Document Type

Article

Publication Date

2025

DOI

10.1111/geb.70003

Publication Title

Global Ecology and Biogeography

Volume

34

Issue

5

Pages

e70003

Abstract

Motivation: Here, we make available a second version of the BioTIME database, which compiles records of abundance estimates for species in sample events of ecological assemblages through time. The updated version expands version 1.0 of the database by doubling the number of studies and includes substantial additional curation to the taxonomic accuracy of the records, as well as the metadata. Moreover, we now provide an R package (BioTIMEr) to facilitate use of the database.

Main Types of Variables Included: The database is composed of one main data table containing the abundance records and 11 metadata tables. The data are organised in a hierarchy of scales where 11,989,233 records are nested in 1,603,067 sample events, from 553,253 sampling locations, which are nested in 708 studies. A study is defined as a sampling methodology applied to an assemblage for a minimum of 2 years.

Spatial Location and Grain: Sampling locations in BioTIME are distributed across the planet, including marine, terrestrial and freshwater realms. Spatial grain size and extent vary across studies depending on sampling methodology. We recommend gridding of sampling locations into areas of consistent size.

Time Period and Grain: The earliest time series in BioTIME start in 1874, and the most recent records are from 2023. Temporal grain and duration vary across studies. We recommend doing sample-level rarefaction to ensure consistent sampling effort through time before calculating any diversity metric.

Major Taxa and Level of Measurement: The database includes any eukaryotic taxa, with a combined total of 56,400 taxa.

Software Format: csv and. SQL.

Rights

© 2025 The Authors.

This is an open access article under the terms of the Creative Commons Attribution 4.0 International (CC BY 4.0) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Data Availability

Article states: "A static stable release of BioTIME version 2.0 can be found in Zenodo (https://doi.org/10.5281/zenodo.10932823). Code used in data curation and standardisation can be found at github.com/bioTIMEHub/BioTIME. The R package BioTIMEr is available in CRAN and can be found at github.com/bioTIMEHub/BioTIMEr."

Original Publication Citation

Dornelas, M., Antao, L. H., Bates, A. E., Brambilla, V., Chase, J. M., Chow, C. F. Y., Fontrodona-Eslava, A., Magurran, A. E., Martins, I. S., Moyes, F., Sagouis, A., Adu-Acheampong, S., Acquah-Lamptey, D., Adam, D., Ajani, P. A., Albaina, A., Almaraz, P., An, J. S., Anderson, R. S.,…Zvuloni, A. (2025). BioTIME 2.0: Expanding and improving a database of biodiversity time series. Global Ecology and Biogeography, 34(5), 1-18, Article e70003. https://doi.org/10.1111/geb.70003

Additional Files
geb70003-sup-0001-files1.pdf (233 kB)
List of database tables with field descriptions and explanations, and table of classifications of abundance and biomass within BioTIME.
geb70003-sup-0002-files2.pdf (289 kB)
Tutorial for data curation.
geb70003-sup-0003-files3.docx (215 kB)
List of data sources.
geb70003-sup-0004-files4.docx (38 kB)
Change Log for Updates compared with BioTIME 1.0
geb70003-sup-0005-files5.csv (1 kB)
Proportional representation of Animalia phyla and Chromista, Fungi, Plantae and Protozoa Kingdoms in BioTIME 2.0.
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