BDPGx — A big data platform for graph-based pharmacogenomics data

Abstract

Pharmacogenomics studies are widely adopted in clinical practices and it helps in understanding the effect of drug and its dosage based on individual's genetic makeup. The pharmacogenomics data available in open repositories are used to find the molecular associations between genes, pathways, diseases and the drug dosage effects. With the advent of various sequencing projects, the data deposited in the repositories are voluminous, multidimensional and are of different formats. The heterogeneous data need to be integrated and visualized in a graphical format to gain meaningful information. We developed a big data platform for querying and visualization of pharmacogenomics data stored in the form of graphs. Initially, the data related to genes, its related pathways and diseases, drugs and chemicals are integrated using Neo4j graph database. A web application is developed to provide an easy to use interface for querying this integrated database. The results are given back in the form of graphs and downloadable text format. The platform is scalable to integrate new databases and extensible to add more properties.