Supporting Biodiversity Dataset Preparation: An Introduction to the TaiBIF Open Data Toolkit

By

Liu, Melissa (Jean-Yi)
Jhang, Jhu-Jyun
Hoh, Daphne
Chang, Chun-I
Tuanmu, Mao-Ning

Type

Article

Date of Publication

2025-1-22

Original Publication

Metabarcoding and metagenomics

Volume

9

Pages

1--4

Subjects

biodiversity data tool , data cleaning , data template , data validation

Contributed by

Pensoft Publishers

Language

English

Published by

Bulgaria Pensoft Publishers 2017-

Identifiers

DOI: https://doi.org/10.3897/biss.9.147432

 

Abstract

The Darwin Core standard (DwC; Darwin Core Task Group 2009) and the Global Biodiversity Information Facility (GBIF) new data model provide a flexible set of biodiversity data fields to accommodate various thematic datasets such as taxonomic checklists, sampling events, eDNA metabarcoding, ecological survey data, etc. However, this flexibility can make it challenging for data providers to get started, often leading to frustration when trying to map their original data fields to DwC terms. Additionally, while data cleaning is crucial for enhancing data quality (Chapman 2005), it requires significant expertise and effort, which may hinder the mobilization of high-quality data. To address these common pain points in data mobilization, the Taiwan Biodiversity Information Facility (TaiBIF) developed the TaiBIF Open Data Toolkit (ODT) by integrating various thematic dataset templates, DwC terms, the Nansen Legacy Excel Template Generator, Excel data editing interfaces (e.g, filter, cell editing, AutoFill), GBIF Data Validator, and the OpenRefine. We combined the strengths of each tool to create a straightforward workflow from data sheet generation (Fig. 1, Fig. 2), data validation (Fig. 3), data cleaning to dataset packaging (Fig. 4). We hope the toolkit aligns with the needs of data publishers and facilitates a smoother and more user-friendly process of data management and publishing.