ACM Home Page
Please provide us with feedback. Feedback
Storing semi-structured data on disk drives
Full text PdfPdf (1.45 MB)
Source
ACM Transactions on Storage (TOS) archive
Volume 5 ,  Issue 2  (June 2009) table of contents
Article No. 6  
Year of Publication: 2009
ISSN:1553-3077
Authors
Medha Bhadkamkar  Florida International University, Miami, FL
Fernando Farfan  Florida International University, Miami, FL
Vagelis Hristidis  Florida International University, Miami, FL
Raju Rangaswami  Florida International University, Miami, FL
Publisher
ACM  New York, NY, USA
Bibliometrics
Downloads (6 Weeks): 64,   Downloads (12 Months): 228,   Citation Count: 0
Additional Information:

abstract   references   index terms   collaborative colleagues  

Tools and Actions: Request Permissions Request Permissions    Review this Article  
DOI Bookmark: Use this link to bookmark this Article: http://doi.acm.org/10.1145/1534912.1534915
What is a DOI?

ABSTRACT

Applications that manage semi-structured data are becoming increasingly commonplace. Current approaches for storing semi-structured data use existing storage machinery; they either map the data to relational databases, or use a combination of flat files and indexes. While employing these existing storage mechanisms provides readily available solutions, there is a need to more closely examine their suitability to this class of data. Particularly, retrofitting existing solutions for semi-structured data can result in a mismatch between the tree structure of the data and the access characteristics of the underlying storage device (disk drive). This study explores various possibilities in the design space of native storage solutions for semi-structured data by exploring alternative approaches that match application data access characteristics to those of the underlying disk drive. For evaluating the effectiveness of the proposed native techniques in relation to the existing solution, we experiment with XML data using the XPathMark benchmark. Extensive evaluation reveals the strengths and weaknesses of the proposed native data layout techniques. While the existing solutions work really well for deep-focused queries into a semi-structured document (those that result in retrieving entire subtrees), the proposed native solutions substantially outperform for the non-deep-focused queries, which we demonstrate are at least as important as the deep-focused. We believe that native data layout techniques offer a unique direction for improving the performance of semi-structured data stores for a variety of important workloads. However, given that the proposed native techniques require circumventing current storage stack abstractions, further investigation is warranted before they can be applied to general-purpose storage systems.


REFERENCES

Note: OCR errors may be found in this Reference List extracted from the full text article. ACM has opted to expose the complete List rather than only correct and linked references.

1
 
2
Afanasiev, L., Manolescu, I., and Michiels, P. 2005. Member: A micro-benchmark repository for XQuery. In Proceedings of the 3rd International XML Database Symposium on Database and XML Technologies (XSym'05). S. Bressan et al., Eds. Lecture Notes in Computer Science, vol. 3671. Springer, 144--161.
 
3
Afanasiev, L. and Marx, M. 2006. An analysis of the current xquery benchmarks. In ExpDB. 9--20.
 
4
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. 1990. Basic local alignment search tool. J. Mol. Biol. 215, 3, 403--410.
 
5
Barbosa, D., Barta, A., Mendelzon, A. O., Mihaila, G. A., Rizzolo, F., and Rodriguez-Guianolli, P. 2001. Tox - The Toronto XML engine. In Proceedings of the Workshop on Information Integration on the Web. 66--73.
 
6
Bedathur, S. and Haritsa, J. 2006. Search-Optimized suffix-tree storage for biological applications. In Proceedings of the12th IEEE International Conference on High Performance Computing (HiPC). D. A. Bader et al., Eds. Lecture Notes in Computer Science, vol. 3769, 29--39.
7
 
8
Bhadkamkar, M., Farfan, F., Hristidis, V., and Rangaswami, R. 2006. Efficient native storage for semi-structured data (extended paper version). http://www.cis.fiu.edu/SSS/NativeXMLextended.pdf.
 
9
 
10
 
11
12
 
13
Bucy, J., Ganger, G., and Contributors. 2003. The DiskSim simulation environment version 3.0 reference manual. Tech. rep. CMU-CS-03-102, Carnegie Mellon University.
14
 
15
CDA. 2007. HL7 clinical document architecture, release 2.0. http://lists.hl7.org/read/attachment/61225/1/CDA-doc 20version.pdf. 2007.
 
16
Delcher, A., Kasif, S., Fleischmann, R., Peterson, J., White, O., and Salzberg, S. 1999. Alignment of whole genomes. Nucleic Acids Res. 27, 11, 2369--2376.
17
 
18
Dimitrijevic, Z., Rangaswami, R., Chang, E., Watson, D., and Acharya, A. 2004. Diskbench: User-Level disk feature extraction tool. Tech. rep. TR-2004-18, University of California at Santa Barbara.
 
19
Dolin, R. H., Alschuler, L., Boyer, S., Beebe, C., Behlen, F. M., Biron, P. V., and Shabo Shvo, A. 2006. HL7 clinical document architecture release 2. J. Amer. Med. Inf. Assoc. 13, 1.
 
20
 
21
Farfan, F., Hristidis, V., and Rangaswami, R. 2007. Beyond lazy XML parsing. In Proceedings of International Conference on Database and Expert Systems Applications (DEXA).
22
 
23
Franceschet, M. 2004. XPathMark: An XPath benchmark for XMark. Tech. rep. PP-2004-04, University of Amsterdam.
 
24
Franceschet, M. 2005. XPathMark: An XPath benchmark for the XMark generated data. Lecture Notes in Computer Science, vol. 3671. Springer, 129--143.
 
25
Galax. 2007. Galax. 2007. Galax homepage. http://www.galaxquery.org.
 
26
Ganger, G. R. 2001. Blurring the line between OSes and storage devices. Tech. rep. CMU-CS-01-166, Carnegie Mellon University.
27
 
28
GML. 2008. Geography markup language. http://opengis.net/gml/.
 
29
 
30
HL7. 2008. Health level seven XML. http://www.hl7.org/special/Committees/xml/xml.htm.
 
31
32
 
33
 
34
Kanne, C. and Moerkotte, G. 1999. Efficient storage of XML data. Tech. rep., Universitaet Mannheim.
35
 
36
37
38
 
39
Kundu, S. and Misra, J. 1977. A linear tree partition algorithm. SIAM J. Comput. 6, 1,151--154.
 
40
Li, Q. and Moon, B. 2001. Indexing and querying XML data for regular path expressions. VLDB J.
 
41
Manolescu, I., Miachon, C., and Michiels, P. 2006. Towards micro-benchmarking Xquery. In Proceedings of the International Workshop on Performance and Evaluation of Data Management Systems (ExpDB), 28--39.
42
 
43
 
44
Mergen, S. L. S. and Heuser, C. A. 2004. Matching of XML schemas and relational schemas. In Proceedings of the Brazilian Symposium on Databases (SBBD).
 
45
MML. 2008. Medical markup language. http://www.ncbi.nlm.nih.gov/.
 
46
Nambiar, U., Lacroix, Z., Bressan, S., Lee, M., and Li, Y. 2001. XML benchmarks put to the test. http://www.comp.nus.edu.sg/~liyg/publication/iiwas01.pdf.
 
47
48
49
50
 
51
ODS. 2008. Open document specification v1.0. http://www.oasis-open.org/committees/download.php/12572/OpenDocument-v1.0-os.pdf.
 
52
OOX. 2008. Openoffice XML file format v1.0.
 
53
 
54
Ramanath, M., Freire, J., Haritsa, J., and Roy, P. 2003. Searching for efficient XML to relational mappings. Tech. rep. TR-2003-01, DSL/SERC.
 
55
 
56
Rokhsar, D. 2007. Computational analysis of genomic sequence data. http://www.nersc.gov/news/annual reports/annrep01/sh BER 06.html.
 
57
 
58
 
59
 
60
 
61
 
62
 
63
 
64
SVG. 2008. Scalable vector graphics. http://www.w3.org/Graphics/SVG/.
 
65
66
 
67
Xalan. 2007. Xalan-Java. http://xml.apache.org/xalan-j.
 
68
XPath. 2007. XML path language (XPath) version 1.0. http://www.w3.org/TR/xpath.
 
69
XT. 2007. XT homepage. http://www.blnz.com/xt/index.html.
 
70

Collaborative Colleagues:
Medha Bhadkamkar: colleagues
Fernando Farfan: colleagues
Vagelis Hristidis: colleagues
Raju Rangaswami: colleagues