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merge ligneous conjunctivitis that was equiv to obsoleted orphanet te…
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…rm (#7545)

* merge ligneous conjunctivitis that was equiv to obsoleted orphanet term

and create new term for ligneous conjunctivitis for the OMIM included entry

@sabrinatoro I'm not sure if this the correct way to do this. I could have kept the original term and make it equiv to the OMIM included term, but I think all the other xrefs were referring to the term it was merged into. So I think this is okay, albeit, a bit different from our usual workflows.

* grouped duplicated lines

---------

Co-authored-by: Sabrina Toro <[email protected]>
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@nicolevasilevsky @sabrinatoro
nicolevasilevsky and sabrinatoro authored Apr 10, 2024
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Showing 1 changed file with 28 additions and 24 deletions.
52 changes: 28 additions & 24 deletions src/ontology/mondo-edit.obo
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Original file line number Diff line number Diff line change
Expand Up @@ -180135,11 +180135,13 @@ property_value: confidence "8.333333333333334" xsd:double
[Term]
id: MONDO:0009009
name: hypoplasminogenemia
def: "Severe hypoplasminogenemia (HPG) or type 1 plasminogen (plg) deficiency is a systemic disease characterized by markedly impaired extracellular fibrinolysis leading to the formation of ligneous (fibrin-rich) pseudomembranes on mucosae during wound healing." [Orphanet:722]
def: "A rare multi-system disease characterized by markedly impaired extracellular fibrinolysis leading to the formation of ligneous (fibrin-rich) pseudomembranes on mucosae." [Orphanet:722]
subset: gard_rare {source="GARD:4380"}
subset: nord_rare {source="MONDO:NORD"}
subset: ordo_disease {source="Orphanet:97231"}
subset: ordo_disease {source="Orphanet:722"}
subset: orphanet_rare {source="Orphanet:722"}
subset: orphanet_rare {source="Orphanet:97231"}
subset: rare
synonym: "hypoplasminogenemia" EXACT CLINGEN_LABEL []
synonym: "ligneous conjunctivitis" RELATED [https://orcid.org/0000-0001-9310-0163, OMIM:217090]
Expand All @@ -180149,19 +180151,28 @@ synonym: "plasminogen deficiency, type I" EXACT [https://orcid.org/0000-0001-931
synonym: "type 1 plasminogen deficiency" EXACT [GARD:0004380, https://orcid.org/0000-0001-9310-0163]
xref: DOID:0111592 {source="MONDO:equivalentTo"}
xref: GARD:4380 {source="Orphanet:722"}
xref: ICD10CM:H10.4 {source="Orphanet:97231/attributed", source="Orphanet:97231/ntbt", source="Orphanet:97231"}
xref: ICD10CM:L90.5 {source="Orphanet:722", source="Orphanet:722/attributed", source="Orphanet:722/ntbt"}
xref: ICD9:372.39 {source="MONDO:relatedTo", source="MONDO:i2s"}
xref: MedDRA:10071570 {source="Orphanet:97231/e", source="Orphanet:97231"}
xref: MESH:C580017 {source="MONDO:equivalentTo"}
xref: OMIM:217090 {source="Orphanet:722", source="MONDO:equivalentTo", source="Orphanet:722/e"}
xref: Orphanet:722 {source="MONDO:equivalentTo", source="OMIM:217090"}
xref: Orphanet:97231 {source="MONDO:relatedTo", source="OMIM:217090"}
xref: Orphanet:97231 {source="MONDO:equivalentObsolete", source="OMIM:217090"}
xref: SCTID:403435005 {source="MONDO:relatedTo"}
xref: SCTID:95840007 {source="MONDO:equivalentTo"}
xref: UMLS:C0398621 {source="Orphanet:722", source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="Orphanet:722/e"}
xref: UMLS:C1274789 {source="MONDO:relatedTo", source="OMIM:217090"}
xref: UMLS:C1274789 {source="MONDO:relatedTo", source="Orphanet:97231/e", source="OMIM:217090", source="Orphanet:97231"}
is_a: MONDO:0002242 {source="MESH:C580017"} ! coagulation protein disease
is_a: MONDO:0003847 {source="MONDO:Redundant", source="Orphanet:722/inferred"} ! hereditary disease
relationship: excluded_subClassOf MONDO:0002314 {source="https://orcid.org/0000-0001-5208-3432", source="https://orcid.org/0000-0002-6601-2165"} ! chronic conjunctivitis
relationship: excluded_subClassOf MONDO:0005328 {source="MONDO:0015937-obsoleted", source="https://orcid.org/0000-0001-5208-3432"} ! eye disorder
relationship: excluded_subClassOf MONDO:0006170 {source="MONDO:Entailed", source="Orphanet:97231", source="https://orcid.org/0000-0001-5208-3432"} ! conjunctival disorder
relationship: has_characteristic MONDO:0021136 {source="MONDO:0020198"} ! rare
relationship: has_characteristic PATO:0001863 ! chronic
relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/9071 {source="MONDO:mim2gene_medgen"} ! PLG
property_value: confidence "12.055555555555557" xsd:double
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7100" xsd:anyURI
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7224" xsd:anyURI

[Term]
id: MONDO:0009010
Expand Down Expand Up @@ -430235,27 +430246,11 @@ is_a: MONDO:0005093 {source="MONDO:0019304-obsoleted"} ! skin disorder

[Term]
id: MONDO:0019946
name: ligneous conjunctivitis
def: "Ligneous conjunctivitis (LC) is a rare form of chronic conjunctivitis characterized by the recurrent formation of pseudomembranous lesions most commonly on the palpebral surfaces. It is most frequently reported as a clinical manifestation of severe homozygous or compound-heterozygous hypoplasminogenemia." [Orphanet:97231]
comment: Reason: duplicate. This will be merged with MONDO:0009009 hypoplasminogenemia
subset: obsoletion_candidate
subset: ordo_disease {source="Orphanet:97231"}
subset: orphanet_rare {source="Orphanet:97231"}
subset: rare
synonym: "conjunctivitis lignosa" EXACT [Orphanet:97231]
xref: ICD10CM:H10.4 {source="Orphanet:97231/attributed", source="Orphanet:97231/ntbt", source="Orphanet:97231"}
xref: ICD9:372.39 {source="MONDO:relatedTo", source="MONDO:i2s"}
xref: MedDRA:10071570 {source="Orphanet:97231/e", source="Orphanet:97231"}
xref: Orphanet:97231 {source="MONDO:equivalentObsolete"}
xref: SCTID:403435005 {source="MONDO:equivalentTo"}
xref: UMLS:C1274789 {source="Orphanet:97231/e", source="MONDO:equivalentTo", source="Orphanet:97231"}
is_a: MONDO:0002314 {source="https://orcid.org/0000-0002-6601-2165"} ! chronic conjunctivitis
is_a: MONDO:0005328 {source="MONDO:0015937-obsoleted"} ! eye disorder
is_a: MONDO:0006170 {source="MONDO:Entailed", source="Orphanet:97231"} ! conjunctival disorder
relationship: has_characteristic MONDO:0021136 {source="MONDO:0020198"} ! rare
relationship: has_characteristic PATO:0001863 ! chronic
name: obsolete ligneous conjunctivitis
property_value: IAO:0000231 MONDO:TermsMerged
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7224" xsd:anyURI
property_value: IAO:0006012 "2024-05-01" xsd:string
is_obsolete: true
replaced_by: MONDO:0009009

[Term]
id: MONDO:0019947
Expand Down Expand Up @@ -513990,6 +513985,15 @@ intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.o
property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0001-5208-3432
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7515" xsd:anyURI

[Term]
id: MONDO:0100560
name: ligneous conjunctivitis
def: "A rare form of chronic conjunctivitis characterized by the development of firm fibrin-rich, woody-like pseudomembraneous lesions mainly on the tarsal conjunctivae. Ligneous conjunctivitis is usually the initial and most common manifestation of type I congenital plasminogen deficiency." [OMIM:217090, PMID:12850227]
xref: OMIM:217090 {source="MONDO:includedEntryInOMIM"}
is_a: MONDO:0006170 {source="OMIM:217090"} ! conjunctival disorder
property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0001-5208-3432
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7224" xsd:anyURI

[Term]
id: MONDO:0200000
name: uterine ligament adenosarcoma
Expand Down

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