Towards Semantic Mediation for GEON: Facilitating Scientific Data Integration using Knowledge Repres

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Towards Semantic Mediation for
GEONFacilitating Scientific Data Integration
using Knowledge Representation

• Bertram Ludäscher
• ludaesch_at_sdsc.edu
• Data and Knowledge Systems
• San Diego Supercomputer Center
• U.C. San Diego

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Acknowledgements
Smart Geologic Map Prototype Kai
Lin klin_at_sdsc.edu Data and Knowledge Systems San
Diego Supercomputer Center Geo-Knowledge-Engineer
Boyan Brodaric brodaric_at_NRCan.gc.ca Natural
Resources Canada ... and many GEONites Dogan,
Krishna, ..., State Geologic Surveys, Chaitan,
Ilya, Michalis, Ashraf, ... (upcoming demo)
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GEON and Semantic Data Integration
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What is Knowledge Representation? Relating Theory
to the World via Formal Models
Source John F. Sowa, Knowledge Representation
Logical, Philosophical, and Computational
Foundations
All models are wrong, but some are useful!
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What is (an) Ontology ??? (... what CS
graduate students need to know ...)

• 1. Ontology as a philosophical discipline
• 2. Ontology as a an informal conceptual system
• 3. Ontology as a formal semantic account
• 4. Ontology as a specification of a
  conceptualization
• 5. Ontology as a representation of a conceptual
  system
• via a logical theory
• 5.1 characterized by specific formal properties
• 5.2 characterized only by its specific purposes
• 6. Ontology as the vocabulary used by a logical
  theory
• 7. Ontology as a (meta-level) specification of a
  logical theory

Guarino95
http//ontology.ip.rm.cnr.it/Papers/KBKS95.pdf
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What is an Ontology? (CSE-291 contd -)

• Given a logical language L ...
• ... a conceptualization is a set of models of L
  which describes the admittable (intended)
  interpretations of its non-logical symbols (the
  vocabulary)
• ... an ontology is a (possibly incomplete)
  axiomatization of a conceptualization.

set of all models M(L)
logic theories
ontology
conceptualization C(L)
Guarino96 http//www-ksl.stanford.edu/KR96/Guari
no-What/P003.html
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Problem Scientific Data Integration ... from
Questions to Queries ...
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?
Complex Multiple-Worlds Mediation
GeoPhysical (gravity contours)
Geologic Map (Virginia)
GeoChronologic (Concordia)
Foliation Map (structure DB)
GeoChemical
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Got Glue? Which one? What for?

• XML (common syntax)
• flexible (semistructured) data model
• used at all levels data / metadata exchange,
  message exchange (SOAP), schemas data types
  (XML Schema), Semantic Web web ontologies
  (RDF(S), OWL), ...
• Grid infrastructure (system interoperation)
• distributed computing and data management
• web services
• Controlled Vocabularies (joins)
• data level joins across different data sets
• but meta-data and ontologies (concept names,
  relationship names, ...) are also data!
• Integrated View Definitions (mediated
  views/virtual databases)
• declarative specification of integration logic
  XQuery, Datalog, ...
• Thesauri (translator for retrieving related
  information)
• synonyms, broader/narrow term, e.g., UMLS
  (meta-thesaurus, ontology)
• Taxonomies (classification)
• shared vocabulary, concept hierarchy (is-a)
• Ontologies (classification additional
  semantics)
• formal specification of a conceptualization,
  shared meaning
• facilitates smart querying, semantic mediation

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Information Integration Challenges

• System aspects Grid Middleware
• distributed data computing
• Web Services, WSDL/SOAP, OGSA,
• sources functions, files, data sets,
• Syntax Structure
• (XML-Based) Data Mediators
• wrapping, restructuring
• (XML) queries and views
• sources (XML) databases
• Semantics
• Model-Based/Semantic Mediators
• conceptual models and declarative views
• Knowledge Representation ontologies, description
  logics (RDF(S),OWL ...)
• sources knowledge bases (DBCMsICs)

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Standard (XML-Based) Mediator Architecture
USER/Client
Query Q ( G (S1,..., Sk) )
Integrated Global (XML) View G
Integrated View Definition G(..)? S1(..)Sk(..)

MEDIATOR
(XML) Queries Results
(XML) View
(XML) View
(XML) View
wrappers implemented as web services
Wrapper
Wrapper
Wrapper
S1
S2
Sk
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XML-Based vs. Semantic Mediation
CM Descr.Logic, ER, UML, RDF(S),
CM-QL F-Logic,
0.0155381,1.54906,2,140,29,Tertiary,Trc,CHINLE
FORMATION,59,57
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GEON Framework for Interoperability in the
Geosciences

• Systems level GEON Grid ...
• enable sharing of data and tools via grid
  services
• based on Open Grid Services Architecture (OGSA)
• acquisition of cluster endpoints and initial
  deployment at some sites underway, including
  SDSC, UTEP, VT, ...,
• Syntactic and schema level Data integration via
  (meta)data standards (often XML-based)
• database mediators create integrated virtual
  databases
• dynamic creation and automatic update of
  data-warehouses
• Semantic level data integration via semantic
  mediation
• Situating 4-D data in context ? spatio-temporal,
  thematic, process contexts can be represented as
  concept spaces
• specifically use of ontologies, and logic-based
  knowledge representation
• development guided/driven by specific scientific
  data integration problems

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Towards Shared Conceptualizations High-level
Domain Ontology Standard Data Model
Adoption of a standard (meta)data model wrap
data sets into unified virtual views
Source NADAM Team (Boyan Brodaric et al.)
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Towards Shared Conceptualizations Data
Contextualization via Concept Spaces
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Towards Knowledge Sharing Rock-type Ontology
Genesis
Fabric
Composition
Texture
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Getting Formal Source Contextualization
Ontology Refinement in Logic
Biomedical Informatics Research
Network http//nbirn.net
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(No Transcript)
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Querying with Multiple Classifications/Ontologies
Age, Composition, Texture, Fabric, Genesis
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What to do with the KR Glue?

• Conceptual-level information, concept spaces,
  ontologies, and other KR techniques for ...
• ... smart data discovery
• ... browsing and querying by themes, disciplines,
  ...
• ... defining virtual/mediated databases at
  conceptual level
• ... support plugging together of data and
  information experiments into Scientific
  Workflows
• (a.k.a. Analytical Pipelines in the SEEK ITR)
• ... smarter user interfaces
• is find felsic sedimentary rocks a meaningful
  (satisfiable) query?
• ...

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Some enabling operations on ontology data

• Concept expansion
• what else to look for when asking for Mafic

Composition
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Some enabling operations on ontology data

• Generalization
• finding data that is like X and Y

Composition
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Towards Knowledge Sharing Rock-type Ontology
Genesis
Fabric
Composition
Texture
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DEMO... do NOT click this ...

• http//kbis.sdsc.edu/GEON/ahm03-demo.html

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Architecture of Integrated Geologic Map Prototype
System
request
response
Map Definition
HTTP Server (Java Server Page)
local layer
remote layer
local layer
MapServer (Minnesota)
Mediator (Java application)
Database (Arizona)
Database (Montana)
Global Ontology Definitions Rock classification
Geologic age
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Data Source Wrapping and Integration
ABBREV
Arizona
PERIOD
FORMATION
Idaho
AGE
NAME
Colorado
PERIOD
LITHOLOGY
Utah
TYPE
PERIOD
Nevada
FMATN
TIME_UNIT
Wyoming
NAME
Livingston formation
FORMATION
PERIOD
Tertiary-Cretaceous
Montana West
AGE
New Mexico
NAME
PERIOD
LITHOLOGY
andesitic sandstone
Montana East
FORMATION
PERIOD
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Ontology-Enabled Query Processing
User Show formations from Cenozoic!
Age Ontology
Cenozoic
Query Rewriting
Quaternary
Tertiary
select FORMATION where AGETertiary or
AGEQuaternary
PERIOD
FORMATION
LITHOLOGY
PERIOD
ABBREV
Arizona
Montana West
Map Rendering
Color Definition
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Integration Challenges

• MANY!
• non-available or non-interoperable data
• Dirty data, no controlled vocabularies
• Many different controlled vocabularies! (clean
  data)
• What is entailed by a vocabulary?
• ? Formal Ontologies
• ? Extensible Ontologies

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Whats next?

• YOU!
• GEON-SCI
• Science questions waiting to be turned into
  queries!
• GEON-KR Working Group activities
• guided (if not driven by) geoscientists
• marry KR technologies to standards (W3C, Semantic
  Web RDF, OWL, ...)
• collect GEON-able KR resources (data models,
  controlled vocabularies, ontologies, ...)
• GEON-DEV
• Generalize and merge current KR/semantic
  mediation architecture with standard Grid
  architecture
• building systems