San Diego Supercomputer Center San Diego Supercomputer Center EDBT'02, Prague EDBT'02, Prague 1 Scientific Data Scientific Data Integration Integration for for Complex Multiple-Worlds Complex Multiple-Worlds Scenarios: Scenarios: Databases Meets Knowledge Databases Meets Knowledge Representation Representation Bertram Lud Bertram Lud ä ä scher scher Data and Knowledge System Data and Knowledge System San Diego Supercomputer San Diego Supercomputer Center Center U.C. San Diego U.C. San Diego
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Bertram Lud ä scher Data and Knowledge System San Diego Supercomputer Center U.C. San Diego
EDBT Panel, March 2002, Prague: Scientific Data Integration for Complex Multiple-Worlds Scenarios: Databases Meets Knowledge Representation. Bertram Lud ä scher Data and Knowledge System San Diego Supercomputer Center U.C. San Diego. ? Information Integration. Crime Stats. - PowerPoint PPT Presentation
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San Diego Supercomputer CenterSan Diego Supercomputer CenterEDBT'02, PragueEDBT'02, Prague 11
EDBT Panel, March 2002, Prague:EDBT Panel, March 2002, Prague: Scientific Data Integration Scientific Data Integration
for for Complex Multiple-WorldsComplex Multiple-Worlds Scenarios: Scenarios: Databases Meets Knowledge RepresentationDatabases Meets Knowledge Representation
EDBT Panel, March 2002, Prague:EDBT Panel, March 2002, Prague: Scientific Data Integration Scientific Data Integration
for for Complex Multiple-WorldsComplex Multiple-Worlds Scenarios: Scenarios: Databases Meets Knowledge RepresentationDatabases Meets Knowledge Representation
Bertram LudBertram Ludääscherscher
Data and Knowledge SystemData and Knowledge System
San Diego Supercomputer Center San Diego Supercomputer Center
U.C. San DiegoU.C. San Diego
Bertram LudBertram Ludääscherscher
Data and Knowledge SystemData and Knowledge System
San Diego Supercomputer Center San Diego Supercomputer Center
U.C. San DiegoU.C. San Diego
A Home Buyer’s Information Integration ProblemA Home Buyer’s Information Integration Problem
What houses for sale under $500k have at least 2 bathrooms, 2 bedrooms, a nearby school ranking in the upper third, in a neighborhood
with below-average crime rate and diverse population?
San Diego Supercomputer CenterSan Diego Supercomputer CenterEDBT'02, PragueEDBT'02, Prague 1010
Semantics-Aware Semantics-Aware BrowsingBrowsing and and QueryingQuerying
Cerebellum
Source 1 Source 2
Source 3
Cerebellar Cortex
Granule Cell Layer
Purkinje Cell layer
Molecular Layer
has a
Purkinje Cell Dendrite
Dendritic spines
Dendritic shaft
Endoplasmic reticulum
Purkinje Neuron
has a
San Diego Supercomputer CenterSan Diego Supercomputer CenterEDBT'02, PragueEDBT'02, Prague 1111
Domain Map = labeled graph with concepts ("classes") and roles ("associations")• additional semantics: expressed as logic rules (F-logic)
Domain Map = labeled graph with concepts ("classes") and roles ("associations")• additional semantics: expressed as logic rules (F-logic)
Domain Map (DM)
Purkinje cells and Pyramidal cells have dendritesthat have higher-order branches that contain spines.Dendritic spines are ion (calcium) regulating components.Spines have ion binding proteins. Neurotransmissioninvolves ionic activity (release). Ion-binding proteinscontrol ion activity (propagation) in a cell. Ion-regulatingcomponents of cells affect ionic activity (release).
Domain Expert Knowledge
DM in Description Logic
Formalizing Glue Knowledge:Formalizing Glue Knowledge:Domain Map for Domain Map for SYNAPSESYNAPSE and and NCMIRNCMIR
San Diego Supercomputer CenterSan Diego Supercomputer CenterEDBT'02, PragueEDBT'02, Prague 1212
Syntactic Joins Syntactic Joins “Semantic” Joins via Glue Maps
DB expert DB expert KRDB + domain experts
San Diego Supercomputer CenterSan Diego Supercomputer CenterEDBT'02, PragueEDBT'02, Prague 1919
Some ObservationsSome Observations• Scientific Data Integration is different Scientific Data Integration is different
– e.g., complex and hidden semantics,...
• Co-Education (CS=>DS, DS=>CS) takes time Co-Education (CS=>DS, DS=>CS) takes time – NIH BioInformatics Research Network (BIRN) – Neuroscientists– DOE Scientific Data Management Center (SDM)– Starting with Ecologists, Geoscientists, ...
• A good thing about standards: A good thing about standards: • There are so many to choose from:There are so many to choose from:
• Syntax is overrated (and its impact underestimated?)Syntax is overrated (and its impact underestimated?)– nobody likes LISP any more, but everybody likes XML ...
• 22ndnd Marriage of Knowledge Representation & Databases: Marriage of Knowledge Representation & Databases:– Semantic Web– (child from 1st marriage: Deductive Databases; aren’t they cute siblings? ;)=> model-based/semantic mediators
San Diego Supercomputer CenterSan Diego Supercomputer CenterEDBT'02, PragueEDBT'02, Prague 2020
Internet2
SOAP
SOA
P
OILOIL
The Road Ahead: Scientific Data Integration with The Road Ahead: Scientific Data Integration with the Semantic Web !?the Semantic Web !?
Data-Grid
Scientific DataScientific Data RDF DOOD rules
WSDL XQuery
DAML-S
RDF DOOD rules
WSDL XQuery
DAML-S
XMLXML RDF RDF
XMLDB
sub
sum
ptio
n
DAML
Logic
descrip
tion
log
ics
RDB
infe
ren
ce
ORDBontologies
’
Integrated Data ViewsIntegrated Data Views
Ivory
Tower
San Diego Supercomputer CenterSan Diego Supercomputer CenterEDBT'02, PragueEDBT'02, Prague 2121
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, Germany, ), Heidelberg, Germany, IEEE Computer Society, April 2001. IEEE Computer Society, April 2001.
• Navigating Virtual Information Sources with Know-MENavigating Virtual Information Sources with Know-ME, X. Qian, B. Ludäscher, , X. Qian, B. Ludäscher, M. E. Martone, A. Gupta, M. E. Martone, A. Gupta, demonstration track, Intl. Conference on Extending demonstration track, Intl. Conference on Extending Database TechnologyDatabase Technology ( (EDBTEDBT), Prague, Czech Republic, March 2002. ), Prague, Czech Republic, March 2002.
• Model-Based Information Integration in a Neuroscience Mediator SystemModel-Based Information Integration in a Neuroscience Mediator System , B. , B. Ludäscher, A. Gupta, M. E. Martone, Ludäscher, A. Gupta, M. E. Martone, demonstration track, 26th Intl. Conference on demonstration track, 26th Intl. Conference on Very Large DatabasesVery Large Databases ( (VLDBVLDB), Cairo, Egypt, September 2000. ), Cairo, Egypt, September 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 Database 12th Intl. Conference on Scientific and Statistical Database ManagementManagement ( (SSDBMSSDBM), Berlin, Germany, IEEE Computer Society, July 2000. ), Berlin, Germany, IEEE Computer Society, July 2000.
• A Cell-Centered Database for Electron Tomographic DataA Cell-Centered Database for Electron Tomographic Data, M. E. Martone, A. , M. E. Martone, A. Gupta, M. Wong, X. Qian, G. Sosinsky, S. Lamont, B. Ludäscher , and M. H. Gupta, M. Wong, X. Qian, G. Sosinsky, S. Lamont, B. Ludäscher , and M. H. Ellisman. Ellisman. Journal of Structural BiologyJournal of Structural Biology, 2002. to appear , 2002. to appear