Pytaxon: A Python software for resolving and correcting taxonomic names in biodiversity data.

IF 1 4区环境科学与生态学 Q3 BIODIVERSITY CONSERVATION Biodiversity Data Journal Pub Date : 2025-01-08 eCollection Date: 2025-01-01 DOI:10.3897/BDJ.13.e138257

Marco A Proença Neto, Marcos P A De Sousa

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Abstract

Background: The standardisation and correction of taxonomic names in large biodiversity databases remain persistent challenges for researchers, as errors in species names can compromise ecological analyses, land-use planning and conservation efforts, particularly when inaccurate data are shared on global biodiversity portals.

New information: We present pytaxon, a Python software designed to resolve and correct taxonomic names in biodiversity data by leveraging the Global Names Verifier (GNV) API and employing fuzzy matching techniques to suggest corrections for discrepancies and nomenclatural inconsistencies. The pytaxon offers both a Command Line Interface (CLI) and a Graphical User Interface (GUI), ensuring accessibility to users with different levels of computing expertise. Tests on spreadsheets derived from datasets published in the Global Biodiversity Information Facility (GBIF) demonstrated its effectiveness in identifying and resolving taxonomic errors. By mitigating the propagation of inaccuracies from researchers' datasets to global biodiversity databases, pytaxon supports more reliable conservation decisions and robust scientific investigations. Its contributions enhance data integrity and promote informed biodiversity management in a rapidly evolving global environment.

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Pytaxon：一个Python软件，用于解析和纠正生物多样性数据中的分类名称。

背景：大型生物多样性数据库中分类名称的标准化和校正一直是研究人员面临的挑战，因为物种名称的错误可能会影响生态分析、土地利用规划和保护工作，特别是当不准确的数据在全球生物多样性门户网站上共享时。新信息：我们提出pytaxon，一个Python软件，旨在通过利用全球名称验证器（GNV） API和模糊匹配技术来解决和纠正生物多样性数据中的分类名称，并建议纠正差异和命名不一致。pytaxon提供命令行界面（CLI）和图形用户界面（GUI），确保具有不同计算专业水平的用户都可以访问。对来自全球生物多样性信息设施（GBIF）公布的数据集的电子表格进行的测试表明，它在识别和解决分类错误方面是有效的。通过减少从研究人员的数据集到全球生物多样性数据库的不准确性传播，pytaxon支持更可靠的保护决策和有力的科学调查。它的贡献增强了数据的完整性，并在快速变化的全球环境中促进了知情的生物多样性管理。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Biodiversity Data Journal Agricultural and Biological Sciences-Ecology, Evolution, Behavior and Systematics

CiteScore

2.20

自引率

7.70%

发文量

283

审稿时长

6 weeks

期刊介绍： Biodiversity Data Journal (BDJ) is a community peer-reviewed, open-access, comprehensive online platform, designed to accelerate publishing, dissemination and sharing of biodiversity-related data of any kind. All structural elements of the articles – text, morphological descriptions, occurrences, data tables, etc. – will be treated and stored as DATA, in accordance with the Data Publishing Policies and Guidelines of Pensoft Publishers. The journal will publish papers in biodiversity science containing taxonomic, floristic/faunistic, morphological, genomic, phylogenetic, ecological or environmental data on any taxon of any geological age from any part of the world with no lower or upper limit to manuscript size.