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talk · Thursday 24 September · 14:38–⁠14:50 · FORUM

Building digital-native species: Transitioning from PDF liberation to semantic-by-design publishing

Laurence · Planning the Libroscope: creating research ready biodiversity from scientific publications

Recording time 6:16:06–6:27:31Open on Vimeo ↗

Summaries and key moments are machine-produced. Check the recording for the speaker’s exact words.

The short versionKeeping data linked and structured from specimen to publication yields FAIR, trusted data on the day of publication.

Overview

What this was about

Laurence presented the 'digital-native species' workflow, noting that it takes on average 21 years from specimen collection to publication and that current practice erases structured data into PDFs only to re-extract it later. In the new model, bulk samples become a biodiversity knowledge graph linking specimens with barcodes, images and genomic data, exported as JSON to Zenodo and carried through an XML-based, semantically enhanced manuscript and peer review to multi-format publication with bidirectional links. She also showed dashboards monitoring institutions and journals, arguing that measuring a journal's FAIRness matters more than impact factor, given that taxonomic references average around 50 years old.

Why it matters. It proposes a way to shorten the long description lag and to produce certified data that can reduce AI hallucination.

Key ideas

In the room

  • On average it takes 21 years from collecting a specimen to publishing about it.
  • The old model erases data into PDFs, which then must be rescued with conversion errors.
  • Digital-native species link physical specimens to digital specimens, DNA barcodes, images and genomic data from the outset, exported as JSON to Zenodo.
  • An XML-based manuscript retains semantic links and identifiers through editing and peer review.
  • XML-first yields FAIR-born, trusted data at the day of publication with bidirectional links.
  • Dashboards (institution, GBIF hosted portal for journals, TreatmentBank) monitor impact and journal FAIRness.
  • The average age of references in taxonomy is about 50 years, making 2- or 5-year impact factors irrelevant.
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Programme abstract

Building digital-native species: Transitioning from PDF liberation to semantic-by-design publishing

Laurence

Scientific publications remain the primary vehicle for communicating biodiversity knowledge. The Bouchout Declaration marked an important step toward opening biodiversity literature and mobilising the taxonomic knowledge embedded within publications. Since then, major efforts have focused on liberating biodiversity data from legacy PDFs through text mining, semantic annotation and automated extraction workflows, enabling large-scale mobilisation of taxonomic names, treatments and material citations.

However, PDF-centric approaches remain limited by the publication format itself. Extracting structured knowledge from PDFs is retrospective, heterogeneous and costly, often requiring complex workflows to recover semantics that were never encoded during publication.

In the framework of the Disentis Roadmap and the Biodiversity Libroscope initiative, this contribution argues for a transition from retrospective data liberation to digital-first and XML-first publishing workflows that generate machine-actionable biodiversity knowledge by design. Central to this vision is the concept of “digital-native species”, in which species descriptions and supporting evidence are created, published and maintained in interoperable semantic environments from the outset.

Publications remain the formal scholarly record but are generated from, and linked to, structured specimen-level evidence including images, sequences, measurements, treatments and collection records. Semantic XML publishing enables fine-grained markup, interoperability across infrastructures and direct integration with natural science collections and global biodiversity platforms.

This contribution discusses how semantic-by-design publishing can create interconnected, computable and AI-ready biodiversity knowledge ecosystems.

Submitted to the conference programme before the talk, so the talk itself may differ.