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TEST Build from main branch with code updates to icd11 component goal…
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… and problematic exclusion script (#637)

* TEST Build from main branch with code updates to icd11 component goal and problematic exclusion script

* remove echo debug statement

* refactor sparql query
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@twhetzel
twhetzel authored Aug 14, 2024
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2 changes: 1 addition & 1 deletion 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/2024-08-07/doid.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-08-13/doid.owl

### Entities and axioms

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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/2024-08-07/gard.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-08-13/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/2024-08-07/icd10cm.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-08-13/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/2024-08-07/icd10who.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-08-13/icd10who.owl

### Entities and axioms

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18 changes: 9 additions & 9 deletions docs/metrics/icd11foundation.md
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**IRI:** http://purl.obolibrary.org/obo/mondo/sources/icd11foundation.owl

**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-08-07/icd11foundation.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-08-13/icd11foundation.owl

### Entities and axioms

| Metric | Value |
| ------ | ----- |
| Annotation properties | 12 |
| Axioms | 422785 |
| Logical axioms | 65410 |
| Classes | 70045 |
| Axioms | 309765 |
| Logical axioms | 65391 |
| Classes | 57711 |
| Object properties | 0 |
| Data properties | 0 |
| Individuals | 0 |
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| Metric | Value |
| ------ | ----- |
| AnnotationAssertion | 287318 |
| AnnotationAssertion | 186651 |
| SubAnnotationPropertyOf | 1 |
| Declaration | 70056 |
| SubClassOf | 65410 |
| Declaration | 57722 |
| SubClassOf | 65391 |


#### Entity namespaces: axiom counts by namespace

| Metric | Value |
| ------ | ----- |
| prefix_unknown | 70047 |
| prefix_unknown | 57713 |
| oboInOwl | 3 |
| owl | 2 |
| rdf | 1 |
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| Metric | Value |
| ------ | ----- |
| Class | 200865 |
| Class | 188493 |


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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2 changes: 1 addition & 1 deletion 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/2024-08-07/ncit.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-08-13/ncit.owl

### Entities and axioms

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16 changes: 8 additions & 8 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/2024-08-07/omim.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-08-13/omim.owl

### Entities and axioms

| Metric | Value |
| ------ | ----- |
| Annotation properties | 19 |
| Axioms | 347287 |
| Axioms | 347317 |
| Logical axioms | 22779 |
| Classes | 19535 |
| Classes | 19534 |
| Object properties | 7 |
| Data properties | 0 |
| Individuals | 0 |
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| Metric | Value |
| ------ | ----- |
| AnnotationAssertion | 304950 |
| AnnotationAssertion | 304981 |
| SubAnnotationPropertyOf | 1 |
| Declaration | 19557 |
| Declaration | 19556 |
| SubClassOf | 22779 |


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| xsd | 1 |
| skos | 1 |
| rdfs | 2 |
| CHR | 1446 |
| CHR | 1445 |
| MONDO | 1 |
| rdf | 1 |
| IAO | 2 |
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| Metric | Value |
| ------ | ----- |
| Class | 65083 |
| ObjectSomeValuesFrom | 17832 |
| Class | 65082 |
| ObjectSomeValuesFrom | 17831 |


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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2 changes: 1 addition & 1 deletion 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/2024-08-07/ordo.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-08-13/ordo.owl

### Entities and axioms

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2 changes: 1 addition & 1 deletion docs/reports/mapped_deprecated.md
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| Ontology | Tot deprecated in Mondo |
|:----------------------------------------------------------|--------------------------:|
| [NCIT](./mapped_deprecated_ncit.md) | 5 |
| [OMIM](./mapped_deprecated_omim.md) | 43 |
| [OMIM](./mapped_deprecated_omim.md) | 44 |
| [ORDO](./mapped_deprecated_ordo.md) | 167 |
| [GARD](./mapped_deprecated_gard.md) | 0 |
| [ICD11FOUNDATION](./mapped_deprecated_icd11foundation.md) | 0 |
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1 change: 1 addition & 0 deletions docs/reports/mapped_deprecated_omim.md
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| MONDO:0010859 | OMIM:600309 | MONDO:equivalentObsolete |
| MONDO:0011111 | OMIM:601563 | MONDO:equivalentObsolete |
| MONDO:0011543 | OMIM:605365 | MONDO:equivalentObsolete |
| MONDO:0011893 | OMIM:607683 | MONDO:equivalentObsolete |
| MONDO:0011910 | OMIM:607801 | MONDO:equivalentObsolete |
| MONDO:0012461 | OMIM:610269 | MONDO:equivalentObsolete |
| MONDO:0012560 | OMIM:610799 | MONDO:equivalentObsolete |
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20 changes: 10 additions & 10 deletions docs/reports/migrate.md
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# Migratable terms
| Ontology | Tot |
|:------------------------------------------------|:-------|
| [GARD](./migrate_gard.md) | 9,370 |
| [ORDO](./migrate_ordo.md) | 84 |
| [DOID](./migrate_doid.md) | 46 |
| [NCIT](./migrate_ncit.md) | 2,209 |
| [OMIM](./migrate_omim.md) | 16 |
| [ICD11FOUNDATION](./migrate_icd11foundation.md) | 12,409 |
| [ICD10WHO](./migrate_icd10who.md) | 119 |
| [ICD10CM](./migrate_icd10cm.md) | 1,892 |
| Ontology | Tot |
|:------------------------------------------------|:------|
| [GARD](./migrate_gard.md) | 9,370 |
| [ORDO](./migrate_ordo.md) | 84 |
| [DOID](./migrate_doid.md) | 47 |
| [ICD11FOUNDATION](./migrate_icd11foundation.md) | 4,594 |
| [NCIT](./migrate_ncit.md) | 2,209 |
| [ICD10WHO](./migrate_icd10who.md) | 119 |
| [ICD10CM](./migrate_icd10cm.md) | 1,892 |
| [OMIM](./migrate_omim.md) | 1 |

### Codebook
`Ontology`: Name of ontology
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3 changes: 2 additions & 1 deletion docs/reports/migrate_doid.md
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| MONDO:0971165 | cerebellar ataxia, impaired intellectual development, and dysequilibrium syndrome 4 | DOID:0070559 | MONDO:equivalentTo | cerebellar ataxia, impaired intellectual development, and dysequilibrium syndrome 4 | | MONDO:0009133 |
| MONDO:0971166 | glucose transporter type 1 deficiency syndrome | DOID:0070560 | MONDO:equivalentTo | glucose transporter type 1 deficiency syndrome | | MONDO:0000429|MONDO:0002908 |
| MONDO:0971167 | fanconi-bickel syndrome | DOID:0070562 | MONDO:equivalentTo | Fanconi-Bickel syndrome | | MONDO:0006025|MONDO:0002908 |
| MONDO:0971168 | glucose-galactose malabsorption | DOID:0070563 | MONDO:equivalentTo | glucose-galactose malabsorption | | MONDO:0002908|MONDO:0006025 |
| MONDO:0971168 | glucose-galactose malabsorption | DOID:0070563 | MONDO:equivalentTo | glucose-galactose malabsorption | | MONDO:0002908|MONDO:0006025 |
| MONDO:0971183 | autosomal recessive pseudohypoaldosteronism type 1 | DOID:0060854 | MONDO:equivalentTo | autosomal recessive pseudohypoaldosteronism type 1 | | MONDO:0018638|MONDO:0006025 |
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