EDAM annotations as URIs rather than labels

Hi,

I'm working on the Research Software Ecosystem, specifically on tools and workflows metadata. I noticed that in the Codex, the EDAM annotations are EDAM labels, and not EDAM URIs. This can cause issues, as classes' main labels can change over time, while URIs are permanent. Another issue is that in some (rare) cases, a class can switch from a subclass to another one (for example, an operation can become a topic). Finally, in some (rare) cases, several classes will have the same main label. While we try to avoid such cases in EDAM, they do happen exceptionally.

An example: the tool `abyss` is annotated with the topic "Sequence assembly", which also happens to be an [operation](http://edamontology.org/operation_0310) and a [data](http://edamontology.org/data_0925) type.

Is it at all feasible to switch from labels to URIs? For now I am doing it on my end, but it's not ideal given the cases mentioned above.

Start by locating how the Codex stores and emits EDAM annotations, then inspect the abyss example and the current label-based representation. Check how EDAM URIs would preserve class identity across label, hierarchy, and duplicate-label changes. Done means annotations consistently expose the intended EDAM URIs without breaking existing tool and workflow metadata.

Written by the indexing model from the issue text.