How should mappings be handled?

[jamesamcl]

I think the general consensus in the SSSOM community is that mappings should be moved out of ontologies (hasDbXref) and into external SSSOM files, because (1) it would allow mappings to be updated without updating the ontology, (2) SSSOM has richer semantics than the mapping annotations currently used in ontologies, and (3) mappings are subjective and there is not always one "correct" mapping for a term. @matentzn please correct me if I am wrong about any of this.

If this happens, OLS will start to lose a lot of mapping links between terms which are extremely important for users to navigate between ontologies. I think there are two possibilities for fixing this:

1. OLS integration with OXO. We had this in OLS3. However mappings were only shown "on demand" when you clicked on the mappings tab as it had to query the OXO API each time, rather than being included in results from the OLS API which I think ideally they should be.

2. OLS loading SSSOM files. We could add a mappings section to the OLS config next to ontologies and load them as part of the OLS "linker" stage. Then they would be materialised in the OLS database.

Just throwing some ideas out there and very interested to hear what you think @henrietteharmse

[henrietteharmse]

I very much agree and support the removal of mappings from ontologies. And yes, this will cause dbXrefs to be lost from OLS.
Solution 2 will give comparable behaviour.