PyRice: a Python package for querying Oryza sativa databases

Abstract

Summary: Currently, gene information available for Oryza sativa species is located in various online heterogeneous data sources. Moreover, methods of access are also diverse, mostly web-based and sometimes query APIs, which might not always be straightforward for domain experts. The challenge is to collect information quickly from these applications and combine it logically, to facilitate scientific research. We developed a Python package named PyRice, a unified programing API to access all supported databases at the same time with consistent output. PyRice design is modular and implements a smart query system, which fits the computing resources to optimize the query speed. As a result, PyRice is easy to use and produces intuitive results.

Availability and implementation: https://github.com/SouthGreenPlatform/PyRice.

Supplementary information: Supplementary data are available at Bioinformatics online.