Distributed XQuery-based integration and visualization of multimodality brain mapping data

Frontiers in Neuroinformatics

Volumn 3, Issue JAN, 2009, Pages

  Detwiler, Landon T ^a   Suciu, Dan ^b   Franklin, Joshua D ^a   Moore, Eider B ^a   Poliakov, Andrew V ^a   Lee, Eunjung S ^a   Corina, David P ^c   Ojemann, George A ^d   Brinkley, James F ^a,b  

^a UNIVERSITY OF WASHINGTON   (United States)

^b University of Washington   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

Author keywords

Brain mapping; Brain visualization; Data integration; Distributed query processing; Neuroinformatics; Query shipping; Semantic web; XQuery

Indexed keywords

EID: 84875804889     PISSN: 16625196     EISSN: None     Source Type: Journal    
DOI: 10.3389/neuro.11.002.2009     Document Type: Article

References (42)

1. Apache Software Foundation. (2007). Apache Tomcat. 2007. Available at: http://tomcat.apache.org/.
2. Bales, N., Brinkley, J, Lee, E. S., Mathur, S., Re, C., Suciu, D. (2005). A Framework for XML-Based Integration of Data, Visualization and Analysis in a Biomedical Domain. Trondheim, Proceedings, Third International XML Database Symposium (XSym 2005), pp. 207-221.
3. Brinkley, J. F. (2008). University of Washington Integrated Brain Project, Home Page. Available at: http://sig.biostr.washington.edu/projects/brain.
4. Brinkley, J. F., Jakobovits, R. M., Poliakov, A. V., Martin, R. F., Gibson, E. R., Corina, D. M., Ojemann, G. A. (2004). An experiment management system for cortical stimulation mapping data. San Diego, Society for Neuroscience Annual Meeting, p. 1032.12.
5. Brinkley, J. F., Myers, L. M., Prothero, J. S., Heil, G. H., Tsuruda, J. S., Maravilla, K. R., Ojemann, G. A., Rosse, C. (1997). A structural information framework for brain mapping. In: Neuroinformatics: An Overview of the Human Brain Project, S. H. Koslow and M. F. Huerta, eds (Mahwah, Lawrence Erlbaum), pp. 309-334.
6. Brinkley, J. F., Suciu, D., Detwiler, L. T., Gennari, J. H., Rosse, C. (2006). A framework for using reference ontologies as a foundation for the semantic web. Proc. AMIA Annu. Fall Symp. 2006, 96-100.
7. Detwiler, L. T., Suciu, D., Brinkley, J. F. (2008). Regular paths in SparQL: querying the NCI thesaurus. Proc. AMIA Annu. Fall Symp. 2008, 161-165.
8. Evans, A. C., Collins, D. L., Mills, S. R., Brown, E. D., Kelly, R. L., Peters, T. M. (1993). 3D Statistical neuroanatomical models from 305 MRI volumes. Proc. IEEE Nucl. Sci. Symp. Med. Imag. Conf. 1993, 1813-1817.
9. Fernandez, M., Jim, T., Morton, K., Onose, N., Simeon, J. (2007). DXQ: A Distributed XQuery Scripting Language. Beijing, XIME-P-2007: 4th International Workshop on XQuery Implementation, Experience and Perspectives.
10. Fernandez, M., Kadiyska, Y., Morishima, A., Suciu, D., Tan, W. (2002). Silkroute: a framework for publishing relational data in XML. ACM Trans. Database Technol. 27, 1-6.
11. Gazzaniga, M. S. (2008). The fMRI Data Center. 2001. Available at: http://www.fmridc.org/.
12. GNU. (2008). QEXO - The GNU Kawa Implementation of XQuery. Available at: http://www.gnu.org/software/qexo/.
13. Hinshaw, K. P., Poliakov, A. V., Martin, R. F., Moore, E. B., Shapiro, L. G., Brinkley, J. F. (2002). Shape-based cortical surface segmentation for visualization brain mapping. Neuroimage 16, 295-316.
14. Kay, M. (2008). SAXON: The XSLT and XQuery Processor. Available at: http://saxon.sourceforge.net/.
15. Keator, D. B., Grethe, J. S., Marcus, D., Ozyurt, B., Gadde, S., Murphy, S., Pieper, S., Greve, D., Notestine, R., Bockholt, H. J., Papadopoulos, P. (2008). A national human neuroimaging collaboratory enabled by the Biomedical Informatics Research Network (BIRN). IEEE Trans. Inf. Technol. Biomed. 12, 162-172.
16. Koslow, S., and Hyman, S. (2000). Human brain project: a program for the new millenium. Einstein Q. J. Biol. Med. 17, 7-15.
17. Laboratory of Neuro Imaging. (2008). LONI Image Database. Available at: http://www.loni.ucla.edu/Research/Databases/.
18. Li, X., Gennari, J. H., Brinkley, J. (2007). XGI: a graphical interface for XQuery creation. Proc. AMIA Annu. Fall Symp. 2007, 453-457.
19. Martone, M. E., Zhang, S., Gupta, A., Qian, X., He, H., Price, D. L., Wong, M., Santini, S., Ellisman, M. H. (2003). The cell-centered database: a database for multiscale structural and protein localization data from light and electron microscopy. Neuroinformatics 1, 379-395.
20. Miller, P. L., Nadkarni, P., Singer, M., Marenco, L., Hines, M., Shepard, G. (2001). Integration of multidisciplinary sensory data: a pilot model of the Human Brain Project approach. J. Am. Med. Assoc. 8, 34-48.
21. Moore, E. B., Poliakov, A. Lincoln, P., Brinkley, J. (2007). MindSeer: a portable and extensible tool for visualization of structural and functional neuroimaging data. BMC Bioinformatics 8, 389.
22. Mork, P., Brinkley, J. F. Rosse, C. (2003). OQAFMA Querying Agent for the Foundational Model of Anatomy: a prototype for providing flexible and effi cient access to large semantic networks. J. Biomed. Inform. 36, 501-517.
23. Nature Neuroscience. (2000). A debate over fMRI data sharing. Nat. Neurosci. 3, 845-846.
24. Ojemann, G., Ojemann, J., Lettich, E., Berger, M. (1989). Cortical language localization in left, dominant hemisphere: an electrical stimulation mapping investigation in 117 patients. J. Neurosurg. 71, 316-326.
25. Oster, S., Langella, S., Hastings, S., Ervin, D., Madduri, R., Phillips, J., Kurc, T., Siebenlist, F., Covitz, P., Shanbhag, K., Foster, I., Saltz, J. (2008). CaGrid 1.0: an enterprise Grid infrastructure for biomedical research. J. Am. Med. Inform. Assoc. 15, 138-149.
26. Ozsu, T., and Valduriez, P. (1999). Principles of Distributed Database Systems. Prentice Hall.
27. Poliakov, A., Hertzenberrg, X., Moore, E. B., Corina, D., Ojemann, G. A., Brinkley, J. F. (2007). Unobtrusive integration of data management with fMRI analysis. Neuroinformatics 5, 3-10.
28. Re, C. (2006). SilkRoute II - Efficient relational publishing to XML. 2006. Available at: http://silkroute.cs.washington.edu/.
29. Re, C., Brinkley, J., Hinshaw, K., Suciu, D. (2004). Distributed XQuery. Proceedings of the Workshop on Information Integration on the Web (IIWeb), pp. 116-121.
30. Rosse, C., and Mejino, J. L. V. (2003). A reference ontology for bioinformatics: the Foundational Model of Anatomy. J. Bioinform. 36, 478-500.
31. Shaw, M., Detwiler, L. T., Brinkley, J. F, Suciu, D. (2008). Generating application ontologies from reference ontologies. Proc. AMIA Annu. Fall Symp. 2008, 672-676.
32. Society for Neuroscience. (2008). Neuroscience Database Gateway. 2008. Avaialable at: http://ndg.sfn.org/.
33. Stalder, D. S., and Brinkley, J. F. (1999). The Digital Anatomist Foundational Model Server. Monterey, Perl Conference 3.0.
34. Structural Informatics Group. (2007a). DXQP - Distributed XQuery Processor. 2007. Available at: http://sig.biostr.washington.edu/projects/dxqp/.
35. Structural Informatics Group. (2007b). WIX: Web Interface for XQuery. 2007. Available at: http://sig.biostr.washington.edu/projects/wix/index. html.
36. Structural Informatics Group. (2008). DXBrain Demo Query. 2007 Available at: http://sig.biostr.washington.edu/projects/dxbrain/demoquery.html.
37. Van Essen, D. (2008). SumsDB. Available at: http://sumsdb.wustl.edu:8081/sums/dispatch.do?forward=index.
38. W3C. (2008). Simple Object Access Protocol (SOAP). Available at: http://www.w3.org/TR/soap/.
39. Wellcome Department of Cognitive Neurology. (2001). Statistical Parametric Mapping. Available at: http://www.fil.ion.ucl.ac.uk/spm/.
40. World Wide Web Consortium. (2005a). Resource Description Framework (RDF). 2005. Available at: http://www.w3.org/RDF/.
41. World Wide Web Consortium. (2005b). SparQL query language for RDF. 2005. Available at: http://www.w3.org/TR/rdf-sparql-query/.
42. World Wide Web Consortium. (2005c). The OWL Web Ontology Language. Available at: http://www.w3.org/TR/owl-features/.