Exact synonym updates - build

monarch-initiative · Jul 3, 2024 · a8d3777 · a8d3777
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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/2024-06-22/doid.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-07-02/doid.owl
 
 ### Entities and axioms
 
 | Metric | Value |
 | ------ | ----- |
 | Annotation properties | 27 |
-| Axioms | 116206 |
-| Logical axioms | 16161 |
-| Classes | 13124 |
+| Axioms | 135174 |
+| Logical axioms | 16200 |
+| Classes | 13147 |
 | Object properties | 0 |
 | Data properties | 0 |
 | Individuals | 0 |
@@ -32,11 +32,11 @@
 
 | Metric | Value |
 | ------ | ----- |
-| AnnotationAssertion | 86894 |
+| AnnotationAssertion | 105800 |
 | SubAnnotationPropertyOf | 1 |
 | DisjointClasses | 26 |
-| Declaration | 13150 |
-| SubClassOf | 16135 |
+| Declaration | 13173 |
+| SubClassOf | 16174 |
 
 
 #### Entity namespaces: axiom counts by namespace
@@ -45,7 +45,7 @@
 | ------ | ----- |
 | oboInOwl | 12 |
 | owl | 2 |
-| DOID | 11577 |
+| DOID | 11600 |
 | HP | 118 |
 | xsd | 1 |
 | CL | 63 |
@@ -70,7 +70,7 @@
 
 | Metric | Value |
 | ------ | ----- |
-| Class | 45606 |
+| Class | 45707 |
 
 
 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/2024-06-22/gard.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-07-02/gard.owl
 
 ### Entities and axioms
 

diff --git a/docs/metrics/icd10cm.md b/docs/metrics/icd10cm.md
@@ -2,14 +2,14 @@
 
 **IRI:** http://purl.obolibrary.org/obo/mondo/sources/icd10cm.owl
 
-**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-22/icd10cm.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-07-02/icd10cm.owl
 
 ### Entities and axioms
 
 | Metric | Value |
 | ------ | ----- |
 | Annotation properties | 7 |
-| Axioms | 302783 |
+| Axioms | 398757 |
 | Logical axioms | 95846 |
 | Classes | 95848 |
 | Object properties | 0 |
@@ -32,7 +32,7 @@
 
 | Metric | Value |
 | ------ | ----- |
-| AnnotationAssertion | 111084 |
+| AnnotationAssertion | 207058 |
 | SubAnnotationPropertyOf | 1 |
 | Declaration | 95852 |
 | SubClassOf | 95846 |

diff --git a/docs/metrics/icd10who.md b/docs/metrics/icd10who.md
@@ -2,14 +2,14 @@
 
 **IRI:** http://purl.obolibrary.org/obo/mondo/sources/icd10who.owl
 
-**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-22/icd10who.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-07-02/icd10who.owl
 
 ### Entities and axioms
 
 | Metric | Value |
 | ------ | ----- |
 | Annotation properties | 8 |
-| Axioms | 50466 |
+| Axioms | 63008 |
 | Logical axioms | 12542 |
 | Classes | 12543 |
 | Object properties | 0 |
@@ -32,7 +32,7 @@
 
 | Metric | Value |
 | ------ | ----- |
-| AnnotationAssertion | 25377 |
+| AnnotationAssertion | 37919 |
 | SubAnnotationPropertyOf | 1 |
 | Declaration | 12546 |
 | SubClassOf | 12542 |

diff --git a/docs/metrics/icd11foundation.md b/docs/metrics/icd11foundation.md
@@ -2,14 +2,14 @@
 
 **IRI:** http://purl.obolibrary.org/obo/mondo/sources/icd11foundation.owl
 
-**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-22/icd11foundation.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-07-02/icd11foundation.owl
 
 ### Entities and axioms
 
 | Metric | Value |
 | ------ | ----- |
 | Annotation properties | 12 |
-| Axioms | 329926 |
+| Axioms | 430290 |
 | Logical axioms | 65410 |
 | Classes | 70045 |
 | Object properties | 0 |
@@ -32,7 +32,7 @@
 
 | Metric | Value |
 | ------ | ----- |
-| AnnotationAssertion | 194459 |
+| AnnotationAssertion | 294823 |
 | SubAnnotationPropertyOf | 1 |
 | Declaration | 70056 |
 | SubClassOf | 65410 |

diff --git a/docs/metrics/ncit.md b/docs/metrics/ncit.md
@@ -2,14 +2,14 @@
 
 **IRI:** http://purl.obolibrary.org/obo/mondo/sources/ncit.owl
 
-**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-22/ncit.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-07-02/ncit.owl
 
 ### Entities and axioms
 
 | Metric | Value |
 | ------ | ----- |
 | Annotation properties | 12 |
-| Axioms | 623834 |
+| Axioms | 623940 |
 | Logical axioms | 33655 |
 | Classes | 15971 |
 | Object properties | 0 |
@@ -32,7 +32,7 @@
 
 | Metric | Value |
 | ------ | ----- |
-| AnnotationAssertion | 574177 |
+| AnnotationAssertion | 574283 |
 | EquivalentClasses | 6260 |
 | DatatypeDefinition | 19 |
 | AnnotationPropertyRangeOf | 1 |

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/2024-06-22/omim.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-07-02/omim.owl
 
 ### Entities and axioms
 
 | Metric | Value |
 | ------ | ----- |
 | Annotation properties | 18 |
-| Axioms | 346174 |
-| Logical axioms | 22747 |
-| Classes | 19514 |
+| Axioms | 346898 |
+| Logical axioms | 22738 |
+| Classes | 19512 |
 | Object properties | 7 |
 | Data properties | 0 |
 | Individuals | 0 |
@@ -32,23 +32,23 @@
 
 | Metric | Value |
 | ------ | ----- |
-| AnnotationAssertion | 303891 |
+| AnnotationAssertion | 304626 |
 | SubAnnotationPropertyOf | 1 |
-| Declaration | 19535 |
-| SubClassOf | 22747 |
+| Declaration | 19533 |
+| SubClassOf | 22738 |
 
 
 #### Entity namespaces: axiom counts by namespace
 
 | Metric | Value |
 | ------ | ----- |
-| prefix_unknown | 18068 |
+| prefix_unknown | 18069 |
 | oboInOwl | 4 |
 | owl | 2 |
 | xsd | 1 |
 | skos | 1 |
 | rdfs | 2 |
-| CHR | 1449 |
+| CHR | 1446 |
 | MONDO | 1 |
 | rdf | 1 |
 | IAO | 2 |
@@ -61,8 +61,8 @@
 
 | Metric | Value |
 | ------ | ----- |
-| Class | 64998 |
-| ObjectSomeValuesFrom | 17818 |
+| Class | 64978 |
+| ObjectSomeValuesFrom | 17808 |
 
 
 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/2024-06-22/ordo.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-07-02/ordo.owl
 
 ### Entities and axioms
 
 | Metric | Value |
 | ------ | ----- |
 | Annotation properties | 16 |
-| Axioms | 206309 |
+| Axioms | 221716 |
 | Logical axioms | 42481 |
 | Classes | 14917 |
 | Object properties | 4 |
@@ -32,7 +32,7 @@
 
 | Metric | Value |
 | ------ | ----- |
-| AnnotationAssertion | 148893 |
+| AnnotationAssertion | 164300 |
 | SubAnnotationPropertyOf | 1 |
 | Declaration | 14934 |
 | SubClassOf | 42481 |

diff --git a/docs/reports/mapped_deprecated.md b/docs/reports/mapped_deprecated.md
@@ -1,7 +1,7 @@
 # Mapped deprecated terms
 | Ontology                                                  |   Tot deprecated in Mondo |
 |:----------------------------------------------------------|--------------------------:|
-| [DOID](./mapped_deprecated_doid.md)                       |                         5 |
+| [DOID](./mapped_deprecated_doid.md)                       |                         6 |
 | [OMIM](./mapped_deprecated_omim.md)                       |                        46 |
 | [ORDO](./mapped_deprecated_ordo.md)                       |                       226 |
 | [NCIT](./mapped_deprecated_ncit.md)                       |                        22 |

diff --git a/docs/reports/mapped_deprecated_doid.md b/docs/reports/mapped_deprecated_doid.md
@@ -6,6 +6,7 @@
 |:--------------|:---------------------|:-------------------------|
 | ID            | A oboInOwl:hasDbXref | >A oboInOwl:source       |
 | MONDO:0001639 | DOID:13121           | MONDO:equivalentObsolete |
+| MONDO:0006886 | DOID:3968            | MONDO:equivalentObsolete |
 | MONDO:0008024 | DOID:0111201         | MONDO:equivalentObsolete |
 | MONDO:0008025 | DOID:0111208         | MONDO:equivalentObsolete |
 | MONDO:0013127 | DOID:0050549         | MONDO:equivalentObsolete |

diff --git a/docs/reports/migrate.md b/docs/reports/migrate.md
@@ -2,12 +2,12 @@
 | Ontology                                        | Tot    |
 |:------------------------------------------------|:-------|
 | [GARD](./migrate_gard.md)                       | 9,370  |
-| [DOID](./migrate_doid.md)                       | 34     |
+| [DOID](./migrate_doid.md)                       | 33     |
 | [NCIT](./migrate_ncit.md)                       | 2,209  |
+| [OMIM](./migrate_omim.md)                       | 2      |
 | [ICD11FOUNDATION](./migrate_icd11foundation.md) | 12,409 |
 | [ICD10WHO](./migrate_icd10who.md)               | 119    |
-| [ICD10CM](./migrate_icd10cm.md)                 | 1,889  |
-| [OMIM](./migrate_omim.md)                       | 0      |
+| [ICD10CM](./migrate_icd10cm.md)                 | 1,892  |
 | [ORDO](./migrate_ordo.md)                       | 0      |
 
 ### Codebook