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Merge pull request #685 from monarch-initiative/_build_develop_8nov2024
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Data build to merge into main
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@twhetzel
twhetzel authored Nov 11, 2024
2 parents 66cd017 + 46d340f commit eceb06a
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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/2024-10-04/doid.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-11-09/doid.owl

### Entities and axioms

| Metric | Value |
| ------ | ----- |
| Annotation properties | 28 |
| Axioms | 133598 |
| Logical axioms | 16341 |
| Classes | 13230 |
| Axioms | 133759 |
| Logical axioms | 16363 |
| Classes | 13250 |
| Object properties | 0 |
| Data properties | 0 |
| Individuals | 0 |
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| Metric | Value |
| ------ | ----- |
| AnnotationAssertion | 103998 |
| AnnotationAssertion | 104117 |
| SubAnnotationPropertyOf | 2 |
| DisjointClasses | 26 |
| Declaration | 13257 |
| SubClassOf | 16315 |
| Declaration | 13277 |
| SubClassOf | 16337 |


#### Entity namespaces: axiom counts by namespace
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| ------ | ----- |
| oboInOwl | 12 |
| owl | 2 |
| DOID | 11672 |
| HP | 114 |
| DOID | 11686 |
| HP | 116 |
| xsd | 1 |
| CL | 62 |
| skos | 5 |
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| rdf | 1 |
| CHEBI | 90 |
| IAO | 2 |
| UBERON | 410 |
| UBERON | 414 |
| SO | 17 |
| obo | 191 |
| GENO | 10 |
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| Metric | Value |
| ------ | ----- |
| Class | 46072 |
| Class | 46136 |


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/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/2024-10-04/gard.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-11-09/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/2024-10-04/icd10cm.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-11-09/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/2024-10-04/icd10who.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-11-09/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/2024-10-04/icd11foundation.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-11-09/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/2024-10-04/ncit.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-11-09/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/2024-10-04/omim.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-11-09/omim.owl

### Entities and axioms

| Metric | Value |
| ------ | ----- |
| Annotation properties | 21 |
| Axioms | 355754 |
| Logical axioms | 26248 |
| Classes | 22976 |
| Axioms | 356115 |
| Logical axioms | 26262 |
| Classes | 23005 |
| Object properties | 7 |
| Data properties | 0 |
| Individuals | 0 |
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| Metric | Value |
| ------ | ----- |
| AnnotationAssertion | 306504 |
| AnnotationAssertion | 306822 |
| SubAnnotationPropertyOf | 2 |
| Declaration | 23000 |
| SubClassOf | 26248 |
| Declaration | 23029 |
| SubClassOf | 26262 |


#### Entity namespaces: axiom counts by namespace

| Metric | Value |
| ------ | ----- |
| prefix_unknown | 21534 |
| prefix_unknown | 21566 |
| oboInOwl | 4 |
| owl | 2 |
| xsd | 1 |
| skos | 1 |
| rdfs | 2 |
| CHR | 1445 |
| CHR | 1442 |
| OMO | 1 |
| MONDO | 1 |
| rdf | 1 |
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| Metric | Value |
| ------ | ----- |
| Class | 75462 |
| ObjectSomeValuesFrom | 21276 |
| Class | 75522 |
| ObjectSomeValuesFrom | 21301 |


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/2024-10-04/ordo.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-11-09/ordo.owl

### Entities and axioms

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4 changes: 2 additions & 2 deletions docs/odk-workflows/ManageDocumentation.md
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Expand Up @@ -38,9 +38,9 @@ The documentation is _not_ automatically updated from the Markdown, and needs to
If everything was successful, you will see a message similar to this one:

```
INFO - Your documentation should shortly be available at: https://monarch-initiative.github.io/mondo-ingest/
INFO - Your documentation should shortly be available at: https://monarch-initiative.github.io/noname/
```
3. Just to double check, you can now navigate to your documentation pages (usually https://monarch-initiative.github.io/mondo-ingest/).
3. Just to double check, you can now navigate to your documentation pages (usually https://monarch-initiative.github.io/noname/).
Just make sure you give GitHub 2-5 minutes to build the pages!


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2 changes: 1 addition & 1 deletion docs/odk-workflows/ReleaseWorkflow.md
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Expand Up @@ -44,7 +44,7 @@ Once your [CI checks](ContinuousIntegration.md) have passed, and your reviews ar

## Create a GitHub release

1. Go to your releases page on GitHub by navigating to your repository, and then clicking on releases (usually on the right, for example: https://github.com/monarch-initiative/mondo-ingest/releases). Then click "Draft new release"
1. Go to your releases page on GitHub by navigating to your repository, and then clicking on releases (usually on the right, for example: https://github.com/monarch-initiative/noname/releases). Then click "Draft new release"
1. As the tag version you **need to choose the date on which your ontologies were build.** You can find this, for example, by looking at the `mondo-ingest.obo` file and check the `data-version:` property. The date needs to be prefixed with a `v`, so, for example `v2020-02-06`.
1. You can write whatever you want in the release title, but we typically write the date again. The description underneath should contain a concise list of changes or term additions.
1. Click "Publish release". Done.
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4 changes: 2 additions & 2 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) | 42 |
| [ORDO](./mapped_deprecated_ordo.md) | 167 |
| [OMIM](./mapped_deprecated_omim.md) | 43 |
| [ORDO](./mapped_deprecated_ordo.md) | 168 |
| [GARD](./mapped_deprecated_gard.md) | 0 |
| [ICD11FOUNDATION](./mapped_deprecated_icd11foundation.md) | 0 |
| [ICD10CM](./mapped_deprecated_icd10cm.md) | 0 |
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1 change: 1 addition & 0 deletions docs/reports/mapped_deprecated_omim.md
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| ID | A oboInOwl:hasDbXref | >A oboInOwl:source |
| MONDO:0000911 | OMIM:613740 | MONDO:equivalentObsolete |
| MONDO:0007061 | OMIM:102590 | MONDO:equivalentObsolete |
| MONDO:0007066 | OMIM:102800 | MONDO:equivalentObsolete |
| MONDO:0007602 | OMIM:134700 | MONDO:equivalentObsolete |
| MONDO:0007659 | OMIM:137560 | MONDO:equivalentObsolete |
| MONDO:0007779 | OMIM:145410 | MONDO:equivalentObsolete |
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1 change: 1 addition & 0 deletions docs/reports/mapped_deprecated_ordo.md
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| MONDO:0015255 | Orphanet:1256 | MONDO:equivalentObsolete |
| MONDO:0015297 | Orphanet:137653 | MONDO:equivalentObsolete |
| MONDO:0015343 | Orphanet:139420 | MONDO:equivalentObsolete |
| MONDO:0015424 | Orphanet:1420 | MONDO:equivalentObsolete |
| MONDO:0015551 | Orphanet:158665 | MONDO:equivalentObsolete |
| MONDO:0015560 | Orphanet:158796 | MONDO:equivalentObsolete |
| MONDO:0015591 | Orphanet:163903 | MONDO:equivalentObsolete |
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4 changes: 2 additions & 2 deletions docs/reports/migrate.md
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| Ontology | Tot |
|:------------------------------------------------|:------|
| [GARD](./migrate_gard.md) | 9,370 |
| [DOID](./migrate_doid.md) | 50 |
| [ICD11FOUNDATION](./migrate_icd11foundation.md) | 4,593 |
| [DOID](./migrate_doid.md) | 37 |
| [OMIM](./migrate_omim.md) | 34 |
| [NCIT](./migrate_ncit.md) | 2,211 |
| [OMIM](./migrate_omim.md) | 15 |
| [ORDO](./migrate_ordo.md) | 13 |
| [ICD10WHO](./migrate_icd10who.md) | 119 |
| [ICD10CM](./migrate_icd10cm.md) | 1,894 |
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