Fix inconsistencies in xrefs related to errors in Synonym sync

[twhetzel]

See #8270 (comment)

FAIL Rule ../sparql/qc/mondo/qc-exact-synonyms-non-exact-mappings.sparql: 4 violation(s)
entity,label,xref,synonym,code
http://purl.obolibrary.org/obo/MONDO_0012817,Ewing sarcoma,NCIT:C7542,PNET of Thoracopulmonary region,MONDO:relatedTo
http://purl.obolibrary.org/obo/MONDO_0020528,ACTH-dependent Cushing syndrome,ICD10CM:E24.0,pituitary-dependent Cushing's disease,MONDO:directSiblingOf
http://purl.obolibrary.org/obo/MONDO_0004471,bacterial arthritis,NCIT:C26700,septic arthritis,MONDO:directSiblingOf
http://purl.obolibrary.org/obo/MONDO_0002514,hepatobiliary neoplasm,DOID:3117,hepatobiliary tumors,MONDO:mondoIsBroaderThanSource

[twhetzel]

It looks like these changes have already been made in the latest version of mondo-edit.obo.

[twhetzel]

Ah, now I see what is happening. The CURIEs that are an issue are the ones that are being added as provenance of a confirmed exact synonym match between Mondo and an external source and that external source has some other xref relationship other than MONDO:equivalentToso the fix that needs to happen is:

• confirm that for these failing cases that there truly is an equivalentTo relationship with the xref
• change the xref source to MONDO:equivalentTo

---

In these two qc check failure cases, the xref does seem correct and should be addressed in the Synonym Sync:

• http://purl.obolibrary.org/obo/MONDO_0012817,Ewing sarcoma,NCIT:C7542,PNET of Thoracopulmonary region,MONDO:relatedTo
• http://purl.obolibrary.org/obo/MONDO_0002514,hepatobiliary neoplasm,DOID:3117,hepatobiliary tumors,MONDO:mondoIsBroaderThanSource
  cc: @joeflack4

[joeflack4]

@twhetzel I will finish looking into these tomorrow! Thanks.

[twhetzel]

Added a ticket to address this in the Synonym Sync pipeline monarch-initiative/mondo-ingest#687