Workshop on Semantic Publishing in Geneva

5 September 2023

A two-day workshop has been organized in the context of the BiCIKl Project by SIB, Plazi, CETAF, Pensoft, European Journal of Taxonomy and MHNParis. The workshop will be in Geneva, Switzerland, and be about Semantic Publishing. The workshop will be an opportunity to discuss why and to demonstrate how to publish semantically enhanced and linked publications. 

There will be presentations, discussions and technical/practical sessions on implementing workflows according to the following agenda:

Thursday afternoon, 14 September, 13:00-17:30



Welcome and Housekeeping

Patrick Ruch

13:15- 13:35

Introductory presentation: What is happening? We have this global biodiversity crisis and we have a lot of published data on biodiversity/ How can we use it to address the crisis?

Donat Agosti


Introductory presentation on the BICIKL project

Lyubomir Penev


The role of publications in research of a natural history institution: How the institution can use the data and work we are doing to build its strategy 

Laurence Bénichou


The semantic publishing landscape: new tools and directions in the next decade (from open access to linked FAIR data)

Lyubomir Penev


From questions to answers: the role of publications as seeds for building knowledge graphs (BiCIKL)

Patrick Ruch


Scientific publications reused: GBIF, Biodiversity Literature Repository (BLR), OpenBiodiv, Biodiversity PMC, Synospecies 

Donat Agosti


The costs of going semantic and the costs of not going there

Laurence Bénichou & Donat Agosti


Phenoscript: a new programming language for writing and publishing FAIR semantic phenotypes

Sergei Tarasov


Coffee break


Questions and answers to the introduction

Lyubomir Penev


Discussion, stakeholder input

Laurence Bénichou

19:00 -23:00


Friday morning, 15 September


9:30 - 12:00    

Technical workshop demonstrating how semantic publishing works

Answering questions about ARPHA and AWT, Métotaxa, Plazi workflow, Biodiversity Literature Repository

Discussion points (1 - 8: 10 minutes each including questions)

1. Retro-conversion (Plazi workflow; BiCIKL)

Demo / DA

2. Publishing: Arpha Writing Tool and Publishing Platform 2.0 (Pensoft, BiCIKL)

Demo / TG

3. Publishing: Metotaxa/Métostem (MNHN/CETAF; BiCIKL, FNSO)

Demo / MS

4. Nanopublications

Demo /TG

5. Visualizations: Dashboards

Demo / TK

6. Reuse: GBIF & other data aggregators

Demo / DA

7. Wikidata

Demo / DM

8. External repositories: Biodiversity Literature Repository, Biodiversity Heritage Library, Biodiversity PMC, OpenBiodiv, Synospecies

Demo / DA/PR/TG

9. Alternative metrics enabling FAIR evaluation of the published content

Disc / LP/LB

10. Current situation: who is doing what in biodiversity & taxonomy publishing 

Disc / All

11. Integration of open Science: start from the theoretical concept to a technical implementation (BKH)

Disc / LP

*The meeting should end in time to allow participants to catch whatever they need to get back - or else start enjoying a weekend in Geneva

Demo: Demonstration

Disc: Discussion


End of meeting and Lunch


Visit at the Garden or BLR/Zenodo (to be decided)

The operators and professionals participating will be discussing the current status of semantic publishing, and how we can use it to provide enhanced data for addressing the current biodiversity crisis. There will be a focus on new semantic publishing tools, and on workflow work.

The target is to establish possible ways to collaborate in the further development of semantic publishing and provide innovative tools and support mechanisms, increasing the awareness of the benefits and opportunities of semantic publishing for publishers (and why this helps against biodiversity decline).

To recap:

Title: Semantic publishing: biodiversity data liberation, linking and FAIRness

When: 14-15 September 2023

Where: HEG Geneva
Tambourine 17, 1227 Carouge - Room B4.05 (Building F, 4th floor)