Metadata Import from RDF to i2b2

Abstract

Metadata management is an important task in medical informatics and highly affects the gain out of existing health information data. Data Warehouse solutions like Informatics for Integrating Biology and the Bedside (i2b2) are common tools for identifying patient cohorts and analyzing collected clinical data while respecting patient privacy. The Resource Description Framework (RDF) is designed for highly interoperable ontology representation in various formats, facilitating ontology and metadata management. Our approach is to combine i2b2's and RDF's benefits by importing the easy-to-edit RDF ontology into the extensive-research-enabling i2b2 software. We do so by using a SPARQL Protocol and RDF Query Language (SPARQL) interface, that enables RDF data queries, and developing a java program, which then generates i2b2-specific SQL insert statements. To demonstrate our solution's feasibility, we transcribe our lung disease specific ontology to RDF and import it into our i2b2 data warehouse.

Keywords: Biological ontologies; automatic data processing; information systems; metadata; organization and administration.