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KNOW-ME ( KNOW ledge- M ap- E xplorer ) Semantic Browsing of Integrated Data using Knowledge Maps

protein structure. protein localization. cell morphometry. neuron physiology. KNOW-ME ( KNOW ledge- M ap- E xplorer ) Semantic Browsing of Integrated Data using Knowledge Maps. Knowledge Map A domain map representing terminological knowledge about experimental data

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KNOW-ME ( KNOW ledge- M ap- E xplorer ) Semantic Browsing of Integrated Data using Knowledge Maps

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  1. protein structure protein localization cell morphometry neuron physiology KNOW-ME(KNOWledge-Map-Explorer)Semantic Browsing of Integrated Data using Knowledge Maps • Knowledge Map • A domain map representing terminological knowledge about experimental data • A process map representing knowledge of state-transitions about temporal phenomena • Links between them

  2. a a get water fill glass c b bring glass b KNOW-ME Features • Query Capabilities • For Concept Maps • “find paths having nodes (N1, ..Nk) and avoiding nodes (N1, ..N m)” … • For Process Maps (STNs) • transition types and parameters • precondition-postcondition descriptions • traversing level of details – elaborations and abstractions • For bridges across concept maps and process maps • “locate a concept satisfying <condition1> associated with some process which exhibits a state transition satisfying <condition2>” elaborate abstract

  3. C C C C C C UMLS 800k concepts 1.9m names KNOW-ME Architecture WebDot Graph Layout (dakswebdot.sdsc.edu) JSP Java Bean Tomcat Servlet/JSP Engine KNOW-ME Query Engine KNOW-ME Web-Browser (anywhere) (pamina2.sdsc.edu) Oracle DB NCMIR CCDB ANATOM Process Maps Domain Maps (birn.sdsc.edu)

  4. KNOW-ME w/ Domain Map

  5. KNOW-ME w/ Process Map

  6. KNOW-ME Result Graph

  7. KNOW-ME Result Data

  8. Summary: KNOW-ME Features • “Semantic” Browsing of Data: • Data “about” a concept • “All electromicrographs of spiny dendrites” • Data “about” a process • “All electrode recordings that show ‘long-term-potentiation’ ” • Data that is “evidence of” a process • “All electromicrographs that suggest ‘synapse generation’ occurs during LTP” Xufei Qian, Bertram Ludäscher, Maryann E. Martone, Amarnath GuptaSan Diego Supercomputer Center & Department of Neurosciences University of California, San Diego

  9. Some Related References: Mediation of Neuroscience Data • Model-Based Mediation with Domain Maps, B. Ludäscher, A. Gupta, M. E. Martone, 17th Intl. Conference on Data Engineering (ICDE), Heidelberg, Germany, IEEE Computer Society, April 2001. • Navigating Virtual Information Sources with Know-ME, X. Qian, B. Ludäscher, M. E. Martone, A. Gupta, demonstration track, Intl. Conference on Extending Database Technology (EDBT), Prague, Czech Republic, March 2002. • Model-Based Information Integration in a Neuroscience Mediator System, B. Ludäscher, A. Gupta, M. E. Martone, demonstration track, 26th Intl. Conference on Very Large Databases (VLDB), Cairo, Egypt, September 2000. • Knowledge-Based Integration of Neuroscience Data Sources, A. Gupta, B. Ludäscher, M. E. Martone, 12th Intl. Conference on Scientific and Statistical Database Management (SSDBM), Berlin, Germany, IEEE Computer Society, July 2000. • A Cell-Centered Database for Electron Tomographic Data, M. E. Martone, A. Gupta, M. Wong, X. Qian, G. Sosinsky, S. Lamont, B. Ludäscher , and M. H. Ellisman. Journal of Structural Biology, 2002. to appear

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