©2011 MFMER | slide-1 The Linked Clinical Data Project Jyotishman Pathak, PhD HCLS TMO October 27, 2010

©2011 MFMER | slide-2 Purpose The Linked Clinical Data (LCD) project aims to investigate emerging Semantic Web technologies for developing an ontology-driven framework for high- throughput phenotyping using Electronic Medical Records (EMRs) to analyze multi-factorial phenotypes. Investigate ontology-based techniques. Develop a framework for publishing and integrating. Propose and validate semantic reasoning techniques to support rapid cohort identification

©2011 MFMER | slide-3 LCD Architecture Med Index Virtuoso RDF View MCLSS Endpoint SPARQL SQL Linked Open Drug Data Endpoints Selector Thick Client Application Thin Client Application Mobile Client Application Health Quest MICS MRIS NRAF MCLSS Databases Web Server Virtual Server Viewer Formatter Linked Data API Response Request

©2011 MFMER | slide-4 Project – Automated SNPedia SNPedia contains a wealth of data but the information in the wiki is manually curated. The focus of this project is to automate the results using patient data. Using MCLSS, identify patients with specific conditions. Join with OMIM to determine the genetic locus associated with those conditions Join with dbSNP to identify potentially associated SNPs. Each of the joins will be done using a single federated SPARQL query. Results will then be compared to data in SNPedia

©2011 MFMER | slide-5 Disease to SNP architecture dbSNP OMIM MCLSS Databases Endpoints Patient Disease SNOMED/ICD9 Gene SNP Request Results RDF View Mapping SPARQL Query

©2011 MFMER | slide-6 Process – Creating dbSNP endpoint No endpoint could be found so one had to be created. Download dbSNP database from a Sybase dump Use Perl to filter the tables in order to isolate desired data and rewrite into tab delimited form. Create tables in mySQL and import the files. Use Virtuoso to link to the tables Create RDF views by mapping the table columns to the desired endpoint subjects

©2011 MFMER | slide-7 dbSNP Schema The filtered tables did not have a primary key so an id column was added to each table. Subjects in our dbSNP endpoint mapped directly to the schema LOC VALRSSNP

©2011 MFMER | slide-8 Hurdles Virtuoso Did not support federated queries until March. March release has bugs Unable to run SPARQL queries against non- local endpoints Federated queries of mixed location crashes the server Endpoints Difficult to find Unreliable up time Schema documentation

©2011 MFMER | slide-9 Status MCLSS endpoint has been created dbSNP endpoint has been created OMIM endpoint has been located Waiting on Virtuoso fix for federated query bug.

©2011 MFMER | slide-10 Questions?