Mining the human phenome using semantic web technologies: a case study for Type 2 Diabetes

AMIA Annu Symp Proc. 2012;2012:699-708. Epub 2012 Nov 3.

Abstract

The ability to conduct genome-wide association studies (GWAS) has enabled new exploration of how genetic variations contribute to health and disease etiology. However, historically GWAS have been limited by inadequate sample size due to associated costs for genotyping and phenotyping of study subjects. This has prompted several academic medical centers to form "biobanks" where biospecimens linked to personal health information, typically in electronic health records (EHRs), are collected and stored on large number of subjects. This provides tremendous opportunities to discover novel genotype-phenotype associations and foster hypothesis generation. In this work, we study how emerging Semantic Web technologies can be applied in conjunction with clinical and genotype data stored at the Mayo Clinic Biobank to mine the phenotype data for genetic associations. In particular, we demonstrate the role of using Resource Description Framework (RDF) for representing EHR diagnoses and procedure data, and enable federated querying via standardized Web protocols to identify subjects genotyped with Type 2 Diabetes for discovering gene-disease associations. Our study highlights the potential of Web-scale data federation techniques to execute complex queries.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Data Mining
  • Diabetes Mellitus, Type 2 / genetics*
  • Electronic Health Records* / standards
  • Genetic Association Studies
  • Genetic Predisposition to Disease
  • Genome-Wide Association Study*
  • Humans
  • Internet / standards
  • Phenotype*
  • Semantics