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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/2024-08-13/doid.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-09-06/doid.owl
 
 ### Entities and axioms
 
 | Metric | Value |
 | ------ | ----- |
 | Annotation properties | 27 |
-| Axioms | 129102 |
-| Logical axioms | 16223 |
-| Classes | 13160 |
+| Axioms | 129444 |
+| Logical axioms | 16297 |
+| Classes | 13204 |
 | Object properties | 0 |
 | Data properties | 0 |
 | Individuals | 0 |
@@ -32,11 +32,11 @@
 
 | Metric | Value |
 | ------ | ----- |
-| AnnotationAssertion | 99692 |
+| AnnotationAssertion | 99916 |
 | SubAnnotationPropertyOf | 1 |
 | DisjointClasses | 26 |
-| Declaration | 13186 |
-| SubClassOf | 16197 |
+| Declaration | 13230 |
+| SubClassOf | 16271 |
 
 
 #### Entity namespaces: axiom counts by namespace
@@ -45,8 +45,8 @@
 | ------ | ----- |
 | oboInOwl | 12 |
 | owl | 2 |
-| DOID | 11614 |
-| HP | 118 |
+| DOID | 11646 |
+| HP | 114 |
 | xsd | 1 |
 | CL | 62 |
 | skos | 5 |
@@ -59,7 +59,7 @@
 | rdf | 1 |
 | CHEBI | 90 |
 | IAO | 2 |
-| UBERON | 394 |
+| UBERON | 410 |
 | SO | 17 |
 | obo | 191 |
 | GENO | 10 |
@@ -70,7 +70,7 @@
 
 | Metric | Value |
 | ------ | ----- |
-| Class | 45766 |
+| Class | 45958 |
 
 
 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/2024-08-13/gard.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-09-06/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/2024-08-13/icd10cm.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-09-06/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/2024-08-13/icd10who.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-09-06/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/2024-08-13/icd11foundation.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-09-06/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/2024-08-13/ncit.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-09-06/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/2024-08-13/omim.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-09-06/omim.owl
 
 ### Entities and axioms
 
 | Metric | Value |
 | ------ | ----- |
 | Annotation properties | 19 |
-| Axioms | 347317 |
-| Logical axioms | 22779 |
-| Classes | 19534 |
+| Axioms | 354395 |
+| Logical axioms | 26211 |
+| Classes | 22954 |
 | Object properties | 7 |
 | Data properties | 0 |
 | Individuals | 0 |
@@ -32,17 +32,17 @@
 
 | Metric | Value |
 | ------ | ----- |
-| AnnotationAssertion | 304981 |
+| AnnotationAssertion | 305207 |
 | SubAnnotationPropertyOf | 1 |
-| Declaration | 19556 |
-| SubClassOf | 22779 |
+| Declaration | 22976 |
+| SubClassOf | 26211 |
 
 
 #### Entity namespaces: axiom counts by namespace
 
 | Metric | Value |
 | ------ | ----- |
-| prefix_unknown | 18092 |
+| prefix_unknown | 21512 |
 | oboInOwl | 4 |
 | owl | 2 |
 | xsd | 1 |
@@ -61,8 +61,8 @@
 
 | Metric | Value |
 | ------ | ----- |
-| Class | 65082 |
-| ObjectSomeValuesFrom | 17831 |
+| Class | 75366 |
+| ObjectSomeValuesFrom | 21258 |
 
 
 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/2024-08-13/ordo.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-09-06/ordo.owl
 
 ### Entities and axioms
 

diff --git a/docs/reports/mapped_deprecated.md b/docs/reports/mapped_deprecated.md
@@ -2,12 +2,12 @@
 | Ontology                                                  |   Tot deprecated in Mondo |
 |:----------------------------------------------------------|--------------------------:|
 | [NCIT](./mapped_deprecated_ncit.md)                       |                         5 |
-| [OMIM](./mapped_deprecated_omim.md)                       |                        44 |
+| [OMIM](./mapped_deprecated_omim.md)                       |                        42 |
+| [DOID](./mapped_deprecated_doid.md)                       |                         3 |
 | [ORDO](./mapped_deprecated_ordo.md)                       |                       167 |
 | [GARD](./mapped_deprecated_gard.md)                       |                         0 |
 | [ICD11FOUNDATION](./mapped_deprecated_icd11foundation.md) |                         0 |
 | [ICD10CM](./mapped_deprecated_icd10cm.md)                 |                         0 |
-| [DOID](./mapped_deprecated_doid.md)                       |                         0 |
 | [ICD10WHO](./mapped_deprecated_icd10who.md)               |                         0 |
 
 `Ontology`: Name of ontology    

diff --git a/docs/reports/mapped_deprecated_doid.md b/docs/reports/mapped_deprecated_doid.md
@@ -2,6 +2,9 @@
 [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:0010542 | DOID:0081164         | MONDO:equivalentObsolete |
+| MONDO:0011893 | DOID:0110578         | MONDO:equivalentObsolete |
+| MONDO:0015701 | DOID:0060015         | MONDO:equivalentObsolete |
diff --git a/docs/reports/mapped_deprecated_omim.md b/docs/reports/mapped_deprecated_omim.md
@@ -16,7 +16,6 @@
 | MONDO:0008126 | OMIM:164891          | MONDO:equivalentObsolete |
 | MONDO:0008204 | OMIM:168850          | MONDO:equivalentObsolete |
 | MONDO:0008415 | OMIM:181515          | MONDO:equivalentObsolete |
-| MONDO:0009489 | OMIM:244850          | MONDO:equivalentObsolete |
 | MONDO:0009535 | OMIM:247440          | MONDO:equivalentObsolete |
 | MONDO:0009654 | OMIM:252700          | MONDO:equivalentObsolete |
 | MONDO:0010045 | OMIM:270710          | MONDO:equivalentObsolete |
@@ -33,7 +32,6 @@
 | MONDO:0010859 | OMIM:600309          | MONDO:equivalentObsolete |
 | MONDO:0011111 | OMIM:601563          | MONDO:equivalentObsolete |
 | MONDO:0011543 | OMIM:605365          | MONDO:equivalentObsolete |
-| MONDO:0011893 | OMIM:607683          | MONDO:equivalentObsolete |
 | MONDO:0011910 | OMIM:607801          | MONDO:equivalentObsolete |
 | MONDO:0012461 | OMIM:610269          | MONDO:equivalentObsolete |
 | MONDO:0012560 | OMIM:610799          | MONDO:equivalentObsolete |

diff --git a/docs/reports/migrate.md b/docs/reports/migrate.md
@@ -2,13 +2,13 @@
 | Ontology                                        | Tot   |
 |:------------------------------------------------|:------|
 | [GARD](./migrate_gard.md)                       | 9,370 |
-| [ORDO](./migrate_ordo.md)                       | 84    |
-| [DOID](./migrate_doid.md)                       | 47    |
+| [OMIM](./migrate_omim.md)                       | 6     |
+| [DOID](./migrate_doid.md)                       | 53    |
 | [ICD11FOUNDATION](./migrate_icd11foundation.md) | 4,594 |
+| [ORDO](./migrate_ordo.md)                       | 22    |
 | [NCIT](./migrate_ncit.md)                       | 2,209 |
 | [ICD10WHO](./migrate_icd10who.md)               | 119   |
 | [ICD10CM](./migrate_icd10cm.md)                 | 1,892 |
-| [OMIM](./migrate_omim.md)                       | 1     |
 
 ### Codebook
 `Ontology`: Name of ontology