1. National Partnership of Advanced Computational Infrastructure San Diego Supercomputer Center KNOW-ME (KNOWledge-Map-Explorer) Semantic Browsing of Integrated Data using Knowledge Maps Knowledge MapKnowledge Map –A domain map representing terminological knowledge about experimental data –A process map representing knowledge of state-transitions about temporal phenomena –Links between them protein localization neuron physiology protein structure cell morphometry

2. National Partnership of Advanced Computational Infrastructure San Diego Supercomputer Center KNOW-ME Features Query CapabilitiesQuery Capabilities –For Concept Maps “find paths having nodes (N 1,..N k ) 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 associated with some process which exhibits a state transition satisfying ” a b get water a b bring glass c fill glass elaborate abstract

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

4. National Partnership of Advanced Computational Infrastructure San Diego Supercomputer Center KNOW-ME w/ Domain Map

5. National Partnership of Advanced Computational Infrastructure San Diego Supercomputer Center KNOW-ME w/ Process Map

6. National Partnership of Advanced Computational Infrastructure San Diego Supercomputer Center KNOW-ME Result Graph

7. National Partnership of Advanced Computational Infrastructure San Diego Supercomputer Center KNOW-ME Result Data

8. National Partnership of Advanced Computational Infrastructure San Diego Supercomputer Center Summary: KNOW-ME Features “Semantic” Browsing of Data:“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 Gupta San Diego Supercomputer Center & Department of Neurosciences University of California, San Diego Xufei Qian, Bertram Ludäscher, Maryann E. Martone, Amarnath Gupta San Diego Supercomputer Center & Department of Neurosciences University of California, San Diego

9. National Partnership of Advanced Computational Infrastructure San Diego Supercomputer Center 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.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.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.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.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 appearA 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