Abstract
Clinical genomics, the marriage of clinical information and knowledge about the human or pathogen genome, holds enormous promise for the healthcare and life sciences domain. Based on a more in-depth understanding of the human and pathogen molecular interaction, clinical genomics can be used to discover new targeted drugs and provide personalized therapies with fewer side effects, at reduced costs, and with higher efficacy. A key enabler of clinical genomics is a sound standards-based biomedical information integration middleware. This middleware must be able to de-identify, integrate and correlate clinical, clinical trials, genomic and images metadata from the various systems. We describe MedII, a novel biomedical information integration research technology that some of its components were integrated in IBM Clinical Genomics solution. We also introduce the need for biomedical information preservation to assist in ensuring that the integrated biomedical information can be read and interpreted decades from now.
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References
IBM Clinical Genomics solution, http://publib.boulder.ibm.com/infocenter/eserver/v1r2/index.jsp?topic=/ddqb/eicavcg.htm
Shabo, A., Rabinovici-Cohen, S., Vortman, P.: Revolutionary impact of XML on biomedical information interoperability. IBM Systems Journal 45(2), 361–373 (2006)
Altman, R.B., Klein, T.E.: Challenges for biomedical informatics and pharmacogenomics. Annual Review of Pharmacology and Toxicology 42, 113–133 (2002)
Hewett, M., Oliver, D.E., Rubin, D.L., Easton, K.L., Stuart, J.M., Altman, R.B., Klein, T.E.: PharmGKB: the Pharmacogenetics Knowledge Base. Nucleic Acids Research (NAR) 30(1), 163–165 (2002)
Astakhov, V., Gupta, A., Santini, S., Grethe, J.S.: Data Integration in the Biomedical Informatics Research Network (BIRN). In: Ludäscher, B., Raschid, L. (eds.) DILS 2005. LNCS (LNBI), vol. 3615, pp. 317–320. Springer, Heidelberg (2005)
Chen, I.A., Kosky, A.S., Markowitz, V.M., Szeto, E., Topaloglou, T.: Advanced Query Mechanisms for Biological Databases. In: 6th Int. Conf. on Intelligent Systems for Molecular Biology (1998)
Haas, L.M., Schwarz, P.M., Kodali, P., Kotlar, E., Rice, J., Swope, W.C.: DiscoveryLink: A System for Integrated Access to Life Sciences Data Sources. IBM Systems Journal 40(2), 489–511 (2001)
Do, H.H., Rahm, E.: Flexible Integration of Molecular-biological Annotation Data: The GenMapper Approach. In: Bertino, E., Christodoulakis, S., Plexousakis, D., Christophides, V., Koubarakis, M., Böhm, K., Ferrari, E. (eds.) EDBT 2004. LNCS, vol. 2992, pp. 811–822. Springer, Heidelberg (2004)
Shaker, R., Mork, P., Brockenbrough, J.S., Donel-son, L., Tarczy-Hornoch, P.: The BioMediator System as a Tool for Integrating Biologic Databases on the Web. In: Workshop on Information Integration on the Web, IIWeb 2004 (2004)
Rahm, E., Bernstein, P.A.: A survey of approaches to automatic schema matching. The VLDB Journal 10(4), 334–350 (2001)
Leser, U., Naumann, F.: (Almost) Hands-Off Information Integration for the Life Sciences. In: Proceedings of the Conference on Innovative Data Systems Research, CIDR (2005)
Mullins, I., Siadaty, M., Lyman, J., Scully, K., Garrett, C., Miller, W., Muller, R., Robson, B., Apte, C., Weiss, S., Rigoustsos, I., Platt, D., Cohen, S., Knaus, W.: Data Mining and Clinical Data Repositories: Insights from a 667,000 Patient Data Set. Journal of Computers in Biology and Medicine (2005)
ISO 14721:2003, Blue Book. Issue 1. CCSDS 650.0-B-1: Reference Model for an Open Archival Information System, OAIS (2002)
Factor, M., Naor, D., Rabinovici-Cohen, S., Ramati, L., Reshef, P., Satran, J., Giaretta, D.L.: Preservation DataStores: Architecture for Preservation Aware Storage. In: 24th IEEE Conference on Mass Storage Systems and Technologies (MSST), San Diego, pp. 3–15 (2007)
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Rabinovici-Cohen, S. (2009). Biomedical Information Integration Middleware for Clinical Genomics. In: Feldman, Y.A., Kraft, D., Kuflik, T. (eds) Next Generation Information Technologies and Systems. NGITS 2009. Lecture Notes in Computer Science, vol 5831. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-04941-5_4
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DOI: https://doi.org/10.1007/978-3-642-04941-5_4
Publisher Name: Springer, Berlin, Heidelberg
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