mondo cycle week 1 data build on main

monarch-initiative · Aug 7, 2024 · d54ae6b · d54ae6b
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diff --git a/docs/metrics/doid.md b/docs/metrics/doid.md
@@ -2,7 +2,7 @@
 
 **IRI:** http://purl.obolibrary.org/obo/mondo/sources/doid.owl
 
-**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-08-05/doid.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-08-07/doid.owl
 
 ### Entities and axioms
 

diff --git a/docs/metrics/gard.md b/docs/metrics/gard.md
@@ -2,7 +2,7 @@
 
 **IRI:** http://purl.obolibrary.org/obo/mondo/sources/gard.owl
 
-**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-08-05/gard.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-08-07/gard.owl
 
 ### Entities and axioms
 

diff --git a/docs/metrics/icd10cm.md b/docs/metrics/icd10cm.md
@@ -2,7 +2,7 @@
 
 **IRI:** http://purl.obolibrary.org/obo/mondo/sources/icd10cm.owl
 
-**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-08-05/icd10cm.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-08-07/icd10cm.owl
 
 ### Entities and axioms
 

diff --git a/docs/metrics/icd10who.md b/docs/metrics/icd10who.md
@@ -2,7 +2,7 @@
 
 **IRI:** http://purl.obolibrary.org/obo/mondo/sources/icd10who.owl
 
-**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-08-05/icd10who.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-08-07/icd10who.owl
 
 ### Entities and axioms
 

diff --git a/docs/metrics/icd11foundation.md b/docs/metrics/icd11foundation.md
@@ -2,7 +2,7 @@
 
 **IRI:** http://purl.obolibrary.org/obo/mondo/sources/icd11foundation.owl
 
-**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-08-05/icd11foundation.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-08-07/icd11foundation.owl
 
 ### Entities and axioms
 

diff --git a/docs/metrics/ncit.md b/docs/metrics/ncit.md
@@ -2,7 +2,7 @@
 
 **IRI:** http://purl.obolibrary.org/obo/mondo/sources/ncit.owl
 
-**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-08-05/ncit.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-08-07/ncit.owl
 
 ### Entities and axioms
 

diff --git a/docs/metrics/omim.md b/docs/metrics/omim.md
@@ -2,7 +2,7 @@
 
 **IRI:** http://purl.obolibrary.org/obo/mondo/sources/omim.owl
 
-**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-08-05/omim.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-08-07/omim.owl
 
 ### Entities and axioms
 

diff --git a/docs/metrics/ordo.md b/docs/metrics/ordo.md
@@ -2,7 +2,7 @@
 
 **IRI:** http://purl.obolibrary.org/obo/mondo/sources/ordo.owl
 
-**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-08-05/ordo.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-08-07/ordo.owl
 
 ### Entities and axioms
 

diff --git a/docs/reports/migrate_ordo.md b/docs/reports/migrate_ordo.md
diff --git a/src/mappings/gard.sssom.tsv b/src/mappings/gard.sssom.tsv
@@ -9,7 +9,7 @@
 #   skos: http://www.w3.org/2004/02/skos/core#
 #   sssom: https://w3id.org/sssom/
 # license: https://w3id.org/sssom/license/unspecified
-# mapping_set_id: https://w3id.org/sssom/mappings/3c611c23-d05e-4312-990f-c025914ba99c
+# mapping_set_id: https://w3id.org/sssom/mappings/2ab29bc2-cbd9-4db0-8353-594cc6b5c645
 subject_id	subject_label	predicate_id	object_id	mapping_justification
 obo:GARD_1	GRACILE syndrome	skos:exactMatch	Orphanet:53693	semapv:UnspecifiedMatching
 obo:GARD_1	GRACILE syndrome	skos:narrowMatch	OMIM:603358	semapv:UnspecifiedMatching

diff --git a/src/mappings/icd10cm.sssom.tsv b/src/mappings/icd10cm.sssom.tsv
@@ -6,6 +6,6 @@
 #   skos: http://www.w3.org/2004/02/skos/core#
 #   sssom: https://w3id.org/sssom/
 # license: https://w3id.org/sssom/license/unspecified
-# mapping_set_id: https://w3id.org/sssom/mappings/90483748-67c5-4945-8598-ede2d3f6495d
+# mapping_set_id: https://w3id.org/sssom/mappings/791877cb-cabc-4c85-ae3c-9d0ed06cf784
 
 
diff --git a/src/mappings/icd10who.sssom.tsv b/src/mappings/icd10who.sssom.tsv
@@ -6,6 +6,6 @@
 #   skos: http://www.w3.org/2004/02/skos/core#
 #   sssom: https://w3id.org/sssom/
 # license: https://w3id.org/sssom/license/unspecified
-# mapping_set_id: https://w3id.org/sssom/mappings/7565cb47-92a8-4403-bb95-60c81d9759d8
+# mapping_set_id: https://w3id.org/sssom/mappings/d7d450f4-1433-481e-bc58-5764cc4bcf1e
 
 
diff --git a/src/mappings/icd11foundation.sssom.tsv b/src/mappings/icd11foundation.sssom.tsv
@@ -6,6 +6,6 @@
 #   skos: http://www.w3.org/2004/02/skos/core#
 #   sssom: https://w3id.org/sssom/
 # license: https://w3id.org/sssom/license/unspecified
-# mapping_set_id: https://w3id.org/sssom/mappings/0ac284d6-092c-4366-af89-ac6075739870
+# mapping_set_id: https://w3id.org/sssom/mappings/a17920dc-cde7-4e7d-920b-90ebad467c84
 
 
diff --git a/src/mappings/mondo-nando.sssom.tsv b/src/mappings/mondo-nando.sssom.tsv
@@ -15,7 +15,7 @@
 # mapping_provider: MONDO:NANDO
 # mapping_set_description: This mapping set is manually curated by the NANDO team at
 #   nanbyodata.jp.
-# mapping_set_id: https://w3id.org/sssom/mappings/05a2c8ab-dce1-4e98-aae8-149fd0b456bc
+# mapping_set_id: https://w3id.org/sssom/mappings/864b7416-dacd-41b5-b47e-e8740578e9aa
 # mapping_set_title: NANDO - Mondo mappings provided by nanbyodata.jp
 subject_id	subject_label	predicate_id	object_id	object_label	mapping_justification
 MONDO:0000050	isolated congenital growth hormone deficiency	skos:closeMatch	NANDO:2200317	Congenital growth hormone deficiency	semapv:MappingInversion

diff --git a/src/mappings/ncit.sssom.tsv b/src/mappings/ncit.sssom.tsv
@@ -9,7 +9,7 @@
 #   skos: http://www.w3.org/2004/02/skos/core#
 #   sssom: https://w3id.org/sssom/
 # license: https://w3id.org/sssom/license/unspecified
-# mapping_set_id: https://w3id.org/sssom/mappings/21440827-20be-4c73-b8ed-d5309ca40f2c
+# mapping_set_id: https://w3id.org/sssom/mappings/8254990e-0ee0-4a2b-bab7-b3acb4c44fb0
 subject_id	subject_label	predicate_id	object_id	mapping_justification
 NCIT:C103222	Popliteal Fossa	oboInOwl:hasDbXref	UBERON:0013069	semapv:UnspecifiedMatching
 NCIT:C103384	Common Iliac Lymph Node	oboInOwl:hasDbXref	UBERON:0015878	semapv:UnspecifiedMatching

diff --git a/src/ontology/external/mondo-omim-genes.robot.owl b/src/ontology/external/mondo-omim-genes.robot.owl
@@ -8,7 +8,7 @@
      xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/mondo/external/nord.robot.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mondo/external/2024-08-05/nord.robot.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mondo/external/2024-08-07/nord.robot.owl"/>
     </owl:Ontology>
 
 

diff --git a/src/ontology/external/nando-mappings.robot.owl b/src/ontology/external/nando-mappings.robot.owl
@@ -8,7 +8,7 @@
      xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/mondo/external/nord.robot.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mondo/external/2024-08-05/nord.robot.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mondo/external/2024-08-07/nord.robot.owl"/>
     </owl:Ontology>
 
 

diff --git a/src/ontology/external/nord.robot.owl b/src/ontology/external/nord.robot.owl
@@ -8,7 +8,7 @@
      xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/mondo/external/nord.robot.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mondo/external/2024-08-05/nord.robot.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mondo/external/2024-08-07/nord.robot.owl"/>
     </owl:Ontology>
 
 

diff --git a/src/ontology/external/ordo-subsets.robot.owl b/src/ontology/external/ordo-subsets.robot.owl
@@ -8,7 +8,7 @@
      xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/mondo/external/nord.robot.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mondo/external/2024-08-05/nord.robot.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mondo/external/2024-08-07/nord.robot.owl"/>
     </owl:Ontology>
 
 

diff --git a/src/ontology/imports/omo_import.owl b/src/ontology/imports/omo_import.owl
@@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/mondo-ingest/imports/omo_import.owl>
-<http://purl.obolibrary.org/obo/mondo-ingest/releases/2024-08-05/imports/omo_import.owl>
+<http://purl.obolibrary.org/obo/mondo-ingest/releases/2024-08-07/imports/omo_import.owl>
 Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/omo/releases/2023-11-02/omo.owl>)
-Annotation(owl:versionInfo "2024-08-05")
+Annotation(owl:versionInfo "2024-08-07")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000031>))
 Declaration(Class(<http://purl.obolibrary.org/obo/IAO_0000027>))

diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl
@@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/mondo-ingest/imports/ro_import.owl>
-<http://purl.obolibrary.org/obo/mondo-ingest/releases/2024-08-05/imports/ro_import.owl>
+<http://purl.obolibrary.org/obo/mondo-ingest/releases/2024-08-07/imports/ro_import.owl>
 Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/ro/releases/2024-04-24/ro.owl>)
-Annotation(owl:versionInfo "2024-08-05")
+Annotation(owl:versionInfo "2024-08-07")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000002>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000003>))

diff --git a/src/ontology/lexmatch/README.md b/src/ontology/lexmatch/README.md
@@ -32,26 +32,26 @@
  * Number of mappings in [`unmapped_ordo_mondo`](mondo-only/unmapped_ordo_mondo.tsv): 868
  * Number of mappings in [`unmapped_ordo_mondo_exact`](mondo-only/unmapped_ordo_mondo.tsv): 868
 ## mondo_XXXXmatch_ontology
- * Number of mappings in [`mondo_exactmatch_orphanet`](split-mapping-set/mondo_exactmatch_orphanet.tsv): 869
  * Number of mappings in [`mondo_broadmatch_orphanet`](split-mapping-set/mondo_broadmatch_orphanet.tsv): 2
  * Number of mappings in [`mondo_closematch_orphanet`](split-mapping-set/mondo_closematch_orphanet.tsv): 114
- * Number of mappings in [`mondo_exactmatch_doid`](split-mapping-set/mondo_exactmatch_doid.tsv): 79
- * Number of mappings in [`mondo_narrowmatch_doid`](split-mapping-set/mondo_narrowmatch_doid.tsv): 2
+ * Number of mappings in [`mondo_exactmatch_orphanet`](split-mapping-set/mondo_exactmatch_orphanet.tsv): 869
  * Number of mappings in [`mondo_closematch_doid`](split-mapping-set/mondo_closematch_doid.tsv): 260
- * Number of mappings in [`mondo_exactmatch_ncit`](split-mapping-set/mondo_exactmatch_ncit.tsv): 128
+ * Number of mappings in [`mondo_narrowmatch_doid`](split-mapping-set/mondo_narrowmatch_doid.tsv): 2
+ * Number of mappings in [`mondo_exactmatch_doid`](split-mapping-set/mondo_exactmatch_doid.tsv): 79
+ * Number of mappings in [`mondo_exactmatch_omim`](split-mapping-set/mondo_exactmatch_omim.tsv): 112
+ * Number of mappings in [`mondo_broadmatch_icd10cm`](split-mapping-set/mondo_broadmatch_icd10cm.tsv): 112
+ * Number of mappings in [`mondo_closematch_icd10cm`](split-mapping-set/mondo_closematch_icd10cm.tsv): 6229
+ * Number of mappings in [`mondo_narrowmatch_icd10cm`](split-mapping-set/mondo_narrowmatch_icd10cm.tsv): 461
+ * Number of mappings in [`mondo_exactmatch_icd10cm`](split-mapping-set/mondo_exactmatch_icd10cm.tsv): 2376
+ * Number of mappings in [`mondo_broadmatch_icd11.foundation`](split-mapping-set/mondo_broadmatch_icd11.foundation.tsv): 293
+ * Number of mappings in [`mondo_closematch_icd11.foundation`](split-mapping-set/mondo_closematch_icd11.foundation.tsv): 6971
+ * Number of mappings in [`mondo_exactmatch_icd11.foundation`](split-mapping-set/mondo_exactmatch_icd11.foundation.tsv): 10617
  * Number of mappings in [`mondo_broadmatch_ncit`](split-mapping-set/mondo_broadmatch_ncit.tsv): 11
  * Number of mappings in [`mondo_closematch_ncit`](split-mapping-set/mondo_closematch_ncit.tsv): 77
- * Number of mappings in [`mondo_exactmatch_omimps`](split-mapping-set/mondo_exactmatch_omimps.tsv): 7
+ * Number of mappings in [`mondo_exactmatch_ncit`](split-mapping-set/mondo_exactmatch_ncit.tsv): 128
  * Number of mappings in [`mondo_closematch_omimps`](split-mapping-set/mondo_closematch_omimps.tsv): 24
- * Number of mappings in [`mondo_exactmatch_omim`](split-mapping-set/mondo_exactmatch_omim.tsv): 112
- * Number of mappings in [`mondo_exactmatch_icd10who`](split-mapping-set/mondo_exactmatch_icd10who.tsv): 1651
- * Number of mappings in [`mondo_narrowmatch_icd10who`](split-mapping-set/mondo_narrowmatch_icd10who.tsv): 221
+ * Number of mappings in [`mondo_exactmatch_omimps`](split-mapping-set/mondo_exactmatch_omimps.tsv): 7
  * Number of mappings in [`mondo_broadmatch_icd10who`](split-mapping-set/mondo_broadmatch_icd10who.tsv): 60
  * Number of mappings in [`mondo_closematch_icd10who`](split-mapping-set/mondo_closematch_icd10who.tsv): 328
- * Number of mappings in [`mondo_exactmatch_icd11.foundation`](split-mapping-set/mondo_exactmatch_icd11.foundation.tsv): 10617
- * Number of mappings in [`mondo_broadmatch_icd11.foundation`](split-mapping-set/mondo_broadmatch_icd11.foundation.tsv): 293
- * Number of mappings in [`mondo_closematch_icd11.foundation`](split-mapping-set/mondo_closematch_icd11.foundation.tsv): 6971
- * Number of mappings in [`mondo_exactmatch_icd10cm`](split-mapping-set/mondo_exactmatch_icd10cm.tsv): 2376
- * Number of mappings in [`mondo_narrowmatch_icd10cm`](split-mapping-set/mondo_narrowmatch_icd10cm.tsv): 461
- * Number of mappings in [`mondo_broadmatch_icd10cm`](split-mapping-set/mondo_broadmatch_icd10cm.tsv): 112
- * Number of mappings in [`mondo_closematch_icd10cm`](split-mapping-set/mondo_closematch_icd10cm.tsv): 6229
+ * Number of mappings in [`mondo_narrowmatch_icd10who`](split-mapping-set/mondo_narrowmatch_icd10who.tsv): 221
+ * Number of mappings in [`mondo_exactmatch_icd10who`](split-mapping-set/mondo_exactmatch_icd10who.tsv): 1651
diff --git a/src/ontology/metadata/doid-metrics.json b/src/ontology/metadata/doid-metrics.json
@@ -26,7 +26,7 @@
     "obj_property_count_incl": 0,
     "ontology_anno_count": 11,
     "ontology_iri": "http://purl.obolibrary.org/obo/mondo/sources/doid.owl",
-    "ontology_version_iri": "http://purl.obolibrary.org/obo/mondo/sources/2024-08-05/doid.owl",
+    "ontology_version_iri": "http://purl.obolibrary.org/obo/mondo/sources/2024-08-07/doid.owl",
     "owl2": true,
     "owl2_dl": true,
     "owl2_el": true,

diff --git a/src/ontology/metadata/gard-metrics.json b/src/ontology/metadata/gard-metrics.json
@@ -26,7 +26,7 @@
     "obj_property_count_incl": 0,
     "ontology_anno_count": 1,
     "ontology_iri": "http://purl.obolibrary.org/obo/mondo/sources/gard.owl",
-    "ontology_version_iri": "http://purl.obolibrary.org/obo/mondo/sources/2024-08-05/gard.owl",
+    "ontology_version_iri": "http://purl.obolibrary.org/obo/mondo/sources/2024-08-07/gard.owl",
     "owl2": true,
     "owl2_dl": true,
     "owl2_el": true,

diff --git a/src/ontology/metadata/icd10cm-metrics.json b/src/ontology/metadata/icd10cm-metrics.json
@@ -26,7 +26,7 @@
     "obj_property_count_incl": 0,
     "ontology_anno_count": 5,
     "ontology_iri": "http://purl.obolibrary.org/obo/mondo/sources/icd10cm.owl",
-    "ontology_version_iri": "http://purl.obolibrary.org/obo/mondo/sources/2024-08-05/icd10cm.owl",
+    "ontology_version_iri": "http://purl.obolibrary.org/obo/mondo/sources/2024-08-07/icd10cm.owl",
     "owl2": true,
     "owl2_dl": true,
     "owl2_el": true,

diff --git a/src/ontology/metadata/icd10who-metrics.json b/src/ontology/metadata/icd10who-metrics.json
@@ -26,7 +26,7 @@
     "obj_property_count_incl": 0,
     "ontology_anno_count": 5,
     "ontology_iri": "http://purl.obolibrary.org/obo/mondo/sources/icd10who.owl",
-    "ontology_version_iri": "http://purl.obolibrary.org/obo/mondo/sources/2024-08-05/icd10who.owl",
+    "ontology_version_iri": "http://purl.obolibrary.org/obo/mondo/sources/2024-08-07/icd10who.owl",
     "owl2": true,
     "owl2_dl": true,
     "owl2_el": true,

diff --git a/src/ontology/metadata/icd11foundation-metrics.json b/src/ontology/metadata/icd11foundation-metrics.json
@@ -26,7 +26,7 @@
     "obj_property_count_incl": 0,
     "ontology_anno_count": 5,
     "ontology_iri": "http://purl.obolibrary.org/obo/mondo/sources/icd11foundation.owl",
-    "ontology_version_iri": "http://purl.obolibrary.org/obo/mondo/sources/2024-08-05/icd11foundation.owl",
+    "ontology_version_iri": "http://purl.obolibrary.org/obo/mondo/sources/2024-08-07/icd11foundation.owl",
     "owl2": true,
     "owl2_dl": true,
     "owl2_el": true,

diff --git a/src/ontology/metadata/ncit-metrics.json b/src/ontology/metadata/ncit-metrics.json
@@ -26,7 +26,7 @@
     "obj_property_count_incl": 0,
     "ontology_anno_count": 7,
     "ontology_iri": "http://purl.obolibrary.org/obo/mondo/sources/ncit.owl",
-    "ontology_version_iri": "http://purl.obolibrary.org/obo/mondo/sources/2024-08-05/ncit.owl",
+    "ontology_version_iri": "http://purl.obolibrary.org/obo/mondo/sources/2024-08-07/ncit.owl",
     "owl2": true,
     "owl2_dl": true,
     "owl2_el": false,

diff --git a/src/ontology/metadata/omim-metrics.json b/src/ontology/metadata/omim-metrics.json
@@ -26,7 +26,7 @@
     "obj_property_count_incl": 7,
     "ontology_anno_count": 1,
     "ontology_iri": "http://purl.obolibrary.org/obo/mondo/sources/omim.owl",
-    "ontology_version_iri": "http://purl.obolibrary.org/obo/mondo/sources/2024-08-05/omim.owl",
+    "ontology_version_iri": "http://purl.obolibrary.org/obo/mondo/sources/2024-08-07/omim.owl",
     "owl2": true,
     "owl2_dl": true,
     "owl2_el": true,

diff --git a/src/ontology/metadata/ordo-metrics.json b/src/ontology/metadata/ordo-metrics.json
@@ -26,7 +26,7 @@
     "obj_property_count_incl": 4,
     "ontology_anno_count": 12,
     "ontology_iri": "http://purl.obolibrary.org/obo/mondo/sources/ordo.owl",
-    "ontology_version_iri": "http://purl.obolibrary.org/obo/mondo/sources/2024-08-05/ordo.owl",
+    "ontology_version_iri": "http://purl.obolibrary.org/obo/mondo/sources/2024-08-07/ordo.owl",
     "owl2": true,
     "owl2_dl": true,
     "owl2_el": true,