bertram lud ä scher data and knowledge system san diego supercomputer center u.c. san diego

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?

?Information Integration


RealtorRealtor DemographicsDemographicsSchool RankingsSchool RankingsCrime StatsCrime Stats

“Simple Multiple-Worlds”Mediation Problem

=> XML-Based Mediator

“Simple Multiple-Worlds”Mediation Problem

=> XML-Based Mediator

http://www.epa.gov/opptintr/kids/hometour/images/house.jpg

http://www.ftb.ca.gov/education/images/schools.jpg

A Neuroscientist’s Information Integration ProblemA Neuroscientist’s Information Integration Problem

What is the cerebellar distribution of rat proteins with more than 70% homology with human NCS-1? Any structure specificity?

How about other rodents?



protein localization(NCMIR)

protein localization(NCMIR)

neurotransmission(SENSELAB)

neurotransmission(SENSELAB)

sequence info(CaPROT)

sequence info(CaPROT) morphometry

(SYNAPSE)

morphometry(SYNAPSE)

“Complex Multiple-Worlds”Mediation Problem

=> Model-Based Mediator

“Complex Multiple-Worlds”Mediation Problem

=> Model-Based Mediator

A Geoscientist’s Information Integration ProblemA Geoscientist’s Information Integration Problem

What is the distribution and U/ Pb zircon ages of A-type plutons in VA? How about their 3-D geometry ?

How does it relate to host rock structures?



Geologic Map(Virginia)

Geologic Map(Virginia) GeoChemicalGeoChemical GeoPhysical

(gravity contours)

GeoPhysical(gravity contours)

GeoChronologic(Concordia)

GeoChronologic(Concordia)

Foliation Map(structure DB)

Foliation Map(structure DB)

“Complex Multiple-Worlds”

Mediation

“Complex Multiple-Worlds”

Mediation


Scientific Data Integration Challenges: Scientific Data Integration Challenges: Heterogeneities in the 4S’s ...Heterogeneities in the 4S’s ...

• System AspectsSystem Aspects– platforms, devices, phys. distribution, transport protocols,

access APIs, impedance mismatch, user interfaces, application integration ...

• SyntaxesSyntaxes– heterogeneous data formats (one for each tool ...)

• StructuresStructures– heterogeneous schemas (one for each DB ...)– heterogeneous data models (RDBs, ORDBs, OODBs,

XMLDBs)

• SemanticsSemantics– unclear semantics: e.g., incoherent terminology, multiple

taxonomies, ...


Data Integration: Approaches / SolutionsData Integration: Approaches / Solutions

SyntaxSyntax

StructureStructure

SemanticsSemantics

System aspectsSystem aspects

• (Data-)Grid / Middleware(Data-)Grid / Middleware– system: distributed data & computing (SDSC

SRB, Globus, web services, WSDL)– source = file or DB

• XML-Based MediatorsXML-Based Mediators– structure: XML queries and views– source = XML-DB

• Model-Based/Semantic MediatorsModel-Based/Semantic Mediators– semantics: conceptual models and declarative

views – source = Knowledge Base (DB+CMs+ICs)

• Semantic Web FormalismsSemantic Web Formalisms– semantics: ontologies, description logics

(RDF(S), DAML+OIL,...)

• Knowledge/Semantic-GridKnowledge/Semantic-Grid– combination


What’s in a Link? What’s in a Link? • Syntactic Joins Syntactic Joins

(X,Y) := X.SSN = Y.SSN equality (X,Y) := X.UMLS-ID = Y.UID

• ““Speciality” JoinsSpeciality” Joins (X,Y,Score) := BLAST(X,Y,Score) similarity

• Semantic/Rule-Based JoinsSemantic/Rule-Based Joins (X,Y,C) :=

X isa C, Y isa C, BLAST(X,Y,S), S>0.8 homology, lub (X,Y,[produces,B,increased_in]) :=

X produces B, B increased_in Y. rule-based

e.g., X=-secretase, B=beta amyloid, Y=Alzheimer’s disease

• Challenge: Challenge: – compile semantic joins into efficient syntactic ones

XY

XML-Based vs. Model-Based MediationXML-Based vs. Model-Based Mediation

Raw DataRaw DataRaw Data

IF THEN IF THEN IF THEN

LogicalDomainConstraints

Integrated-CM :=

CM-QL(Src1-CM,...)

Integrated-CM :=

CM-QL(Src1-CM,...)

. . ....

....

........ (XML)Objects

Conceptual Models

XMLElements

XML Models

C2 C3

C1

R

Classes,Relations,Ontologiesis-a, has-a, ...

“Glue” Maps Domain Maps Process Maps

“Glue” Maps Domain Maps Process Maps

Integrated-DTD :=

XQuery(Src1-DTD,...)

Integrated-DTD :=

XQuery(Src1-DTD,...)

No DomainConstraints

A = (B*|C),DB = ...

Structural Constraints (DTDs),Parent, Child, Sibling, ...

CM ~ {Descr.Logic, ER, UML, RDF/XML(-Schema), …} CM-QL ~ {F-Logic, DAML+OIL, …}

NCMIR ANATOM NCMIR ANATOM Domain Map:Domain Map:• conceptsconcepts• relationsrelations• logic ruleslogic rules


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


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


Source Registration/Data ContextualizationSource Registration/Data Contextualization

Source registers data with an existing ontology, using description logics it may also refine the mediator’s

domain map... [ICDE01]

sources can register new concepts at the mediator ...


Source Registration: Semantic Annotations Source Registration: Semantic Annotations


Multiple Ways of Querying DataMultiple Ways of Querying Data

Brain

Cerebellum

Purkinje Cell Layer

Purkinje cell

neuron

has a

has a

has a

is aSpatial Representation (Atlases)

Ontologies

Transformations


S1 S2

S3

(XML-Wrapper) (XML-Wrapper) (XML-Wrapper)

CM-Wrapper CM-Wrapper CM-Wrapper

USER/ClientUSER/Client

CM (Integrated View)

MediatorEngine

FL rule proc.

LP rule proc.

Graph proc.XSB Engine

GCM

CM S1

GCM

CM S2

GCM

CM S3

CM Queries & Results (exchanged in XML)

Domain MapsDMs

Domain MapsDMs

Domain MapsDMs

Domain MapsDMs

Domain MapsDMs

Process MapsPMs

“Glue” MapsGMs

semanticcontextCON(S)

Integrated View Definition IVD

Model-Based Mediator Architecture

First Results & Demos:[SSDBM’00] [VLDB’00]

[ICDE’01] [HBP’01] [EDBT’02][BNCOD’02]

Conceptual Model =• Object Model • Knowledge Base• Contextualization

Conceptual Model =• Object Model • Knowledge Base• Contextualization


Model-Based Mediation Methodology ...Model-Based Mediation Methodology ...

• Lift Sources to export CMs: Lift Sources to export CMs:

CM(S) = OM(S) + KB(S) + CON(S)

• Object Model OM(Object Model OM(SS):):– complex objects (frames), class hierarchy, OO constraints

• Knowledge Base KB(Knowledge Base KB(SS):):– explicit representation of (“hidden”) source semantics

– logic rules over OM(S)

• Contextualization CON(Contextualization CON(SS):):– situate OM(S) data using “glue maps” (GMs): domain maps DMs (ontology)

= terminological knowledge: concepts + roles process maps PMs

= “procedural knowledge”: states + transitions


... Model-Based Mediation Methodology... Model-Based Mediation Methodology

• Integrated View Definition (IVD)Integrated View Definition (IVD)– declarative (logic) rules with object-oriented features

– defined over CM(S), domain maps, process maps

– needs “mediation engineers” = domain + KRDB experts

• Knowledge-Based Querying and Browsing (runtime):Knowledge-Based Querying and Browsing (runtime):– mediator composes the user query Q with the IVD

... rewrites (Q o IVD), sends subqueries to sources

... post-processes returned results (e.g., situate in context)


Mediation Scenarios & TechniquesMediation Scenarios & TechniquesFederated Databases XML-Based Mediation Model-Based Mediation

One-World One-/Multiple-Worlds Complex Multiple-Worlds

Common Schema Mediated Schema Common Glue Maps

SQL, rules XML query languages DOOD query languages

Schema Transformations Syntax-Aware Mappings Semantics-Aware Mappings

Syntactic Joins Syntactic Joins “Semantic” Joins via Glue Maps

DB expert DB expert KRDB + domain experts


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:

– SQL, http, HTML, XML, XQuery, XSLT, XML Schema, RDF(S), DAML+OIL, DAML-S, UMLS, GO, XMI, SOAP, WSDL, ...

• 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


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


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

bertram lud ä scher data and knowledge system san diego supercomputer center u.c. san diego

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