Merge pull request #427 from monarch-initiative/r2024-02-04

release 2024-02-04
monarch-initiative · Feb 5, 2024 · 4da94a7 · 4da94a7
2 parents ac7d676 + c35f1c2
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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/2024-02-02/doid.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-02-04/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/2024-02-02/gard.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-02-04/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/2024-02-02/icd10cm.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-02-04/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/2024-02-02/icd10who.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-02-04/icd10who.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/2024-02-02/ncit.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-02-04/ncit.owl
 
 ### Entities and axioms
 

diff --git a/docs/metrics/omim.md b/docs/metrics/omim.md
@@ -2,16 +2,16 @@
 
 **IRI:** http://purl.obolibrary.org/obo/mondo/sources/omim.owl
 
-**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-02-02/omim.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-02-04/omim.owl
 
 ### Entities and axioms
 
 | Metric | Value |
 | ------ | ----- |
 | Annotation properties | 13 |
-| Axioms | 320435 |
-| Logical axioms | 19151 |
-| Classes | 19389 |
+| Axioms | 320535 |
+| Logical axioms | 19160 |
+| Classes | 19392 |
 | Object properties | 6 |
 | Data properties | 0 |
 | Individuals | 0 |
@@ -32,16 +32,16 @@
 
 | Metric | Value |
 | ------ | ----- |
-| AnnotationAssertion | 281880 |
-| Declaration | 19404 |
-| SubClassOf | 19151 |
+| AnnotationAssertion | 281968 |
+| Declaration | 19407 |
+| SubClassOf | 19160 |
 
 
 #### Entity namespaces: axiom counts by namespace
 
 | Metric | Value |
 | ------ | ----- |
-| prefix_unknown | 17943 |
+| prefix_unknown | 17946 |
 | MONDO | 1 |
 | oboInOwl | 3 |
 | owl | 2 |
@@ -59,8 +59,8 @@
 
 | Metric | Value |
 | ------ | ----- |
-| Class | 57685 |
-| ObjectSomeValuesFrom | 14302 |
+| Class | 57706 |
+| ObjectSomeValuesFrom | 14306 |
 
 
 More information about the source can be found [in the documentation](../sources.md). The raw data (ontology metrics) can be found [on GitHub](https://github.com/monarch-initiative/mondo-ingest/tree/main/src/ontology/metadata).

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/2024-02-02/ordo.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-02-04/ordo.owl
 
 ### Entities and axioms
 

diff --git a/docs/reports/mapped_deprecated.md b/docs/reports/mapped_deprecated.md
@@ -5,9 +5,9 @@
 | [DOID](./mapped_deprecated_doid.md)         |                         3 |
 | [ORDO](./mapped_deprecated_ordo.md)         |                       225 |
 | [NCIT](./mapped_deprecated_ncit.md)         |                        12 |
-| [GARD](./mapped_deprecated_gard.md)         |                         0 |
 | [ICD10CM](./mapped_deprecated_icd10cm.md)   |                         0 |
 | [ICD10WHO](./mapped_deprecated_icd10who.md) |                         0 |
+| [GARD](./mapped_deprecated_gard.md)         |                         0 |
 
 `Ontology`: Name of ontology    
 `Tot deprecated in Mondo`: Total terms that the ontology source itself has deprecated which have existing xrefs in Mondo

diff --git a/docs/reports/migrate.md b/docs/reports/migrate.md
@@ -3,10 +3,10 @@
 |:----------------------------------|:------|
 | [ORDO](./migrate_ordo.md)         | 97    |
 | [GARD](./migrate_gard.md)         | 9,370 |
+| [OMIM](./migrate_omim.md)         | 32    |
 | [NCIT](./migrate_ncit.md)         | 2,179 |
 | [DOID](./migrate_doid.md)         | 188   |
 | [ICD10WHO](./migrate_icd10who.md) | 119   |
-| [OMIM](./migrate_omim.md)         | 107   |
 | [ICD10CM](./migrate_icd10cm.md)   | 1,889 |
 
 ### Codebook

diff --git a/docs/reports/migrate_omim.md b/docs/reports/migrate_omim.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/507f869a-cd95-40b2-9636-aed115ae3b63
+# mapping_set_id: https://w3id.org/sssom/mappings/4a15181d-230f-4c48-9f33-2a5a80faec32
 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/db4b5640-7248-4db2-a2a2-f05262b8d103
+# mapping_set_id: https://w3id.org/sssom/mappings/b8f1cbe0-0a0c-4135-8cdd-4bd589a50a90
 
 
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/a58dd7c8-fc9f-43b9-b5db-504d4693a86a
+# mapping_set_id: https://w3id.org/sssom/mappings/a220a858-0168-4443-aa72-d961958866e0
 
 
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/0ce5f93a-6922-44f2-b5c9-7941df418456
+# mapping_set_id: https://w3id.org/sssom/mappings/e712f5c8-defd-4d42-8a0c-95f94f9e7b28
 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/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/2024-02-02/imports/omo_import.owl>
+<http://purl.obolibrary.org/obo/mondo-ingest/releases/2024-02-04/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 "2024-02-02")
+Annotation(owl:versionInfo "2024-02-04")
 
 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/2024-02-02/imports/ro_import.owl>
+<http://purl.obolibrary.org/obo/mondo-ingest/releases/2024-02-04/imports/ro_import.owl>
 Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/ro/releases/2023-08-18/ro.owl>)
-Annotation(owl:versionInfo "2024-02-02")
+Annotation(owl:versionInfo "2024-02-04")
 
 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
@@ -28,24 +28,24 @@
  * Number of mappings in [`unmapped_ordo_mondo`](mondo-only/unmapped_ordo_mondo.tsv): 903
  * Number of mappings in [`unmapped_ordo_mondo_exact`](mondo-only/unmapped_ordo_mondo.tsv): 903
 ## mondo_XXXXmatch_ontology
- * Number of mappings in [`mondo_exactmatch_icd10who`](split-mapping-set/mondo_exactmatch_icd10who.tsv): 1217
- * Number of mappings in [`mondo_closematch_icd10who`](split-mapping-set/mondo_closematch_icd10who.tsv): 147
- * Number of mappings in [`mondo_narrowmatch_icd10who`](split-mapping-set/mondo_narrowmatch_icd10who.tsv): 24
- * Number of mappings in [`mondo_broadmatch_icd10who`](split-mapping-set/mondo_broadmatch_icd10who.tsv): 31
- * Number of mappings in [`mondo_exactmatch_ncit`](split-mapping-set/mondo_exactmatch_ncit.tsv): 110
  * Number of mappings in [`mondo_closematch_ncit`](split-mapping-set/mondo_closematch_ncit.tsv): 72
  * Number of mappings in [`mondo_broadmatch_ncit`](split-mapping-set/mondo_broadmatch_ncit.tsv): 10
- * Number of mappings in [`mondo_exactmatch_doid`](split-mapping-set/mondo_exactmatch_doid.tsv): 242
- * Number of mappings in [`mondo_closematch_doid`](split-mapping-set/mondo_closematch_doid.tsv): 653
- * Number of mappings in [`mondo_narrowmatch_doid`](split-mapping-set/mondo_narrowmatch_doid.tsv): 13
- * Number of mappings in [`mondo_broadmatch_doid`](split-mapping-set/mondo_broadmatch_doid.tsv): 1
- * Number of mappings in [`mondo_exactmatch_omimps`](split-mapping-set/mondo_exactmatch_omimps.tsv): 14
- * Number of mappings in [`mondo_closematch_omimps`](split-mapping-set/mondo_closematch_omimps.tsv): 8
- * Number of mappings in [`mondo_exactmatch_orphanet`](split-mapping-set/mondo_exactmatch_orphanet.tsv): 929
+ * Number of mappings in [`mondo_exactmatch_ncit`](split-mapping-set/mondo_exactmatch_ncit.tsv): 110
+ * Number of mappings in [`mondo_closematch_omim`](split-mapping-set/mondo_closematch_omim.tsv): 75
+ * Number of mappings in [`mondo_exactmatch_omim`](split-mapping-set/mondo_exactmatch_omim.tsv): 132
  * Number of mappings in [`mondo_closematch_orphanet`](split-mapping-set/mondo_closematch_orphanet.tsv): 68
- * Number of mappings in [`mondo_exactmatch_icd10cm`](split-mapping-set/mondo_exactmatch_icd10cm.tsv): 1934
+ * Number of mappings in [`mondo_exactmatch_orphanet`](split-mapping-set/mondo_exactmatch_orphanet.tsv): 929
+ * Number of mappings in [`mondo_closematch_omimps`](split-mapping-set/mondo_closematch_omimps.tsv): 8
+ * Number of mappings in [`mondo_exactmatch_omimps`](split-mapping-set/mondo_exactmatch_omimps.tsv): 14
  * Number of mappings in [`mondo_closematch_icd10cm`](split-mapping-set/mondo_closematch_icd10cm.tsv): 6008
- * Number of mappings in [`mondo_narrowmatch_icd10cm`](split-mapping-set/mondo_narrowmatch_icd10cm.tsv): 57
  * Number of mappings in [`mondo_broadmatch_icd10cm`](split-mapping-set/mondo_broadmatch_icd10cm.tsv): 72
- * Number of mappings in [`mondo_exactmatch_omim`](split-mapping-set/mondo_exactmatch_omim.tsv): 132
- * Number of mappings in [`mondo_closematch_omim`](split-mapping-set/mondo_closematch_omim.tsv): 75
+ * Number of mappings in [`mondo_exactmatch_icd10cm`](split-mapping-set/mondo_exactmatch_icd10cm.tsv): 1934
+ * Number of mappings in [`mondo_narrowmatch_icd10cm`](split-mapping-set/mondo_narrowmatch_icd10cm.tsv): 57
+ * Number of mappings in [`mondo_closematch_doid`](split-mapping-set/mondo_closematch_doid.tsv): 653
+ * Number of mappings in [`mondo_broadmatch_doid`](split-mapping-set/mondo_broadmatch_doid.tsv): 1
+ * Number of mappings in [`mondo_exactmatch_doid`](split-mapping-set/mondo_exactmatch_doid.tsv): 242
+ * Number of mappings in [`mondo_narrowmatch_doid`](split-mapping-set/mondo_narrowmatch_doid.tsv): 13
+ * Number of mappings in [`mondo_closematch_icd10who`](split-mapping-set/mondo_closematch_icd10who.tsv): 147
+ * Number of mappings in [`mondo_broadmatch_icd10who`](split-mapping-set/mondo_broadmatch_icd10who.tsv): 31
+ * Number of mappings in [`mondo_exactmatch_icd10who`](split-mapping-set/mondo_exactmatch_icd10who.tsv): 1217
+ * Number of mappings in [`mondo_narrowmatch_icd10who`](split-mapping-set/mondo_narrowmatch_icd10who.tsv): 24