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Text Mining and Biodiversity Research Infrastructure

Workshop at SwissText 2023, Neuchâtel, June 12 pm


Call for participation

We invite interested researchers to participate in the workshop on Biodiversity, Open Access, and Text Mining, at the SwissText conference in Neuchatel on June 12. The workshop will offer an invited presentation by Christophe Dessimoz, head of the Swiss Institute of Bioinformatics, brief presentations of text mining tools for scientific literature access, and an open panel discussion on Open Access to the scientific literature and the benefits for the scientific community.

We invite contributions (e.g. opinions, tools, posters) from the Swiss biodiversity community at large, including scientists at Natural History Museums and Botanical gardens, as well as university research teams interested in studying biological diversity, including biochemists working with natural products, evolutionary biologists, etc.

We also offer the possibility to present relevant text mining tools. Please send a brief note stating your interest to Fabio Rinaldi ( by May 3th.


The scientific knowledge on biodiversity is imprisoned in a daily growing corpus of hundred millions of pages of scientific publications. This knowledge is needed to better understand the dynamics and dimensions of the global biodiversity crisis, to understand the impact of climate change on the distribution of species or to understand the viral spillover from animals to humans. This knowledge is very difficult to access because it is unstructured, in printed formats, including portable data format (PDF), which are difficult to machine operate, or closed access. The power of access to millions of machine actionable articles in PMC, including millions of supplementary data files, or tens of millions of abstracts in PubMed and tools to annotate and mine and discover new facts is obvious. These tools could be used for TDM and annotations of biodiversity literature - but the PMC/PubMed equivalent has not been available for publications in the biodiversity domain, hence the need for a BiodiversityPMC !

In this workshop we will introduce the fledgling “biodiversity PMC” built and maintained by SIBiLS, Zenodo and Plazi, making use of the recently reviewed copyright law in Switzerland. Legal, institutional, technical aspects from processing to long term storage and accessing and annotating of the data will be discussed. This will be complemented by the research questions driving this effort from discovering known biodiversity, to extracting traits to study the impact of climate change to annotating biotic interactions to understand viral spillover to build question/answer systems.

Tentative program

Title Duration Speakers and notes
Introduction 10 Patrick and Fabio
Keynote 20 Christophe Dessimoz
Tool presentation 30 OGER / ArthroMine BiodiversityPMC/SIBiLS Biotic Interaction Explorer eBioDiv Matching service Plazi workflow Synospecies
Opinion presentation and Panel discussion 60 Moderator: Fabio Rinaldi Christophe Dessimoz (SIB) Patrick Furrer (CHUV) Pierre-Marie Allard (UniFR) Donat Agosti (Plazi) Rainer Krug, UNIZH Nils Arrigo, Info Fauna
Coffee break & demo session tbc See tool presentation


Abstract submissions: May 9th, 2023

Response: May 16th, 2023

Abstracts should be sent to:

Scientific committee

  • Donat Agosti, Plazi
  • Pierre-Marie Allard, UNIFR
  • Nadir Alvarez (tbc)
  • Laurence Bénichou
  • Fabio Rinaldi
  • Patrick Ruch
  • Robert Waterhouse