An ongoing success story!
The 3rd Ontologies4Chem Workshop, hosted by NFDI4Chem and co-organised by NFDI4Cat, took place from 9 to 11 December 2024. The online event, which has been going since 2022, was a great success again this year, with more than 60 international participants and many renowned speakers from all over the world. The main goal of the Ontologies4Chem Workshop series is to create a space where experts working on different ontology projects, domain and ontology specialists, software developers, and service providers from NFDI4Chem and other NFDI consortia related to chemistry can meet and exchange ideas. This helps identify synergies and create new opportunities for collaboration.
The main topic of the first day was chemical ontologies and their application with a focus on status reports, new developments and industry collaborations. A short introduction with a review of the last two Ontologies4Chem Workshops was followed by a status report from NFDI4Chem on the activities in the field of ontology development/curation. In addition, there were also updates on the latest developments of the NFDI4Chem Terminology Service & Search Service as well as the work in the area of Minimum Information about Chemical Investigations (MIChI’s), e.g. in the field of NMR, in order to be able to capture domain-specific metadata using ontologies in the future. Various initiatives and international projects, such as the Physical Sciences Data Infrastructure (PSDI), Pistoia Alliance, The World Avatar and IUPAC’s Gold Book also presented themselves and their activities.
The workshop’s second day focused on the representation of chemical entities using Chemical Entities of Biological Interest (ChEBI) and other chemical ontologies. It began with presentations on the use of AI and advanced algorithms for the automated classification of chemical compounds based on their structure, which sparked a lively discussion. This set the stage for talks from NFDI4Chem and NFDI4Cat, which highlighted critical shortcomings of ChEBI in meeting their key use cases. The ChEBI team followed with an update on efforts to migrate ChEBI to a more robust infrastructure, acknowledging the previously discussed limitations and emphasizing the need for a community-driven approach to fix such issues, due to the current funding situation. One such proposal was given by Chris Mungall on the example of simplifying ChEBI to better serve the biology community, in which he stressed the importance of fixing ChEBI’s foundational problems rather than creating a new ontology. The day concluded with a constructive discussion, where the audience agreed on the need for closer collaboration. While the path forward remains to be defined, it was agreed that future workshops should be held to continue these discussions. However, indexing all relevant ontologies in the NFDI4Chem Terminology Service to facilitate comparisons and mappings, fostering a more rigorous analysis of their similarities and potential synergies, was well received as a first pragmatic step.
Day 3, though shorter, was equally impactful, focusing on the representation of chemical reactions. Mark Dörr discussed the challenges of modeling chemical reactions on a mechanistic level and proposed a minimalistic ontology approach for reaction modeling, which should be augmented by AI when necessary. Carles Bo presented the ioChem-BD repository and its integration with the ontoRXN knowledge graph, which supports FAIR reaction mechanisms and enables detailed querying of reaction data. The NFDI4Chem team highlighted the current state of the Named Reaction Ontology (RXNO) and the Molecular Process Ontology (MOP), pointing out structural flaws that need addressing. The day ended with a productive open discussion, where participants proposed future collaborative efforts, including hackathons and GitHub repositories, to improve data annotation, address current ontology issues, and explore the development of new reaction ontologies.
As usual from the last two Ontologies4Chem Workshops, the workshop agenda and the slides of the presentations are freely available. In addition, the recordings of all presentations will be available on our NFDI4Chem YouTube channel very soon.
