Release 231107

monarch-initiative · Nov 7, 2023 · 0ae368f · 0ae368f
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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/2023-08-19/doid.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2023-11-07/doid.owl
 
 ### Entities and axioms
 
 | Metric | Value |
 | ------ | ----- |
 | Annotation properties | 25 |
-| Axioms | 112727 |
-| Logical axioms | 15803 |
-| Classes | 12899 |
+| Axioms | 113059 |
+| Logical axioms | 15835 |
+| Classes | 12928 |
 | Object properties | 2 |
 | Data properties | 0 |
 | Individuals | 0 |
@@ -32,10 +32,10 @@
 
 | Metric | Value |
 | ------ | ----- |
-| AnnotationAssertion | 84000 |
+| AnnotationAssertion | 84271 |
 | DisjointClasses | 26 |
-| Declaration | 12924 |
-| SubClassOf | 15777 |
+| Declaration | 12953 |
+| SubClassOf | 15809 |
 
 
 #### Entity namespaces: axiom counts by namespace
@@ -44,22 +44,22 @@
 | ------ | ----- |
 | oboInOwl | 11 |
 | owl | 2 |
-| DOID | 11369 |
-| HP | 109 |
+| DOID | 11388 |
+| HP | 115 |
 | xsd | 1 |
-| CL | 60 |
+| CL | 61 |
 | skos | 5 |
 | BFO | 2 |
 | rdfs | 2 |
 | FOODON | 24 |
-| NCBITaxon | 319 |
+| NCBITaxon | 320 |
 | TRANS | 13 |
 | SYMP | 306 |
 | dc11 | 2 |
 | rdf | 1 |
 | CHEBI | 90 |
 | IAO | 2 |
-| UBERON | 391 |
+| UBERON | 393 |
 | SO | 17 |
 | obo | 191 |
 | GENO | 10 |
@@ -70,7 +70,7 @@
 
 | Metric | Value |
 | ------ | ----- |
-| Class | 44665 |
+| Class | 44758 |
 
 
 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/2023-08-19/gard.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2023-11-07/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/2023-08-19/icd10cm.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2023-11-07/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/2023-08-19/icd10who.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2023-11-07/icd10who.owl
 
 ### Entities and axioms
 

diff --git a/docs/metrics/ncit.md b/docs/metrics/ncit.md
@@ -2,16 +2,16 @@
 
 **IRI:** http://purl.obolibrary.org/obo/mondo/sources/ncit.owl
 
-**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2023-08-19/ncit.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2023-11-07/ncit.owl
 
 ### Entities and axioms
 
 | Metric | Value |
 | ------ | ----- |
 | Annotation properties | 12 |
-| Axioms | 553075 |
-| Logical axioms | 30475 |
-| Classes | 14732 |
+| Axioms | 612683 |
+| Logical axioms | 32780 |
+| Classes | 15628 |
 | Object properties | 0 |
 | Data properties | 0 |
 | Individuals | 0 |
@@ -32,19 +32,19 @@
 
 | Metric | Value |
 | ------ | ----- |
-| AnnotationAssertion | 507838 |
-| EquivalentClasses | 5479 |
+| AnnotationAssertion | 564245 |
+| EquivalentClasses | 6027 |
 | DatatypeDefinition | 19 |
-| Declaration | 14762 |
-| SubClassOf | 24977 |
+| Declaration | 15658 |
+| SubClassOf | 26734 |
 
 
 #### Entity namespaces: axiom counts by namespace
 
 | Metric | Value |
 | ------ | ----- |
 | prefix_unknown | 1 |
-| NCIT | 14754 |
+| NCIT | 15650 |
 | oboInOwl | 3 |
 | owl | 2 |
 | rdf | 1 |
@@ -58,8 +58,8 @@
 
 | Metric | Value |
 | ------ | ----- |
-| Class | 82584 |
-| ObjectIntersectionOf | 5479 |
+| Class | 88896 |
+| ObjectIntersectionOf | 6027 |
 
 
 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/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/2023-08-20/omim.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2023-11-07/omim.owl
 
 ### Entities and axioms
 
 | Metric | Value |
 | ------ | ----- |
 | Annotation properties | 13 |
-| Axioms | 347642 |
-| Logical axioms | 36016 |
-| Classes | 31451 |
+| Axioms | 348742 |
+| Logical axioms | 36188 |
+| Classes | 31563 |
 | Object properties | 6 |
 | Data properties | 0 |
 | Individuals | 0 |
@@ -32,22 +32,22 @@
 
 | Metric | Value |
 | ------ | ----- |
-| AnnotationAssertion | 280160 |
-| Declaration | 31466 |
-| SubClassOf | 36016 |
+| AnnotationAssertion | 280976 |
+| Declaration | 31578 |
+| SubClassOf | 36188 |
 
 
 #### Entity namespaces: axiom counts by namespace
 
 | Metric | Value |
 | ------ | ----- |
-| prefix_unknown | 30006 |
+| prefix_unknown | 30117 |
 | oboInOwl | 3 |
 | owl | 2 |
 | xsd | 1 |
 | skos | 1 |
 | rdfs | 2 |
-| CHR | 1444 |
+| CHR | 1445 |
 | MONDO | 1 |
 | rdf | 1 |
 | IAO | 2 |
@@ -60,8 +60,8 @@
 
 | Metric | Value |
 | ------ | ----- |
-| Class | 103477 |
-| ObjectSomeValuesFrom | 14185 |
+| Class | 103933 |
+| ObjectSomeValuesFrom | 14240 |
 
 
 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/2023-08-20/ordo.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2023-11-07/ordo.owl
 
 ### Entities and axioms
 

diff --git a/docs/reports/mapped_deprecated.md b/docs/reports/mapped_deprecated.md
@@ -2,10 +2,10 @@
 | Ontology                                    |   Tot deprecated in Mondo |
 |:--------------------------------------------|--------------------------:|
 | [OMIM](./mapped_deprecated_omim.md)         |                        45 |
-| [NCIT](./mapped_deprecated_ncit.md)         |                         3 |
+| [DOID](./mapped_deprecated_doid.md)         |                         2 |
+| [NCIT](./mapped_deprecated_ncit.md)         |                        11 |
 | [ORDO](./mapped_deprecated_ordo.md)         |                         0 |
 | [ICD10CM](./mapped_deprecated_icd10cm.md)   |                         0 |
-| [DOID](./mapped_deprecated_doid.md)         |                         0 |
 | [ICD10WHO](./mapped_deprecated_icd10who.md) |                         0 |
 | [GARD](./mapped_deprecated_gard.md)         |                         0 |
 

diff --git a/docs/reports/mapped_deprecated_doid.md b/docs/reports/mapped_deprecated_doid.md
@@ -2,6 +2,8 @@
 [Interactive FlatGithub table](https://flatgithub.com/monarch-initiative/mondo-ingest?filename=src/ontology/reports/doid_mapped_deprecated_terms.robot.template.tsv)
 
 ### Mapped deprecated terms
-| mondo_id   | source_id            | source             |
-|:-----------|:---------------------|:-------------------|
-| ID         | A oboInOwl:hasDbXref | >A oboInOwl:source |
+| mondo_id      | source_id            | source                   |
+|:--------------|:---------------------|:-------------------------|
+| ID            | A oboInOwl:hasDbXref | >A oboInOwl:source       |
+| MONDO:0002546 | DOID:955             | MONDO:equivalentObsolete |
+| MONDO:0004398 | DOID:7922            | MONDO:equivalentObsolete |
diff --git a/docs/reports/mapped_deprecated_ncit.md b/docs/reports/mapped_deprecated_ncit.md
@@ -6,5 +6,13 @@
 |:--------------|:---------------------|:-------------------------|
 | ID            | A oboInOwl:hasDbXref | >A oboInOwl:source       |
 | MONDO:0003998 | NCIT:C40257          | MONDO:equivalentObsolete |
+| MONDO:0004204 | NCIT:C4462           | MONDO:equivalentObsolete |
+| MONDO:0004419 | NCIT:C39822          | MONDO:equivalentObsolete |
+| MONDO:0004819 | NCIT:C7150           | MONDO:equivalentObsolete |
+| MONDO:0005065 | NCIT:C3234           | MONDO:equivalentObsolete |
+| MONDO:0005362 | NCIT:C34801          | MONDO:equivalentObsolete |
+| MONDO:0015040 | NCIT:C7167           | MONDO:equivalentObsolete |
 | MONDO:0017308 | NCIT:C75007          | MONDO:equivalentObsolete |
+| MONDO:0020804 | NCIT:C7586           | MONDO:equivalentObsolete |
+| MONDO:0020805 | NCIT:C4743           | MONDO:equivalentObsolete |
 | MONDO:0020842 | NCIT:C8998           | MONDO:equivalentObsolete |
diff --git a/docs/reports/mapped_deprecated_omim.md b/docs/reports/mapped_deprecated_omim.md
@@ -31,7 +31,6 @@
 | MONDO:0010804 | OMIM:600048          | MONDO:equivalentObsolete |
 | MONDO:0010859 | OMIM:600309          | MONDO:equivalentObsolete |
 | MONDO:0011111 | OMIM:601563          | MONDO:equivalentObsolete |
-| MONDO:0011499 | OMIM:604916          | MONDO:equivalentObsolete |
 | MONDO:0011543 | OMIM:605365          | MONDO:equivalentObsolete |
 | MONDO:0011882 | OMIM:607655          | MONDO:equivalentObsolete |
 | MONDO:0011910 | OMIM:607801          | MONDO:equivalentObsolete |
@@ -41,6 +40,7 @@
 | MONDO:0013596 | OMIM:614157          | MONDO:equivalentObsolete |
 | MONDO:0013617 | OMIM:614192          | MONDO:equivalentObsolete |
 | MONDO:0013701 | OMIM:614339          | MONDO:equivalentObsolete |
+| MONDO:0014695 | OMIM:616568          | MONDO:equivalentObsolete |
 | MONDO:0014849 | OMIM:616958          | MONDO:equivalentObsolete |
 | MONDO:0017996 | OMIM:615057          | MONDO:equivalentObsolete |
 | MONDO:0018138 | OMIM:103470          | MONDO:equivalentObsolete |

diff --git a/docs/reports/migrate.md b/docs/reports/migrate.md
@@ -1,12 +1,12 @@
 # Migratable terms
 | Ontology                          | Tot   |
 |:----------------------------------|:------|
-| [DOID](./migrate_doid.md)         | 95    |
 | [GARD](./migrate_gard.md)         | 9,370 |
-| [NCIT](./migrate_ncit.md)         | 2,113 |
+| [ORDO](./migrate_ordo.md)         | 3     |
+| [OMIM](./migrate_omim.md)         | 204   |
+| [NCIT](./migrate_ncit.md)         | 2,161 |
 | [ICD10WHO](./migrate_icd10who.md) | 119   |
-| [ORDO](./migrate_ordo.md)         | 110   |
-| [OMIM](./migrate_omim.md)         | 101   |
+| [DOID](./migrate_doid.md)         | 113   |
 | [ICD10CM](./migrate_icd10cm.md)   | 1,889 |
 
 ### Codebook