Geographic And Taxonomic Occurrence R-based Scrubbing (gatoRs): An R package and workflow for processing biodiversity data

IF 2.7 3区生物学 Q2 PLANT SCIENCES

Applications in Plant Sciences Pub Date : 2024-03-21 DOI:10.1002/aps3.11575

Natalie N. Patten, Michelle L. Gaynor, Douglas E. Soltis, Pamela S. Soltis

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引用次数: 0

Abstract

Premise

Digitized biodiversity data offer extensive information; however, obtaining and processing biodiversity data can be daunting. Complexities arise during data cleaning, such as identifying and removing problematic records. To address these issues, we created the R package Geographic And Taxonomic Occurrence R-based Scrubbing (gatoRs).

Methods and Results

The gatoRs workflow includes functions that streamline downloading records from the Global Biodiversity Information Facility (GBIF) and Integrated Digitized Biocollections (iDigBio). We also created functions to clean downloaded specimen records. Unlike previous R packages, gatoRs accounts for differences in download structure between GBIF and iDigBio and allows for user control via interactive cleaning steps.

Conclusions

Our pipeline enables the scientific community to process biodiversity data efficiently and is accessible to the R coding novice. We anticipate that gatoRs will be useful for both established and beginning users. Furthermore, we expect our package will facilitate the introduction of biodiversity-related concepts into the classroom via the use of herbarium specimens.

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基于 R 的地理和分类出现率擦除 (gatoRs)：处理生物多样性数据的 R 软件包和工作流程

前提条件数字化的生物多样性数据提供了大量信息；然而，获取和处理生物多样性数据的工作可能非常艰巨。数据清理过程中会出现一些复杂问题，如识别和删除有问题的记录。为了解决这些问题，我们创建了基于 R 的地理与分类出现清理（Geographic And Taxonomic Occurrence R-based Scrubbing，gatoRs）软件包。方法与结果 gatoRs 工作流程包括简化从全球生物多样性信息基金（GBIF）和综合数字化生物收集（iDigBio）下载记录的功能。我们还创建了清理下载标本记录的函数。与以前的 R 软件包不同，gatoRs 考虑到了 GBIF 和 iDigBio 下载结构的差异，并允许用户通过交互式清理步骤进行控制。我们预计，gatoRs 对成熟用户和初学者都很有用。此外，我们还希望我们的软件包能通过标本馆标本的使用，促进将生物多样性相关概念引入课堂。

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来源期刊

Applications in Plant Sciences PLANT SCIENCES-

CiteScore

7.30

自引率

0.00%

发文量

审稿时长

12 weeks

期刊介绍： Applications in Plant Sciences (APPS) is a monthly, peer-reviewed, open access journal promoting the rapid dissemination of newly developed, innovative tools and protocols in all areas of the plant sciences, including genetics, structure, function, development, evolution, systematics, and ecology. Given the rapid progress today in technology and its application in the plant sciences, the goal of APPS is to foster communication within the plant science community to advance scientific research. APPS is a publication of the Botanical Society of America, originating in 2009 as the American Journal of Botany''s online-only section, AJB Primer Notes & Protocols in the Plant Sciences. APPS publishes the following types of articles: (1) Protocol Notes describe new methods and technological advancements; (2) Genomic Resources Articles characterize the development and demonstrate the usefulness of newly developed genomic resources, including transcriptomes; (3) Software Notes detail new software applications; (4) Application Articles illustrate the application of a new protocol, method, or software application within the context of a larger study; (5) Review Articles evaluate available techniques, methods, or protocols; (6) Primer Notes report novel genetic markers with evidence of wide applicability.