Semantic Mediation of Scientific Data via LogicBased Data Federation Software

1
Semantic Mediation of Scientific Data via
Logic-Based Data Federation Software

• Amarnath Gupta
• Bertram Ludäscher
• Reagan Moore
• San Diego Supercomputer Center
• University of California, San Diego

2
Information Integration / Mediation

• Goal
• combine data from different sources s.t. the
  integrated whole is more than the sum of its
  isolated parts
• gt SDSC/CSE MIX project (Mediation of Information
  in XML)
• Standard Scenarios
• C2B, e.g. comparison shopping
  
• AddAll IntegratedView(amazon, barnesnoble,
  ...)
• B2B, e.g. marketplaces
• Virt_Market IntegratedView(supplier_1, ...
  supplier_n)
• C2M, e.g. home-buyer
• Full_Picture IntegratedView(Realtor, Crime,
  Schools, ...)

One-World Mediation e.g. join on ISBN
Simple Multiple-World Mediation e.g. join on ZIP
3
MIX Mediation Challenges

• MIX Mediator Architecture (middleware)
• wrappers wrap different data into common format
  (XML)
• mediator combines sources XML views into
  IntegratedView
• MIX Mediator Components
• declarative mediator view definition language
• XMAS (XML Matching And Structuring) language,
  algebra, and first prototype 1999
  SIGMOD99,EDBT00,...
• query composition and rewriting esp. with limited
  source capabilities
• on-demand (lazy) query processing of virtual
  XML docs (DOM-VXD)
• Blended Browsing and Querying user interface
  (BBQ)

4
New MIX Challenges from Scientific Applications

• Complex Data (S2S)
• SDSCs Scientific Data Applications
  (current/planned, e.g. Neurosciences SciDAC/SDM,
  NCMIR, NIH BIRN, Earth sciences, ...) show that
  syntactic/structural integration is insufficient
  for ...
• Complex Multiple-World Mediation Problems
• complex, disjoint, seemingly unrelated data
• hidden semantics in complex, indirect
  relationships
• gt Semantic (aka Model/Knowledge-Based) Mediation
  
• lift mediation to the level of conceptual models
  (CMs)
• use domain experts knowledge formalized as rules
  over CMs
• gt Specialized Extensions
• temporal, geospatial, statistical, DQ/accuracy...
  operations
• gt Extend Mediation Scope and Power via Deductive
  Rules

5
A Neuroscience Question
What is the cerebellar distribution of rat
proteins with more than 70 homology with human
NCS-1? Any structure specificity? How about other
rodents?
6
Example for Formalizing Domain KnowledgeDomain
Map (Ontology) for SYNAPSE and NCMIR

• A domain map comprises
• Description Logic facts ...
• - concepts ("classes")
• - roles ("associations")
• derived properties ...
• ... expressed as logic rules
• - (e.g. F-logic)

7
Domain Map Refinement
... source can register new concepts at the
mediator ...
8
Semantic Annotation Tool for Domain Scientists
9
Extended Mediator Architecture for Semantic
Mediation
USER/Client
CM (Integrated View)
Domain Map DM
Integrated View Definition IVD
Mediator Repository DB
CM Plug-In
CM Queries Results (exchanged in XML)
first results demos SSDBM00
VLDB00 ICDE01 NIH-HBP01
Logic API (capabilities)
S3
S2
10
ANATOM Domain Map with Registered Data
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Query Processing
12
Mediator System Architecture
13
Mediation ServicesSource Registration (System
Issues)
14
Mediation Services Source Registration
(Semantics Issues)

• Domain Map Registration
• provide concept space/ontology
• as a private object (myANATOM)
• merge with others (give semantic bridges)
• and check for conflicts
• Conceptual Model Registration
• schema classes, associations, attributes
• domain constraints
• put data into context (linking data to the
  domain map)

15
Mediation Services Client Registration
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Other Existing Infrastructure

• Transparent Access to Remote Data Collections
  Storage Resource Broker (SRB) and Metadata
  Catalog (MCAT)
• Production-Level Software
• PPDG interface to LBNL Storage Manager,
  collection creation, replication management
• Use of manual and automatic wrapper technology
  (Minerva, Roadrunner, V. Crescenzi, Universita di
  Roma Tre)
• gt XWrap Elite

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SRB and the Particle Physics Data Grid
S-Commands
S-Commands
Wisc Client 2
SRB Server _at_Wisc
Wisc Client 1
SRB Server _at_LBL
SRB Server _at_LBL
Disk cache
file caching
esrb.driver
esrb.driver
IPC
IPC
Stage() purge() fileStatus()
file purging
File caching request
Stage() purge() fileStatus()
HRM
FC
esrb.server
Stage() purge() fileStatus()
18
Year 1 Deliverables

• define interface metadata format (Critchlow)
• extend XWrap to generate wrappers using the
  interface metadata description instead of
  requiring human interaction (GT)
• develop a canonical XML-based query and response
  format as a dynamic interface between query
  engine and wrappers (Critchlow, GT, SDSC)
• communication via agent protocols? How about
  using digital library infrastructure (e.g. Simple
  Digital Library Interoperability Protocol, SDLIP)
• use extended XWrap to create wrappers for the
  genomics domain for evaluation (GT)
• extend the SDSC query and metadata architecture
  to interoperate with the LLNL DataFoundry (SDSC,
  Critchlow)
• ... interoperation at the wrapper level Minerva
  wrappers, XWrap

19
References

• 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 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.