This study demonstrates harmonization and semantic annotation work for pharmacogenomics data dictionaries collected from PGRN research groups. A semi-automated system was developed to support the harmonization/annotation process, which includes four individual steps, (1) pre-processing PGRN variables; (2) decomposing and normalizing variable descriptions; (3) semantically annotating words and phrases using controlled terminologies; (4) grouping PGRN variables into categories based on the annotation results and semantic types, for total 1514 PGRN variables.
Our results demonstrate that there is a significant amount of variability in how pharmacogenomics data is represented and that additional standardization efforts are needed. This represents a critical first step toward identifying and creating data standards for pharmacogenomics studies.