From Web 1.0  Web 3.0: Is RDF access to RDB enough? Vipul Kashyap Senior Medical Informatician, Clinical Informatics R&D Partners Healthcare System Martin Flanagan, CTO, InSilico Discovery W3C Workshop on RDF Access to Relational Databases October 26 th, 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 Entrez Access Mechanism: Web Services For what gene(s) is a given SNP, e.g.., rs 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 (

Ontology based RDF Query Specification prefix example prefix ns select distinct ?v0, ?v1 where { ?v0 ns:type example:gene ?v0 example:has_gene_region ?v1 ?v0 example:gname ‘CPNE’ } SPARQL Query Generated:

Mapping to Relational Databases Mapping to Oracle Databases Mapping to Gene Names Mediator Class

Mapping to Web Services Mapping to GetGenomeLocations in gene_regions Mediator class

Mapping to Excel Spreadsheets Mapping to Spreadsheet Data Mapping to Gene Names Mediator Class

Translators Query Translation and Execution This one SPARQL statement ‘joins’ data From NCBI, Excel, Oracle – “who did what assay matching this sequence data …”

A Generalized Framework for RDF Access Ontology Classes and Properties Gene, GeneRegion has_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 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

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 Excel Spreadsheets Generalized Transformation Language GRDDL Relational Algebra

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)