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merged 'human anaplasmosis' to 'anaplasmosis' #6557

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merged 'human anaplasmosis' to 'anaplasmosis' #6557

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7 changes: 2 additions & 5 deletions src/ontology/components/mondo-subsets.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -177338,10 +177338,7 @@

<!-- http://purl.obolibrary.org/obo/MONDO_0044747 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/MONDO_0044747">
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/mondo#nord_rare"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/mondo#rare"/>
</owl:Class>
<owl:Class rdf:about="http://purl.obolibrary.org/obo/MONDO_0044747"/>



Expand Down Expand Up @@ -189501,5 +189498,5 @@



<!-- Generated by the OWL API (version 4.5.25) https://github.com/owlcs/owlapi -->
<!-- Generated by the OWL API (version 4.5.25.2023-02-15T19:15:49Z) https://github.com/owlcs/owlapi -->
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can you confirm that you intended to make these changes and this is okay?

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I don't know... :-)

@matentzn I obsoleted a term with "nord-rare", and removed the "nord-rare" subset annotation for that obsoleted term. I assume this is why this change is showing and that it is ok. BUT I don't know for sure.
Could you please confirm? Thank you!

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No, you can't change that file manually! No rare subset should be edited manually by us, even during obsoletion!

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It wasn't changed manually, it was changed automatically by changing things in the ontology (so I guess it is semi-manual?).
We, therefore, need to answer the following question: What do we do when obsoleting a term that is in the rare disease subset (whether it is because of merge or obsoletion alone)? Do we leave the rare subset annotations on the obsoleted term? (and wait for the release to clean it up)?
(is this going to be a problem with QC?)

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Do we leave the rare subset annotations on the obsoleted term? (and wait for the release to clean it up)?

Not only do we leave them on the obsoleted terms - for the rare subset, we keep them there. We want to reflect the subset with 100% fidelity to what we have been provided with - if this means that an obsoleted term is used, this should be reflected. Only the rare disease resources should be able to fix this, and we need to establish a line of communications with them to enable them how to do so.


24 changes: 10 additions & 14 deletions src/ontology/mondo-edit.obo
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Expand Up @@ -419906,14 +419906,20 @@ def: "A disease or disorder caused by infection with Anaplasma." [MONDO:patterns
synonym: "anaplasma caused disease or disorder" EXACT [MONDO:patterns/specific_infectious_disease_by_agent]
synonym: "anaplasma disease or disorder" EXACT []
synonym: "anaplasma infectious disease" EXACT []
synonym: "anaplasmoses" EXACT [MESH:D000712]
synonym: "human anaplasmosis" EXACT [MONDO:0044747]
xref: ICD9:082.49
xref: MESH:D000712 {source="https://orcid.org/0000-0003-1967-3726", source="MONDO:equivalentTo"}
xref: NCIT:C128425 {source="MONDO:equivalentTo"}
xref: SCTID:13906002 {source="MONDO:equivalentTo"}
xref: SCTID:427481004 {source="MONDO:equivalentTo"}
is_a: MONDO:0006922 {source="MONDO:Redundant"} ! Anaplasmataceae infectious disease
is_a: MONDO:0025294 {source="MONDO:Redundant"} ! tick-borne infectious disease
intersection_of: MONDO:0005550 ! infectious disease
intersection_of: MONDO:0100332 NCBITaxon:768 ! disease has primary infectious agent Anaplasma
relationship: transmitted_by NCBITaxon:6944 ! Ixodes
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/5537" xsd:anyURI
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/5897" xsd:anyURI

[Term]
id: MONDO:0025351
Expand Down Expand Up @@ -444448,21 +444454,11 @@ is_obsolete: true

[Term]
id: MONDO:0044747
name: human anaplasmosis
def: "An infection that is caused by Anaplasma phagocytophilum, which is transmitted to humans by infected ticks; it is characterized by fever, headache, chills, and myalgia." [NCIT:C128425]
comment: Reason: duplicate. This will be merged with MONDO:0025303 anaplasmosis
subset: obsoletion_candidate
synonym: "anaplasmoses" BROAD [MESH:D000712]
synonym: "anaplasmosis" BROAD [NCIT:C128425]
synonym: "human anaplasmosis" EXACT []
xref: ICD9:082.49
xref: NCIT:C128425 {source="MONDO:equivalentTo"}
xref: SCTID:427481004 {source="MONDO:equivalentTo"}
is_a: MONDO:0025303 ! anaplasmosis
relationship: transmitted_by NCBITaxon:6944 ! Ixodes
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/5537" xsd:anyURI
name: obsolete human anaplasmosis
property_value: IAO:0000231 MONDO:TermsMerged
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/5897" xsd:anyURI
property_value: IAO:0006012 "2023-08-01" xsd:string
is_obsolete: true
replaced_by: MONDO:0025303

[Term]
id: MONDO:0044748
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