From 08274445211807199c2e562f7a46b027e399ab8b Mon Sep 17 00:00:00 2001 From: twhetzel Date: Wed, 20 Nov 2024 23:40:40 +0000 Subject: [PATCH 1/4] [create-pull-request] automated change --- src/ontology/mondo-edit.obo | 17 ++++++++++++----- 1 file changed, 12 insertions(+), 5 deletions(-) diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo index 969c015f66..402909c608 100644 --- a/src/ontology/mondo-edit.obo +++ b/src/ontology/mondo-edit.obo @@ -7520,6 +7520,7 @@ is_a: MONDO:0002211 {source="DOID:0060026"} ! B cell deficiency id: MONDO:0000584 name: obsolete B cell linker protein deficiency subset: gard_rare {source="MONDO:GARD"} +is_a: MONDO:0015977 {source="DOID:0060027"} ! agammaglobulinemia property_value: IAO:0000231 MONDO:TermsMerged property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7612" xsd:anyURI is_obsolete: true @@ -11819,6 +11820,7 @@ replaced_by: MONDO:0015690 id: MONDO:0000884 name: obsolete myeloid and lymphoid neoplasms associated with FGFR1 abnormalities subset: gard_rare {source="MONDO:GARD"} +is_a: MONDO:0015688 {source="DOID:0080167"} ! myeloid/lymphoid neoplasms associated with eosinophilia and abnormality of PDGFRA, PDGFRB, FGFR1 or JAK2 property_value: IAO:0000231 MONDO:TermsMerged property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7614" xsd:anyURI is_obsolete: true @@ -74343,6 +74345,7 @@ intersection_of: disease_has_location UBERON:0000056 ! ureter id: MONDO:0004031 name: obsolete ovary mixed epithelial carcinoma subset: gard_rare {source="MONDO:GARD"} +is_a: MONDO:0005140 {source="DOID:6898"} ! ovarian carcinoma property_value: IAO:0000231 MONDO:TermsMerged property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7609" xsd:anyURI is_obsolete: true @@ -153524,7 +153527,7 @@ xref: OMIM:132090 {source="Orphanet:25968", source="MONDO:equivalentTo", source= xref: Orphanet:25968 {source="MONDO:equivalentTo", source="OMIM:132090"} xref: UMLS:C1851549 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:377052"} is_a: MONDO:0015650 {source="https://orcid.org/0000-0001-5208-3432"} ! epilepsy syndrome -is_a: MONDO:0020072 {source="https://orcid.org/0000-0001-5208-3432", source="https://www.epilepsydiagnosis.org/syndrome/epilepsy-syndrome-groupoverview.html"} ! childhood-onset epilepsy syndrome +is_a: MONDO:0020072 {source="Orphanet:25968", source="https://orcid.org/0000-0001-5208-3432", source="https://www.epilepsydiagnosis.org/syndrome/epilepsy-syndrome-groupoverview.html"} ! childhood-onset epilepsy syndrome relationship: excluded_subClassOf MONDO:0020072 {source="Orphanet:25968", source="https://orcid.org/0000-0001-5208-3432"} ! childhood-onset epilepsy syndrome property_value: seeAlso "https://rarediseases.info.nih.gov/diseases/2170/epilepsy-benign-occipital" xsd:anyURI {source="GARD:0002170"} @@ -179446,6 +179449,8 @@ xref: NORD:1789 {source="MONDO:NORD"} xref: OMIM:190351 {source="MONDO:obsoleteEquivalent"} xref: Orphanet:77258 {source="OMIM:190351"} xref: UMLS:C1860823 {source="MEDGEN:349899", source="MONDO:obsoleteEquivalent", source="MONDO:MEDGEN"} +is_a: MONDO:0000426 {source="DOID:0080376"} ! autosomal dominant disease +is_a: MONDO:0017951 {source="OMIM:190351"} ! trichorhinophalangeal syndrome property_value: IAO:0000231 OMO:0001000 {source="MONDO:excludeHistoricalDisease"} property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/4948" xsd:anyURI property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6749" xsd:anyURI @@ -244358,6 +244363,7 @@ xref: NCIT:C141441 xref: Orphanet:101046 {source="MONDO:equivalentTo", source="OMIM:600512", source="DOID:0060748"} xref: UMLS:C1838062 {source="MONDO:equivalentTo", source="MEDGEN:325326", source="MONDO:MEDGEN"} is_a: MONDO:0005027 {source="DOID:0060748/inferred", source="MESH:C537297/inferred", source="MONDO:Redundant", source="NCIT:C141441", source="OMIM:600512/inferred"} ! epilepsy +is_a: MONDO:0005115 {source="DOID:0060748"} ! temporal lobe epilepsy is_a: MONDO:0017704 {source="Orphanet:101046"} ! familial partial epilepsy relationship: curated_content_resource https://search.clinicalgenome.org/kb/conditions/MONDO:0010898 {source="MONDO:CLINGEN"} relationship: excluded_subClassOf MONDO:0005115 {source="DC-OMIM:600512", source="DOID:0060748", source="OMIM:600512", source="https://orcid.org/0000-0001-5208-3432"} ! temporal lobe epilepsy @@ -463044,7 +463050,7 @@ xref: DOID:0080472 {source="MONDO:equivalentTo"} xref: MEDGEN:1626137 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: OMIM:617711 {source="MONDO:equivalentTo"} xref: UMLS:C4540199 {source="MEDGEN:1626137", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} -is_a: MONDO:0100062 {source="OMIM:617711"} ! developmental and epileptic encephalopathy +is_a: MONDO:0100062 {source="DOID:0080472", source="OMIM:617711"} ! developmental and epileptic encephalopathy relationship: excluded_subClassOf MONDO:0020627 {source="OMIM:617711", source="https://orcid.org/0000-0001-5208-3432"} ! epileptic encephalopathy, infantile or early childhood property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/4521" xsd:anyURI @@ -463064,7 +463070,7 @@ xref: MEDGEN:1638319 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: OMIM:617829 {source="MONDO:equivalentTo"} xref: Orphanet:442835 {source="OMIM:617829"} xref: UMLS:C4693362 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:1638319"} -is_a: MONDO:0100062 {source="OMIM:617829", source="https://orcid.org/0000-0001-5208-3432"} ! developmental and epileptic encephalopathy +is_a: MONDO:0100062 {source="DOID:0080471", source="OMIM:617829", source="https://orcid.org/0000-0001-5208-3432"} ! developmental and epileptic encephalopathy relationship: excluded_subClassOf MONDO:0020627 {source="OMIM:617829", source="https://orcid.org/0000-0001-5208-3432"} ! epileptic encephalopathy, infantile or early childhood property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/4521" xsd:anyURI @@ -463084,7 +463090,7 @@ xref: MEDGEN:1642888 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: OMIM:618012 {source="MONDO:equivalentTo"} xref: Orphanet:442835 {source="OMIM:618012"} xref: UMLS:C4693934 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:1642888"} -is_a: MONDO:0100062 {source="OMIM:618012"} ! developmental and epileptic encephalopathy +is_a: MONDO:0100062 {source="DOID:0112275", source="OMIM:618012"} ! developmental and epileptic encephalopathy relationship: excluded_subClassOf MONDO:0020627 {source="OMIM:618012", source="https://orcid.org/0000-0001-5208-3432"} ! epileptic encephalopathy, infantile or early childhood property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/4521" xsd:anyURI @@ -488147,6 +488153,7 @@ subset: otar {source="MONDO:OTAR"} xref: GARD:17893 {source="MONDO:obsoleteEquivalent", source="MONDO:GARD"} xref: MEDGEN:1798905 {source="MONDO:obsoleteEquivalent", source="MONDO:MEDGEN"} xref: UMLS:C5567482 {source="MEDGEN:1798905", source="MONDO:obsoleteEquivalent", source="MONDO:MEDGEN"} +is_a: MONDO:0015653 {source="Orphanet:488613"} ! monogenic epilepsy property_value: IAO:0000231 MONDO:TermsMerged property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7597" xsd:anyURI is_obsolete: true @@ -556598,7 +556605,7 @@ xref: MEDGEN:1841215 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: OMIM:620422 {source="MONDO:equivalentTo"} xref: UMLS:C5830579 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:1841215"} is_a: MONDO:0003847 {source="OMIM:620422", source="https://orcid.org/0000-0001-5208-3432"} ! hereditary disease -is_a: MONDO:0019200 {source="https://orcid.org/0000-0001-5208-3432"} ! retinitis pigmentosa +is_a: MONDO:0019200 {source="OMIM:620422", source="https://orcid.org/0000-0001-5208-3432"} ! retinitis pigmentosa relationship: excluded_from_qc_check http://purl.obolibrary.org/obo/mondo/sparql/qc/mondo/qc-omim-subsumption.sparql [Term] From 46384aed296919311bdbe8ecdeb270b06b59f6ec Mon Sep 17 00:00:00 2001 From: Trish Whetzel Date: Wed, 20 Nov 2024 16:22:21 -0800 Subject: [PATCH 2/4] remove incorrectly added subclass axiom --- src/ontology/mondo-edit.obo | 6 ------ 1 file changed, 6 deletions(-) diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo index 402909c608..a021c46157 100644 --- a/src/ontology/mondo-edit.obo +++ b/src/ontology/mondo-edit.obo @@ -7520,7 +7520,6 @@ is_a: MONDO:0002211 {source="DOID:0060026"} ! B cell deficiency id: MONDO:0000584 name: obsolete B cell linker protein deficiency subset: gard_rare {source="MONDO:GARD"} -is_a: MONDO:0015977 {source="DOID:0060027"} ! agammaglobulinemia property_value: IAO:0000231 MONDO:TermsMerged property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7612" xsd:anyURI is_obsolete: true @@ -11820,7 +11819,6 @@ replaced_by: MONDO:0015690 id: MONDO:0000884 name: obsolete myeloid and lymphoid neoplasms associated with FGFR1 abnormalities subset: gard_rare {source="MONDO:GARD"} -is_a: MONDO:0015688 {source="DOID:0080167"} ! myeloid/lymphoid neoplasms associated with eosinophilia and abnormality of PDGFRA, PDGFRB, FGFR1 or JAK2 property_value: IAO:0000231 MONDO:TermsMerged property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7614" xsd:anyURI is_obsolete: true @@ -74345,7 +74343,6 @@ intersection_of: disease_has_location UBERON:0000056 ! ureter id: MONDO:0004031 name: obsolete ovary mixed epithelial carcinoma subset: gard_rare {source="MONDO:GARD"} -is_a: MONDO:0005140 {source="DOID:6898"} ! ovarian carcinoma property_value: IAO:0000231 MONDO:TermsMerged property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7609" xsd:anyURI is_obsolete: true @@ -179449,8 +179446,6 @@ xref: NORD:1789 {source="MONDO:NORD"} xref: OMIM:190351 {source="MONDO:obsoleteEquivalent"} xref: Orphanet:77258 {source="OMIM:190351"} xref: UMLS:C1860823 {source="MEDGEN:349899", source="MONDO:obsoleteEquivalent", source="MONDO:MEDGEN"} -is_a: MONDO:0000426 {source="DOID:0080376"} ! autosomal dominant disease -is_a: MONDO:0017951 {source="OMIM:190351"} ! trichorhinophalangeal syndrome property_value: IAO:0000231 OMO:0001000 {source="MONDO:excludeHistoricalDisease"} property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/4948" xsd:anyURI property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6749" xsd:anyURI @@ -488153,7 +488148,6 @@ subset: otar {source="MONDO:OTAR"} xref: GARD:17893 {source="MONDO:obsoleteEquivalent", source="MONDO:GARD"} xref: MEDGEN:1798905 {source="MONDO:obsoleteEquivalent", source="MONDO:MEDGEN"} xref: UMLS:C5567482 {source="MEDGEN:1798905", source="MONDO:obsoleteEquivalent", source="MONDO:MEDGEN"} -is_a: MONDO:0015653 {source="Orphanet:488613"} ! monogenic epilepsy property_value: IAO:0000231 MONDO:TermsMerged property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7597" xsd:anyURI is_obsolete: true From 44ca58c67637ecbb8208c7a8ef6454f6f8c841c5 Mon Sep 17 00:00:00 2001 From: Trish Whetzel Date: Wed, 20 Nov 2024 17:25:13 -0800 Subject: [PATCH 3/4] remove parent classes that are stated to be excluded --- src/ontology/mondo-edit.obo | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo index a021c46157..165d31b926 100644 --- a/src/ontology/mondo-edit.obo +++ b/src/ontology/mondo-edit.obo @@ -153524,7 +153524,6 @@ xref: OMIM:132090 {source="Orphanet:25968", source="MONDO:equivalentTo", source= xref: Orphanet:25968 {source="MONDO:equivalentTo", source="OMIM:132090"} xref: UMLS:C1851549 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:377052"} is_a: MONDO:0015650 {source="https://orcid.org/0000-0001-5208-3432"} ! epilepsy syndrome -is_a: MONDO:0020072 {source="Orphanet:25968", source="https://orcid.org/0000-0001-5208-3432", source="https://www.epilepsydiagnosis.org/syndrome/epilepsy-syndrome-groupoverview.html"} ! childhood-onset epilepsy syndrome relationship: excluded_subClassOf MONDO:0020072 {source="Orphanet:25968", source="https://orcid.org/0000-0001-5208-3432"} ! childhood-onset epilepsy syndrome property_value: seeAlso "https://rarediseases.info.nih.gov/diseases/2170/epilepsy-benign-occipital" xsd:anyURI {source="GARD:0002170"} @@ -244358,7 +244357,6 @@ xref: NCIT:C141441 xref: Orphanet:101046 {source="MONDO:equivalentTo", source="OMIM:600512", source="DOID:0060748"} xref: UMLS:C1838062 {source="MONDO:equivalentTo", source="MEDGEN:325326", source="MONDO:MEDGEN"} is_a: MONDO:0005027 {source="DOID:0060748/inferred", source="MESH:C537297/inferred", source="MONDO:Redundant", source="NCIT:C141441", source="OMIM:600512/inferred"} ! epilepsy -is_a: MONDO:0005115 {source="DOID:0060748"} ! temporal lobe epilepsy is_a: MONDO:0017704 {source="Orphanet:101046"} ! familial partial epilepsy relationship: curated_content_resource https://search.clinicalgenome.org/kb/conditions/MONDO:0010898 {source="MONDO:CLINGEN"} relationship: excluded_subClassOf MONDO:0005115 {source="DC-OMIM:600512", source="DOID:0060748", source="OMIM:600512", source="https://orcid.org/0000-0001-5208-3432"} ! temporal lobe epilepsy From f01bc1929cb44cf3a0a1d319ed64e52e1e1e4d59 Mon Sep 17 00:00:00 2001 From: Trish Whetzel Date: Thu, 21 Nov 2024 16:24:49 -0800 Subject: [PATCH 4/4] add back subclassof and remove excluded_subclassof relationship --- src/ontology/mondo-edit.obo | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo index 165d31b926..00e2f9d3d3 100644 --- a/src/ontology/mondo-edit.obo +++ b/src/ontology/mondo-edit.obo @@ -153524,7 +153524,7 @@ xref: OMIM:132090 {source="Orphanet:25968", source="MONDO:equivalentTo", source= xref: Orphanet:25968 {source="MONDO:equivalentTo", source="OMIM:132090"} xref: UMLS:C1851549 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:377052"} is_a: MONDO:0015650 {source="https://orcid.org/0000-0001-5208-3432"} ! epilepsy syndrome -relationship: excluded_subClassOf MONDO:0020072 {source="Orphanet:25968", source="https://orcid.org/0000-0001-5208-3432"} ! childhood-onset epilepsy syndrome +is_a: MONDO:0020072 {source="https://orcid.org/0000-0001-5208-3432", source="https://www.epilepsydiagnosis.org/syndrome/epilepsy-syndrome-groupoverview.html"} ! childhood-onset epilepsy syndrome property_value: seeAlso "https://rarediseases.info.nih.gov/diseases/2170/epilepsy-benign-occipital" xsd:anyURI {source="GARD:0002170"} [Term]