Species occurrence cubes in GBIF

Aggregating occurrence data along spatial, temporal and taxonomic dimensions to create “data cubes” for biodiversity management and policy decisions

hero-cubes-2 — Illustration of a Pacific Pilot Whale *Pacific Globicephala macrorhynchus* Gray, 1846 from The marine mammals of the north-western coast of North America, New York, 1974. Shared under Public Domain by the Biodiversity Heritage Library.

GBIF allows users to create and download data cubes to be used as basis for models and indicators of past, current and future biodiversity. While the generation of cubes relies on the GBIF SQL download API, users can easily define cubes by selecting the desired taxonomic, temporal and/or spatial dimension from a simple pre-set list of options. The generated SQL query may be further customized before the download is launched.

Dimensions

Options for generating cubes include

Taxonomic dimension: Kingdom, phylum, class, order, family, genus, species, accepted taxon, exact taxon
Temporal dimension: Year, year and month, date
Spatial dimension: EEA reference grid, extended quarter degree grid (QDGC), ISEA3H, military grid reference system (MGRS)

Users may add additional dimensions based on categorical data, e.g., life stages, IUCN Red List categories, etc. by refining the SQL query.

Measures

For each combination of dimension categories (group), a measure is calculated. As a minimum, this includes a count of occurrences, but the user may also select to add information about coordinate and temporal uncertainty.

Format, metadata and FAIRness

As with other GBIF occurrence download formats, cubes are generated as tab-delimited CSV files. Cube metadata will be preserved in a download page detailing the SQL query, the underlying GBIF datasets contributing to the cube as well as a link to download the cube. Like regular downloads, cubes are assigned DOIs for easy citation.

Technical documentation and examples

Please refer to the documentation for full details on options for creating, customizing and submitting queries for occurrence cubes.

More information about species occurrence cubes

Desmet P, Oldoni D, Blissett M, Robertson T (2023). Specification for species occurrence cubes and their production. https://docs.b-cubed.eu/guides/occurrence-cube/
Groom Q, Abraham L, Adriaens T, Breugelmans L, Clarke D, Fernández M, et al. B-Cubed: Leveraging Analysis-Ready Biodiversity Datasets and Cloud Computing for Timely and Actionable Biodiversity Monitoring. Biodiversity Information Science and Standards [Internet]. 2023 Aug 9;7. Available from: https://doi.org/10.3897/biss.7.110734
Oldoni D, Groom Q, Adriaens T, Davis AJS, Reyserhove L, Strubbe D, et al. Occurrence cubes: a new paradigm for aggregating species occurrence data. 2020 Mar 25; Available from: https://doi.org/10.1101/2020.03.23.983601

	The GBIF development of species occurrence cubes is part of B³ (Biodiversity Building Blocks for policy) Work Package 2, led by the Research Institute for Nature and Forest (INBO) and funded by the European Union’s Horizon Europe Research and Innovation Programme (ID No 101059592).