Merge pull request #506 from monarch-initiative/build-2024-05-01

Build 2024-05-01
monarch-initiative · May 1, 2024 · 5a54e99 · 5a54e99
2 parents adc2015 + 07cb6b3
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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/2024-04-19/doid.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-05-01/doid.owl
 
 ### Entities and axioms
 
 | Metric | Value |
 | ------ | ----- |
 | Annotation properties | 27 |
-| Axioms | 115826 |
-| Logical axioms | 16084 |
-| Classes | 13084 |
+| Axioms | 115964 |
+| Logical axioms | 16110 |
+| Classes | 13099 |
 | Object properties | 2 |
 | Data properties | 0 |
 | Individuals | 0 |
@@ -32,11 +32,11 @@
 
 | Metric | Value |
 | ------ | ----- |
-| AnnotationAssertion | 86629 |
+| AnnotationAssertion | 86726 |
 | SubAnnotationPropertyOf | 1 |
 | DisjointClasses | 26 |
-| Declaration | 13112 |
-| SubClassOf | 16058 |
+| Declaration | 13127 |
+| SubClassOf | 16084 |
 
 
 #### Entity namespaces: axiom counts by namespace
@@ -45,10 +45,10 @@
 | ------ | ----- |
 | oboInOwl | 12 |
 | owl | 2 |
-| DOID | 11539 |
+| DOID | 11552 |
 | HP | 118 |
 | xsd | 1 |
-| CL | 61 |
+| CL | 63 |
 | skos | 5 |
 | BFO | 2 |
 | rdfs | 2 |
@@ -71,7 +71,7 @@
 
 | Metric | Value |
 | ------ | ----- |
-| Class | 45412 |
+| Class | 45479 |
 
 
 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/2024-04-19/gard.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-05-01/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/2024-04-19/icd10cm.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-05-01/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/2024-04-19/icd10who.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-05-01/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/2024-04-19/icd11foundation.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-05-01/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/2024-04-19/ncit.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-05-01/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/2024-04-19/omim.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-05-01/omim.owl
 
 ### Entities and axioms
 
 | Metric | Value |
 | ------ | ----- |
 | Annotation properties | 18 |
-| Axioms | 345408 |
-| Logical axioms | 22664 |
-| Classes | 19465 |
+| Axioms | 345588 |
+| Logical axioms | 22689 |
+| Classes | 19482 |
 | Object properties | 7 |
 | Data properties | 0 |
 | Individuals | 0 |
@@ -32,23 +32,23 @@
 
 | Metric | Value |
 | ------ | ----- |
-| AnnotationAssertion | 303257 |
+| AnnotationAssertion | 303395 |
 | SubAnnotationPropertyOf | 1 |
-| Declaration | 19486 |
-| SubClassOf | 22664 |
+| Declaration | 19503 |
+| SubClassOf | 22689 |
 
 
 #### Entity namespaces: axiom counts by namespace
 
 | Metric | Value |
 | ------ | ----- |
-| prefix_unknown | 18022 |
+| prefix_unknown | 18036 |
 | oboInOwl | 4 |
 | owl | 2 |
 | xsd | 1 |
 | skos | 1 |
 | rdfs | 2 |
-| CHR | 1446 |
+| CHR | 1449 |
 | MONDO | 1 |
 | rdf | 1 |
 | IAO | 2 |
@@ -61,8 +61,8 @@
 
 | Metric | Value |
 | ------ | ----- |
-| Class | 64785 |
-| ObjectSomeValuesFrom | 17773 |
+| Class | 64850 |
+| ObjectSomeValuesFrom | 17792 |
 
 
 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/2024-04-19/ordo.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-05-01/ordo.owl
 
 ### Entities and axioms
 

diff --git a/docs/reports/mapped_deprecated.md b/docs/reports/mapped_deprecated.md
@@ -1,8 +1,8 @@
 # Mapped deprecated terms
 | Ontology                                                  |   Tot deprecated in Mondo |
 |:----------------------------------------------------------|--------------------------:|
-| [OMIM](./mapped_deprecated_omim.md)                       |                        46 |
-| [DOID](./mapped_deprecated_doid.md)                       |                         4 |
+| [DOID](./mapped_deprecated_doid.md)                       |                         5 |
+| [OMIM](./mapped_deprecated_omim.md)                       |                        45 |
 | [ORDO](./mapped_deprecated_ordo.md)                       |                       225 |
 | [NCIT](./mapped_deprecated_ncit.md)                       |                        12 |
 | [GARD](./mapped_deprecated_gard.md)                       |                         0 |

diff --git a/docs/reports/mapped_deprecated_doid.md b/docs/reports/mapped_deprecated_doid.md
@@ -5,6 +5,7 @@
 | mondo_id      | source_id            | source                   |
 |:--------------|:---------------------|:-------------------------|
 | ID            | A oboInOwl:hasDbXref | >A oboInOwl:source       |
+| MONDO:0001639 | DOID:13121           | 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/mapped_deprecated_omim.md b/docs/reports/mapped_deprecated_omim.md
@@ -25,7 +25,6 @@
 | 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 |

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)                       | 42     |
-| [ORDO](./migrate_ordo.md)                       | 26     |
-| [OMIM](./migrate_omim.md)                       | 24     |
+| [DOID](./migrate_doid.md)                       | 56     |
 | [NCIT](./migrate_ncit.md)                       | 2,176  |
 | [ICD10WHO](./migrate_icd10who.md)               | 119    |
+| [ORDO](./migrate_ordo.md)                       | 11     |
 | [ICD11FOUNDATION](./migrate_icd11foundation.md) | 10,581 |
+| [OMIM](./migrate_omim.md)                       | 10     |
 | [ICD10CM](./migrate_icd10cm.md)                 | 1,889  |
 
 ### Codebook