Biodiversity Literature Repository: a repository and gateway to data in publications

Zenodo, hosted at CERN, is a general-purpose research repository designed to preserve and disseminate the long tail of research across all disciplines. While Zenodo has a long tradition of enabling FAIR (Findable, Accessible, Interoperable, Reusable) research outputs, domain-specific communities—such as biodiversity science—require richer metadata, structured deposition workflows, and support for highly interlinked digital objects.

TreatmentBank, Plazi’s taxonomic literature processing pipeline exemplifies this need by converting biodiversity publications into machine-actionable outputs—including over one Million taxonomic treatments, figures, and digital specimens from 103,000 converted publications—published in the Biodiversity Literature Repository (BLR) community on Zenodo. Through Zenodo’s deposition policy and community management model, these deposits are systematically organized and transparently linked to downstream infrastructures such as GBIF. Each deposit receives extensive metadata, a DataCite DOI, licence information, and both human- and machine-readable representations. Visual materials are further enhanced through the IIIF viewer, enabling deep zoom, annotation display, and interoperability with external biodiversity platforms.

To support these sophisticated domain workflows, Zenodo introduced custom metadata, allowing communities like Plazi, the Berlin Museum für Naturkunde Dark Taxon project, and the Bat Literature Project to embed vocabulary-based semantic annotations (e.g., Darwin Core, Audubon Core) directly into deposits. This ensures accurate representation of interlinked objects and long-term FAIR compliance, even for granular items such as individual treatments, physical objects, or figures.

All components—including deposition, metadata enhancement, and cross-platform linking—are powered by REST APIs and are exposed as open metadata datasets, enabling automated workflows and self-sustaining community ecosystems. The BiCIKL project demonstrates how such an infrastructure can serve as a modular building block for an integrated biodiversity knowledge graph. The Biodiversity PMC is an example of how BLR can be used as a launch pad for downstream usage in research of conservation projects or for detailed annotations. 

Using in an exemplary way Zenodo’s Biodiversity Literature Repository community, this poster explains the concepts underpinning the Zenodo repository, governance and community management, Zenodo’s community-driven deposition model, the role of custom metadata, and IIIF support to produce very rich FAIR, interlinked, and interoperable biodiversity data.