Time for periodic drama: are we still planning to use ontologies? As it stands, the ontology information is not used anywhere outside meta.yml. In particular, they are not used by any tool that I know of, and are not displayed on the website. At the same time, they are a major PITA during code review. I remember the plan was to use it to detect possible connections, but that seems to have stalled long ago. Are we still planning to move forward with this?

I would say yes

Perhaps.jpg

@mashehu you have more insights

My opinion has not changed in the last year: https://nfcore.slack.com/archives/C043UU89KKQ/p1742371935409379

For me tools should be able to pick up ontologies based on the extension

> Once we have these identifiers, we can start to build a whole lot of tooling. For example, automatically matching and validating which processes can go together. Use in the language server to validate channel types when you’re writing code to identify mistakes in real time. In code reviews, Copilot has been good at flagging processes / channels wrongly matched but that was not by using EDAM. It was thanks to the file extensions annotations we put in the Yaml file, and the code itself. In particular, fasta vs fasta.gz. I don’t think there’s an EDAM for fasta.gz. Then if you want to add the notion of regular gzip vs bgzip etc … I’m afraid I don’t think EDAM would enable the sort of things we’d wish to have

My write up from the thread above boils down to this. Though I must admit that I'm slightly less in favour of it than I used to be.