The b3verse: Research Software as a Reproducible Engine for Transnational Biodiversity Indicators

The transition from raw monitoring data to actionable policy indicators must be transparent, reproducible, and scalable to effectively address the global biodiversity crisis. The B3 project (Biodiversity Building Blocks for Policy) demonstrates how research software can function as a first-class scientific output by developing the b3verse, a modular suite of twelve interconnected R packages that transform heterogeneous biodiversity data, such as GBIF occurrence records, into standardized occurrence cubes and policy-relevant indicators.
Built around a shared occurrence cube structure, the b3verse enables interoperability across taxa, regions, and monitoring schemes while preserving methodological flexibility. Standardized interfaces allow specialized packages to implement diverse indicator approaches, including general biodiversity indicators (b3gbi), phylogenetic diversity (pdindicatoR), and alien species impact (impIndicator), while producing comparable and harmonized outputs. Integrated uncertainty estimation and validation procedures ensure statistically robust and reproducible results.
Developed through collaboration across nine countries and twelve research institutes, the b3verse reflects interdisciplinary expertise spanning biodiversity science, ecological modelling, data engineering, and science-policy integration. A shared development guide defines standards for interfaces, testing, and documentation, ensuring consistent quality and long-term maintainability across packages. Distribution via R-Universe supports coordinated releases and straightforward adoption.
All releases and associated data snapshots are archived on Zenodo to provide stable, citable references beyond the project lifespan. Framed as reusable research infrastructure rather than a single analytical workflow, the b3verse strengthens transnational biodiversity monitoring through open and reproducible software and supports coordinated, evidence-based policy action.

Transcript

1. Biodiversity Building Blocks for policy Ward Langeraert Research Institute for Nature and Forest (INBO) The b3verse: Research Software as a Reproducible Engine for Transnational Biodiversity Indicators BioMonWeek/05-2026/Montpellier
2. Biodiversity Building Blocks for policy The Challenge: From Raw Data to Policy Impact Why occurrence cubes? Challenges Opportunities Aim
3. Biodiversity Building Blocks for policy The Challenge: From Raw Data to Policy Impact What occurrence cubes? • Occurrence cubes: first developed during TrIAS project • Aggregate GBIF occurrences • taxonomically, e.g. species • temporally, e.g. year • spatially, e.g. EEA grid 1x1km Oldoni D., Groom Q. & Desmet P. (2020) https://speakerdeck.com/damianooldoni/occurrence-cubes year eea_cell_code speciesKey n min_coord_uncertainty 2014 1kmE3886N3121 2889173 51 10 2014 1kmE3886N3122 2889173 109 10 ... ... ... ... ... 2018 1kmE4047N3067 2889173 1 2828
4. Biodiversity Building Blocks for policy The Challenge: From Raw Data to Policy Impact Development of a package ecosystem • B-Cubed: create reproducible and robust workflow • Generate cubes • Process cubes • Analyse cubes • Statistical models • Indicator calculation • Visualise and interpret results
5. Biodiversity Building Blocks for policy The Challenge: From Raw Data to Policy Impact Development of a package ecosystem • Approach: Group of interconnected R packages • b3verse • Challenges: • Cooperation • Interoperability • Automation • Accessibility
6. Biodiversity Building Blocks for policy The Workflow: From GBIF to Actionable Indicators
7. Biodiversity Building Blocks for policy The Workflow: From GBIF to Actionable Indicators
8. Biodiversity Building Blocks for policy The Workflow: From GBIF to Actionable Indicators
9. Biodiversity Building Blocks for policy The Workflow: From GBIF to Actionable Indicators Indicator calculation
10. Biodiversity Building Blocks for policy The Workflow: From GBIF to Actionable Indicators
11. Biodiversity Building Blocks for policy The Workflow: From GBIF to Actionable Indicators Visualisation and interpretation
12. Biodiversity Building Blocks for policy The Engine: Reliability by Design Technical governance • Shared software development guide • Quality assurance • Cooperation on GitHub + automated checks https://docs.b-cubed.eu/guides/software-development/
13. Biodiversity Building Blocks for policy The Engine: Reliability by Design Impact and accessibility • R-universe package repository platform (“personal CRAN”, more info) • Searchable catalogue • Automatic updates and compilation • Visible and accessible https://b-cubed-eu.r-universe.dev/
14. Biodiversity Building Blocks for policy The Engine: Reliability by Design Impact and accessibility • b3data: Dedicated Frictionless data package for b3verse packages • Example occurrence cubes • Spatial reference grids • All datasets are version-controlled on Zenodo • Can be loaded directly into R
15. Biodiversity Building Blocks for policy Conclusion Ongoing development
16. Biodiversity Building Blocks for policy Conclusion Summary • b3verse: a reusable research infrastructure for occurrence cubes • Transparent and interoperable • Scalable • Reliable and actionable
17. Biodiversity Building Blocks for policy This project receives funding from the European Union’s Horizon Europe Research and Innovation Programme (ID No 101059592). Views and opinions expressed are those of the author(s) only and do not necessarily reflect those of the European Union or the European Commission. Neither the EU nor the EC can be held responsible for them. Thank you! Ward Langeraert1 B-Cubed Newsletter @b-cubed.eu B-Cubed Project @BCubedProject b-cubed.eu B-Cubed Project Coauthors: Lissa Breugelmans2, Peter Desmet1, Shawn Dove3, Sabrina Kumschick4, Sandra MacFadyen4, Damiano Oldoni1, Hanno Seebens3, Maarten Trekels2, Mukhtar Muhammed Yahaya4, Toon Van Daele1 1Research Institute for Nature and Forest (INBO), 2Meise Botanic Garden (MeiseBG), 3Justus-Liebig-Universität Gießen (JLU), 4Stellenbosch University (SUN)