data Eng., vol. 17, no. 12, 2005, pp. 1595–1609.
16. M.M. Moro, L. Lipyeow, and Y.C. Chang, "Schema Advisor for Hybrid Relational-XML DBMS," Proc. ACM Sigmod Int'l Conf. Management of Data, ACM Press, 2007; doi:10.1145/1247480.1247592.
17. M. Nicola and V. Rodrigues, A Performance Comparison of DB2 9 pureXML and CLOB or Shredded XML Storage, tech. report, IBM, 2006; www.ibm.com/developerworks/db2/library/techarticle/ dm-0612nicolaindex.html.
18. T. Grust, J. Rittinger, and J. Teubner, "Why Off-the-Shelf RDBMSs Are Better at XPath Than You Might Expect," Proc. ACM Sigmod Int'l Conf. Management of Data, ACM Press, 2007, doi:10.1145/1247480.1247591.
28 ms
(Ver 2.0)

Marketing Automation Platform Marketing Automation Tool