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Merge pull request #498 from monarch-initiative/build-2024-04-19
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Build: 2024-04-19
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matentzn authored Apr 23, 2024
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8 changes: 4 additions & 4 deletions docs/metrics/doid.md
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**IRI:** http://purl.obolibrary.org/obo/mondo/sources/doid.owl

**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-04-07/doid.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-04-19/doid.owl

### Entities and axioms

| Metric | Value |
| ------ | ----- |
| Annotation properties | 27 |
| Axioms | 114627 |
| Axioms | 115826 |
| Logical axioms | 16084 |
| Classes | 13084 |
| Object properties | 2 |
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| Metric | Value |
| ------ | ----- |
| AnnotationAssertion | 85431 |
| AnnotationAssertion | 86629 |
| SubAnnotationPropertyOf | 1 |
| DisjointClasses | 26 |
| Declaration | 13111 |
| Declaration | 13112 |
| SubClassOf | 16058 |


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2 changes: 1 addition & 1 deletion docs/metrics/gard.md
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**IRI:** http://purl.obolibrary.org/obo/mondo/sources/gard.owl

**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-04-07/gard.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-04-19/gard.owl

### Entities and axioms

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2 changes: 1 addition & 1 deletion docs/metrics/icd10cm.md
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**IRI:** http://purl.obolibrary.org/obo/mondo/sources/icd10cm.owl

**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-04-07/icd10cm.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-04-19/icd10cm.owl

### Entities and axioms

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2 changes: 1 addition & 1 deletion docs/metrics/icd10who.md
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**IRI:** http://purl.obolibrary.org/obo/mondo/sources/icd10who.owl

**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-04-07/icd10who.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-04-19/icd10who.owl

### Entities and axioms

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46 changes: 23 additions & 23 deletions docs/metrics/icd11foundation.md
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# Metrics HTTP://PURL.OBOLIBRARY.ORG/OBO/MONDO-INGEST/COMPONENTS/ICD11FOUNDATION
# Metrics ICD11FOUNDATION

**IRI:** http://purl.obolibrary.org/obo/mondo-ingest/components/icd11foundation.owl
**IRI:** http://purl.obolibrary.org/obo/mondo/sources/icd11foundation.owl

**Version IRI:** http://purl.obolibrary.org/obo/mondo-ingest/releases/2024-02-17/components/icd11foundation.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-04-19/icd11foundation.owl

### Entities and axioms

| Metric | Value |
| ------ | ----- |
| Annotation properties | 21 |
| Axioms | 570662 |
| Logical axioms | 130473 |
| Classes | 100002 |
| Object properties | 70 |
| Annotation properties | 12 |
| Axioms | 367211 |
| Logical axioms | 87706 |
| Classes | 87537 |
| Object properties | 0 |
| Data properties | 0 |
| Individuals | 0 |

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| Metric | Value |
| ------ | ----- |
| Expressivity | CINTEH |
| Expressivity | |
| OWL2 | True |
| OWL2 DL | True |
| OWL2 EL | True |
| OWL2 QL | False |
| OWL2 RL | False |
| OWL2 QL | True |
| OWL2 RL | True |

#### Axiom types

| Metric | Value |
| ------ | ----- |
| AnnotationAssertion | 340100 |
| EquivalentClasses | 5075 |
| SubObjectPropertyOf | 51 |
| Declaration | 100089 |
| SubClassOf | 125347 |
| AnnotationAssertion | 191956 |
| SubAnnotationPropertyOf | 1 |
| Declaration | 87548 |
| SubClassOf | 87706 |


#### Entity namespaces: axiom counts by namespace

| Metric | Value |
| ------ | ----- |
| prefix_unknown | 100084 |
| owl | 3 |
| prefix_unknown | 87539 |
| oboInOwl | 3 |
| owl | 2 |
| rdf | 1 |
| IAO | 1 |
| xsd | 1 |
| skos | 5 |
| rdfs | 1 |
| rdfs | 2 |
| obo | 1 |
| dc | 1 |


#### Class expressions used

| Metric | Value |
| ------ | ----- |
| Class | 392111 |
| ObjectSomeValuesFrom | 40919 |
| ObjectIntersectionOf | 19706 |
| Class | 262949 |


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).
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7 changes: 4 additions & 3 deletions docs/metrics/ncit.md
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**IRI:** http://purl.obolibrary.org/obo/mondo/sources/ncit.owl

**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-04-07/ncit.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-04-19/ncit.owl

### Entities and axioms

| Metric | Value |
| ------ | ----- |
| Annotation properties | 12 |
| Axioms | 612683 |
| Axioms | 612685 |
| Logical axioms | 32780 |
| Classes | 15628 |
| Object properties | 0 |
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| Metric | Value |
| ------ | ----- |
| AnnotationAssertion | 564245 |
| AnnotationAssertion | 564246 |
| EquivalentClasses | 6027 |
| DatatypeDefinition | 19 |
| AnnotationPropertyRangeOf | 1 |
| Declaration | 15658 |
| SubClassOf | 26734 |

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20 changes: 10 additions & 10 deletions docs/metrics/omim.md
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**IRI:** http://purl.obolibrary.org/obo/mondo/sources/omim.owl

**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-04-07/omim.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-04-19/omim.owl

### Entities and axioms

| Metric | Value |
| ------ | ----- |
| Annotation properties | 18 |
| Axioms | 345359 |
| Logical axioms | 22654 |
| Classes | 19458 |
| Axioms | 345408 |
| Logical axioms | 22664 |
| Classes | 19465 |
| Object properties | 7 |
| Data properties | 0 |
| Individuals | 0 |
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| Metric | Value |
| ------ | ----- |
| AnnotationAssertion | 303225 |
| AnnotationAssertion | 303257 |
| SubAnnotationPropertyOf | 1 |
| Declaration | 19479 |
| SubClassOf | 22654 |
| Declaration | 19486 |
| SubClassOf | 22664 |


#### Entity namespaces: axiom counts by namespace

| Metric | Value |
| ------ | ----- |
| prefix_unknown | 18015 |
| prefix_unknown | 18022 |
| oboInOwl | 4 |
| owl | 2 |
| xsd | 1 |
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| Metric | Value |
| ------ | ----- |
| Class | 64758 |
| ObjectSomeValuesFrom | 17767 |
| Class | 64785 |
| ObjectSomeValuesFrom | 17773 |


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).
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12 changes: 6 additions & 6 deletions docs/metrics/ordo.md
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**IRI:** http://purl.obolibrary.org/obo/mondo/sources/ordo.owl

**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-04-07/ordo.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-04-19/ordo.owl

### Entities and axioms

| Metric | Value |
| ------ | ----- |
| Annotation properties | 15 |
| Axioms | 205027 |
| Annotation properties | 16 |
| Axioms | 206309 |
| Logical axioms | 42481 |
| Classes | 14917 |
| Object properties | 4 |
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| Metric | Value |
| ------ | ----- |
| AnnotationAssertion | 147612 |
| AnnotationAssertion | 148893 |
| SubAnnotationPropertyOf | 1 |
| Declaration | 14933 |
| Declaration | 14934 |
| SubClassOf | 42481 |


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| IAO | 1 |
| xsd | 2 |
| BFO | 1 |
| rdfs | 1 |
| rdfs | 2 |
| RO | 3 |
| obo | 1 |
| dc | 3 |
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19 changes: 10 additions & 9 deletions docs/reports/mapped_deprecated.md
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# Mapped deprecated terms
| Ontology | Tot deprecated in Mondo |
|:--------------------------------------------|--------------------------:|
| [OMIM](./mapped_deprecated_omim.md) | 46 |
| [DOID](./mapped_deprecated_doid.md) | 4 |
| [ORDO](./mapped_deprecated_ordo.md) | 225 |
| [NCIT](./mapped_deprecated_ncit.md) | 12 |
| [GARD](./mapped_deprecated_gard.md) | 0 |
| [ICD10CM](./mapped_deprecated_icd10cm.md) | 0 |
| [ICD10WHO](./mapped_deprecated_icd10who.md) | 0 |
| Ontology | Tot deprecated in Mondo |
|:----------------------------------------------------------|--------------------------:|
| [OMIM](./mapped_deprecated_omim.md) | 46 |
| [DOID](./mapped_deprecated_doid.md) | 4 |
| [ORDO](./mapped_deprecated_ordo.md) | 225 |
| [NCIT](./mapped_deprecated_ncit.md) | 12 |
| [GARD](./mapped_deprecated_gard.md) | 0 |
| [ICD11FOUNDATION](./mapped_deprecated_icd11foundation.md) | 0 |
| [ICD10CM](./mapped_deprecated_icd10cm.md) | 0 |
| [ICD10WHO](./mapped_deprecated_icd10who.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
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7 changes: 7 additions & 0 deletions docs/reports/mapped_deprecated_icd11foundation.md
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## ICD11FOUNDATION
[Interactive FlatGithub table](https://flatgithub.com/monarch-initiative/mondo-ingest?filename=src/ontology/reports/icd11foundation_mapped_deprecated_terms.robot.template.tsv)

### Mapped deprecated terms
| mondo_id | source_id | source |
|:-----------|:---------------------|:-------------------|
| ID | A oboInOwl:hasDbXref | >A oboInOwl:source |
19 changes: 10 additions & 9 deletions docs/reports/migrate.md
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# Migratable terms
| Ontology | Tot |
|:----------------------------------|:------|
| [GARD](./migrate_gard.md) | 9,370 |
| [DOID](./migrate_doid.md) | 40 |
| [ORDO](./migrate_ordo.md) | 21 |
| [NCIT](./migrate_ncit.md) | 2,176 |
| [OMIM](./migrate_omim.md) | 14 |
| [ICD10WHO](./migrate_icd10who.md) | 119 |
| [ICD10CM](./migrate_icd10cm.md) | 1,889 |
| Ontology | Tot |
|:------------------------------------------------|:-------|
| [GARD](./migrate_gard.md) | 9,370 |
| [DOID](./migrate_doid.md) | 42 |
| [ORDO](./migrate_ordo.md) | 26 |
| [OMIM](./migrate_omim.md) | 24 |
| [NCIT](./migrate_ncit.md) | 2,176 |
| [ICD10WHO](./migrate_icd10who.md) | 119 |
| [ICD11FOUNDATION](./migrate_icd11foundation.md) | 10,581 |
| [ICD10CM](./migrate_icd10cm.md) | 1,889 |

### Codebook
`Ontology`: Name of ontology
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4 changes: 3 additions & 1 deletion docs/reports/migrate_doid.md
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| MONDO:0958317 | neurodevelopmental disorder with poor growth and behavioral abnormalities | DOID:0081444 | MONDO:equivalentTo | neurodevelopmental disorder with poor growth and behavioral abnormalities | An autosomal recessive intellectual developmental disorder that is characterized by global developmental delay, moderately to severely impaired intellectual development, often with absent speech, and behavioral abnormalities, including hyperactivity, short attention span, and ADHD and that has_material_basis_in homozygous or compound heterozygous mutation in the ATP9A gene on chromosome 20q13. | MONDO:0019502 |
| MONDO:0958318 | chronic inflammatory demyelinating polyneuritis | DOID:2536 | MONDO:equivalentTo | chronic inflammatory demyelinating polyneuritis | | MONDO:0002336 |
| MONDO:0958319 | congenital kyphosis | DOID:4668 | MONDO:equivalentTo | congenital kyphosis | | |
| MONDO:0958320 | postural kyphosis | DOID:9373 | MONDO:equivalentTo | postural kyphosis | | |
| MONDO:0958320 | postural kyphosis | DOID:9373 | MONDO:equivalentTo | postural kyphosis | | |
| MONDO:0958359 | childhood spinal muscular atrophy | DOID:0060160 | MONDO:equivalentTo | childhood spinal muscular atrophy | | MONDO:0001516 |
| MONDO:0958360 | cholesterol-ester transfer protein deficiency | DOID:0111368 | MONDO:equivalentTo | cholesterol-ester transfer protein deficiency | | MONDO:0002525 |
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