Apr 21, 2020

PyRice: a Python package for querying Oryza Sativa functional databases

BioRxiv : the Preprint Server for Biology
Q. H. DOPierre Larmande

Abstract

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 programming API to access all supported databases at the same time with consistent output. PyRice design is modular and can be easily extended with new databases. Furthermore, the package 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. It is available under MIT Licence on PyPi package repository, while the source code and the documentation are available on GitHub. Availability and implementation. https://github.com/SouthGreenPlatform/PyRice. Contact: pierre.larmande at ird.fr. Licence information: MIT. Supplementary information: Supplementary data are available at https://pyrice.readthedocs.io

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Mentioned in this Paper

In Vivo
Patterns
Abnormal Degeneration
Entire Retina
HDAC9 gene
Vision
Nerve Degeneration
Retinal Diseases
PDE6C protein, human
Histone Deacetylase

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