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mass obsolete children of psychiatric disorder (#6697)
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* mass obsolete children of psychiatric disorder

close #6695

* reclassify children

* fix source
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@nicolevasilevsky
nicolevasilevsky authored Sep 25, 2023
1 parent 400c9de commit 3756e3c
Showing 1 changed file with 37 additions and 67 deletions.
104 changes: 37 additions & 67 deletions src/ontology/mondo-edit.obo
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Original file line number Diff line number Diff line change
Expand Up @@ -98309,7 +98309,6 @@ xref: UMLS:C1510489 {source="MONDO:notFoundInDiseaseSubset", source="Orphanet:85
is_a: MONDO:0011057 {source="EFO:0006790", source="ICD10CM:I68.0/inferred", source="MESH:D016657/inferred", source="NCIT:C84625", source="Orphanet:85458/inferred"} ! cerebrovascular disorder
is_a: MONDO:0018634 {source="Orphanet:85458"} ! hereditary amyloidosis
is_a: MONDO:0019065 {source="DOID:9246", source="MESH:D016657", source="MONDO:Redundant", source="Orphanet:85458"} ! amyloidosis
is_a: MONDO:0020144 {source="Orphanet:85458"} ! cerebrovascular dementia

[Term]
id: MONDO:0005621
Expand Down Expand Up @@ -134558,12 +134557,11 @@ xref: OMIMPS:125310 {source="MONDO:equivalentTo"}
xref: Orphanet:136 {source="DOID:13945", source="OMIM:125310"}
xref: UMLS:C1272305 {source="MONDO:ncbi_mim2gene_medline", source="MONDO:notFoundInDiseaseSubset"}
is_a: MONDO:0002254 {source="NCIT:C84606"} ! syndromic disease
is_a: MONDO:0015547 {source="MONDO:Redundant", source="Orphanet:136", source="Orphanet:136/inferred"} ! hereditary dementia
is_a: MONDO:0020144 {source="Orphanet:136"} ! cerebrovascular dementia
is_a: MONDO:0005385 {source="https://orcid.org/0000-0001-5208-3432"} ! vascular disorder
relationship: excluded_subClassOf MONDO:0015368 {source="MONDO:0020262-obsoleted"} ! neuro-ophthalmological disease
relationship: excluded_subClassOf MONDO:0015547 {source="Orphanet:136"} ! hereditary dementia
relationship: excluded_subClassOf MONDO:0019046 {source="DOID:13945"} ! leukodystrophy
relationship: has_characteristic MONDO:0021152 {source="OMIMPS:125310"} ! inherited
property_value: confidence "0.9675925925925928" xsd:double

[Term]
id: MONDO:0007433
Expand Down Expand Up @@ -202363,7 +202361,7 @@ xref: MESH:C567479 {source="MONDO:equivalentTo"}
xref: OMIM:300699 {source="MONDO:equivalentTo", source="DOID:0060823"}
xref: Orphanet:364028 {source="DOID:0060823", source="OMIM:300699"}
xref: UMLS:C2678051 {source="MONDO:equivalentTo", source="MONDO:ncbi_mim2gene_medline", source="OMIM:300699"}
is_a: MONDO:0018222 ! X-linked intellectual disability due to GRIA3 anomalies
is_a: MONDO:0020119 {source="OMIM:300699"} ! X-linked syndromic intellectual disability
relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/4573 {source="MONDO:mim2gene_medgen"} ! GRIA3
property_value: confidence "1.84375" xsd:double
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/4521" xsd:anyURI
Expand Down Expand Up @@ -204920,8 +204918,8 @@ xref: UMLS:C1845055 {source="NCIT:C118631", source="MONDO:equivalentTo", source=
is_a: MONDO:0002254 {source="MONDO:Redundant", source="NCIT:C118631"} ! syndromic disease
is_a: MONDO:0005151 ! endocrine system disorder
is_a: MONDO:0016513 {source="Orphanet:847"} ! alpha-thalassemia-related diseases
is_a: MONDO:0016980 {source="Orphanet:847"} ! ATR-X-related syndrome
is_a: MONDO:0020040 ! 46,XY disorder of sex development
is_a: MONDO:0020119 {source="https://orcid.org/0000-0001-5208-3432"} ! X-linked syndromic intellectual disability
relationship: has_characteristic HP:0001417 ! X-linked inheritance
relationship: has_characteristic MONDO:0021136 ! rare
relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/886 {source="MONDO:mim2gene_medgen"} ! ATRX
Expand Down Expand Up @@ -208823,7 +208821,8 @@ xref: UMLS:C0796159 {source="MONDO:equivalentTo", source="Orphanet:93974"}
xref: UMLS:CN205653 {source="MONDO:equivalentTo", source="MONDO:preferredExternal"}
xref: UMLS:CN206716 {source="MONDO:equivalentTo"}
xref: UMLS:CN206718 {source="MONDO:equivalentTo"}
is_a: MONDO:0016980 {source="Orphanet:73220"} ! ATR-X-related syndrome
is_a: MONDO:0002254 {source="https://orcid.org/0000-0001-5208-3432"} ! syndromic disease
is_a: MONDO:0003847 {source="https://orcid.org/0000-0001-5208-3432"} ! hereditary disease
relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/886 {source="MONDO:mim2gene_medgen"} ! ATRX
property_value: confidence "37.50000000000002" xsd:double
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/4521" xsd:anyURI
Expand Down Expand Up @@ -259483,7 +259482,6 @@ xref: MESH:C567858 {source="MONDO:equivalentTo"}
xref: OMIM:612936 {source="DOID:0110802", source="MONDO:equivalentTo"}
xref: Orphanet:280763 {source="DOID:0110802", source="OMIM:612936"}
xref: UMLS:C2752008 {source="MONDO:equivalentTo", source="MONDO:ncbi_mim2gene_medline", source="OMIM:612936"}
is_a: MONDO:0017241 {source="Orphanet:280763/btnt"} ! AP4-related intellectual disability and spastic paraplegia
is_a: MONDO:0019064 {source="DOID:0110802", source="MESH:C567858", source="MONDO:Redundant", source="OMIM:612936"} ! hereditary spastic paraplegia
intersection_of: MONDO:0019064 ! hereditary spastic paraplegia
intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/574 ! AP4M1
Expand Down Expand Up @@ -267078,7 +267076,6 @@ xref: DOID:0110803 {source="MONDO:equivalentTo"}
xref: OMIM:613744 {source="MONDO:equivalentTo", source="DOID:0110803"}
xref: Orphanet:280763 {source="DOID:0110803", source="OMIM:613744"}
xref: UMLS:C3151056 {source="MONDO:equivalentTo", source="MONDO:ncbi_mim2gene_medline", source="OMIM:613744"}
is_a: MONDO:0017241 {source="Orphanet:280763/btnt"} ! AP4-related intellectual disability and spastic paraplegia
is_a: MONDO:0019064 {source="DOID:0110803", source="MONDO:Redundant", source="OMIM:613744"} ! hereditary spastic paraplegia
intersection_of: MONDO:0019064 ! hereditary spastic paraplegia
intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/573 ! AP4E1
Expand Down Expand Up @@ -270173,7 +270170,6 @@ xref: NCIT:C164224 {source="MONDO:equivalentTo"}
xref: OMIM:614066 {source="DOID:0110799", source="MONDO:equivalentTo"}
xref: Orphanet:280763 {source="DOID:0110799", source="OMIM:614066"}
xref: UMLS:C3279738 {source="MONDO:equivalentTo", source="MONDO:ncbi_mim2gene_medline", source="OMIM:614066"}
is_a: MONDO:0017241 {source="Orphanet:280763/btnt"} ! AP4-related intellectual disability and spastic paraplegia
is_a: MONDO:0019064 {source="DOID:0110799", source="MONDO:Redundant", source="OMIM:614066"} ! hereditary spastic paraplegia
intersection_of: MONDO:0019064 ! hereditary spastic paraplegia
intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/572 ! AP4B1
Expand All @@ -270199,7 +270195,6 @@ xref: DOID:0110804 {source="MONDO:equivalentTo"}
xref: OMIM:614067 {source="DOID:0110804", source="MONDO:equivalentTo"}
xref: Orphanet:280763 {source="DOID:0110804", source="OMIM:614067"}
xref: UMLS:C3279743 {source="MONDO:equivalentTo", source="MONDO:ncbi_mim2gene_medline", source="OMIM:614067"}
is_a: MONDO:0017241 {source="Orphanet:280763/btnt"} ! AP4-related intellectual disability and spastic paraplegia
is_a: MONDO:0019064 {source="DOID:0110804", source="MONDO:Redundant", source="OMIM:614067"} ! hereditary spastic paraplegia
intersection_of: MONDO:0019064 ! hereditary spastic paraplegia
intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/575 ! AP4S1
Expand Down Expand Up @@ -290174,7 +290169,7 @@ xref: OMIM:616158 {source="Orphanet:438216", source="MONDO:equivalentTo", source
xref: Orphanet:438216 {source="MONDO:equivalentTo"}
xref: UMLS:C4015357 {source="MONDO:equivalentTo", source="MONDO:ncbi_mim2gene_medline"}
xref: UMLS:CN237609 {source="MONDO:equivalentTo"}
is_a: MONDO:0018580 {source="Orphanet:438216"} ! PURA-related severe neonatal hypotonia-seizures-encephalopathy syndrome
is_a: MONDO:0003847 {source="https://orcid.org/0000-0001-5208-3432"} ! hereditary disease
relationship: excluded_subClassOf MONDO:0015802 {source="DOID:0070061"} ! autosomal dominant non-syndromic intellectual disability
relationship: has_characteristic HP:0000006 ! Autosomal dominant inheritance
relationship: has_characteristic SO:1000008 ! point_mutation
Expand Down Expand Up @@ -332150,21 +332145,17 @@ property_value: confidence "2.461538461538462" xsd:double

[Term]
id: MONDO:0016980
name: ATR-X-related syndrome
comment: Reason of obsoletion: out of scope - MONDO:excludeGrouping. This is part of a large mass-obsoletione effort for ORDO terms.
subset: disease_grouping
subset: obsoletion_candidate
subset: ordo_group_of_disorders {source="Orphanet:263355"}
name: obsolete ATR-X-related syndrome
synonym: "ATR-X-related syndrome" EXACT CLINGEN_PREFERRED []
xref: Orphanet:263355 {source="MONDO:equivalentObsolete"}
xref: UMLS:CN202282 {source="MONDO:equivalentTo"}
is_a: MONDO:0002254 {source="https://orcid.org/0000-0001-5208-3432"} ! syndromic disease
is_a: MONDO:0020119 {source="https://clinicalgenome.org/affiliation/40060/"} ! X-linked syndromic intellectual disability
xref: Orphanet:263355 {source="MONDO:obsoleteEquivalentObsolete"}
xref: UMLS:CN202282 {source="MONDO:obsoleteEquivalent"}
relationship: excluded_subClassOf MONDO:0015159 {source="Orphanet:263355"} ! multiple congenital anomalies/dysmorphic syndrome-intellectual disability
relationship: excluded_subClassOf MONDO:0020119 {source="Orphanet:263355"} ! X-linked syndromic intellectual disability
property_value: IAO:0000231 OMO:0001000 {source="MONDO:excludeGrouping"}
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/5114" xsd:anyURI
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/5588" xsd:anyURI
property_value: IAO:0006012 "2023-09-01" xsd:string
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6695" xsd:anyURI
is_obsolete: true

[Term]
id: MONDO:0016981
Expand Down Expand Up @@ -335964,26 +335955,18 @@ property_value: IAO:0006012 "2023-09-01" xsd:string

[Term]
id: MONDO:0017241
name: AP4-related intellectual disability and spastic paraplegia
def: "A disorder that presents with spastic paraplegia and intellectual disability in which the cause of the disease is a mutation in the AP4B1 gene." [https://www.clinicalgenome.org/affiliation/40006/, PMID:29193663, PMID:29430868, PMID:30543385, PMID:321171285]
comment: Reason of obsoletion: out of scope - MONDO:excludeGrouping. This is part of a large mass-obsoletione effort for ORDO terms.
subset: obsoletion_candidate
subset: ordo_disease {source="Orphanet:280763"}
name: obsolete AP4-related intellectual disability and spastic paraplegia
def: "OBSOLETE. A disorder that presents with spastic paraplegia and intellectual disability in which the cause of the disease is a mutation in the AP4B1 gene." [https://www.clinicalgenome.org/affiliation/40006/, PMID:29193663, PMID:29430868, PMID:30543385, PMID:321171285]
synonym: "AP4 deficiency syndrome" EXACT [Orphanet:280763]
synonym: "AP4 related intellectual disability and spastic paraplegia" EXACT [https://github.com/monarch-initiative/mondo/issues/1728]
synonym: "severe intellectual disability and progressive spastic paraplegia" NARROW [Orphanet:280763]
xref: Orphanet:280763 {source="MONDO:equivalentTo"}
xref: UMLS:CN202757 {source="MONDO:equivalentTo"}
is_a: MONDO:0000508 {source="Orphanet:280763", source="https://clinicalgenome.org/affiliation/40060/"} ! syndromic intellectual disability
is_a: MONDO:0015089 {source="Orphanet:280763"} ! autosomal recessive complex spastic paraplegia
union_of: MONDO:0013048 ! hereditary spastic paraplegia 50
union_of: MONDO:0013401 ! hereditary spastic paraplegia 51
union_of: MONDO:0013551 ! hereditary spastic paraplegia 47
union_of: MONDO:0013552 ! hereditary spastic paraplegia 52
relationship: has_characteristic MONDO:0021136 {source="MONDO:0015983"} ! rare
xref: Orphanet:280763 {source="MONDO:obsoleteEquivalent"}
xref: UMLS:CN202757 {source="MONDO:obsoleteEquivalent"}
property_value: IAO:0000231 OMO:0001000 {source="MONDO:excludeGrouping"}
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/5114" xsd:anyURI
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/5588" xsd:anyURI
property_value: IAO:0006012 "2023-09-01" xsd:string
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6695" xsd:anyURI
is_obsolete: true

[Term]
id: MONDO:0017242
Expand Down Expand Up @@ -344318,8 +344301,8 @@ xref: ICD10CM:Q93.5 {source="Orphanet:314655/attributed", source="Orphanet:31465
xref: Orphanet:314655 {source="MONDO:equivalentTo"}
xref: SCTID:768555009 {source="MONDO:equivalentTo"}
xref: UMLS:CN203780 {source="MONDO:equivalentTo"}
is_a: MONDO:0002254 {source="https://orcid.org/0000-0001-5208-3432"} ! syndromic disease
is_a: MONDO:0016904 {source="Orphanet:314655"} ! partial deletion of the long arm of chromosome 5
is_a: MONDO:0018580 {source="Orphanet:314655"} ! PURA-related severe neonatal hypotonia-seizures-encephalopathy syndrome
relationship: disease_arises_from_structure CHR:9606-chr5q31.3 {source="https://orcid.org/0000-0002-4142-7153"} ! 5q31.3 (Human)
relationship: has_characteristic SO:1000029 {source="https://orcid.org/0000-0002-4142-7153"} ! chromosomal_deletion
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/3664" xsd:anyURI
Expand Down Expand Up @@ -351238,17 +351221,14 @@ is_a: MONDO:0015193 {source="NCIT:C111904", source="Orphanet:364013"} ! hydrops

[Term]
id: MONDO:0018222
name: X-linked intellectual disability due to GRIA3 anomalies
comment: Reason of obsoletion: out of scope - MONDO:excludeGrouping. This is part of a large mass-obsoletion effort for ORDO terms.
subset: obsoletion_candidate
subset: ordo_disease {source="Orphanet:364028"}
name: obsolete X-linked intellectual disability due to GRIA3 anomalies
xref: ICD10CM:F72 {source="Orphanet:364028", source="Orphanet:364028/attributed", source="Orphanet:364028/ntbt"}
xref: Orphanet:364028 {source="MONDO:equivalentTo"}
is_a: MONDO:0015159 {source="Orphanet:364028"} ! multiple congenital anomalies/dysmorphic syndrome-intellectual disability
is_a: MONDO:0020119 {source="Orphanet:364028", source="https://clinicalgenome.org/affiliation/40060/"} ! X-linked syndromic intellectual disability
xref: Orphanet:364028 {source="MONDO:obsoleteEquivalent"}
property_value: IAO:0000231 OMO:0001000 {source="MONDO:excludeGrouping"}
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/5114" xsd:anyURI
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/5588" xsd:anyURI
property_value: IAO:0006012 "2023-09-01" xsd:string
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6695" xsd:anyURI
is_obsolete: true

[Term]
id: MONDO:0018223
Expand Down Expand Up @@ -356936,18 +356916,14 @@ property_value: IAO:0006012 "2023-09-01" xsd:string

[Term]
id: MONDO:0018580
name: PURA-related severe neonatal hypotonia-seizures-encephalopathy syndrome
comment: Reason of obsoletion: out of scope - MONDO:excludeGrouping. This is part of a large mass-obsoletion effort for ORDO terms.
subset: obsoletion_candidate
subset: ordo_disease {source="Orphanet:438213"}
name: obsolete PURA-related severe neonatal hypotonia-seizures-encephalopathy syndrome
xref: ICD10CM:G40.4 {source="Orphanet:438213/attributed", source="Orphanet:438213/ntbt", source="Orphanet:438213"}
xref: Orphanet:438213 {source="MONDO:equivalentTo"}
xref: UMLS:CN237608 {source="MONDO:equivalentTo"}
is_a: MONDO:0000508 {source="Orphanet:438213"} ! syndromic intellectual disability
is_a: MONDO:0015159 {source="Orphanet:438213"} ! multiple congenital anomalies/dysmorphic syndrome-intellectual disability
relationship: has_characteristic MONDO:0021136 {source="MONDO:0015162"} ! rare
xref: Orphanet:438213 {source="MONDO:obsoleteEquivalent"}
xref: UMLS:CN237608 {source="MONDO:obsoleteEquivalent"}
property_value: IAO:0000231 OMO:0001000 {source="MONDO:excludeGrouping"}
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/5114" xsd:anyURI
property_value: IAO:0006012 "2023-10-01" xsd:string
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6695" xsd:anyURI
is_obsolete: true

[Term]
id: MONDO:0018581
Expand Down Expand Up @@ -384257,19 +384233,13 @@ is_a: MONDO:0019245 ! lysosomal lipid storage disorder

[Term]
id: MONDO:0020144
name: cerebrovascular dementia
comment: Reason of obsoletion: out of scope - MONDO:excludeGrouping. This is part of a large mass-obsoletione effort for ORDO terms.
subset: disease_grouping
subset: obsoletion_candidate
subset: ordo_group_of_disorders {source="Orphanet:98549"}
name: obsolete cerebrovascular dementia
synonym: "rare cerebrovascular dementia" RELATED [Orphanet:98549]
xref: Orphanet:98549 {source="MONDO:equivalentTo"}
is_a: MONDO:0001627 {source="MONDO:Redundant", source="Orphanet:98549"} ! dementia
intersection_of: MONDO:0001627 ! dementia
intersection_of: disease_has_basis_in_dysfunction_of UBERON:0008998 ! vasculature of brain
relationship: has_characteristic MONDO:0021136 {source="MONDO:0019515"} ! rare
xref: Orphanet:98549 {source="MONDO:obsoleteEquivalent"}
property_value: IAO:0000231 OMO:0001000 {source="MONDO:excludeGrouping"}
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/5114" xsd:anyURI
property_value: IAO:0006012 "2023-10-01" xsd:string
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6695" xsd:anyURI
is_obsolete: true

[Term]
id: MONDO:0020145
Expand Down

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