Merge pull request #548 from monarch-initiative/icd11-branches

Update ICD11 relevant SPARQL query to exclude classes in the Extension Code branch
monarch-initiative · May 29, 2024 · 33b18ae · 33b18ae
2 parents cc7d392 + 5bce47d
commit 33b18ae
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diff --git a/docs/metrics/doid.md b/docs/metrics/doid.md
@@ -2,14 +2,14 @@
 
 **IRI:** http://purl.obolibrary.org/obo/mondo/sources/doid.owl
 
-**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-05-01/doid.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-05-28/doid.owl
 
 ### Entities and axioms
 
 | Metric | Value |
 | ------ | ----- |
 | Annotation properties | 27 |
-| Axioms | 115964 |
+| Axioms | 115971 |
 | Logical axioms | 16110 |
 | Classes | 13099 |
 | Object properties | 2 |
@@ -32,7 +32,7 @@
 
 | Metric | Value |
 | ------ | ----- |
-| AnnotationAssertion | 86726 |
+| AnnotationAssertion | 86733 |
 | SubAnnotationPropertyOf | 1 |
 | DisjointClasses | 26 |
 | Declaration | 13127 |

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/2024-05-01/gard.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-05-28/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/2024-05-01/icd10cm.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-05-28/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/2024-05-01/icd10who.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-05-28/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/2024-05-01/icd11foundation.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-05-28/icd11foundation.owl
 
 ### Entities and axioms
 
 | Metric | Value |
 | ------ | ----- |
 | Annotation properties | 12 |
-| Axioms | 367211 |
-| Logical axioms | 87706 |
-| Classes | 87537 |
+| Axioms | 329926 |
+| Logical axioms | 65410 |
+| Classes | 70045 |
 | Object properties | 0 |
 | Data properties | 0 |
 | Individuals | 0 |
@@ -32,17 +32,17 @@
 
 | Metric | Value |
 | ------ | ----- |
-| AnnotationAssertion | 191956 |
+| AnnotationAssertion | 194459 |
 | SubAnnotationPropertyOf | 1 |
-| Declaration | 87548 |
-| SubClassOf | 87706 |
+| Declaration | 70056 |
+| SubClassOf | 65410 |
 
 
 #### Entity namespaces: axiom counts by namespace
 
 | Metric | Value |
 | ------ | ----- |
-| prefix_unknown | 87539 |
+| prefix_unknown | 70047 |
 | oboInOwl | 3 |
 | owl | 2 |
 | rdf | 1 |
@@ -57,7 +57,7 @@
 
 | Metric | Value |
 | ------ | ----- |
-| Class | 262949 |
+| Class | 200865 |
 
 
 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
@@ -2,16 +2,16 @@
 
 **IRI:** http://purl.obolibrary.org/obo/mondo/sources/ncit.owl
 
-**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-05-01/ncit.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-05-28/ncit.owl
 
 ### Entities and axioms
 
 | Metric | Value |
 | ------ | ----- |
 | Annotation properties | 12 |
-| Axioms | 612685 |
-| Logical axioms | 32780 |
-| Classes | 15628 |
+| Axioms | 623834 |
+| Logical axioms | 33655 |
+| Classes | 15971 |
 | Object properties | 0 |
 | Data properties | 0 |
 | Individuals | 0 |
@@ -32,20 +32,20 @@
 
 | Metric | Value |
 | ------ | ----- |
-| AnnotationAssertion | 564246 |
-| EquivalentClasses | 6027 |
+| AnnotationAssertion | 574177 |
+| EquivalentClasses | 6260 |
 | DatatypeDefinition | 19 |
 | AnnotationPropertyRangeOf | 1 |
-| Declaration | 15658 |
-| SubClassOf | 26734 |
+| Declaration | 16001 |
+| SubClassOf | 27376 |
 
 
 #### Entity namespaces: axiom counts by namespace
 
 | Metric | Value |
 | ------ | ----- |
 | prefix_unknown | 1 |
-| NCIT | 15650 |
+| NCIT | 15993 |
 | oboInOwl | 3 |
 | owl | 2 |
 | rdf | 1 |
@@ -59,8 +59,8 @@
 
 | Metric | Value |
 | ------ | ----- |
-| Class | 88896 |
-| ObjectIntersectionOf | 6027 |
+| Class | 91288 |
+| ObjectIntersectionOf | 6260 |
 
 
 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/2024-05-01/omim.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-05-28/omim.owl
 
 ### Entities and axioms
 
 | Metric | Value |
 | ------ | ----- |
 | Annotation properties | 18 |
-| Axioms | 345588 |
-| Logical axioms | 22689 |
-| Classes | 19482 |
+| Axioms | 346016 |
+| Logical axioms | 22718 |
+| Classes | 19502 |
 | Object properties | 7 |
 | Data properties | 0 |
 | Individuals | 0 |
@@ -32,17 +32,17 @@
 
 | Metric | Value |
 | ------ | ----- |
-| AnnotationAssertion | 303395 |
+| AnnotationAssertion | 303774 |
 | SubAnnotationPropertyOf | 1 |
-| Declaration | 19503 |
-| SubClassOf | 22689 |
+| Declaration | 19523 |
+| SubClassOf | 22718 |
 
 
 #### Entity namespaces: axiom counts by namespace
 
 | Metric | Value |
 | ------ | ----- |
-| prefix_unknown | 18036 |
+| prefix_unknown | 18056 |
 | oboInOwl | 4 |
 | owl | 2 |
 | xsd | 1 |
@@ -61,8 +61,8 @@
 
 | Metric | Value |
 | ------ | ----- |
-| Class | 64850 |
-| ObjectSomeValuesFrom | 17792 |
+| Class | 64928 |
+| ObjectSomeValuesFrom | 17803 |
 
 
 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/2024-05-01/ordo.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-05-28/ordo.owl
 
 ### Entities and axioms
 

diff --git a/docs/reports/mapped_deprecated.md b/docs/reports/mapped_deprecated.md
@@ -2,9 +2,9 @@
 | Ontology                                                  |   Tot deprecated in Mondo |
 |:----------------------------------------------------------|--------------------------:|
 | [DOID](./mapped_deprecated_doid.md)                       |                         5 |
-| [OMIM](./mapped_deprecated_omim.md)                       |                        45 |
+| [OMIM](./mapped_deprecated_omim.md)                       |                        47 |
 | [ORDO](./mapped_deprecated_ordo.md)                       |                       225 |
-| [NCIT](./mapped_deprecated_ncit.md)                       |                        12 |
+| [NCIT](./mapped_deprecated_ncit.md)                       |                        22 |
 | [GARD](./mapped_deprecated_gard.md)                       |                         0 |
 | [ICD11FOUNDATION](./mapped_deprecated_icd11foundation.md) |                         0 |
 | [ICD10CM](./mapped_deprecated_icd10cm.md)                 |                         0 |

diff --git a/docs/reports/mapped_deprecated_ncit.md b/docs/reports/mapped_deprecated_ncit.md
@@ -6,13 +6,23 @@
 |:--------------|:---------------------|:-------------------------|
 | ID            | A oboInOwl:hasDbXref | >A oboInOwl:source       |
 | MONDO:0002063 | NCIT:C6977           | MONDO:equivalentObsolete |
+| MONDO:0002938 | NCIT:C66903          | MONDO:equivalentObsolete |
+| MONDO:0003222 | NCIT:C5504           | MONDO:equivalentObsolete |
+| MONDO:0003450 | NCIT:C4173           | MONDO:equivalentObsolete |
 | MONDO:0003998 | NCIT:C40257          | MONDO:equivalentObsolete |
+| MONDO:0004141 | NCIT:C9499           | 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:0005104 | NCIT:C9419           | MONDO:equivalentObsolete |
 | MONDO:0005362 | NCIT:C34801          | MONDO:equivalentObsolete |
+| MONDO:0005369 | NCIT:C2915           | MONDO:equivalentObsolete |
+| MONDO:0006475 | NCIT:C27892          | MONDO:equivalentObsolete |
+| MONDO:0013171 | NCIT:C3963           | MONDO:equivalentObsolete |
 | MONDO:0015040 | NCIT:C7167           | MONDO:equivalentObsolete |
+| MONDO:0015540 | NCIT:C35439          | MONDO:equivalentObsolete |
+| MONDO:0016747 | NCIT:C5505           | MONDO:equivalentObsolete |
 | MONDO:0017308 | NCIT:C75007          | MONDO:equivalentObsolete |
 | MONDO:0020804 | NCIT:C7586           | MONDO:equivalentObsolete |
 | MONDO:0020805 | NCIT:C4743           | MONDO:equivalentObsolete |

diff --git a/docs/reports/mapped_deprecated_omim.md b/docs/reports/mapped_deprecated_omim.md
@@ -16,6 +16,8 @@
 | MONDO:0008126 | OMIM:164891          | MONDO:equivalentObsolete |
 | MONDO:0008204 | OMIM:168850          | MONDO:equivalentObsolete |
 | MONDO:0008415 | OMIM:181515          | MONDO:equivalentObsolete |
+| MONDO:0008873 | OMIM:210730          | MONDO:equivalentObsolete |
+| MONDO:0009455 | OMIM:242870          | MONDO:equivalentObsolete |
 | MONDO:0009535 | OMIM:247440          | MONDO:equivalentObsolete |
 | MONDO:0009586 | OMIM:249660          | MONDO:equivalentObsolete |
 | MONDO:0009654 | OMIM:252700          | 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)                       | 56     |
-| [NCIT](./migrate_ncit.md)                       | 2,176  |
+| [DOID](./migrate_doid.md)                       | 8      |
+| [NCIT](./migrate_ncit.md)                       | 2,209  |
+| [OMIM](./migrate_omim.md)                       | 13     |
+| [ICD11FOUNDATION](./migrate_icd11foundation.md) | 12,409 |
 | [ICD10WHO](./migrate_icd10who.md)               | 119    |
-| [ORDO](./migrate_ordo.md)                       | 11     |
-| [ICD11FOUNDATION](./migrate_icd11foundation.md) | 10,581 |
-| [OMIM](./migrate_omim.md)                       | 10     |
+| [ORDO](./migrate_ordo.md)                       | 10     |
 | [ICD10CM](./migrate_icd10cm.md)                 | 1,889  |
 
 ### Codebook