pandasGWAS: a Python package for easy retrieval of GWAS catalog data

Abstract

Background: Since the NHGRI-EBI Catalog of human genome-wide association studies was established by NHGRI in 2008, research on it has attracted more and more researchers as the amount of data has grown rapidly. Easy-to-use, open-source, general-purpose programs for accessing the NHGRI-EBI Catalog of human genome-wide association studies are in great demand for current Python data analysis pipeline. Results: In this work we present pandasGWAS, a Python package that provides programmatic access to the NHGRI-EBI Catalog of human genome-wide association studies. Instead of downloading all data locally, pandasGWAS queries data based on input criteria and handles paginated data gracefully. The data is then transformed into multiple associated pandas.DataFrame objects according to its hierarchical relationships, which makes it easy to integrate into current Python-based data analysis toolkits. Conclusions: pandasGWAS is an open-source Python package that provides the first Python client interface to the GWAS Catalog REST API. Compared with existing tools, the data structure of pandasGWAS is more consistent with the design specification of GWAS Catalog REST API, and provides many easy-to-use mathematical symbol operations.