TDWG2026
Home / Talks / FORUM
talk · Thursday 24 September · 14:14–⁠14:26 · FORUM

Biodiversity literature as FAIR and AI-ready data by design (and how to get there)

Chris Le Coquet · Planning the Libroscope: creating research ready biodiversity from scientific publications

Recording time 6:04:02–6:15:22Open on Vimeo ↗

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

The short versionDon't just liberate biodiversity literature, publish it liberated.

Overview

What this was about

Chris Le Coquet argued that the next step is not liberating more literature but changing how it is published. Rather than creating PDFs that must later be mined, XML-first single-source workflows (e.g. MitoTaxa, annotated in JATS TaxPub via GoldenGate) capture structure, references, semantic markup and persistent identifiers during production. Shared standards provide a common grammar, PIDs make entities unambiguous, and together they make publications FAIR by design, part of the Libroscope network and genuinely AI-ready.

Why it matters. Stopping the creation of new PDF backlog would free liberation effort for legacy literature and give AI trustworthy, structured inputs.

Key ideas

In the room

  • Publications are infrastructure through which knowledge is validated, connected and reused.
  • Plazi has liberated more than one million treatments from legacy literature; the question is whether this should remain the way we publish.
  • In XML-first workflows, machine-readable structure exists from the start and many outputs derive from one source.
  • References become structured objects that can be matched and resolved, preserving relationships for knowledge graphs.
  • Semantic markup turns material citations into explicit entities and relationships.
  • Machine-readable is not interoperable: standards (JATS TaxPub, Darwin Core, ontologies) give a common grammar and PIDs give identity.
  • AI readiness is a consequence of good semantic publishing; the challenge now is scale and community convergence.
Jump in

Notable moments

In their words

Transcript

Automatically generated captions can contain mistakes, especially in names and technical terms. Times are relative to the room recording.

Read the transcript ↓
Loading transcript…
Keep exploring

Related talks.

See the map ↗
talk · 24 Sept · 14:26–⁠14:38 · FORUM

Realtime Access to Data in new Taxonomic Publications

Plazi can deliver interlinked, machine-actionable data from new taxonomic papers within hours, and XML-first publishing removes most of the costly effort.

Guido Sautter
talk · 24 Sept · 14:02–⁠14:14 · FORUM

The future is the future - thought about access to data in publications

Liberating data from literature works, but the future lies in use-case-driven, digital-first publishing that also targets the undescribed majority of species.

Donat Agosti
talk · 25 Sept · 10:30–⁠10:45 · SAL B

The LIB Open Knowledge Space: A semantic architecture for FAIR, CLEAR, and AI-ready biodiversity knowledge

Knowledge can enter the LIB Open Knowledge Space as natural language immediately and be formalised step by step, so content becomes FAIR, CLEAR and AI-ready incrementally.

Lars Vogt
Programme abstract

Biodiversity literature as FAIR and AI-ready data by design (and how to get there)

Chris Le Coquet

Since the earliest observations of the living world, scientific literature has been the primary medium for documenting and disseminating biodiversity knowledge. Over centuries, this process has generated a vast corpus of taxonomic, ecological, biogeographic, and recently also molecular information. Yet, much of these data remain embedded in PDF-based publications, limiting their findability, accessibility, interoperability, and computational reuse.

Although data extraction and annotation tools have been produced to address this issue and unlock biodiversity data from PDFs, it is crucial to stop extending the legacy backlog. According to the Disentis vision, this presentation proposes to shift toward semantically enhanced publishing workflows designed to readily produce FAIR, interlinked, and AI-ready data, a process that started more than a decade ago as part of the ViBRANT FP7 project and was subsequently carried out successfully through the pro-iBiosphere, EU BON, and BiCIKL projects.

XML-first workflows for prospective literature (MetoTaxa, ARPHA) will be presented from semantic markup to enrichment and publication through interconnected infrastructures. Particular emphasis will be placed on the standards (e.g., JATS-TaxPub), vocabularies (e.g., Darwin Core), and resolvable persistent identifiers.

By supporting large-scale knowledge integration and machine-actionable biodiversity data, such workflows create new opportunities for emerging AI applications and also improve support for many other machine driven forms of reuse.

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