Dear Peter, On Sat, 24 Jan 2026 at 13:44, Peter Murray-Rust via Blueobelisk-discuss < [email protected]> wrote:
> On "How do we assess [Structural Biology and small molecule design]". It's > sponsored by CODATA and Schroedinger. I'm slightly out of touch with > cheminformatics and would value up-to-date view. > I do not think I can do a full up-to-date view on cheminformatics, but I have some pointers that may be useful. Of course, browsing recent Journal of Cheminformatics journal article titles give you a broad overview on what has been going on. > I want to make the point that we cannot easily access work that is not > Open, and that we absolutely need Open ontologies and validation processes > to do this effectively and impartially. This is possible in crystallography > because of the Open ethos and requirement to share data, the CIF > ontologies, the databanks, the Commissions on experimental data. > In the BO we have tried to create shared open ontologies and syntaxes. How > has this progressed? can we produce data in a sharable, frictionless form > ? And have any large companies (esp Schoedinger) made useful contributions > to Openness? > For ontologies, there are indeed things going on. Two recent chemistry ontology papers: - 2024: Ontologies4Cat: investigating the landscape of ontologies for catalysis research data management, https://doi.org/10.1186/s13321-024-00807-2 - 2022: Ontologies4Chem: the landscape of ontologies in chemistry, https://doi.org/10.1515/pac-2021-2007 These discuss multiple ontology, mostly available in the OWL. For our team in Maastricht, we're working on a second paper about the eNanoMapper (application) ontology, and a recent workshop ( https://nfdi4chem.de/event/4-workshop-ontologies4chem/) work started on a second major release of the CHEMINF ontology. I have the feeling there is literature missing (at least from before 2016), but maybe this Scholia page about "chemistry AND ontology" has some additional pointers: https://qlever.scholia.wiki/topics/Q2329,Q324254 I hope this helps and is the start for further discussion, Egon -- -- E.L. Willighagen Department of Translational Genomics NUTRIM Institute of Nutrition and Translational Research in Metabolism Maastricht University Blog: https://chem-bla-ics.linkedchemistry.info/ Mastodon: https://social.edu.nl/@egonw PubList: https://orcid.org/0000-0001-7542-0286
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