Scaling up interoperable and FAIR biodiversity genomics across Europe

Biodiversity Genomics Europe plus (BGE+) is a Horizon Europe project funded under HORIZON-CL6-2025-01-BIODIV-03, and coordinated by Naturalis Biodiversity Center. It builds on the previous Biodiversity Genomics Europe project to scale up the production and use of genomic evidence for taxonomy, biodiversity monitoring and policy.

BGE+ brings together the European communities around iBOL Europe (International Barcode of Life) for DNA barcoding, ERGA (European Reference Genome Atlas) and CETAF (Consortium of European Taxonomic Facilities). This project aims to turn distributed biodiversity genomics activities into a more coherent European system, with shared protocols, interoperable data and sustainable services.

Objectives

  1. Broaden participation and capacity for biodiversity genomics across Europe.
  2. Remove technical barriers to producing and analysing DNA barcodes and whole-genome sequence data.
  3. Increase the uptake of genomic evidence in biodiversity monitoring, environmental management and policy.
  4. Establish the foundations for a sustainable distributed European biodiversity genomics system.

The project combines cascade funding and training with the development of laboratory protocols, bioinformatics tools and FAIR data infrastructure. It will also develop policy-oriented roadmaps for DNA barcoding, metabarcoding and whole-genome approaches, while investigating how biodiversity genomics services could become part of existing European Research Infrastructures.

FAIR data and RO-Crate

BGE+ follows an open science, open data and open source approach. Sequence data will be deposited in established repositories such as ENA and BOLD, while biodiversity observations and other outputs will use appropriate FAIR repositories and community standards.

RO-Crate provides an important part of the project’s FAIR Digital Object (FDO) and provenance approach. BGE+ will use RO-Crate to package tabular data and associated metadata, describe computational analyses and workflow runs, and connect datasets, workflows, provenance and publications.

RO-Crate is used for:

  • laboratory metadata from distributed metabarcoding experiments will be captured as FAIR RO-Crates
  • sequence repositories and biodiversity infrastructures will be aligned with FAIR Digital Object approaches including RO-Crate and FAIR Signposting
  • workflows and datasets will use RO-Crate to capture rich metadata, provenance and citation information
  • RO-Crate editor e.g. Crate-O to be integrated with the ARPHA scholarly publishing system for publisher Pensoft
  • a generalised Publication RO-Crate profile will be developed for linking articles with biodiversity repositories and detailed data provenance
  • an updated RO-Crate profile for metabarcoding will document analytical steps so that archived data can be audited, reprocessed and reused.

eScience Lab involvement

The eScience Lab contributes its expertise in RO-Crate, FAIR provenance and research workflows.

  • WP4: Improving laboratory protocols and approaches (lead: NHMUK)
    • Task T4.5: Laboratory Intercalibration Framework for DNA Metabarcoding (lead: CIBIO)
    • Deliverable D4.4: Intercalibration Protocol Package (lead: CIBIO)
  • WP5: Improving bioinformatic tools and services (lead: EMBL)
    • Task T5.4: Scaling up interoperability between sequence repositories and biodiversity infrastructures (lead: EMBL-EBI)
    • Deliverable D5.3: Integrated system of sequence and biodiversity infrastructures (lead: EMBL)
    • Task T5.5: Streamlining publication with FAIR access to biodiversity genomics data (lead: Pensoft)
    • Milestone MS5.6: Pilot implementation of RO-Crate system for data and metadata associated with journal articles (lead: Pensoft)
    • Deliverable D5.6: Tools and workflows for scholarly publishing of barcoding and reference genome biodiversity data (lead: Pensoft)
    • Task T5.7: Pilot framework for future-proofing metabarcoding-based monitoring (lead: EMBL-EBI)
    • Deliverable D5.7: Validation and calibration of DNA metabarcoding analysis framework (lead: EMBL)