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Merge pull request #566 from monarch-initiative/data-load-12062024
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Update all Mondo Ingest data files (12 June 2024)
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@matentzn
matentzn authored Jun 14, 2024
2 parents 7631849 + 75952bf commit 0b790b6
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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/2024-06-05/doid.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-13/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/2024-06-05/gard.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-13/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/2024-06-05/icd10cm.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-13/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/2024-06-05/icd10who.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-13/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/2024-06-05/icd11foundation.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-13/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/2024-06-05/ncit.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-13/ncit.owl

### Entities and axioms

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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/2024-06-05/omim.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-13/omim.owl

### Entities and axioms

| Metric | Value |
| ------ | ----- |
| Annotation properties | 18 |
| Axioms | 346108 |
| Logical axioms | 22736 |
| Classes | 19509 |
| Axioms | 346158 |
| Logical axioms | 22739 |
| Classes | 19512 |
| Object properties | 7 |
| Data properties | 0 |
| Individuals | 0 |
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| Metric | Value |
| ------ | ----- |
| AnnotationAssertion | 303841 |
| AnnotationAssertion | 303885 |
| SubAnnotationPropertyOf | 1 |
| Declaration | 19530 |
| SubClassOf | 22736 |
| Declaration | 19533 |
| SubClassOf | 22739 |


#### Entity namespaces: axiom counts by namespace

| Metric | Value |
| ------ | ----- |
| prefix_unknown | 18063 |
| prefix_unknown | 18066 |
| oboInOwl | 4 |
| owl | 2 |
| xsd | 1 |
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| Metric | Value |
| ------ | ----- |
| Class | 64971 |
| ObjectSomeValuesFrom | 17811 |
| Class | 64980 |
| ObjectSomeValuesFrom | 17813 |


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/2024-06-05/ordo.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-13/ordo.owl

### Entities and axioms

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4 changes: 2 additions & 2 deletions docs/reports/mapped_deprecated.md
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| Ontology | Tot deprecated in Mondo |
|:----------------------------------------------------------|--------------------------:|
| [DOID](./mapped_deprecated_doid.md) | 5 |
| [OMIM](./mapped_deprecated_omim.md) | 47 |
| [ORDO](./mapped_deprecated_ordo.md) | 225 |
| [OMIM](./mapped_deprecated_omim.md) | 46 |
| [ORDO](./mapped_deprecated_ordo.md) | 226 |
| [NCIT](./mapped_deprecated_ncit.md) | 22 |
| [GARD](./mapped_deprecated_gard.md) | 0 |
| [ICD11FOUNDATION](./mapped_deprecated_icd11foundation.md) | 0 |
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1 change: 0 additions & 1 deletion docs/reports/mapped_deprecated_omim.md
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| MONDO:0008873 | OMIM:210730 | MONDO:equivalentObsolete |
| MONDO:0009455 | OMIM:242870 | MONDO:equivalentObsolete |
| MONDO:0009535 | OMIM:247440 | MONDO:equivalentObsolete |
| MONDO:0009586 | OMIM:249660 | MONDO:equivalentObsolete |
| MONDO:0009654 | OMIM:252700 | MONDO:equivalentObsolete |
| MONDO:0010045 | OMIM:270710 | MONDO:equivalentObsolete |
| MONDO:0010291 | OMIM:300274 | MONDO:equivalentObsolete |
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1 change: 1 addition & 0 deletions docs/reports/mapped_deprecated_ordo.md
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| MONDO:0012414 | Orphanet:228337 | MONDO:equivalentObsolete |
| MONDO:0012588 | Orphanet:228366 | MONDO:equivalentObsolete |
| MONDO:0013297 | Orphanet:238755 | MONDO:equivalentObsolete |
| MONDO:0013621 | Orphanet:306507 | MONDO:equivalentObsolete |
| MONDO:0013866 | Orphanet:314629 | MONDO:equivalentObsolete |
| MONDO:0014147 | Orphanet:352709 | MONDO:equivalentObsolete |
| MONDO:0014788 | Orphanet:466801 | MONDO:equivalentObsolete |
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2 changes: 1 addition & 1 deletion docs/reports/migrate.md
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| [GARD](./migrate_gard.md) | 9,370 |
| [DOID](./migrate_doid.md) | 34 |
| [NCIT](./migrate_ncit.md) | 2,209 |
| [OMIM](./migrate_omim.md) | 13 |
| [OMIM](./migrate_omim.md) | 16 |
| [ICD11FOUNDATION](./migrate_icd11foundation.md) | 12,409 |
| [ICD10WHO](./migrate_icd10who.md) | 119 |
| [ORDO](./migrate_ordo.md) | 10 |
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5 changes: 4 additions & 1 deletion docs/reports/migrate_omim.md
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| MONDO:0970993 | immunodeficiency 119 | OMIM:620825 | MONDO:equivalentTo | immunodeficiency 119 | | MONDO:0021094 |
| MONDO:0970994 | immunodeficiency 120 | OMIM:620836 | MONDO:equivalentTo | immunodeficiency 120 | | MONDO:0021094 |
| MONDO:0970995 | premature ovarian failure 24 | OMIM:620840 | MONDO:equivalentTo | premature ovarian failure 24 | | MONDO:0019852 |
| MONDO:0970996 | mhc class ii deficiency | OMIMPS:209920 | MONDO:equivalentTo | MHC class II deficiency | | |
| MONDO:0970996 | mhc class ii deficiency | OMIMPS:209920 | MONDO:equivalentTo | MHC class II deficiency | | |
| MONDO:0970998 | auroneurodental syndrome | OMIM:620830 | MONDO:equivalentTo | auroneurodental syndrome | | |
| MONDO:0970999 | spermatogenic failure 92 | OMIM:620848 | MONDO:equivalentTo | spermatogenic failure 92 | | MONDO:0004983 |
| MONDO:0971000 | spermatogenic failure 93 | OMIM:620849 | MONDO:equivalentTo | spermatogenic failure 93 | | |
4 changes: 2 additions & 2 deletions docs/reports/unmapped.md
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| [NCIT](./unmapped_ncit.md) | 191,123 | 169,937 | 5,221 | 5,199 | 15,965 | 3,675 | 12,290 | 77.0% |
| [ICD11FOUNDATION](./unmapped_icd11foundation.md) | 100,382 | 30,335 | 6,587 | 6,587 | 64,451 | 0 | 64,451 | 100.0% |
| [GARD](./unmapped_gard.md) | 12,004 | 0 | 0 | 0 | 12,004 | 0 | 12,004 | 100.0% |
| [ORDO](./unmapped_ordo.md) | 15,402 | 6,212 | 1,391 | 1,166 | 9,190 | 9,127 | 63 | 0.7% |
| [ORDO](./unmapped_ordo.md) | 15,402 | 6,212 | 1,391 | 1,165 | 9,190 | 9,127 | 63 | 0.7% |
| [DOID](./unmapped_doid.md) | 14,058 | 2,655 | 2,483 | 2,468 | 11,401 | 11,367 | 34 | 0.3% |
| [OMIM](./unmapped_omim.md) | 29,357 | 19,260 | 1,364 | 1,317 | 8,734 | 8,712 | 22 | 0.3% |
| [OMIM](./unmapped_omim.md) | 29,360 | 19,260 | 1,364 | 1,318 | 8,737 | 8,712 | 25 | 0.3% |

`Ontology`: Name of ontology
`Tot terms`: Total terms in ontology
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3 changes: 3 additions & 0 deletions docs/reports/unmapped_omim.md
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| OMIM:620657 | amyloidosis, hereditary systemic 3 |
| OMIM:620658 | amyloidosis, hereditary systemic 5 |
| OMIM:620659 | amyloidosis, hereditary systemic 6 |
| OMIM:620830 | auroneurodental syndrome |
| OMIM:620806 | developmental and epileptic encephalopathy 116 |
| OMIM:620820 | el hayek-chahrour neurodevelopmental syndrome |
| OMIM:620825 | immunodeficiency 119 |
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| OMIM:620840 | premature ovarian failure 24 |
| OMIM:620819 | rothmund-thomson syndrome, type 4 |
| OMIM:620838 | spermatogenic failure 91 |
| OMIM:620848 | spermatogenic failure 92 |
| OMIM:620849 | spermatogenic failure 93 |
| OMIM:301119 | spermatogenic failure, x-linked, 8 |
2 changes: 1 addition & 1 deletion src/mappings/gard.sssom.tsv
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# skos: http://www.w3.org/2004/02/skos/core#
# sssom: https://w3id.org/sssom/
# license: https://w3id.org/sssom/license/unspecified
# mapping_set_id: https://w3id.org/sssom/mappings/bf20857c-043d-409a-b7a2-0aaf8997d749
# mapping_set_id: https://w3id.org/sssom/mappings/3307157d-269d-484d-8e06-41bb182eeb18
subject_id subject_label predicate_id object_id mapping_justification
obo:GARD_1 GRACILE syndrome skos:exactMatch Orphanet:53693 semapv:UnspecifiedMatching
obo:GARD_1 GRACILE syndrome skos:narrowMatch OMIM:603358 semapv:UnspecifiedMatching
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2 changes: 1 addition & 1 deletion src/mappings/icd10cm.sssom.tsv
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# skos: http://www.w3.org/2004/02/skos/core#
# sssom: https://w3id.org/sssom/
# license: https://w3id.org/sssom/license/unspecified
# mapping_set_id: https://w3id.org/sssom/mappings/f20d5636-2b78-431a-856a-bf2d25670274
# mapping_set_id: https://w3id.org/sssom/mappings/31eb5c24-9668-4254-ab1a-254b5120643c


2 changes: 1 addition & 1 deletion src/mappings/icd10who.sssom.tsv
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# skos: http://www.w3.org/2004/02/skos/core#
# sssom: https://w3id.org/sssom/
# license: https://w3id.org/sssom/license/unspecified
# mapping_set_id: https://w3id.org/sssom/mappings/f1f32f22-d5e8-4142-a91f-1f8d5ba9ba08
# mapping_set_id: https://w3id.org/sssom/mappings/425592e1-c66c-434b-a6a8-e0e984eab321


2 changes: 1 addition & 1 deletion src/mappings/icd11foundation.sssom.tsv
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# skos: http://www.w3.org/2004/02/skos/core#
# sssom: https://w3id.org/sssom/
# license: https://w3id.org/sssom/license/unspecified
# mapping_set_id: https://w3id.org/sssom/mappings/78841ed6-2aa6-4079-87ce-ad140e19741c
# mapping_set_id: https://w3id.org/sssom/mappings/16710c1c-e2ed-4759-ae4e-59d2b40613ea


2 changes: 1 addition & 1 deletion src/mappings/mondo-nando.sssom.tsv
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# mapping_provider: MONDO:NANDO
# mapping_set_description: This mapping set is manually curated by the NANDO team at
# nanbyodata.jp.
# mapping_set_id: https://w3id.org/sssom/mappings/4817534d-c1fe-4f66-8800-65e7e4c26d56
# mapping_set_id: https://w3id.org/sssom/mappings/67e59146-3141-455c-9d53-7d0d4eee2e39
# mapping_set_title: NANDO - Mondo mappings provided by nanbyodata.jp
subject_id subject_label predicate_id object_id object_label mapping_justification
MONDO:0000050 isolated congenital growth hormone deficiency skos:closeMatch NANDO:2200317 Congenital growth hormone deficiency semapv:MappingInversion
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2 changes: 1 addition & 1 deletion src/mappings/ncit.sssom.tsv
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# skos: http://www.w3.org/2004/02/skos/core#
# sssom: https://w3id.org/sssom/
# license: https://w3id.org/sssom/license/unspecified
# mapping_set_id: https://w3id.org/sssom/mappings/f1f8d9d9-2cee-40bc-b4c6-b19d8c97520c
# mapping_set_id: https://w3id.org/sssom/mappings/66648e7f-532b-4149-94fc-23c100d2699f
subject_id subject_label predicate_id object_id mapping_justification
NCIT:C103222 Popliteal Fossa oboInOwl:hasDbXref UBERON:0013069 semapv:UnspecifiedMatching
NCIT:C103384 Common Iliac Lymph Node oboInOwl:hasDbXref UBERON:0015878 semapv:UnspecifiedMatching
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