The BIEN R package: A tool to access the Botanical Information and Ecology Network (BIEN) database
The BIEN R package: A tool to access the Botanical Information and Ecology Network (BIEN) database
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DOI：
10.1111/2041-210x.12861
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发表时间：
2018-02-01
影响因子：
6.6
通讯作者：
Enquist, Brian J.
中科院分区：
文献类型：
--
作者：
Maitner, Brian S.;Boyle, Brad;Enquist, Brian J.
1.迫切需要大规模的植物学数据来提高我们对群落组装、共存、植物地理学、进化和许多其他基本生物过程的理解。了解这些过程对于预测和处理人类-生物多样性相互作用和全球变化动态（如粮食和能源安全、生态系统服务、气候变化和物种入侵）至关重要。植物信息和生态网络（BIEN）数据库包括前所未有的清洁和标准化的植物学数据，包含大约8100万个发生记录，从c。375，000种，C. 915，000个性状观察，来自c. 93，000个物种，来自全球110，000个生态地块的共现记录，以及100，000个新世界物种的范围地图和100个复制的物种起源（每个包含81，274个物种）。在这里，我们描述了一个R包，它提供了对这些数据的轻松访问。BIEN R软件包允许用户访问BIEN数据库中的多种类型的数据。此包中的函数通过将用户输入转换为优化的PostgreSQL函数来查询BIEN数据库。函数名称遵循一个约定，旨在使每个函数的功能易于理解。我们还开发了一个协议，用于为通过BIEN R软件包下载的数据提供定制的引文和植物标本检索。4. BIEN数据库的开发是生物数据整合、清理和标准化方面的一项重大成就。同样，BIEN R软件包代表了开放科学的重要工具，使BIEN数据库对每个人都可以自由轻松地访问。
1. There is an urgent need for large-scale botanical data to improve our understanding of community assembly, coexistence, biogeography, evolution, and many other fundamental biological processes. Understanding these processes is critical for predicting and handling human-biodiversity interactions and global change dynamics such as food and energy security, ecosystem services, climate change, and species invasions.2. The Botanical Information and Ecology Network (BIEN) database comprises an unprecedented wealth of cleaned and standardised botanical data, containing roughly 81 million occurrence records from c. 375,000 species, c. 915,000 trait observations across 28 traits from c. 93,000 species, and co-occurrence records from 110,000 ecological plots globally, as well as 100,000 range maps and 100 replicated phylogenies (each containing 81,274 species) for New World species. Here, we describe an R package that provides easy access to these data.3. The BIEN R package allows users to access the multiple types of data in the BIEN database. Functions in this package query the BIEN database by turning user inputs into optimised PostgreSQL functions. Function names follow a convention designed to make it easy to understand what each function does. We have also developed a protocol for providing customised citations and herbarium acknowledgements for data downloaded through the BIEN R package.4. The development of the BIEN database represents a significant achievement in biological data integration, cleaning and standardization. Likewise, the BIEN R package represents an important tool for open science that makes the BIEN database freely and easily accessible to everyone.