Merge branch 'main' into bugfix-mapped-deprecated-mondo-obsoletes

monarch-initiative · Jun 22, 2023 · 17f48f8 · 17f48f8
2 parents 63040d2 + d256fa3
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diff --git a/.gitignore b/.gitignore
@@ -77,6 +77,7 @@ src/scripts/.ipynb_checkpoints/*
 src/ontology/.template.db
 src/mappings/mondo-sources-all-lexical.sssom.tsv
 src/scripts/mondo_unmapped.tsv
+src/ontology/reports/mondo-ingest-edit.owl-obo-report.tsv
 
 # Test
 test/output/

diff --git a/docs/metrics/doid.md b/docs/metrics/doid.md
@@ -2,7 +2,7 @@
 
 **IRI:** http://purl.obolibrary.org/obo/mondo/sources/doid.owl
 
-**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2023-06-15/doid.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2023-06-18/doid.owl
 
 ### Entities and axioms
 

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/2023-06-15/gard.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2023-06-18/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/2023-06-15/icd10cm.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2023-06-18/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/2023-06-15/icd10who.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2023-06-18/icd10who.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/2023-06-15/ncit.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2023-06-18/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/2023-06-15/omim.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2023-06-18/omim.owl
 
 ### Entities and axioms
 
 | Metric | Value |
 | ------ | ----- |
 | Annotation properties | 13 |
-| Axioms | 369825 |
-| Logical axioms | 35719 |
-| Classes | 31254 |
+| Axioms | 371144 |
+| Logical axioms | 35911 |
+| Classes | 31395 |
 | Object properties | 6 |
 | Data properties | 0 |
 | Individuals | 0 |
@@ -32,22 +32,22 @@
 
 | Metric | Value |
 | ------ | ----- |
-| AnnotationAssertion | 302837 |
-| Declaration | 31269 |
-| SubClassOf | 35719 |
+| AnnotationAssertion | 303823 |
+| Declaration | 31410 |
+| SubClassOf | 35911 |
 
 
 #### Entity namespaces: axiom counts by namespace
 
 | Metric | Value |
 | ------ | ----- |
-| prefix_unknown | 29814 |
+| prefix_unknown | 29954 |
 | oboInOwl | 3 |
 | owl | 2 |
 | xsd | 1 |
 | skos | 1 |
 | rdfs | 2 |
-| CHR | 1439 |
+| CHR | 1440 |
 | MONDO | 1 |
 | rdf | 1 |
 | IAO | 2 |
@@ -60,8 +60,8 @@
 
 | Metric | Value |
 | ------ | ----- |
-| Class | 102686 |
-| ObjectSomeValuesFrom | 14071 |
+| Class | 103211 |
+| ObjectSomeValuesFrom | 14134 |
 
 
 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/2023-06-15/ordo.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2023-06-18/ordo.owl
 
 ### Entities and axioms
 

diff --git a/docs/reports/mapped_deprecated.md b/docs/reports/mapped_deprecated.md
@@ -1,13 +1,13 @@
 # Mapped deprecated terms
 | Ontology                                    |   Tot deprecated in Mondo |
 |:--------------------------------------------|--------------------------:|
-| [ORDO](./mapped_deprecated_ordo.md)         |                       574 |
 | [OMIM](./mapped_deprecated_omim.md)         |                        44 |
-| [NCIT](./mapped_deprecated_ncit.md)         |                        33 |
-| [DOID](./mapped_deprecated_doid.md)         |                         0 |
-| [GARD](./mapped_deprecated_gard.md)         |                         0 |
-| [ICD10CM](./mapped_deprecated_icd10cm.md)   |                         0 |
+| [DOID](./mapped_deprecated_doid.md)         |                         4 |
+| [NCIT](./mapped_deprecated_ncit.md)         |                         3 |
+| [ORDO](./mapped_deprecated_ordo.md)         |                       113 |
 | [ICD10WHO](./mapped_deprecated_icd10who.md) |                         0 |
+| [ICD10CM](./mapped_deprecated_icd10cm.md)   |                         0 |
+| [GARD](./mapped_deprecated_gard.md)         |                         0 |
 
 `Ontology`: Name of ontology    
 `Tot deprecated in Mondo`: Total terms that the ontology source itself has deprecated which have existing xrefs in Mondo

diff --git a/docs/reports/mapped_deprecated_omim.md b/docs/reports/mapped_deprecated_omim.md
@@ -14,7 +14,6 @@
 | MONDO:0008091 | OMIM:162820          | MONDO:equivalentObsolete |
 | MONDO:0008126 | OMIM:164891          | MONDO:equivalentObsolete |
 | MONDO:0008204 | OMIM:168850          | MONDO:equivalentObsolete |
-| MONDO:0008409 | OMIM:181430          | MONDO:equivalentObsolete |
 | MONDO:0008415 | OMIM:181515          | MONDO:equivalentObsolete |
 | MONDO:0009535 | OMIM:247440          | MONDO:equivalentObsolete |
 | MONDO:0009654 | OMIM:252700          | MONDO:equivalentObsolete |
@@ -29,12 +28,13 @@
 | MONDO:0010601 | OMIM:306500          | MONDO:equivalentObsolete |
 | MONDO:0010666 | OMIM:309605          | MONDO:equivalentObsolete |
 | MONDO:0010804 | OMIM:600048          | MONDO:equivalentObsolete |
-| MONDO:0010859 | OMIM:600309          | MONDO:equivalentObsolete |
-| MONDO:0010975 | OMIM:600996          | MONDO:equivalentObsolete |
 | MONDO:0011111 | OMIM:601563          | MONDO:equivalentObsolete |
+| MONDO:0011333 | OMIM:603530          | MONDO:equivalentObsolete |
+| MONDO:0011499 | OMIM:604916          | MONDO:equivalentObsolete |
 | MONDO:0011543 | OMIM:605365          | MONDO:equivalentObsolete |
+| MONDO:0011882 | OMIM:607655          | MONDO:equivalentObsolete |
 | MONDO:0011910 | OMIM:607801          | MONDO:equivalentObsolete |
-| MONDO:0012279 | OMIM:609456          | MONDO:equivalentObsolete |
+| MONDO:0012144 | OMIM:608890          | MONDO:equivalentObsolete |
 | MONDO:0012461 | OMIM:610269          | MONDO:equivalentObsolete |
 | MONDO:0012560 | OMIM:610799          | MONDO:equivalentObsolete |
 | MONDO:0013596 | OMIM:614157          | MONDO:equivalentObsolete |

diff --git a/docs/reports/migrate.md b/docs/reports/migrate.md
@@ -4,10 +4,10 @@
 | [GARD](./migrate_gard.md)         | 9,370 |
 | [ORDO](./migrate_ordo.md)         | 70    |
 | [NCIT](./migrate_ncit.md)         | 2,113 |
+| [OMIM](./migrate_omim.md)         | 128   |
 | [ICD10WHO](./migrate_icd10who.md) | 119   |
 | [DOID](./migrate_doid.md)         | 112   |
 | [ICD10CM](./migrate_icd10cm.md)   | 1,888 |
-| [OMIM](./migrate_omim.md)         | 1     |
 
 ### Codebook
 `Ontology`: Name of ontology