Add QC check for proper treatment of preferredExternal annotations #8012
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Adding check that ensures that: 1) Xrefs with preferred external must have a corresponding equivalentto on the same class 2) Xrefs with preferred external must be related to another class which are equivalent as well
| @@ -447927,7 +447924,6 @@ def: "OBSOLETE. Holmes-Gang syndrome is an X-linked mental retardation (XLMR) sy | |||
| comment: Reason: out of scope. Term to consider: alpha thalassemia-X-linked intellectual disability syndrome' | |||
| subset: ordo_malformation_syndrome {source="Orphanet:93970"} | |||
| xref: ICD10CM:Q87.0 {source="Orphanet:93970/attributed", source="Orphanet:93970/ntbt", source="Orphanet:93970"} | |||
| xref: Orphanet:93970 {source="MONDO:obsoleteEquivalentObsolete"} | |||
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Removed because this was flagged in a proxy merge conflict with MONDO_0010663 and MONDO_0019774.
| @@ -447948,7 +447944,6 @@ def: "OBSOLETE. Juberg-Marsidi syndrome is an X-linked mental retardation (XLMR) | |||
| subset: ordo_malformation_syndrome {source="Orphanet:93972"} | |||
| synonym: "juberg Marsidi syndrome" EXACT [] | |||
| xref: MESH:C537457 {source="Orphanet:93972", source="Orphanet:93972/e"} | |||
| xref: Orphanet:93972 {source="MONDO:obsoleteEquivalentObsolete"} | |||
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Removed since flagged in proxy merge with MONDO_0019776 and MONDO_0010663.
| @@ -572324,7 +572319,7 @@ id: MONDO:1011429 | |||
| name: hepatic lipidosis, non-human animal | |||
| def: "Hepatic lipidosis that occurs in non-human animals." [MONDO:patterns/nonhuman_disease] | |||
| xref: OMIA:000548 {source="MONDO:equivalentTo"} | |||
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OMIA:000548 is marked as "redundant" (https://omia.org/OMIA000548/9685/). Do you want to change this to "MONDO:equivalentObsolete"?
| @@ -573443,7 +573438,7 @@ id: MONDO:1011527 | |||
| name: hepatic lipidosis, domestic cat | |||
| def: "Hepatic lipidosis that occurs in domestic cat." [MONDO:patterns/nonhuman_disease] | |||
| xref: OMIA:000548-9685 {source="MONDO:equivalentTo"} | |||
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OMIA:000548-9685 is marked as "redundant" (https://omia.org/OMIA000548/9685/). Consider changing to "MONDO:equivalentObsolete".
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- you set a bunch of orphanet x-ref as "Mondo:equivalentObsolete", indicating that the orphanet record is obsoleted. However, it is not obsoleted as I can find it in orphanet (even though they don't have much information)
- there are a bunch of changes related to changes in NCBITaxon. For example (see photo below). Are these changes expected? Where do they come from?
| @@ -230447,7 +230445,7 @@ xref: OMIM:300612 {source="DOID:0060829", source="Orphanet:3056", source="MONDO: | |||
| xref: OMIM:300706 {source="MONDO:equivalentObsolete", source="DOID:0060811", source="Orphanet:85328", source="Orphanet:85328/e"} | |||
| xref: OMIM:309590 {source="Orphanet:3056", source="MONDO:equivalentTo"} | |||
| xref: Orphanet:3056 {source="DOID:0060829", source="MONDO:equivalentObsolete", source="OMIM:300612"} | |||
| xref: Orphanet:85328 {source="OMIM:300706", source="MONDO:equivalentObsolete", source="OMIM:309590", source="DOID:0060811", source="MONDO:preferredExternal"} | |||
| xref: Orphanet:85328 {source="OMIM:300706", source="MONDO:equivalentObsolete", source="OMIM:309590", source="DOID:0060811"} | |||
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This term is not obsolete in orphanet: https://www.orpha.net/en/disease/detail/85328?name=85328&mode=orpha
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How does Mondo handle this statement:
This entity has been excluded from the Orphanet nomenclature of rare diseases and moved to [Non-specific syndromic intellectual disability](https://www.orpha.net/en/disease/detail/528084)?
And are you saying it should be MONDO:equivalentTo?
If an Orphanet term is not obsolete when moved to another term then xref: Orphanet:3056 is also not obsolete.
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I did not see the message that "This entity has been excluded from the Orphanet nomenclature of rare diseases and moved to Non-specific syndromic intellectual disability?"
My apologies. What you did, using "MONDO:equivalentObsolete" was correct. Thank you!
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Ok, just to note it was originally "MONDO:equivalentObsolete", that was not a change I made.
It's fixed now.
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@twhetzel, my apologies for not seeing the messages about terms being excluded and moved to another orphanet record.
What you did, using the source "MONDO:equivalentObsolete" was correct.
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Thanks for the comment. I reverted the one change I made from your earlier comments, but nothing else needed to be changed/reverted so once it passes QC again it's ready for your review. |
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Everything looks good now. I am approving and merging this PR.
Thank you @twhetzel
Fixes #7872
This PR adds a qc check that ensures that