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data build on main following mondo release (#676)
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* data build on main following mondo release

* remove logs file
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@twhetzel
twhetzel authored Oct 4, 2024
1 parent 0f7fe00 commit 66cd017
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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/2024-09-27/doid.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-10-04/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/2024-09-27/gard.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-10-04/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/2024-09-27/icd10cm.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-10-04/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/2024-09-27/icd10who.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-10-04/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/2024-09-27/icd11foundation.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-10-04/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/2024-09-27/ncit.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-10-04/ncit.owl

### Entities and axioms

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23 changes: 12 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/2024-09-27/omim.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-10-04/omim.owl

### Entities and axioms

| Metric | Value |
| ------ | ----- |
| Annotation properties | 20 |
| Axioms | 355637 |
| Logical axioms | 26237 |
| Classes | 22971 |
| Annotation properties | 21 |
| Axioms | 355754 |
| Logical axioms | 26248 |
| Classes | 22976 |
| Object properties | 7 |
| Data properties | 0 |
| Individuals | 0 |
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| Metric | Value |
| ------ | ----- |
| AnnotationAssertion | 306404 |
| AnnotationAssertion | 306504 |
| SubAnnotationPropertyOf | 2 |
| Declaration | 22994 |
| SubClassOf | 26237 |
| Declaration | 23000 |
| SubClassOf | 26248 |


#### Entity namespaces: axiom counts by namespace

| Metric | Value |
| ------ | ----- |
| prefix_unknown | 21529 |
| prefix_unknown | 21534 |
| oboInOwl | 4 |
| owl | 2 |
| xsd | 1 |
| skos | 1 |
| rdfs | 2 |
| CHR | 1445 |
| OMO | 1 |
| MONDO | 1 |
| rdf | 1 |
| IAO | 2 |
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| Metric | Value |
| ------ | ----- |
| Class | 75435 |
| ObjectSomeValuesFrom | 21274 |
| Class | 75462 |
| ObjectSomeValuesFrom | 21276 |


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/2024-09-27/ordo.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-10-04/ordo.owl

### Entities and axioms

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2 changes: 1 addition & 1 deletion docs/reports/migrate.md
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| Ontology | Tot |
|:------------------------------------------------|:------|
| [GARD](./migrate_gard.md) | 9,370 |
| [OMIM](./migrate_omim.md) | 9 |
| [ICD11FOUNDATION](./migrate_icd11foundation.md) | 4,593 |
| [DOID](./migrate_doid.md) | 37 |
| [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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8 changes: 7 additions & 1 deletion docs/reports/migrate_omim.md
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| MONDO:0975800 | spinocerebellar ataxia 51 | OMIM:620947 | MONDO:equivalentTo | spinocerebellar ataxia 51 | | MONDO:0020380 |
| MONDO:0975801 | encephalopathy, acute transient | OMIM:620950 | MONDO:equivalentTo | encephalopathy, acute transient | | |
| MONDO:0975802 | homocystinuria-megaloblastic anemia | OMIMPS:236270 | MONDO:equivalentTo | Homocystinuria-megaloblastic anemia | | |
| MONDO:0975803 | methylmalonic aciduria | OMIMPS:251000 | MONDO:equivalentTo | Methylmalonic aciduria | | |
| MONDO:0975803 | methylmalonic aciduria | OMIMPS:251000 | MONDO:equivalentTo | Methylmalonic aciduria | | |
| MONDO:0975805 | foveal hypoplasia 3 | OMIM:620958 | MONDO:equivalentTo | foveal hypoplasia 3 | | MONDO:0044203 |
| MONDO:0975806 | multiple mitochondrial dysfunctions syndrome 10 | OMIM:620960 | MONDO:equivalentTo | multiple mitochondrial dysfunctions syndrome 10 | | MONDO:0017338 |
| MONDO:0975807 | cholestasis, progressive familial intrahepatic, 13 | OMIM:620962 | MONDO:equivalentTo | cholestasis, progressive familial intrahepatic, 13 | | MONDO:0015762 |
| MONDO:0975808 | congenital myopathy 25 | OMIM:620964 | MONDO:equivalentTo | congenital myopathy 25 | | MONDO:0019952 |
| MONDO:0975809 | microphthalmia/coloboma 13 | OMIM:620968 | MONDO:equivalentTo | microphthalmia/coloboma 13 | | |
| MONDO:0975810 | short stature with nonspecific skeletal abnormalities | OMIMPS:616255 | MONDO:equivalentTo | Short stature with nonspecific skeletal abnormalities | | |
2 changes: 1 addition & 1 deletion docs/reports/unmapped.md
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| [GARD](./unmapped_gard.md) | 12,004 | 0 | 0 | 0 | 12,004 | 0 | 12,004 | 100.0% |
| [ORDO](./unmapped_ordo.md) | 15,561 | 6,270 | 1,424 | 1,257 | 9,291 | 9,214 | 77 | 0.8% |
| [DOID](./unmapped_doid.md) | 14,158 | 2,660 | 2,488 | 2,478 | 11,496 | 11,458 | 38 | 0.3% |
| [OMIM](./unmapped_omim.md) | 29,473 | 19,341 | 1,366 | 1,324 | 8,767 | 8,758 | 9 | 0.1% |
| [OMIM](./unmapped_omim.md) | 29,489 | 19,348 | 1,366 | 1,324 | 8,776 | 8,759 | 17 | 0.2% |

`Ontology`: Name of ontology
`Tot terms`: Total terms in ontology
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8 changes: 8 additions & 0 deletions docs/reports/unmapped_omim.md
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|:--------------|:---------------------------------------------------------------------------------------------------|
| OMIMPS:236270 | Homocystinuria-megaloblastic anemia |
| OMIMPS:251000 | Methylmalonic aciduria |
| OMIMPS:616255 | Short stature with nonspecific skeletal abnormalities |
| OMIM:620943 | brain malformation renal syndrome |
| OMIM:620962 | cholestasis, progressive familial intrahepatic, 13 |
| OMIM:620964 | congenital myopathy 25 |
| OMIM:620950 | encephalopathy, acute transient |
| OMIM:620958 | foveal hypoplasia 3 |
| OMIM:620952 | homocystinuria-megaloblastic anemia, cbld type |
| OMIM:620937 | kariminejad-reversade neurodevelopmental syndrome |
| OMIM:620940 | methylmalonic aciduria and homocystinuria, cbll type |
| OMIM:620953 | methylmalonic aciduria, cbld type |
| OMIM:620968 | microphthalmia/coloboma 13 |
| OMIM:620960 | multiple mitochondrial dysfunctions syndrome 10 |
| OMIM:620939 | myelofibrosis, congenital, with anemia, neutropenia, developmental delay, and ocular abnormalities |
| OMIM:620938 | spastic paraplegia 93, autosomal recessive |
| OMIM:620947 | spinocerebellar ataxia 51 |
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/a18a538b-ede7-49ec-87cd-9de708a78ba7
# mapping_set_id: https://w3id.org/sssom/mappings/dbe19073-b69b-4537-8a59-d4696fe42fb8
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/1436dca0-2b74-4db6-bf37-db22c44b84ca
# mapping_set_id: https://w3id.org/sssom/mappings/5f0af989-719f-4598-a831-bba89bceb133


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/79dcd770-f17b-4e53-922d-53d0790729ff
# mapping_set_id: https://w3id.org/sssom/mappings/407735a7-0a26-4029-9f0d-4b16e0721b3f


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/fc744708-b1ae-474f-aa0a-fb1d5c6dfb1e
# mapping_set_id: https://w3id.org/sssom/mappings/e36646ed-63a0-4bd7-8cf3-79d50591b979


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/5c6175fe-1e15-4556-af2a-97162743263c
# mapping_set_id: https://w3id.org/sssom/mappings/64c84b64-26cc-4b36-b359-56587bc44478
# 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/b8e0acc7-e2b5-45fe-adbc-ed9377a12c9a
# mapping_set_id: https://w3id.org/sssom/mappings/aee502af-5c5c-4076-a72e-b161f397d08c
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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