Engaging communities to turn publications into FAIR, open biodiversity data

In the digital age, taxonomic information can be systematically extracted from scholarly publications and transformed into FAIR data—findable, accessible, interoperable, and reusable. Once liberated, these data are deposited in multiple online repositories covering different dimensions of biodiversity knowledge. TreatmentBank (TB), a service provided by Plazi, supports this process by extracting taxonomic treatments from the literature and converting, enriching, linking, storing, and disseminating them as FAIR data.

The information liberated by Plazi feeds the Biodiversity Literature Repository (BLR), a community within Zenodo that enables the creation of FAIR data through the use of custom metadata, and mints persistent identifiers for datasets. It also contributes structured articles as treatment datasets, and geographic occurrence data to the Global Biodiversity Information Facility (GBIF), and provides machine-actionable versions of publications to Biodiversity PMC. To date, Plazi has processed 124 320 papers, resulting in the liberation of 1 172 582 taxonomic treatments. A feedback mechanism between GBIF and Plazi allows the curation of data, or refinement of the data for additional reuses. Data and data transfer standards used in the biodiversity community are applied to guarantee a wide as possible reuse of the data.

Researchers, collaborators, and the broader scientific community are invited to join Plazi’s mission to support persistent, openly accessible digital taxonomic literature by exploring its search tools and reusing its openly available data. Through Plazi’s databases, users can access extensive information contained in taxonomic treatments, including names, descriptions, distributions, material citations, synonymic lists, images, tables, and bibliographic references. To cultivate a vibrant community of publication converters, Plazi provides online training courses, a certification programme, on-site workshops, and mentoring for ongoing projects.

The extraction workflow consists of three steps: (1) locating specific information within a publication, (2) highlighting and analysing it, and (3) making the resulting structured data available in other repositories or formats. Using Plazi’s data, users can assess their own contributions to biodiversity knowledge or generate dashboards focused on individual researchers, journals, institutions, or taxonomic groups processed by Plazi and its collaborators.