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

Vipul Kashyapvkashyap1@partners.org

Senior Medical Informatician, Clinical Informatics R&DPartners Healthcare System

Martin Flanagan,mflanagan@insilicodiscovery.com

CTO, InSilico Discovery

W3C Workshop on RDF Access to Relational DatabasesOctober 26th , 2007

Outline

• Position

• Use Case Scenario

• Solution Approach

• A Generalized Framework for RDF Access

• Next Steps:— Proposed Roadmap

— Research Topics

There is a need for a generalized framework (format, representation language, algebra?) for RDF access to:

(A) Relational Databases(B) Tabular Data Sources, e.g., Excel Spreadsheets(C) Web Services

Motivation:(A) Large amounts of “tabular” data and increasing number of

web services in the Healthcare and Life Sciences(B) Learn from the relational database success story: Declarative

query language + Algebra + Opportunities for optimization(C) Potential for providing incremental value, increasing the

adoption and acceptance of the Semantic Web.

Position

Use Case Scenario:Biological 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

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)

Ontology based RDF Query Specification

prefix example <http://www.semanticdiscoverysystems.com/Example.owl#>prefix ns <http://www.w3.org/1999/02/22-rdf-syntax-ns#>select distinct ?v0, ?v1where{?v0 ns:type example:gene?v0 example:has_gene_region ?v1?v0 example:gname ‘CPNE’}

SPARQL Query Generated:

Mapping to Relational Databases

Mapping to OracleDatabases

Mapping to Gene NamesMediator Class

Mapping to Web Services

Mapping to Web Services

Mapping to GetGenomeLocationsin gene_regions Mediator class

Mapping to Excel Spreadsheets

Mapping to Spreadsheet Data

Mapping to Gene NamesMediator Class

Translators

Query Translation and Execution

This one SPARQL statement ‘joins’ dataFrom NCBI, Excel, Oracle – “who did what assay

matching this sequence data …”

A Generalized Framework for RDF Access

Ontology Classes and PropertiesGene, GeneRegionhas_gene_region, gname

RDB specific classes:oracle.mdl

Web service specific classes:ncbi.mdl, keg.mdl

Mediator Framework Classes:gene.mdl, gene_region.mdl, gene_names.mdl, …

Excel specific classes:excel.mdl

The SDS Platform is based on the Mediator Definition Languagework done by Val Tannen and his students at U. Pennsylvania.

Was earlier implemented in the K3 system and was widely used in Pharma

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

Next Steps: Proposed Roadmap

RDF

XML Relational Databases

WSDL ExcelSpreadsheets

Generalized Transformation Language

GRDDLRelationalAlgebra

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)