Merge pull request #468 from monarch-initiative/odk15_datarelease

Update data release
monarch-initiative · Mar 15, 2024 · 0cb6fe7 · 0cb6fe7
2 parents 5546363 + dc7e411
commit 0cb6fe7
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diff --git a/.gitignore b/.gitignore
@@ -114,3 +114,4 @@ src/scripts/dataframes/*
 src/ontology/reports/gard.subclass.added-obsolete.robot.tsv
 src/ontology/reports/gard.subclass.added.robot.tsv
 src/ontology/reports/gard.subclass.confirmed.robot.tsv
+src/ontology/reports/basic-report.tsv
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/2024-02-09/doid.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-03-07/doid.owl
 
 ### Entities and axioms
 
 | Metric | Value |
 | ------ | ----- |
-| Annotation properties | 25 |
-| Axioms | 114236 |
-| Logical axioms | 16021 |
-| Classes | 13047 |
+| Annotation properties | 27 |
+| Axioms | 114485 |
+| Logical axioms | 16033 |
+| Classes | 13057 |
 | Object properties | 2 |
 | Data properties | 0 |
 | Individuals | 0 |
@@ -32,19 +32,20 @@
 
 | Metric | Value |
 | ------ | ----- |
-| AnnotationAssertion | 85143 |
+| AnnotationAssertion | 85367 |
+| SubAnnotationPropertyOf | 1 |
 | DisjointClasses | 26 |
-| Declaration | 13072 |
-| SubClassOf | 15995 |
+| Declaration | 13084 |
+| SubClassOf | 16007 |
 
 
 #### Entity namespaces: axiom counts by namespace
 
 | Metric | Value |
 | ------ | ----- |
-| oboInOwl | 11 |
+| oboInOwl | 12 |
 | owl | 2 |
-| DOID | 11503 |
+| DOID | 11513 |
 | HP | 117 |
 | xsd | 1 |
 | CL | 61 |
@@ -61,7 +62,7 @@
 | IAO | 2 |
 | UBERON | 394 |
 | SO | 17 |
-| obo | 190 |
+| obo | 191 |
 | GENO | 10 |
 | dc | 1 |
 
@@ -70,7 +71,7 @@
 
 | Metric | Value |
 | ------ | ----- |
-| Class | 45249 |
+| Class | 45283 |
 
 
 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/2024-02-09/gard.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-03-07/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/2024-02-09/icd10cm.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-03-07/icd10cm.owl
 
 ### Entities and axioms
 
 | Metric | Value |
 | ------ | ----- |
-| Annotation properties | 5 |
-| Axioms | 302780 |
+| Annotation properties | 7 |
+| Axioms | 302783 |
 | Logical axioms | 95846 |
 | Classes | 95848 |
 | Object properties | 0 |
@@ -33,7 +33,8 @@
 | Metric | Value |
 | ------ | ----- |
 | AnnotationAssertion | 111084 |
-| Declaration | 95850 |
+| SubAnnotationPropertyOf | 1 |
+| Declaration | 95852 |
 | SubClassOf | 95846 |
 
 
@@ -43,9 +44,10 @@
 | ------ | ----- |
 | prefix_unknown | 95847 |
 | owl | 2 |
-| oboInOwl | 2 |
+| oboInOwl | 3 |
 | rdf | 1 |
 | rdfs | 2 |
+| obo | 1 |
 
 
 #### Class expressions used

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/2024-02-09/icd10who.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-03-07/icd10who.owl
 
 ### Entities and axioms
 
 | Metric | Value |
 | ------ | ----- |
-| Annotation properties | 6 |
-| Axioms | 50463 |
+| Annotation properties | 8 |
+| Axioms | 50466 |
 | Logical axioms | 12542 |
 | Classes | 12543 |
 | Object properties | 0 |
@@ -33,7 +33,8 @@
 | Metric | Value |
 | ------ | ----- |
 | AnnotationAssertion | 25377 |
-| Declaration | 12544 |
+| SubAnnotationPropertyOf | 1 |
+| Declaration | 12546 |
 | SubClassOf | 12542 |
 
 
@@ -43,9 +44,10 @@
 | ------ | ----- |
 | prefix_unknown | 12542 |
 | owl | 2 |
-| oboInOwl | 2 |
+| oboInOwl | 3 |
 | rdf | 1 |
 | rdfs | 3 |
+| obo | 1 |
 
 
 #### Class expressions used

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/2024-02-09/ncit.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-03-07/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/2024-02-09/omim.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-03-07/omim.owl
 
 ### Entities and axioms
 
 | Metric | Value |
 | ------ | ----- |
-| Annotation properties | 16 |
-| Axioms | 344611 |
-| Logical axioms | 22561 |
-| Classes | 19399 |
+| Annotation properties | 18 |
+| Axioms | 344965 |
+| Logical axioms | 22612 |
+| Classes | 19433 |
 | Object properties | 7 |
 | Data properties | 0 |
 | Individuals | 0 |
@@ -32,35 +32,37 @@
 
 | Metric | Value |
 | ------ | ----- |
-| AnnotationAssertion | 302632 |
-| Declaration | 19418 |
-| SubClassOf | 22561 |
+| AnnotationAssertion | 302898 |
+| SubAnnotationPropertyOf | 1 |
+| Declaration | 19454 |
+| SubClassOf | 22612 |
 
 
 #### Entity namespaces: axiom counts by namespace
 
 | Metric | Value |
 | ------ | ----- |
-| prefix_unknown | 17956 |
-| MONDO | 1 |
-| oboInOwl | 3 |
+| prefix_unknown | 17990 |
+| oboInOwl | 4 |
 | owl | 2 |
-| rdf | 1 |
-| IAO | 2 |
 | xsd | 1 |
 | skos | 1 |
 | rdfs | 2 |
 | CHR | 1446 |
+| MONDO | 1 |
+| rdf | 1 |
+| IAO | 2 |
 | biolink | 2 |
 | RO | 7 |
+| obo | 1 |
 
 
 #### Class expressions used
 
 | Metric | Value |
 | ------ | ----- |
-| Class | 64513 |
-| ObjectSomeValuesFrom | 17706 |
+| Class | 64649 |
+| ObjectSomeValuesFrom | 17737 |
 
 
 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
@@ -2,17 +2,17 @@
 
 **IRI:** http://purl.obolibrary.org/obo/mondo/sources/ordo.owl
 
-**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-02-09/ordo.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-03-07/ordo.owl
 
 ### Entities and axioms
 
 | Metric | Value |
 | ------ | ----- |
-| Annotation properties | 8 |
-| Axioms | 162312 |
+| Annotation properties | 15 |
+| Axioms | 205027 |
 | Logical axioms | 42481 |
 | Classes | 14917 |
-| Object properties | 3 |
+| Object properties | 4 |
 | Data properties | 0 |
 | Individuals | 0 |
 
@@ -32,23 +32,28 @@
 
 | Metric | Value |
 | ------ | ----- |
-| AnnotationAssertion | 104905 |
-| Declaration | 14926 |
+| AnnotationAssertion | 147612 |
+| SubAnnotationPropertyOf | 1 |
+| Declaration | 14933 |
 | SubClassOf | 42481 |
 
 
 #### Entity namespaces: axiom counts by namespace
 
 | Metric | Value |
 | ------ | ----- |
+| dc11 | 1 |
 | prefix_unknown | 14917 |
-| oboInOwl | 5 |
-| owl | 1 |
+| oboInOwl | 6 |
+| owl | 2 |
 | rdf | 1 |
 | IAO | 1 |
-| xsd | 1 |
+| xsd | 2 |
+| BFO | 1 |
 | rdfs | 1 |
 | RO | 3 |
+| obo | 1 |
+| dc | 3 |
 
 
 #### Class expressions used

diff --git a/docs/reports/mapped_deprecated.md b/docs/reports/mapped_deprecated.md
@@ -1,9 +1,9 @@
 # Mapped deprecated terms
 | Ontology                                    |   Tot deprecated in Mondo |
 |:--------------------------------------------|--------------------------:|
-| [OMIM](./mapped_deprecated_omim.md)         |                        43 |
+| [OMIM](./mapped_deprecated_omim.md)         |                        44 |
 | [DOID](./mapped_deprecated_doid.md)         |                         3 |
-| [ORDO](./mapped_deprecated_ordo.md)         |                       225 |
+| [ORDO](./mapped_deprecated_ordo.md)         |                       224 |
 | [NCIT](./mapped_deprecated_ncit.md)         |                        12 |
 | [GARD](./mapped_deprecated_gard.md)         |                         0 |
 | [ICD10CM](./mapped_deprecated_icd10cm.md)   |                         0 |

diff --git a/docs/reports/mapped_deprecated_omim.md b/docs/reports/mapped_deprecated_omim.md
@@ -17,6 +17,7 @@
 | MONDO:0008204 | OMIM:168850          | MONDO:equivalentObsolete |
 | MONDO:0008415 | OMIM:181515          | MONDO:equivalentObsolete |
 | MONDO:0009535 | OMIM:247440          | MONDO:equivalentObsolete |
+| MONDO:0009586 | OMIM:249660          | MONDO:equivalentObsolete |
 | MONDO:0009654 | OMIM:252700          | MONDO:equivalentObsolete |
 | MONDO:0010045 | OMIM:270710          | MONDO:equivalentObsolete |
 | MONDO:0010291 | OMIM:300274          | MONDO:equivalentObsolete |

diff --git a/docs/reports/mapped_deprecated_ordo.md b/docs/reports/mapped_deprecated_ordo.md
@@ -13,7 +13,6 @@
 | MONDO:0007779 | Orphanet:306588      | MONDO:equivalentObsolete |
 | MONDO:0008018 | Orphanet:587         | MONDO:equivalentObsolete |
 | MONDO:0008083 | Orphanet:228343      | MONDO:equivalentObsolete |
-| MONDO:0008136 | Orphanet:137902      | MONDO:equivalentObsolete |
 | MONDO:0008157 | Orphanet:1306        | MONDO:equivalentObsolete |
 | MONDO:0008227 | Orphanet:1795        | MONDO:equivalentObsolete |
 | MONDO:0008767 | Orphanet:228346      | MONDO:equivalentObsolete |

diff --git a/docs/reports/migrate.md b/docs/reports/migrate.md
@@ -1,11 +1,11 @@
 # Migratable terms
 | Ontology                          | Tot   |
 |:----------------------------------|:------|
-| [ORDO](./migrate_ordo.md)         | 97    |
 | [GARD](./migrate_gard.md)         | 9,370 |
-| [OMIM](./migrate_omim.md)         | 8     |
-| [NCIT](./migrate_ncit.md)         | 2,179 |
-| [DOID](./migrate_doid.md)         | 188   |
+| [ORDO](./migrate_ordo.md)         | 65    |
+| [OMIM](./migrate_omim.md)         | 21    |
+| [NCIT](./migrate_ncit.md)         | 2,176 |
+| [DOID](./migrate_doid.md)         | 198   |
 | [ICD10WHO](./migrate_icd10who.md) | 119   |
 | [ICD10CM](./migrate_icd10cm.md)   | 1,889 |