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2026

SwissGA4GH Workshop: Interoperability for genomic variants, practical use of GA4GH standards

Date: 3 September 2026
Time: 09:30 - 15:00
Location: Campus Biotech, Geneva, Switzerland
Room: H4.02-A

This SwissGA4GH workshop will focus on the practical use of GA4GH standards to improve interoperability in genomic variant representation and federated discovery.

The session will address challenges arising from heterogeneous variant data across clinical, cohort, research, literature-derived and public resources. It will examine how standards such as VRS, Categorical VRS and Beacon can support consistent modelling, matching and discovery of variants across distributed infrastructures.

Through presentations and discussions, participants will explore practical examples of standard adoption, implementation challenges and federated discovery workflows. The workshop will conclude with a discussion on current barriers, open questions and future directions.

No prior GA4GH experience is required, the workshop is open to all interested participants.

Registration (free): register

For any questions about the workshop, please contact: anais.mottaz@hesge.ch

Speakers

  • Michael Baudis
  • Worawich Phornsiricharoenphant
  • Anaïs Mottaz
  • Patrick Ruch
  • Venkata Satagopam
  • Hinri Kerstens (in person or remote, to be confirmed)
  • Emidio Capriotti (tentative)

Schedule (tentative)

Time Session Description
09:30-09:45 Introduction and context Scope of the workshop and interoperability challenges in genomic variant data
09:45-10:30 GA4GH standards for variant representation Introduction to GA4GH standards for variant representation, with a focus on VRS and Categorical VRS
10:30-11:30 Practical perspectives on variant representation Examples of VRS use in national genomic platforms, public variant resources such as ClinVar, literature-derived variant standardisation efforts and challenges, and VRS-Python
11:30-12:00 From observed variants to interpretation and reporting Clinical bioinformatics perspectives on connecting observed variants to interpretation and reporting workflows
12:00-13:30 Lunch break
13:30-14:15 Federated discovery Introduction to the GA4GH Discovery Work Stream and the Beacon protocol, including use for federated discovery across distributed resources
14:15-14:45 Implementation perspectives Implementation experiences from deploying GA4GH standards in practice
14:45-15:00 Wrap-up and open discussion Key messages, open questions and future directions

WBF2026 - Workshop : « Biodiversity Evidence: Foundations of a Community of Practice to streamline and innovate literature workflows »

We are pleased to announce our participation in the CON20 workshop, “Biodiversity Evidence: Foundations of a Community of Practice to streamline and innovate literature workflows” at the World Biodiversity Forum 2026 (Davos, 14-19 June 2026).

The workshop addresses the growing challenge of navigating an expanding body of biodiversity literature, including both peer-reviewed publications and grey literature. It will bring together invited participants to review existing tools and approaches for literature identification, screening, and preparation for synthesis, and to discuss current gaps and needs.

Through short presentations and breakout discussions, participants will work toward establishing the foundations of a Community of Practice (CoPLit) aimed at improving and coordinating literature workflows. The session is part of a broader series at WBF2026 focused on biodiversity evidence.

Registration form 📝: https://tinyurl.com/WBF-CON20

Details 🔎: https://meetingorganizer.copernicus.org/WBF2026/session/55598

Scalable Biodiversity Monitoring by Broadening Article Acquisition

For over a decade, the Swiss Institute of Bioinformatics and HES-SO/HEG Geneva have maintained the SIB Literature Services (SIBiLS, Gobeill et al. 2020). SIBiLS is also an ELIXIR Data Resource, supported by the Data Platform commissioned services.

In 2023, SIBiLS received a significant upgrade with the launch of the Biodiversity PMC digital library. SIBiLS is indeed operating the backend of Biodiversity PMC, which has emerged as the main user portal of SIBiLS. Biodiversity PMC is indeed becoming a global resource in the field: Biodiversity PMC is the largest digitally-native repository of articles for biodiversity research and related disciplines; thus delivering a broad coverage “One Health” library with a broader biodiversity-related coverage than PubMed of EuropePMC.

ScaleBioM aims to enhance Biodiversity PMC to : 1) broaden the coverage by harvesting contents directly from OpenAlex, 2. maintain topical consistency by using automatic filtering methods to harvest only biodiversity related contents from OpenAlex.

We will evaluate how these services can help ecologists - and in particular our partner, Prof. Clara Zemp, from the University of Neuchâtel - to monitor biodiversity on island ecosystems. The development of the automatic filtering services will also benefit from the support from assessments performed by the IPBES.