The Plazi Workflow to liberate PDF-imprisoned biodiversity data

Scholarly knowledge about biodiversity is published in a rapidly increasing corpus of scientific publications. A substantial portion of taxonomic literature is available as unstructured portable document format (PDF) electronic documents. But the data contained, including occurrence records and characteristics, are locked up within these PDFs. 

Semantic enhancement, applied either retrospectively to legacy literature or prospectively through innovative cybertaxonomic publishing models, allows for the electronic mobilization of these data. Of course, a large portion of legacy taxonomic literature is not even digitized in the sense of having the pages scanned and converted into a PDF electronic document, much less having the underlying data mobilized. Even when we publish open access, the data remain closed. The Plazi semantic enhancement workflow facilitates the conversion of publications into findable, open accessible, interoperable, reusable (FAIR) data. 

So far, over 32K publications have been converted, resulting in 350K figures, 375K taxonomic treatments, 406K materials cited accessible through the Biodiversity Literature Repository. The data is directly reused by the Global Biodiversity Information Facility (GBIF)  where it is the sole contributor of over 45,000 species, mainly insects, for which no other digital data is available. The system permits the building of applications focused on images (e.g. Ocellus) or taxonomic names (e.g. Synospecies). This workflow described in this presentation can be applied manually to selected legacy publications, or employ automation to process related articles in batches. Further changes in taxonomic publishing practices could lead to having electronic data elements routinely linked and mobilized.