June release (#7777)

* June release * June release - updating all the release files - updating gitignore
monarch-initiative · Jun 4, 2024 · 08555a0 · 08555a0
1 parent db51338
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diff --git a/.gitignore b/.gitignore
@@ -113,3 +113,6 @@ src/ontology/subsets/*_nodes.tsv
 src/ontology/mondo_nodes.tsv
 src/ontology/mondo_edges.tsv
 src/ontology/mondo-simple.*
+mondo-simple.*
+mondo_edges.*
+mondo_nodes.*
diff --git a/components/mondo-tags.owl b/components/mondo-tags.owl
@@ -4334,14 +4334,6 @@
 
 
 
-    <!-- http://purl.obolibrary.org/obo/MONDO_0001998 -->
-
-    <owl:Class rdf:about="http://purl.obolibrary.org/obo/MONDO_0001998">
-        <mondo:excluded_from_qc_check rdf:resource="http://purl.obolibrary.org/obo/mondo/sparql/qc/general/qc-single-child.sparql"/>
-    </owl:Class>
-
-
-
     <!-- http://purl.obolibrary.org/obo/MONDO_0002008 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/MONDO_0002008">
@@ -24693,6 +24685,14 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/MONDO_0015991 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/MONDO_0015991">
+        <mondo:should_conform_to rdf:resource="http://purl.obolibrary.org/obo/mondo/patterns/OMIM_phenotypic_series.yaml"/>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/MONDO_0015993 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/MONDO_0015993">

diff --git a/imports/equivalencies.json b/imports/equivalencies.json
@@ -37234,15 +37234,6 @@
     }, {
       "representativeNodeId" : "http://purl.obolibrary.org/obo/DOID_9997",
       "nodeIds" : [ "http://purl.obolibrary.org/obo/DOID_9997", "http://purl.obolibrary.org/obo/MONDO_0018920" ]
-    }, {
-      "representativeNodeId" : "http://purl.obolibrary.org/obo/GARD_18955",
-      "nodeIds" : [ "http://purl.obolibrary.org/obo/GARD_18955", "http://purl.obolibrary.org/obo/MONDO_0000698" ]
-    }, {
-      "representativeNodeId" : "http://purl.obolibrary.org/obo/GARD_21957",
-      "nodeIds" : [ "http://purl.obolibrary.org/obo/GARD_21957", "http://purl.obolibrary.org/obo/MONDO_0700264" ]
-    }, {
-      "representativeNodeId" : "http://purl.obolibrary.org/obo/GARD_22195",
-      "nodeIds" : [ "http://purl.obolibrary.org/obo/GARD_22195", "http://purl.obolibrary.org/obo/MONDO_0100567" ]
     }, {
       "representativeNodeId" : "http://purl.obolibrary.org/obo/ICD10CM_A00",
       "nodeIds" : [ "http://purl.obolibrary.org/obo/ICD10CM_A00", "http://purl.obolibrary.org/obo/MONDO_0015766" ]
@@ -60757,6 +60748,9 @@
     }, {
       "representativeNodeId" : "http://purl.obolibrary.org/obo/MONDO_0005639",
       "nodeIds" : [ "http://purl.obolibrary.org/obo/MONDO_0005639", "http://www.ebi.ac.uk/efo/EFO_0007137" ]
+    }, {
+      "representativeNodeId" : "http://purl.obolibrary.org/obo/MONDO_0005641",
+      "nodeIds" : [ "http://purl.obolibrary.org/obo/MONDO_0005641", "http://www.ebi.ac.uk/efo/EFO_0007139" ]
     }, {
       "representativeNodeId" : "http://purl.obolibrary.org/obo/MONDO_0005643",
       "nodeIds" : [ "http://purl.obolibrary.org/obo/MONDO_0005643", "http://www.ebi.ac.uk/efo/EFO_0007142" ]
@@ -60937,6 +60931,9 @@
     }, {
       "representativeNodeId" : "http://purl.obolibrary.org/obo/MONDO_0005675",
       "nodeIds" : [ "http://purl.obolibrary.org/obo/MONDO_0005675", "http://www.ebi.ac.uk/efo/EFO_0007177" ]
+    }, {
+      "representativeNodeId" : "http://purl.obolibrary.org/obo/MONDO_0005676",
+      "nodeIds" : [ "http://purl.obolibrary.org/obo/MONDO_0005676", "http://www.ebi.ac.uk/efo/EFO_0007178" ]
     }, {
       "representativeNodeId" : "http://purl.obolibrary.org/obo/MONDO_0005677",
       "nodeIds" : [ "http://purl.obolibrary.org/obo/MONDO_0005677", "http://www.ebi.ac.uk/efo/EFO_0007179" ]
@@ -67243,9 +67240,6 @@
     }, {
       "representativeNodeId" : "http://purl.obolibrary.org/obo/MONDO_0007734",
       "nodeIds" : [ "http://purl.obolibrary.org/obo/MONDO_0007734", "https://omim.org/entry/142946" ]
-    }, {
-      "representativeNodeId" : "http://purl.obolibrary.org/obo/MONDO_0007736",
-      "nodeIds" : [ "http://purl.obolibrary.org/obo/MONDO_0007736", "https://omim.org/entry/143020" ]
     }, {
       "representativeNodeId" : "http://purl.obolibrary.org/obo/MONDO_0007737",
       "nodeIds" : [ "http://purl.obolibrary.org/obo/MONDO_0007737", "http://purl.obolibrary.org/obo/icd11.foundation_518723993" ]
@@ -96442,9 +96436,6 @@
     }, {
       "representativeNodeId" : "http://purl.obolibrary.org/obo/MONDO_0015541",
       "nodeIds" : [ "http://purl.obolibrary.org/obo/MONDO_0015541", "http://snomed.info/id/398250003" ]
-    }, {
-      "representativeNodeId" : "http://purl.obolibrary.org/obo/MONDO_0015541",
-      "nodeIds" : [ "http://purl.obolibrary.org/obo/MONDO_0015541", "http://www.orpha.net/ORDO/Orphanet_158038" ]
     }, {
       "representativeNodeId" : "http://purl.obolibrary.org/obo/MONDO_0015541",
       "nodeIds" : [ "http://purl.obolibrary.org/obo/MONDO_0015541", "http://www.orpha.net/ORDO/Orphanet_540" ]
@@ -97300,6 +97291,9 @@
     }, {
       "representativeNodeId" : "http://purl.obolibrary.org/obo/MONDO_0015991",
       "nodeIds" : [ "http://purl.obolibrary.org/obo/MONDO_0015991", "http://www.orpha.net/ORDO/Orphanet_187" ]
+    }, {
+      "representativeNodeId" : "http://purl.obolibrary.org/obo/MONDO_0015991",
+      "nodeIds" : [ "http://purl.obolibrary.org/obo/MONDO_0015991", "https://omim.org/phenotypicSeries/PS215700" ]
     }, {
       "representativeNodeId" : "http://purl.obolibrary.org/obo/MONDO_0015995",
       "nodeIds" : [ "http://purl.obolibrary.org/obo/MONDO_0015995", "http://www.orpha.net/ORDO/Orphanet_1879" ]
@@ -114442,6 +114436,9 @@
     }, {
       "representativeNodeId" : "http://purl.obolibrary.org/obo/MONDO_0800176",
       "nodeIds" : [ "http://purl.obolibrary.org/obo/MONDO_0800176", "http://snomed.info/id/217666004" ]
+    }, {
+      "representativeNodeId" : "http://purl.obolibrary.org/obo/MONDO_0800306",
+      "nodeIds" : [ "http://purl.obolibrary.org/obo/MONDO_0800306", "https://omim.org/entry/620681" ]
     }, {
       "representativeNodeId" : "http://purl.obolibrary.org/obo/MONDO_0800436",
       "nodeIds" : [ "http://purl.obolibrary.org/obo/MONDO_0800436", "http://snomed.info/id/720635002" ]
@@ -115606,9 +115603,6 @@
     }, {
       "representativeNodeId" : "http://purl.obolibrary.org/obo/MONDO_0958199",
       "nodeIds" : [ "http://purl.obolibrary.org/obo/MONDO_0958199", "https://omim.org/entry/254780" ]
-    }, {
-      "representativeNodeId" : "http://purl.obolibrary.org/obo/MONDO_0958201",
-      "nodeIds" : [ "http://purl.obolibrary.org/obo/MONDO_0958201", "https://omim.org/entry/620681" ]
     }, {
       "representativeNodeId" : "http://purl.obolibrary.org/obo/MONDO_0958204",
       "nodeIds" : [ "http://purl.obolibrary.org/obo/MONDO_0958204", "https://omim.org/entry/620700" ]
@@ -115705,6 +115699,24 @@
     }, {
       "representativeNodeId" : "http://purl.obolibrary.org/obo/MONDO_0968947",
       "nodeIds" : [ "http://purl.obolibrary.org/obo/MONDO_0968947", "https://omim.org/entry/620784" ]
+    }, {
+      "representativeNodeId" : "http://purl.obolibrary.org/obo/MONDO_0968978",
+      "nodeIds" : [ "http://purl.obolibrary.org/obo/MONDO_0968978", "https://omim.org/entry/620789" ]
+    }, {
+      "representativeNodeId" : "http://purl.obolibrary.org/obo/MONDO_0968980",
+      "nodeIds" : [ "http://purl.obolibrary.org/obo/MONDO_0968980", "https://omim.org/entry/620792" ]
+    }, {
+      "representativeNodeId" : "http://purl.obolibrary.org/obo/MONDO_0968982",
+      "nodeIds" : [ "http://purl.obolibrary.org/obo/MONDO_0968982", "https://omim.org/entry/620795" ]
+    }, {
+      "representativeNodeId" : "http://purl.obolibrary.org/obo/MONDO_0968983",
+      "nodeIds" : [ "http://purl.obolibrary.org/obo/MONDO_0968983", "https://omim.org/entry/620796" ]
+    }, {
+      "representativeNodeId" : "http://purl.obolibrary.org/obo/MONDO_0968986",
+      "nodeIds" : [ "http://purl.obolibrary.org/obo/MONDO_0968986", "http://www.orpha.net/ORDO/Orphanet_645285" ]
+    }, {
+      "representativeNodeId" : "http://purl.obolibrary.org/obo/MONDO_0968987",
+      "nodeIds" : [ "http://purl.obolibrary.org/obo/MONDO_0968987", "http://www.orpha.net/ORDO/Orphanet_645297" ]
     }, {
       "representativeNodeId" : "http://purl.obolibrary.org/obo/MONDO_1010001",
       "nodeIds" : [ "http://purl.obolibrary.org/obo/MONDO_1010001", "http://purl.obolibrary.org/obo/OMIA_000344" ]

diff --git a/imports/equivalencies.obo b/imports/equivalencies.obo
@@ -20942,18 +20942,6 @@ equivalent_to: MONDO:0004946
 id: DOID:9997
 equivalent_to: MONDO:0018920
 
-[Term]
-id: GARD:18955
-equivalent_to: MONDO:0000698
-
-[Term]
-id: GARD:21957
-equivalent_to: MONDO:0700264
-
-[Term]
-id: GARD:22195
-equivalent_to: MONDO:0100567
-
 [Term]
 id: ICD10CM:A00
 equivalent_to: MONDO:0015766
@@ -49810,6 +49798,10 @@ equivalent_to: NCIT:C34505
 id: MONDO:0005639
 equivalent_to: EFO:0007137
 
+[Term]
+id: MONDO:0005641
+equivalent_to: EFO:0007139
+
 [Term]
 id: MONDO:0005643
 equivalent_to: EFO:0007142
@@ -49936,6 +49928,10 @@ equivalent_to: Orphanet:363976
 id: MONDO:0005675
 equivalent_to: EFO:0007177
 
+[Term]
+id: MONDO:0005676
+equivalent_to: EFO:0007178
+
 [Term]
 id: MONDO:0005677
 equivalent_to: EFO:0007179
@@ -54654,10 +54650,6 @@ id: MONDO:0007734
 equivalent_to: https://omim.org/entry/142946
 equivalent_to: NCIT:C75475
 
-[Term]
-id: MONDO:0007736
-equivalent_to: https://omim.org/entry/143020
-
 [Term]
 id: MONDO:0007737
 equivalent_to: http://snomed.info/id/205329008
@@ -78490,7 +78482,6 @@ equivalent_to: Orphanet:158032
 id: MONDO:0015541
 equivalent_to: http://snomed.info/id/398250003
 equivalent_to: https://omim.org/phenotypicSeries/PS267700
-equivalent_to: Orphanet:158038
 equivalent_to: Orphanet:540
 
 [Term]
@@ -79129,6 +79120,7 @@ equivalent_to: Orphanet:185
 [Term]
 id: MONDO:0015991
 equivalent_to: http://snomed.info/id/124711003
+equivalent_to: https://omim.org/phenotypicSeries/PS215700
 equivalent_to: icd11.foundation:640937125
 equivalent_to: NCIT:C84639
 equivalent_to: Orphanet:187
@@ -95176,6 +95168,10 @@ equivalent_to: https://omim.org/entry/619858
 id: MONDO:0800176
 equivalent_to: http://snomed.info/id/217666004
 
+[Term]
+id: MONDO:0800306
+equivalent_to: https://omim.org/entry/620681
+
 [Term]
 id: MONDO:0800436
 equivalent_to: http://snomed.info/id/720635002
@@ -96677,10 +96673,6 @@ equivalent_to: https://omim.org/entry/620569
 id: MONDO:0958199
 equivalent_to: https://omim.org/entry/254780
 
-[Term]
-id: MONDO:0958201
-equivalent_to: https://omim.org/entry/620681
-
 [Term]
 id: MONDO:0958204
 equivalent_to: https://omim.org/entry/620700
@@ -96809,6 +96801,30 @@ equivalent_to: https://omim.org/entry/620782
 id: MONDO:0968947
 equivalent_to: https://omim.org/entry/620784
 
+[Term]
+id: MONDO:0968978
+equivalent_to: https://omim.org/entry/620789
+
+[Term]
+id: MONDO:0968980
+equivalent_to: https://omim.org/entry/620792
+
+[Term]
+id: MONDO:0968982
+equivalent_to: https://omim.org/entry/620795
+
+[Term]
+id: MONDO:0968983
+equivalent_to: https://omim.org/entry/620796
+
+[Term]
+id: MONDO:0968986
+equivalent_to: Orphanet:645285
+
+[Term]
+id: MONDO:0968987
+equivalent_to: Orphanet:645297
+
 [Term]
 id: MONDO:1010001
 equivalent_to: OMIA:000344