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

By

Proença Neto, Marco
De Sousa, Marcos

Type

Article

Date of Publication

2025-1-8

Original Publication

Biodiversity data journal

Volume

13

Pages

1--13

Subjects

biodiversity informatics , data cleaning , scientific names , species name matching , taxonomy

Contributed by

Pensoft Publishers

Language

English

Published by

Sofia Pensoft Publishers [2013]-

Identifiers

DOI: https://doi.org/10.3897/BDJ.13.e138257

 

Abstract

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.<br> 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.