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From Web 1.0 Web 3.0: Is RDF access to RDB enough

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Data Repository: RDBMS containing dbSNP and regulatory region data, Access ... Data Repository: Excel Spreadsheet containing the co-expression patterns of ... – PowerPoint PPT presentation

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Title: From Web 1.0 Web 3.0: Is RDF access to RDB enough


1
From Web 1.0 ? Web 3.0 Is RDF access to RDB
enough?
  • Vipul Kashyap
  • vkashyap1_at_partners.org
  • Senior Medical Informatician, Clinical
    Informatics RD
  • Partners Healthcare System
  • Martin Flanagan,
  • mflanagan_at_insilicodiscovery.com
  • CTO, InSilico Discovery
  • W3C Workshop on RDF Access to Relational
    Databases
  • October 26th , 2007

2
Outline
  • Position
  • Use Case Scenario
  • Solution Approach
  • A Generalized Framework for RDF Access
  • Next Steps
  • Proposed Roadmap
  • Research Topics

3
Position
  • There is a need for a generalized framework
    (format, representation language, algebra?) for
    RDF access to
  • Relational Databases
  • Tabular Data Sources, e.g., Excel Spreadsheets
  • Web Services
  • Motivation
  • Large amounts of tabular data and increasing
    number of web services in the Healthcare and Life
    Sciences
  • Learn from the relational database success
    story Declarative query language Algebra
    Opportunities for optimization
  • Potential for providing incremental value,
    increasing the adoption and acceptance of the
    Semantic Web.

4
Use Case ScenarioBiological Explanations for
Statistical Correlations
  • What is the location of a given Gene, e.g., CPNE1
    on the Human Genome?Data Repository NCBI
    EntrezAccess Mechanism Web Services
  • For what gene(s) is a given SNP, e.g.., rs6060535
    in the upstream regulatory region?Data
    Repository RDBMS containing dbSNP and regulatory
    region data, Access Mechanism JDBC/SQL
  • What genes have been found to be "coexpressed"
    with CPNE1 and in what study?Data Repository
    Excel Spreadsheet containing the co-expression
    patterns of various genes in various
    studies.Access Mechanism .NET API, MS Office API

5
Solution Approach
  • Ontology based RDF query specification
  • Mapping Framework
  • Relational Databases
  • Excel Spreadsheets
  • Web Services
  • Query Translations and Execution
  • Illustrations of a working system based on the
    Semantic Discovery System by InSilico Discovery
    (http//www.insilicodiscovery.com)

6
Ontology based RDF Query Specification
7
Mapping to Relational Databases
8
Mapping to Web Services
9
Mapping to Excel Spreadsheets
10
Query Translation and Execution
This one SPARQL statement joins data From NCBI,
Excel, Oracle who did what assay matching
this sequence data
Translators
11
A Generalized Framework for RDF Access
The SDS Platform is based on the Mediator
Definition Language work done by Val Tannen and
his students at U. Pennsylvania. Was earlier
implemented in the K3 system and was widely used
in Pharma
12
Conclusions
  • Need to think of various types of
    structured/semi-structured/tabular data sources
    in a wholistic manner
  • XML Documents (GRDDL Transforms)
  • Relational Databases
  • Web Services
  • Excel Spreadsheets
  • Other Tabular and Tree data sources
  • Potential for providing value beyond relational
    databases
  • Accelerate the transition to the Semantic Web
  • Increase Adoption and Acceptance

13
Next Steps Proposed Roadmap
RDF
Generalized Transformation Language
Relational Algebra
GRDDL
Relational Databases
WSDL
XML
Excel Spreadsheets
14
Next Steps Research
  • Extension of Relational Algebra?
  • XQuery
  • RDF
  • GRDDL Transformations
  • WSDL
  • Read only Web Service Choreography/Composition
  • What aspects of the above can be webified?
  • Access Transformation Languages
  • Mapping Languages Is XQuery or RDF enough?
  • Existing efforts in Mediator research
  • E.g., Mediator Definition Language (MDL)
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