data build

monarch-initiative · Aug 6, 2024 · eaa7ce2 · eaa7ce2
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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/2024-07-09/doid.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-08-05/doid.owl
 
 ### Entities and axioms
 
 | Metric | Value |
 | ------ | ----- |
 | Annotation properties | 27 |
-| Axioms | 116493 |
-| Logical axioms | 16200 |
-| Classes | 13147 |
+| Axioms | 129102 |
+| Logical axioms | 16223 |
+| Classes | 13160 |
 | Object properties | 0 |
 | Data properties | 0 |
 | Individuals | 0 |
@@ -32,11 +32,11 @@
 
 | Metric | Value |
 | ------ | ----- |
-| AnnotationAssertion | 87119 |
+| AnnotationAssertion | 99692 |
 | SubAnnotationPropertyOf | 1 |
 | DisjointClasses | 26 |
-| Declaration | 13173 |
-| SubClassOf | 16174 |
+| Declaration | 13186 |
+| SubClassOf | 16197 |
 
 
 #### Entity namespaces: axiom counts by namespace
@@ -45,10 +45,10 @@
 | ------ | ----- |
 | oboInOwl | 12 |
 | owl | 2 |
-| DOID | 11600 |
+| DOID | 11614 |
 | HP | 118 |
 | xsd | 1 |
-| CL | 63 |
+| CL | 62 |
 | skos | 5 |
 | rdfs | 2 |
 | FOODON | 24 |
@@ -70,7 +70,7 @@
 
 | Metric | Value |
 | ------ | ----- |
-| Class | 45707 |
+| Class | 45766 |
 
 
 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/2024-07-09/gard.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-08-05/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/2024-07-09/icd10cm.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-08-05/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/2024-07-09/icd10who.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-08-05/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/2024-07-09/icd11foundation.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-08-05/icd11foundation.owl
 
 ### Entities and axioms
 
 | Metric | Value |
 | ------ | ----- |
 | Annotation properties | 12 |
-| Axioms | 329926 |
+| Axioms | 422785 |
 | Logical axioms | 65410 |
 | Classes | 70045 |
 | Object properties | 0 |
@@ -32,7 +32,7 @@
 
 | Metric | Value |
 | ------ | ----- |
-| AnnotationAssertion | 194459 |
+| AnnotationAssertion | 287318 |
 | 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/2024-07-09/ncit.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-08-05/ncit.owl
 
 ### Entities and axioms
 
 | Metric | Value |
 | ------ | ----- |
 | Annotation properties | 12 |
-| Axioms | 623834 |
+| Axioms | 623839 |
 | Logical axioms | 33655 |
 | Classes | 15971 |
 | Object properties | 0 |
@@ -32,7 +32,7 @@
 
 | Metric | Value |
 | ------ | ----- |
-| AnnotationAssertion | 574177 |
+| AnnotationAssertion | 574182 |
 | 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/2024-07-09/omim.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-08-05/omim.owl
 
 ### Entities and axioms
 
 | Metric | Value |
 | ------ | ----- |
-| Annotation properties | 18 |
-| Axioms | 346439 |
-| Logical axioms | 22746 |
-| Classes | 19517 |
+| Annotation properties | 19 |
+| Axioms | 347287 |
+| Logical axioms | 22779 |
+| Classes | 19535 |
 | Object properties | 7 |
 | Data properties | 0 |
 | Individuals | 0 |
@@ -32,17 +32,17 @@
 
 | Metric | Value |
 | ------ | ----- |
-| AnnotationAssertion | 304154 |
+| AnnotationAssertion | 304950 |
 | SubAnnotationPropertyOf | 1 |
-| Declaration | 19538 |
-| SubClassOf | 22746 |
+| Declaration | 19557 |
+| SubClassOf | 22779 |
 
 
 #### Entity namespaces: axiom counts by namespace
 
 | Metric | Value |
 | ------ | ----- |
-| prefix_unknown | 18074 |
+| prefix_unknown | 18092 |
 | oboInOwl | 4 |
 | owl | 2 |
 | xsd | 1 |
@@ -54,15 +54,15 @@
 | IAO | 2 |
 | biolink | 2 |
 | RO | 7 |
-| obo | 1 |
+| obo | 2 |
 
 
 #### Class expressions used
 
 | Metric | Value |
 | ------ | ----- |
-| Class | 64999 |
-| ObjectSomeValuesFrom | 17812 |
+| Class | 65083 |
+| ObjectSomeValuesFrom | 17832 |
 
 
 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/2024-07-09/ordo.owl
+**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-08-05/ordo.owl
 
 ### Entities and axioms
 
 | Metric | Value |
 | ------ | ----- |
 | Annotation properties | 16 |
-| Axioms | 213414 |
+| Axioms | 227556 |
 | Logical axioms | 42867 |
 | Classes | 15089 |
 | Object properties | 4 |
@@ -32,7 +32,7 @@
 
 | Metric | Value |
 | ------ | ----- |
-| AnnotationAssertion | 155440 |
+| AnnotationAssertion | 169582 |
 | SubAnnotationPropertyOf | 1 |
 | Declaration | 15106 |
 | SubClassOf | 42867 |

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 |
 |:----------------------------------------------------------|--------------------------:|
-| [DOID](./mapped_deprecated_doid.md)                       |                         6 |
-| [OMIM](./mapped_deprecated_omim.md)                       |                        46 |
-| [ORDO](./mapped_deprecated_ordo.md)                       |                       260 |
-| [NCIT](./mapped_deprecated_ncit.md)                       |                        22 |
+| [NCIT](./mapped_deprecated_ncit.md)                       |                         5 |
+| [OMIM](./mapped_deprecated_omim.md)                       |                        43 |
+| [ORDO](./mapped_deprecated_ordo.md)                       |                       167 |
 | [GARD](./mapped_deprecated_gard.md)                       |                         0 |
 | [ICD11FOUNDATION](./mapped_deprecated_icd11foundation.md) |                         0 |
 | [ICD10CM](./mapped_deprecated_icd10cm.md)                 |                         0 |
+| [DOID](./mapped_deprecated_doid.md)                       |                         0 |
 | [ICD10WHO](./mapped_deprecated_icd10who.md)               |                         0 |
 
 `Ontology`: Name of ontology    

diff --git a/docs/reports/mapped_deprecated_doid.md b/docs/reports/mapped_deprecated_doid.md
@@ -2,12 +2,6 @@
 [Interactive FlatGithub table](https://flatgithub.com/monarch-initiative/mondo-ingest?filename=src/ontology/reports/doid_mapped_deprecated_terms.robot.template.tsv)
 
 ### Mapped deprecated terms
-| mondo_id      | source_id            | source                   |
-|:--------------|:---------------------|:-------------------------|
-| 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 |
-| MONDO:0015353 | DOID:0111204         | MONDO:equivalentObsolete |
+| mondo_id   | source_id            | source             |
+|:-----------|:---------------------|:-------------------|
+| ID         | A oboInOwl:hasDbXref | >A oboInOwl:source |
diff --git a/docs/reports/mapped_deprecated_ncit.md b/docs/reports/mapped_deprecated_ncit.md
@@ -6,24 +6,7 @@
 |:--------------|:---------------------|:-------------------------|
 | 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 |
 | MONDO:0020842 | NCIT:C8998           | MONDO:equivalentObsolete |
diff --git a/docs/reports/mapped_deprecated_omim.md b/docs/reports/mapped_deprecated_omim.md
@@ -16,8 +16,7 @@
 | 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:0009489 | OMIM:244850          | MONDO:equivalentObsolete |
 | MONDO:0009535 | OMIM:247440          | MONDO:equivalentObsolete |
 | MONDO:0009654 | OMIM:252700          | MONDO:equivalentObsolete |
 | MONDO:0010045 | OMIM:270710          | MONDO:equivalentObsolete |
@@ -34,9 +33,7 @@
 | MONDO:0010859 | OMIM:600309          | MONDO:equivalentObsolete |
 | MONDO:0011111 | OMIM:601563          | MONDO:equivalentObsolete |
 | MONDO:0011543 | OMIM:605365          | MONDO:equivalentObsolete |
-| MONDO:0011798 | OMIM:607236          | MONDO:equivalentObsolete |
 | MONDO:0011910 | OMIM:607801          | 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 |