Add support for deprecated/obsolete identifiers

[gaurav]

We've had a bunch of requests for deprecated or obsolete terms in Babel:

• CHEBI should normalize old identifiers NodeNormalization#17
• CHEBI:2386 returns null NodeNormalization#264
• include previous versions of panther #25
• UMLS IDs where labels still aren't retrieved #70
• MONDO and MESH IDs where labels and equivalent IDs aren't being retrieved (response is null) #71
• Add additional ENSEMBL identifiers #84
• Babel 2023may18 is missing some Ensembl IDs that worked previously #160
• Add HMDB secondary accessions to cliques? #177
• Why do we have obsolete/deprecated MONDO terms? #241
• Note or remove obsolete/deprecated terms from MONDO and HP #243

Note that in some cases (e.g. MONDO) deprecated terms can point to a non-deprecated term that replaces them, while in other cases (e.g. UMLS) there does not appear to be a clear mapping to a non-deprecated term.

Should we add deprecated terms to Babel? If we do that, we will need to mark them in some way so that we can ensure (1) that deprecated terms are never used as the primary identifier of a clique, and (2) so that NodeNorm and NameRes can warn users not to use deprecated terms.

This issue is to discuss whether this would be useful, what changes would be necessary in NodeNorm and NameRes to support them, and how we should go about including them.

[cmungall]

Note that in some cases (e.g. MONDO) deprecated terms can point to a non-deprecated term that replaces them, while in other cases (e.g. UMLS) there does not appear to be a clear mapping to a non-deprecated term.

Not just MONDO, but any OBO ontology commits to never deleting IDs. It's not always possible to specify a replacement of course.

https://incatools.github.io/ontology-access-kit/guide/obsoletion.html