Using Clinical Element Models for Pharmacogenomic Study Data Standardization

Standardized representations for pharmacogenomics data are seldom used, which leads to data heterogeneity and hinders data reuse and integration. In this study, we attempted to represent data elements from the Pharmacogenomics Research Network (PGRN) that are related to four categories, patient, drug, disease and laboratory, in a standard way using Clinical Element Models (CEMs), which have been adopted in the Strategic Health IT Advanced Research Project, secondary use of EHR (SHARPn) as a library of common logical models that facilitate consistent data representation, interpretation, and exchange within and across heterogeneous sources and applications. This was accomplished by grouping PGRN data elements into categories based on UMLS semantic type, then mapping each to one or more CEM attributes using a web-based tool that was developed to support curation activities. This study demonstrates the successful application of SHARPn CEMs to the pharmacogenomic domain. It also identified several categories of data elements that are not currently supported by SHARPn CEMs, which represent opportunities for further development and collaboration.