Abstract
Biomedical data are becoming increasingly complex and heterogeneous in nature. The data are stored in distributed information systems, using a variety of data models, and are processed by increasingly more complex tools that analyze and visualize them. We present in this paper our framework for integrating biomedical research data and tools into a unique Web front end. Our framework is applied to the University of Washington’s Human Brain Project. Specifically, we present solutions to four integration tasks: definition of complex mappings from relational sources to XML, distributed XQuery processing, generation of heterogeneous output formats, and the integration of heterogeneous data visualization and analysis tools.
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References
Abiteboul, S., Benjelloun, O., Cautis, B., Manolescu, I., Milo, T., Preda, N.: Lazy query evaluation for active XML. In: SIGMOD (2004)
Abiteboul, S., Benjelloun, O., Milo, T.: Positive active xml. In: PODS (2004)
Abiteboul, S., Bonifati, A., Cobena, G., Manolescu, I., Milo, T.: Dynamic xml documents with distribution and replication. In: SIGMOD, pp. 527–538 (2003)
Augurusa, E., Braga, D., Campi, A., Ceri, S.: Design of a graphical interface to XQuery. In: Proceedings of the ACM Symposium on Applied Computing (SAC), pp. 226–231 (2003)
Brinkley, J., Jakobovits, R., Rosse, C.: An online image management system for anatomy teaching. In: Proc. AMIA Fall Symposium, p. 983 (2002)
Brinkley, J., Wong, B., Hinshaw, K., Rosse, C.: Design of an anatomy information system. Computer Graphics and Applications 19(3), 38–48 (1999) (invited paper)
Brinkley, J.F., Myers, L.M., Prothero, J.S., Heil, G.H., Tsuruda, J.S., Maravilla, K.R., Ojemann, G.A., Rosse, C.: A structural information framework for brain mapping. In: Neuroinformatics: An Overview of the Human Brain Project, pp. 309–334. Lawrence Erlbaum, Mahwah (1997), See also http://sig.biostr.washington.edu/projects/brain/
Carey, M., Florescu, D., Ives, Z., Lu, Y., Shanmugasundaram, J., Shekita, E., Subramanian, S.: XPERANTO: publishing object-relational data as XML. In: Proceedings of WebDB, Dallas, TX (May 2000)
Carey, M.J.: BEA liquid data for WebLogic: XML-based enterprise information integration. In: ICDE, pp. 800–803 (2004)
Eisenberg, A., Melton, J.: SQL/XML is making good progress. SIGMOD Record 31(2), 101–108 (2002)
Fernandez, M., Kadiyska, Y., Morishima, A., Suciu, D., Tan, W.: SilkRoute: a framework for publishing relational data in XML. ACM Transactions on Database Technology 27(4) (December 2002)
Fernandez, M., Morishima, A., Suciu, D.: Efficient evaluation of XML middleware queries. In: Proceedings of ACM SIGMOD Conference on Management of Data, Santa Barbara (2001)
Fernandez, M., Simeon, J.: Galax: the XQuery implementation for discriminating hackers (2002), Available from http://db.bell-labs.com/galax/
Fernandez, M., Suciu, D., Tan, W.: SilkRoute: trading between relations and XML. In: Proceedings of the WWW9, Amsterdam, pp. 723–746 (2000)
Fernandez, M.F., Florescu, D., Levy, A.Y., Suciu, D.: Declarative specification of web sites with strudel. VLDB Journal 9(1), 38–55 (2000)
Funderburk, J., Kiernan, G., Shanmugasundaram, J., Shekita, E., Wei, C.: Technical note - XTABLES: Bridging relational technology and XML. IBM Systems Journal 42(3), 538 (2003)
Gardner, P., Maffeis, S.: Modelling dynamic Web data. In: Lausen, G., Suciu, D. (eds.) DBPL 2003. LNCS, vol. 2921, pp. 75–84. Springer, Heidelberg (2004)
Hertzenberg, X., Poliakov, A., Corina, D., Ojemann, G., Brinkley, J.: X-batch: Embedded data management for fmri analysis. In: Society for Neuroscience Annual Meeting, San Diego, p. 694.21 (2004)
Hinshaw, K., Poliakov, A., Martin, R., Moore, E., Shapiro, L., Brinkley, J.: Shapebased cortical surface segmentation for visualization brain mapping. Neuroimage 16(2), 295–316 (2002)
Jakobovits, R., Rosse, C., Brinkley, J.: An open source toolkit for building biomedical web applications. J. Am. Med. Ass. 9(6), 557–590 (2002)
Koslow, S., Hyman, S.: Human brain project: A program for the new millenium. Einstein Quarterly J. Biol. Med. 17, 7–15 (2000)
Kossmann, D.: The state of the art in distributed query processing. ACM Comput. Surv. 32(4), 422–469 (2000)
Krishnamurthy, R., Kaushik, R., Naughton, J.: Efficient XML-to-SQL query translation: Where to add the intelligence? In: VLDB, pp. 144–155 (2004)
Krishnaprasad, M., Liu, Z., Manikutty, A., Warner, J., Arora, V., Kotsovolos, S.: Query rewrite for XML in oracle XML DB. In: VLDB, pp. 1122–1133 (2004)
Library, M.: Creating xml views by using annotated xsd schemas (2005)
Moore, E., Poliakov, A., Brinkley, J.: Brain visualization in java3d. In: Proceedings, MEDINFO, San Francisco, CA, p. 1761 (2004)
Mork, P., Brinkley, J.F., Rosse, C.: OQAFMA querying agent for the foundational model of anatomy: a prototype for providing flexible and efficient access to large semantic networks. J. Biomedical Informatics 36(6), 501–517 (2003)
Re, C., Brinkley, J., Hinshaw, K., Suciu, D.: Distributed XQuery. In: Workshop on Information Integration on the Web (IIWeb), September 2004, pp. 116–121 (2004)
Re, C., Brinkley, J., Suciu, D.: Efficient publishing of relational data to XML (submitted)
Rosse, C., Mejino, J.L.V.: A reference ontology for bioinformatics: the foundational model of anatomy. Journal of Bioinformatics 36(6), 478–500 (2003)
Sahuguet, A., Tannen, V.: ubQL, a language for programming distributed query systems. In: WebDB, pp. 37–42 (2001)
Shaker, R., Mork, P., Brockenbrough, J., Donelson, L., Tarczy-Hornoch, P.: The biomediator system as a tool for integrating biologic databases on the web. In: Proc. Workshop on Information Integration on the Web, held in conjunction with VLDB (2004)
Shanmugasundaram, J., Kiernana, J., Shekita, E., Fan, C., Funderburk, J.: Querying XML views of relational data. In: Proceedings of VLDB, Rome, Italy, September 2001, pp. 261–270 (2001)
Shanmugasundaram, J., Shekita, E., Barr, R., Carey, M., Lindsay, B., Pirahesh, H., Reinwald, B.: Efficiently publishing relational data as XML documents. In: Proceedings of VLDB, Cairo, Egypt, September 2000, pp. 65–76 (2000)
Tang, Z., Kadiyska, Y., Li, H., Suciu, D., Brinkley, J.F.: Dynamic XML-based exchange of relational data: application to the Human Brain Project. In: Proceedings, Annual Fall Symposium of the American Medical Informatics Association, Washington, D.C., pp. 649–653 (2003), http://quad.biostr.washington.edu:8080/xbrain/index.jsp
Tang, Z., Kadiyska, Y., Suciu, D., Brinkley, J.: Results visualization in the xbrain xml interface to a relational database. In: Proceedings, MEDINFO, San Francisco, CA, p. 1878 (2004)
Tatarinov, I., Viglas, S., Beyer, K., Shanmugasundaram, J., Shekita, E., Zhang, C.: Storing and querying ordered XML using a relational database system. In: SIGMOD (May 2002)
Wiederhold, G.: Mediators in the architecture of future information systems. IEEE Computer, pp. 38–49 (March 1992)
Wong, L.: The functional guts of the Kleisli query system. In: Proceedings of ICFP, pp. 1–10 (2000)
Zloof, M.M.: Query-by-example: A data base language. IBM Systems Journal 16(4), 324–343 (1977)
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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. In: Bressan, S., et al. Database and XML Technologies. XSym 2005. Lecture Notes in Computer Science, vol 3671. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11547273_15
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DOI: https://doi.org/10.1007/11547273_15
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