PyRice：一个用于查询水稻数据库的 Python 包。

PyRice: a Python package for querying Oryza sativa databases.

机构信息

University of Science and Technology of Hanoi (USTH), Hanoi, Vietnam.

DIADE, Univ Montpellier, IRD, Montpellier, France.

出版信息

Bioinformatics. 2021 May 17;37(7):1037-1038. doi: 10.1093/bioinformatics/btaa694.

DOI:10.1093/bioinformatics/btaa694

PMID:32735312

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.

摘要

目前，可供稻属物种使用的基因信息位于各种在线异构数据源中。此外，访问方法也多种多样，主要基于网络，有时也使用查询 API，但对于领域专家来说，这些方法并不总是直接适用。挑战在于从这些应用程序中快速收集信息，并进行逻辑组合，以方便科学研究。我们开发了一个名为 PyRice 的 Python 包，这是一个统一的编程 API，可以同时访问所有支持的数据库，并具有一致的输出。PyRice 的设计是模块化的，并实现了一个智能查询系统，可以根据计算资源进行调整，以优化查询速度。因此，PyRice 使用方便，结果直观。