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Merge pull request #713 from monarch-initiative/_TEST_build_develop_2…
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…7Nov2024

Data build from `develop`
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@twhetzel
twhetzel authored Nov 28, 2024
2 parents 52541e9 + 8a87302 commit 7dda447
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3 changes: 0 additions & 3 deletions .gitignore
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Expand Up @@ -108,7 +108,4 @@ src/scripts/mondo_unmapped.tsv
tests/output/*
!tests/output/.gitkeep
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
22 changes: 11 additions & 11 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/2024-11-23/doid.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-11-27/doid.owl

### Entities and axioms

| Metric | Value |
| ------ | ----- |
| Annotation properties | 28 |
| Axioms | 133761 |
| Logical axioms | 16363 |
| Classes | 13250 |
| Axioms | 134099 |
| Logical axioms | 16396 |
| Classes | 13274 |
| Object properties | 0 |
| Data properties | 0 |
| Individuals | 0 |
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| Metric | Value |
| ------ | ----- |
| AnnotationAssertion | 104119 |
| AnnotationAssertion | 104400 |
| SubAnnotationPropertyOf | 2 |
| DisjointClasses | 26 |
| Declaration | 13277 |
| SubClassOf | 16337 |
| Declaration | 13301 |
| SubClassOf | 16370 |


#### Entity namespaces: axiom counts by namespace
Expand All @@ -45,10 +45,10 @@
| ------ | ----- |
| oboInOwl | 12 |
| owl | 2 |
| DOID | 11686 |
| DOID | 11710 |
| HP | 116 |
| xsd | 1 |
| CL | 62 |
| CL | 61 |
| skos | 5 |
| rdfs | 2 |
| FOODON | 24 |
Expand All @@ -61,7 +61,7 @@
| CHEBI | 90 |
| IAO | 2 |
| UBERON | 414 |
| SO | 17 |
| SO | 18 |
| obo | 191 |
| GENO | 10 |
| dc | 1 |
Expand All @@ -71,7 +71,7 @@

| Metric | Value |
| ------ | ----- |
| Class | 46136 |
| Class | 46226 |


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/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/2024-11-23/icd10cm.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-11-27/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/2024-11-23/icd10who.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-11-27/icd10who.owl

### Entities and axioms

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2 changes: 1 addition & 1 deletion 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/2024-11-23/icd11foundation.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-11-27/icd11foundation.owl

### Entities and axioms

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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/2024-11-23/ncit.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-11-27/ncit.owl

### Entities and axioms

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22 changes: 11 additions & 11 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/2024-11-23/omim.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-11-27/omim.owl

### Entities and axioms

| Metric | Value |
| ------ | ----- |
| Annotation properties | 21 |
| Axioms | 358729 |
| Logical axioms | 28206 |
| Classes | 23591 |
| Axioms | 358797 |
| Logical axioms | 28211 |
| Classes | 23596 |
| Object properties | 7 |
| Data properties | 0 |
| Individuals | 0 |
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| Metric | Value |
| ------ | ----- |
| AnnotationAssertion | 306906 |
| AnnotationAssertion | 306964 |
| SubAnnotationPropertyOf | 2 |
| Declaration | 23615 |
| SubClassOf | 28206 |
| Declaration | 23620 |
| SubClassOf | 28211 |


#### Entity namespaces: axiom counts by namespace

| Metric | Value |
| ------ | ----- |
| prefix_unknown | 22152 |
| prefix_unknown | 22158 |
| oboInOwl | 4 |
| owl | 2 |
| xsd | 1 |
| skos | 1 |
| rdfs | 2 |
| CHR | 1442 |
| CHR | 1441 |
| OMO | 1 |
| MONDO | 1 |
| rdf | 1 |
Expand All @@ -62,8 +62,8 @@

| Metric | Value |
| ------ | ----- |
| Class | 79998 |
| ObjectSomeValuesFrom | 23242 |
| Class | 80013 |
| ObjectSomeValuesFrom | 23248 |


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/2024-11-23/ordo.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-11-27/ordo.owl

### Entities and axioms

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1 change: 0 additions & 1 deletion docs/odk-workflows/RepositoryFileStructure.md
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Expand Up @@ -31,7 +31,6 @@ These are the components in MONDO-INGEST
| Filename | URL |
| -------- | --- |
| doid.owl | http://purl.obolibrary.org/obo/doid.owl |
| gard.owl | https://github.com/monarch-initiative/gard/releases/latest/download/gard.owl |
| icd10cm.owl | https://data.bioontology.org/ontologies/ICD10CM/submissions/23/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb |
| icd10who.owl | https://github.com/monarch-initiative/icd10who/releases/latest/download/icd10who.ttl |
| icd11foundation.owl | https://github.com/monarch-initiative/icd11/releases/latest/download/icd11foundation.owl |
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5 changes: 2 additions & 3 deletions 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) | 46 |
| [OMIM](./mapped_deprecated_omim.md) | 47 |
| [DOID](./mapped_deprecated_doid.md) | 2 |
| [ORDO](./mapped_deprecated_ordo.md) | 169 |
| [DOID](./mapped_deprecated_doid.md) | 1 |
| [GARD](./mapped_deprecated_gard.md) | 0 |
| [ICD11FOUNDATION](./mapped_deprecated_icd11foundation.md) | 0 |
| [ICD10CM](./mapped_deprecated_icd10cm.md) | 0 |
| [ICD10WHO](./mapped_deprecated_icd10who.md) | 0 |
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3 changes: 2 additions & 1 deletion docs/reports/mapped_deprecated_doid.md
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| mondo_id | source_id | source |
|:--------------|:---------------------|:-------------------------|
| ID | A oboInOwl:hasDbXref | >A oboInOwl:source |
| MONDO:0011893 | DOID:0110578 | MONDO:equivalentObsolete |
| MONDO:0011893 | DOID:0110578 | MONDO:equivalentObsolete |
| MONDO:0013209 | DOID:0080546 | MONDO:equivalentObsolete |
7 changes: 0 additions & 7 deletions docs/reports/mapped_deprecated_gard.md
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1 change: 1 addition & 0 deletions docs/reports/mapped_deprecated_omim.md
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| MONDO:0010760 | OMIM:314800 | MONDO:equivalentObsolete |
| MONDO:0010804 | OMIM:600048 | MONDO:equivalentObsolete |
| MONDO:0010859 | OMIM:600309 | MONDO:equivalentObsolete |
| MONDO:0010996 | OMIM:601101 | MONDO:equivalentObsolete |
| MONDO:0011111 | OMIM:601563 | MONDO:equivalentObsolete |
| MONDO:0011543 | OMIM:605365 | MONDO:equivalentObsolete |
| MONDO:0011893 | OMIM:607683 | MONDO:equivalentObsolete |
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5 changes: 2 additions & 3 deletions docs/reports/migrate.md
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# Migratable terms
| Ontology | Tot |
|:------------------------------------------------|:------|
| [GARD](./migrate_gard.md) | 9,370 |
| [DOID](./migrate_doid.md) | 50 |
| [DOID](./migrate_doid.md) | 73 |
| [ICD11FOUNDATION](./migrate_icd11foundation.md) | 4,593 |
| [OMIM](./migrate_omim.md) | 37 |
| [OMIM](./migrate_omim.md) | 39 |
| [NCIT](./migrate_ncit.md) | 2,211 |
| [ORDO](./migrate_ordo.md) | 13 |
| [ICD10WHO](./migrate_icd10who.md) | 119 |
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