PODD - Towards an extensible, domain-agnostic scientific data management system

Proceedings - 2010 6th IEEE International Conference on e-Science, eScience 2010

Volumn , Issue , 2010, Pages 137-144

  Li, Yuan Fang ^a   Kennedy, Gavin ^a   Davies, Faith ^a   Hunter, Jane ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

Data management systems; Ontology centric architecture; OWL; Phenomics; PODD

Indexed keywords

DATA MANAGEMENT SYSTEM; ONTOLOGY-CENTRIC; OWL; PHENOMICS; PODD;

ARCHITECTURE; ONTOLOGY; PROJECT MANAGEMENT; QUERY LANGUAGES; RECONNAISSANCE AIRCRAFT; SEMANTICS;

INFORMATION MANAGEMENT;

EID: 79951829337     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/eScience.2010.44     Document Type: Conference Paper

References (26)

1. J. Gray, D. T. Liu, M. Nieto-Santisteban, A. Szalay, D. J. DeWitt, and G. Heber, "Scientific data management in the coming decade," SIGMOD Rec., vol. 34, no. 4, pp. 34-41, 2005.
2. A. Shah, M. Singhal, K. Klicker, E. Stephan, H. Wiley, and K. Waters, "Enabling high-throughput data management for systems biology: The bioinformatics resource manager," Bioinformatics, vol. 23, no. 7, pp. 906-909, 2007.
3. T. Berners-Lee, "Linked Data," 2007, http://www.w3.org/ DesignIssues/LinkedData.html.
4. S. Auer, C. Bizer, G. Kobilarov, J. Lehmann, R. Cyganiak, and Z. Ives, "DBpedia: A Nucleus for a Web of Open Data," in Proceedings of 6th International Semantic Web Conference, 2nd Asian Semantic Web Conference (ISWC+ASWC 2007), November 2008, pp. 722-735. [Online]. Available: http://dx.doi.org/10.1007/978-3-540-76298-0 52
5. A. Ruttenberg, J. Rees, M. Samwald, and M. S. Marshall, "Life Sciences on the Semantic Web: the Neurocommons and Beyond," Briefings in Bioinformatics, vol. 10, no. 2, pp. 193-204, 2009.
6. B. Smith, M. Ashburner, C. Rosse et al., "The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration," Nature Biotechnology, vol. 25, no. 11, pp. 1251-1255, November 2007.
7. M. Ashburner, C. A. Ball, J. A. Blake et al., "Gene Ontology: Tool for the Unification of Biology," Nat Genet, vol. 25, no. 1, pp. 25-29, May 2000. [Online]. Available: http://dx.doi.org/10.1038/75556
8. C. Bizer, T. Heath, and T. Berners-Lee, "Linked data - the story so far," International Journal on Semantic Web and Information Systems (IJSWIS), vol. 5, no. 3, pp. 1-22, 2009.
9. Y.-F. Li, G. Kennedy, F. Davies, and J. Hunter, "PODD: An Ontologydriven Data Repository for Collaborative Phenomics Research," in Proceedings of 12th International Conference on Asian Digital Libraries (ICADL 2010). Springer-Verlag, Jun. 2010, pp. 179-188.
10. W. Hoschek, F. J. Jaén-Martínez, A. Samar, H. Stockinger, and K. Stockinger, "Data management in an international data grid project," in GRID '00: Proceedings of the First IEEE/ACM International Workshop on Grid Computing. London, UK: Springer-Verlag, 2000, pp. 77-90.
11. E. W. Sayers et al., "Database resources of the national center for biotechnology information." Nucleic acids research, vol. 37, no. Database issue, pp. D5-15, January 2009. [Online]. Available: http://dx.doi.org/10.1093/ nar/gkn741
12. C. H. Wu, R. Apweiler, A. Bairoch, D. A. Natale, W. C. Barker, B. Boeckmann, S. Ferro, E. Gasteiger, H. Huang, R. Lopez, M. Magrane, M. J. Martin, R. Mazumder, C. O'Donovan, N. Redaschi, and B. Suzek, "The universal protein resource (uniprot): an expanding universe of protein information," Nucl. Acids Res., vol. 34, no. suppl 1, pp. D187-191, January 2006. [Online]. Available: http://dx.doi.org/10.1093/nar/gkj161
13. F. Wang, P.-E. Bourgué, G. Hackenberg, M. Wang, D. Kaltschmidt, and P. Liu, "Sciport: an adaptable scientific data integration platform for collaborative scientific research," in VLDB '07: Proceedings of the 33rd international conference on Very large data bases. VLDB Endowment, 2007, pp. 1310-1313.
14. C. Baru, R. Moore, A. Rajasekar, and M. Wan, "The SDSC storage resource broker," in CASCON '98: Proceedings of the 1998 conference of the Centre for Advanced Studies on Collaborative research. IBM Press, 1998, p. 5.
15. K. Krauter, R. Buyya, and M. Maheswaran, "A taxonomy and survey of grid resource management systems for distributed computing," Softw. Pract. Exper., vol. 32, no. 2, pp. 135-164, 2002.
16. O. Corcho, P. Alper, I. Kotsiopoulos, P. Missier, S. Bechhofer, and C. Goble, "An overview of s-ogsa: A reference semantic grid architecture," Web Semantics: Science, Services and Agents on the World Wide Web, vol. 4, no. 2, pp. 102-115, June 2006. [Online]. Available: http://dx.doi.org/10.1016/j.websem.2006.03.001
17. D. B. Krafft et al., "Vivo: Enabling national networking of scientists," in Proceedings of the Web Science Conference 2010 (WebSci'10), Apr. 2010, pp. 1310-1313.
18. S. Sufi and B. Mathews, "CCLRC Scientific Metadata Model: Version 2," 2004. [Online]. Available: http://epubs.cclrc.ac.uk/bitstream/485/
19. L. N. Soldatova and R. D. King, "An ontology of scientific experiments." Journal of the Royal Society, Interface, vol. 3, no. 11, pp. 795-803, December 2006. [Online]. Available: http://dx.doi.org/10.1098/rsif. 2006.0134
20. A. Brazma et al., "Minimum information about a microarray experiment (MIAME) - toward standards for microarray data," Nat Genet, vol. 29, no. 4, pp. 365-371, December 2001. [Online]. Available: http://dx.doi.org/10.1038/ ng1201-365
21. A. R. Jones, M. Miller, R. Aebersold et al., "The Functional Genomics Experiment model (FuGE): an Extensible Framework for Standards in Functional Genomics," Nature Biotechnology, vol. 25, no. 10, pp. 1127-1133, October 2007.
22. I. Horrocks, P. F. Patel-Schneider, and F. van Harmelen, "From SHIQ and RDF to OWL: The Making of a Web Ontology Language," Journal of Web Semantics, vol. 1, no. 1, pp. 7-26, 2003.
23. E. Prud'hommeaux and A. Seaborne, "SPARQL Query Language for RDF," Apr. 2006, http://www.w3.org/TR/2006/CR-rdf-sparql-query-20060406/.
24. S. Avraham, C.-W. Tung, K. Ilic, P. Jaiswal, E. A. Kellogg, S. Mccouch, A. Pujar, L. Reiser, S. Y. Rhee, M. M. Sachs, M. Schaeffer, L. Stein, P. Stevens, L. Vincent, F. Zapata, and D. Ware, "The plant ontology database: a community resource for plant structure and developmental stages controlled vocabulary and annotations," Nucl. Acids Res., vol. 36, no. suppl 1, pp. D449-454, January 2008. [Online]. Available: http://dx.doi.org/10.1093/nar/ gkm908
25. 2Bench: A SPARQL Performance Benchmark," in Proceedings of 2009 IEEE International Conference on Data Engineering (ICDE'09). IEEE Computer Society, 2009, pp. 222-233.
26. C. Bizer and A. Schultz, "The Berlin SPARQL Benchmark," International Journal On Semantic Web and Information Systems (IJSWIS), 2009, Special Issue on Scalability and Performance of Semantic Web Systems.