National Partnership of Advanced Computational Infrastructure San Diego Supercomputer Center

KNOW-MEKNOW-ME ((KNOWKNOWledge-ledge-MMap-ap-EExplorerxplorer))Semantic Browsing of Integrated Data using Knowledge MapsSemantic Browsing of Integrated Data using Knowledge Maps

• Knowledge MapKnowledge Map– A A domain mapdomain map representing representing

terminological knowledge about terminological knowledge about experimental dataexperimental data

– A A process mapprocess map representing representing knowledge of state-transitions knowledge of state-transitions about temporal phenomenaabout temporal phenomena

– Links between themLinks between them

protein localization

neuronphysiology

proteinstructure

cellmorphometry

National Partnership of Advanced Computational Infrastructure San Diego Supercomputer Center

KNOW-MEKNOW-ME Features Features• Query CapabilitiesQuery Capabilities

– For Concept MapsFor Concept Maps• “find paths having nodes (N1, ..Nk) and avoiding

nodes (N1, ..N m)” …

– For Process Maps (STNs)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 For bridges across concept maps and process mapsmaps

• “locate a concept satisfying <condition1> associated with some process which exhibits a state transition satisfying <condition2>”

a

b

get water

a

b

bring glass

c

fill glass

elaborate

abstract

National Partnership of Advanced Computational Infrastructure San Diego Supercomputer Center

KNOW-ME Query EngineKNOW-ME Query Engine

NCMIRCCDB

WebDot Graph Layout

Tomcat Servlet/JSP Engine

JSP Java Bean

KNOW-MEKNOW-ME Architecture Architecture

(pamina2.sdsc.edu)

(birn.sdsc.edu)

(dakswebdot.sdsc.edu)

KNOW-ME Web-Browser

(anywhere)

CC

C

UMLS800k concepts1.9m names

CC

C

ANATOMProcess MapsDomain Maps

Oracle DB

National Partnership of Advanced Computational Infrastructure San Diego Supercomputer Center

KNOW-MEKNOW-ME w/ Domain Map w/ Domain Map

National Partnership of Advanced Computational Infrastructure San Diego Supercomputer Center

KNOW-MEKNOW-ME w/ Process Map w/ Process Map

National Partnership of Advanced Computational Infrastructure San Diego Supercomputer Center

KNOW-MEKNOW-ME Result Graph Result Graph

National Partnership of Advanced Computational Infrastructure San Diego Supercomputer Center

KNOW-MEKNOW-ME Result Data Result Data

National Partnership of Advanced Computational Infrastructure San Diego Supercomputer Center

Summary:Summary: KNOW-ME KNOW-ME Features Features• ““Semantic” Browsing of Data:Semantic” Browsing of Data:

– Data “about” a concept Data “about” a concept • “All electromicrographs of spiny dendrites”

– Data “about” a processData “about” a process• “All electrode recordings that show ‘long-term-potentiation’ ”

– Data that is “evidence of” a processData 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

Xufei Qian, Bertram Ludäscher, Maryann E. Martone, Amarnath GuptaSan Diego Supercomputer Center & Department of Neurosciences

University of California, San Diego

National Partnership of Advanced Computational Infrastructure San Diego Supercomputer Center

Some Related References: Some Related References: Mediation of Neuroscience DataMediation of Neuroscience Data

• Model-Based Mediation with Domain MapsModel-Based Mediation with Domain Maps, B. Ludäscher, A. Gupta, M. E. , B. Ludäscher, A. Gupta, M. E. Martone, Martone, 17th Intl. Conference on Data Engineering17th Intl. Conference on Data Engineering ( (ICDEICDE), Heidelberg, ), Heidelberg, Germany, IEEE Computer Society, April 2001. Germany, IEEE Computer Society, April 2001.

• Navigating Virtual Information Sources with Know-MENavigating Virtual Information Sources with Know-ME, X. Qian, B. , X. Qian, B. Ludäscher, M. E. Martone, A. Gupta, Ludäscher, M. E. Martone, A. Gupta, demonstration track, Intl. Conference on demonstration track, Intl. Conference on Extending Database TechnologyExtending Database Technology ( (EDBTEDBT), Prague, Czech Republic, March ), Prague, Czech Republic, March 2002. 2002.

• Model-Based Information Integration in a Neuroscience Mediator Model-Based Information Integration in a Neuroscience Mediator SystemSystem, B. Ludäscher, A. Gupta, M. E. Martone, , B. Ludäscher, A. Gupta, M. E. Martone, demonstration track, 26th demonstration track, 26th Intl. Conference on Very Large DatabasesIntl. Conference on Very Large Databases ( (VLDBVLDB), Cairo, Egypt, September ), Cairo, Egypt, September 2000. 2000.

• Knowledge-Based Integration of Neuroscience Data SourcesKnowledge-Based Integration of Neuroscience Data Sources, A. Gupta, B. , A. Gupta, B. Ludäscher, M. E. Martone, Ludäscher, M. E. Martone, 12th Intl. Conference on Scientific and Statistical 12th Intl. Conference on Scientific and Statistical Database ManagementDatabase Management ( (SSDBMSSDBM), Berlin, Germany, IEEE Computer Society, ), Berlin, Germany, IEEE Computer Society, July 2000. July 2000.

• A Cell-Centered Database for Electron Tomographic DataA Cell-Centered Database for Electron Tomographic Data, M. E. Martone, , M. E. Martone, A. Gupta, M. Wong, X. Qian, G. Sosinsky, S. Lamont, B. Ludäscher , and M. A. Gupta, M. Wong, X. Qian, G. Sosinsky, S. Lamont, B. Ludäscher , and M. H. Ellisman. H. Ellisman. Journal of Structural BiologyJournal of Structural Biology, 2002. to appear , 2002. to appear