Merge pull request #782 from monarch-initiative/_main_data-build-2_10…

…Feb2025 Data build files following mondo release
monarch-initiative · Feb 17, 2025 · b70200b · b70200b
2 parents a73277c + 82f6b14
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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/2025-01-10/doid.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2025-02-11/doid.owl
 
 ### Entities and axioms
 
 | Metric | Value |
 | ------ | ----- |
-| Annotation properties | 28 |
-| Axioms | 134288 |
-| Logical axioms | 16444 |
-| Classes | 13297 |
+| Annotation properties | 29 |
+| Axioms | 134604 |
+| Logical axioms | 16498 |
+| Classes | 13354 |
 | Object properties | 0 |
 | Data properties | 0 |
 | Individuals | 0 |
@@ -32,11 +32,11 @@
 
 | Metric | Value |
 | ------ | ----- |
-| AnnotationAssertion | 104518 |
+| AnnotationAssertion | 104722 |
 | SubAnnotationPropertyOf | 2 |
 | DisjointClasses | 26 |
-| Declaration | 13324 |
-| SubClassOf | 16418 |
+| Declaration | 13382 |
+| SubClassOf | 16472 |
 
 
 #### Entity namespaces: axiom counts by namespace
@@ -45,7 +45,7 @@
 | ------ | ----- |
 | oboInOwl | 12 |
 | owl | 2 |
-| DOID | 11733 |
+| DOID | 11767 |
 | HP | 116 |
 | xsd | 1 |
 | CL | 61 |
@@ -56,13 +56,13 @@
 | TRANS | 13 |
 | SYMP | 306 |
 | OMO | 1 |
-| dc11 | 2 |
+| dc11 | 3 |
 | rdf | 1 |
 | CHEBI | 90 |
 | IAO | 2 |
 | UBERON | 414 |
 | SO | 18 |
-| obo | 191 |
+| obo | 214 |
 | GENO | 10 |
 | dc | 1 |
 
@@ -71,7 +71,7 @@
 
 | Metric | Value |
 | ------ | ----- |
-| Class | 46345 |
+| Class | 46510 |
 
 
 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/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/2025-01-10/icd10cm.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2025-02-11/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/2025-01-10/icd10who.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2025-02-11/icd10who.owl
 
 ### Entities and axioms
 

diff --git a/docs/metrics/icd11foundation.md b/docs/metrics/icd11foundation.md
@@ -2,16 +2,16 @@
 
 **IRI:** http://purl.obolibrary.org/obo/mondo/sources/icd11foundation.owl
 
-**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2025-01-10/icd11foundation.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2025-02-11/icd11foundation.owl
 
 ### Entities and axioms
 
 | Metric | Value |
 | ------ | ----- |
 | Annotation properties | 12 |
-| Axioms | 309765 |
-| Logical axioms | 65391 |
-| Classes | 57711 |
+| Axioms | 310944 |
+| Logical axioms | 65559 |
+| Classes | 57872 |
 | Object properties | 0 |
 | Data properties | 0 |
 | Individuals | 0 |
@@ -32,17 +32,17 @@
 
 | Metric | Value |
 | ------ | ----- |
-| AnnotationAssertion | 186651 |
+| AnnotationAssertion | 187501 |
 | SubAnnotationPropertyOf | 1 |
-| Declaration | 57722 |
-| SubClassOf | 65391 |
+| Declaration | 57883 |
+| SubClassOf | 65559 |
 
 
 #### Entity namespaces: axiom counts by namespace
 
 | Metric | Value |
 | ------ | ----- |
-| prefix_unknown | 57713 |
+| prefix_unknown | 57874 |
 | oboInOwl | 3 |
 | owl | 2 |
 | rdf | 1 |
@@ -57,7 +57,7 @@
 
 | Metric | Value |
 | ------ | ----- |
-| Class | 188493 |
+| Class | 188990 |
 
 
 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/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/2025-01-10/ncit.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2025-02-11/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/2025-01-10/omim.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2025-02-11/omim.owl
 
 ### Entities and axioms
 
 | Metric | Value |
 | ------ | ----- |
 | Annotation properties | 23 |
-| Axioms | 373394 |
-| Logical axioms | 28251 |
-| Classes | 23615 |
+| Axioms | 373793 |
+| Logical axioms | 28321 |
+| Classes | 23654 |
 | Object properties | 7 |
 | Data properties | 0 |
 | Individuals | 0 |
@@ -32,23 +32,23 @@
 
 | Metric | Value |
 | ------ | ----- |
-| AnnotationAssertion | 321500 |
+| AnnotationAssertion | 321790 |
 | SubAnnotationPropertyOf | 2 |
-| Declaration | 23641 |
-| SubClassOf | 28251 |
+| Declaration | 23680 |
+| SubClassOf | 28321 |
 
 
 #### Entity namespaces: axiom counts by namespace
 
 | Metric | Value |
 | ------ | ----- |
-| prefix_unknown | 22176 |
+| prefix_unknown | 22214 |
 | oboInOwl | 6 |
 | owl | 2 |
 | xsd | 1 |
 | skos | 1 |
 | rdfs | 2 |
-| CHR | 1442 |
+| CHR | 1443 |
 | OMO | 1 |
 | MONDO | 1 |
 | rdf | 1 |
@@ -62,8 +62,8 @@
 
 | Metric | Value |
 | ------ | ----- |
-| Class | 80112 |
-| ObjectSomeValuesFrom | 23268 |
+| Class | 80291 |
+| ObjectSomeValuesFrom | 23324 |
 
 
 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
@@ -2,14 +2,14 @@
 
 **IRI:** http://purl.obolibrary.org/obo/mondo/sources/ordo.owl
 
-**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2025-01-10/ordo.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2025-02-11/ordo.owl
 
 ### Entities and axioms
 
 | Metric | Value |
 | ------ | ----- |
-| Annotation properties | 16 |
-| Axioms | 228273 |
+| Annotation properties | 19 |
+| Axioms | 180845 |
 | Logical axioms | 43059 |
 | Classes | 15157 |
 | Object properties | 4 |
@@ -32,25 +32,26 @@
 
 | Metric | Value |
 | ------ | ----- |
-| AnnotationAssertion | 170039 |
+| AnnotationAssertion | 122608 |
 | SubAnnotationPropertyOf | 1 |
-| Declaration | 15174 |
+| Declaration | 15177 |
 | SubClassOf | 43059 |
 
 
 #### Entity namespaces: axiom counts by namespace
 
 | Metric | Value |
 | ------ | ----- |
-| dc11 | 1 |
 | prefix_unknown | 15157 |
 | oboInOwl | 6 |
 | owl | 2 |
-| rdf | 1 |
-| IAO | 1 |
 | xsd | 2 |
+| skos | 3 |
 | BFO | 1 |
 | rdfs | 2 |
+| dc11 | 1 |
+| rdf | 1 |
+| IAO | 1 |
 | RO | 3 |
 | obo | 1 |
 | dc | 3 |

diff --git a/docs/reports/mapped_deprecated.md b/docs/reports/mapped_deprecated.md
@@ -2,10 +2,10 @@
 | Ontology                                                  |   Tot deprecated in Mondo |
 |:----------------------------------------------------------|--------------------------:|
 | [NCIT](./mapped_deprecated_ncit.md)                       |                         5 |
-| [OMIM](./mapped_deprecated_omim.md)                       |                        45 |
+| [OMIM](./mapped_deprecated_omim.md)                       |                        44 |
+| [ICD11FOUNDATION](./mapped_deprecated_icd11foundation.md) |                         3 |
 | [ORDO](./mapped_deprecated_ordo.md)                       |                       171 |
 | [DOID](./mapped_deprecated_doid.md)                       |                         1 |
-| [ICD11FOUNDATION](./mapped_deprecated_icd11foundation.md) |                         0 |
 | [ICD10CM](./mapped_deprecated_icd10cm.md)                 |                         0 |
 | [ICD10WHO](./mapped_deprecated_icd10who.md)               |                         0 |
 

diff --git a/docs/reports/mapped_deprecated_icd11foundation.md b/docs/reports/mapped_deprecated_icd11foundation.md
@@ -2,6 +2,9 @@
 [Interactive FlatGithub table](https://flatgithub.com/monarch-initiative/mondo-ingest?filename=src/ontology/reports/icd11foundation_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:0000481 | icd11.foundation:632668568  | MONDO:equivalentObsolete |
+| MONDO:0015376 | icd11.foundation:1956658224 | MONDO:equivalentObsolete |
+| MONDO:0021512 | icd11.foundation:1583331018 | 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:0008868 | OMIM:210550          | MONDO:equivalentObsolete |
 | MONDO:0009455 | OMIM:242870          | MONDO:equivalentObsolete |
 | MONDO:0009535 | OMIM:247440          | MONDO:equivalentObsolete |
 | MONDO:0009654 | OMIM:252700          | MONDO:equivalentObsolete |

diff --git a/docs/reports/migrate.md b/docs/reports/migrate.md
@@ -1,11 +1,11 @@
 # Migratable terms
 | Ontology                                        | Tot   |
 |:------------------------------------------------|:------|
-| [DOID](./migrate_doid.md)                       | 94    |
+| [OMIM](./migrate_omim.md)                       | 63    |
 | [ORDO](./migrate_ordo.md)                       | 62    |
-| [OMIM](./migrate_omim.md)                       | 47    |
-| [ICD11FOUNDATION](./migrate_icd11foundation.md) | 4,593 |
-| [NCIT](./migrate_ncit.md)                       | 2,211 |
+| [ICD11FOUNDATION](./migrate_icd11foundation.md) | 4,587 |
+| [NCIT](./migrate_ncit.md)                       | 2,250 |
+| [DOID](./migrate_doid.md)                       | 128   |
 | [ICD10WHO](./migrate_icd10who.md)               | 119   |
 | [ICD10CM](./migrate_icd10cm.md)                 | 1,894 |