Review strategy of update of x-refs to obsoleted terms

[sabrinatoro]

This issue is derived from reviewing this PR

It looks like the x-ref are updated such that, if they are mapping to an obsolete MONDO term, they get "MONDO:obsoleteEquivalent". For example:

EDITED: can we confirm that it is something that WE are doing in the pipeline? Do we want to continue doing this?

We need this workflow to be modified:
1) in cases when the Mondo term is obsoleted because it was merged to a new Mondo term (ie there is a "term replaced by" annotation), the x-ref should be added to the "term replaced by" as MONDO:EquivalentTo. In the example above, EFO:0006471 should be added as equivalent to MONDO:0005184

UPDATE: The issue we want to solve is the fact that in cases like term merged, having the same x-ref to both the obsoleted term and the "replaced by" term create QC fails because of proxy-merges.

2) we need a report that will be shared with sources for

• all external x-ref that mapped to MONDO obsolete term and given the source "MONDO:obsoleteEquivalent".
• all external x-ref that mapped to MONDO term-1 that was merged to another Mondo term-2 (ie Mondo term-1 is obsolete and replaced by Mondo term-2). We also need indication whether the external x-ref already mapped to Mondo term-2.

[matentzn]

Not 100% if I agree with (1); if the xrefs are provided by an external provider, then we should not redirect them, even to a merged term. Probably for externally provided content, it is better to remove and report?

[sabrinatoro]

Whatever we decide, we do need the reports in place. And when we share this report with the resources (planned to happen after the release, though we might want to do that after the x-ref update), we should be clear about what we did (either remove them completely, or redirect them.