Making species data open and FAIR

Paper proposes a reproducible and semi-automatic workflow for turning traditional checklists into FAIR datasets discoverable through GBIF

Aucuba japonica
Aucuba japonica Thunb. observed in Belgium by toftof (CC BY-NC 4.0)

Lists of taxa typically sharing a geographic or temporal distribution, checklists are important sources of information for use in research and policy. Publishing checklists to GBIF allows for open and FAIR (Findable, Accessible, Interoperable and Reproducible) sharing of data about species.

This paper proposes a reproducible and semi-automatic workflow for transforming traditional checklist data into FAIR data to be ingested and shared through GBIF. Combining source data management, reproducible data transformation according to accepted standards, version control, and data documentation, the approach provides a holistic solution to FAIR checklist publication.

Taking advantage of collaborative platforms for managing content, code and metadata, such as Google Docs, GitHub, and the Integrated Publishing Toolkit (IPT), the authors provide proof of concept by employing the proposed workflow to publish the Manual of the Alien Plants of Belgium containing all invaders in the country since 1800, thoroughly documenting each step of the process.

The code and examples described in the paper are freely available for anyone to copy, modify, use and distribute as they see fit, provided the copyright and license notices are preserved.

Reyserhove L, Desmet P, Oldoni D, Adriaens T, Strubbe D, Davis AJS, Vanderhoeven S, Verloove F and Groom Q (2020) A checklist recipe: making species data open and FAIR. Database. Oxford University Press (OUP) 2020. Available at: