TGX in Brno: second half of the ELIXIR exchange with RECETOX

From 24 to 28 August, Egon, Denise, Javier and Marvin drove to Brno for a week at RECETOX, Masaryk University. This was the return leg of an ELIXIR-funded staff exchange: Helge Hecht and Robin Durník had visited our group in April, and this time Helge hosted us in Brno.

Elliott Price took us through the labs, with their mass spectrometers for metabolomics and exposomics and a biobank behind it, and much of the first day went into hearing what RECETOX is and what they do. We were also given a walkthrough of Galaxy and how this is managed. On Wednesday, Pavel Babica, Antonio Rico Guerrero and Lola Bajard joined to talk about PARC and their work on non-genotoxic carcinogens and Marvin presented VHP4Safety, molecular AOPs, omics analysis with AOPs and the AOP-Wiki RDF. Javier showed his work on rdfsolve, which was later also successfully used for LLM-based SPARQL query construction in Galaxy.

On Thursday, the technical work picked up where April left off. Robin presented the latest aop-tk, the RECETOX Galaxy tool that mines literature for chemical evidence behind AOP key events. Marvin tested it on the molecular initiating event "PXR activation" in liver and got candidate chemicals from over 1700 papers. We also worked on mapping chemical names from text to structures and classes, and Antonio and Pavel got a first introduction to WikiPathways and PathVisio, with a molecular pathway on intercellular communication as a possible joint curation project.

Besides hosting us at the university, Helge also showed us around the city, the Mendel Museum, and Brno's cuisine. Overall, it was a great and fruitful week.

Are you also curious about Helge Hecht and Robin Durník’s visit to us in April of this year? Read more about it here!