Merge branch 'main' into develop

monarch-initiative · Apr 11, 2024 · 9d97d73 · 9d97d73
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diff --git a/docs/external/nord.md b/docs/external/nord.md
@@ -8,7 +8,7 @@
 
 NORD provides three datatypes to us:
 
-* Cross-references to  NORD content
+* Cross-references to NORD content
 * Subset-declarations, which basically correspond to "what NORD considers a Rare Disease"
 * Preferred Names for certain diseases
 

diff --git a/docs/metrics/doid.md b/docs/metrics/doid.md
@@ -2,16 +2,16 @@
 
 **IRI:** http://purl.obolibrary.org/obo/mondo/sources/doid.owl
 
-**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-03-15/doid.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-04-07/doid.owl
 
 ### Entities and axioms
 
 | Metric | Value |
 | ------ | ----- |
 | Annotation properties | 27 |
-| Axioms | 114485 |
-| Logical axioms | 16033 |
-| Classes | 13057 |
+| Axioms | 114627 |
+| Logical axioms | 16084 |
+| Classes | 13084 |
 | Object properties | 2 |
 | Data properties | 0 |
 | Individuals | 0 |
@@ -32,11 +32,11 @@
 
 | Metric | Value |
 | ------ | ----- |
-| AnnotationAssertion | 85367 |
+| AnnotationAssertion | 85431 |
 | SubAnnotationPropertyOf | 1 |
 | DisjointClasses | 26 |
-| Declaration | 13084 |
-| SubClassOf | 16007 |
+| Declaration | 13111 |
+| SubClassOf | 16058 |
 
 
 #### Entity namespaces: axiom counts by namespace
@@ -45,8 +45,8 @@
 | ------ | ----- |
 | oboInOwl | 12 |
 | owl | 2 |
-| DOID | 11513 |
-| HP | 117 |
+| DOID | 11539 |
+| HP | 118 |
 | xsd | 1 |
 | CL | 61 |
 | skos | 5 |
@@ -71,7 +71,7 @@
 
 | Metric | Value |
 | ------ | ----- |
-| Class | 45283 |
+| Class | 45412 |
 
 
 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/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/2024-03-15/gard.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-04-07/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/2024-03-15/icd10cm.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-04-07/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/2024-03-15/icd10who.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-04-07/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/2024-03-15/ncit.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-04-07/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/2024-03-15/omim.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-04-07/omim.owl
 
 ### Entities and axioms
 
 | Metric | Value |
 | ------ | ----- |
 | Annotation properties | 18 |
-| Axioms | 345057 |
-| Logical axioms | 22622 |
-| Classes | 19439 |
+| Axioms | 345359 |
+| Logical axioms | 22654 |
+| Classes | 19458 |
 | Object properties | 7 |
 | Data properties | 0 |
 | Individuals | 0 |
@@ -32,17 +32,17 @@
 
 | Metric | Value |
 | ------ | ----- |
-| AnnotationAssertion | 302974 |
+| AnnotationAssertion | 303225 |
 | SubAnnotationPropertyOf | 1 |
-| Declaration | 19460 |
-| SubClassOf | 22622 |
+| Declaration | 19479 |
+| SubClassOf | 22654 |
 
 
 #### Entity namespaces: axiom counts by namespace
 
 | Metric | Value |
 | ------ | ----- |
-| prefix_unknown | 17996 |
+| prefix_unknown | 18015 |
 | oboInOwl | 4 |
 | owl | 2 |
 | xsd | 1 |
@@ -61,8 +61,8 @@
 
 | Metric | Value |
 | ------ | ----- |
-| Class | 64675 |
-| ObjectSomeValuesFrom | 17745 |
+| Class | 64758 |
+| ObjectSomeValuesFrom | 17767 |
 
 
 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/2024-03-15/ordo.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-04-07/ordo.owl
 
 ### Entities and axioms
 

diff --git a/docs/reports/mapped_deprecated.md b/docs/reports/mapped_deprecated.md
@@ -1,9 +1,9 @@
 # Mapped deprecated terms
 | Ontology                                    |   Tot deprecated in Mondo |
 |:--------------------------------------------|--------------------------:|
-| [OMIM](./mapped_deprecated_omim.md)         |                        44 |
-| [DOID](./mapped_deprecated_doid.md)         |                         3 |
-| [ORDO](./mapped_deprecated_ordo.md)         |                       224 |
+| [OMIM](./mapped_deprecated_omim.md)         |                        46 |
+| [DOID](./mapped_deprecated_doid.md)         |                         4 |
+| [ORDO](./mapped_deprecated_ordo.md)         |                       225 |
 | [NCIT](./mapped_deprecated_ncit.md)         |                        12 |
 | [GARD](./mapped_deprecated_gard.md)         |                         0 |
 | [ICD10CM](./mapped_deprecated_icd10cm.md)   |                         0 |

diff --git a/docs/reports/mapped_deprecated_doid.md b/docs/reports/mapped_deprecated_doid.md
@@ -7,4 +7,5 @@
 | ID            | A oboInOwl:hasDbXref | >A oboInOwl:source       |
 | MONDO:0008024 | DOID:0111201         | MONDO:equivalentObsolete |
 | MONDO:0008025 | DOID:0111208         | MONDO:equivalentObsolete |
+| MONDO:0013127 | DOID:0050549         | MONDO:equivalentObsolete |
 | MONDO:0015353 | DOID:0111204         | MONDO:equivalentObsolete |
diff --git a/docs/reports/mapped_deprecated_omim.md b/docs/reports/mapped_deprecated_omim.md
@@ -25,6 +25,7 @@
 | MONDO:0010357 | OMIM:300551          | MONDO:equivalentObsolete |
 | MONDO:0010387 | OMIM:300640          | MONDO:equivalentObsolete |
 | MONDO:0010394 | OMIM:300660          | MONDO:equivalentObsolete |
+| MONDO:0010425 | OMIM:300778          | MONDO:equivalentObsolete |
 | MONDO:0010470 | OMIM:300881          | MONDO:equivalentObsolete |
 | MONDO:0010527 | OMIM:301590          | MONDO:equivalentObsolete |
 | MONDO:0010601 | OMIM:306500          | MONDO:equivalentObsolete |
@@ -33,6 +34,7 @@
 | MONDO:0010859 | OMIM:600309          | MONDO:equivalentObsolete |
 | MONDO:0011111 | OMIM:601563          | MONDO:equivalentObsolete |
 | MONDO:0011543 | OMIM:605365          | MONDO:equivalentObsolete |
+| MONDO:0011798 | OMIM:607236          | MONDO:equivalentObsolete |
 | MONDO:0011910 | OMIM:607801          | MONDO:equivalentObsolete |
 | MONDO:0012144 | OMIM:608890          | MONDO:equivalentObsolete |
 | MONDO:0012461 | OMIM:610269          | MONDO:equivalentObsolete |

diff --git a/docs/reports/mapped_deprecated_ordo.md b/docs/reports/mapped_deprecated_ordo.md
@@ -223,6 +223,7 @@
 | MONDO:0020742 | Orphanet:1317        | MONDO:equivalentObsolete |
 | MONDO:0020871 | Orphanet:623         | MONDO:equivalentObsolete |
 | MONDO:0021062 | Orphanet:306539      | MONDO:equivalentObsolete |
+| MONDO:0022414 | Orphanet:1526        | MONDO:equivalentObsolete |
 | MONDO:0022921 | Orphanet:2861        | MONDO:equivalentObsolete |
 | MONDO:0023072 | Orphanet:1939        | MONDO:equivalentObsolete |
 | MONDO:0034556 | Orphanet:493348      | MONDO:equivalentObsolete |

diff --git a/docs/reports/migrate.md b/docs/reports/migrate.md
@@ -2,10 +2,10 @@
 | Ontology                          | Tot   |
 |:----------------------------------|:------|
 | [GARD](./migrate_gard.md)         | 9,370 |
-| [ORDO](./migrate_ordo.md)         | 65    |
-| [OMIM](./migrate_omim.md)         | 24    |
+| [DOID](./migrate_doid.md)         | 40    |
+| [ORDO](./migrate_ordo.md)         | 21    |
 | [NCIT](./migrate_ncit.md)         | 2,176 |
-| [DOID](./migrate_doid.md)         | 198   |
+| [OMIM](./migrate_omim.md)         | 14    |
 | [ICD10WHO](./migrate_icd10who.md) | 119   |
 | [ICD10CM](./migrate_icd10cm.md)   | 1,889 |