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Create mondo-nando.sssom.tsv - build #552

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Create mondo-nando.sssom.tsv - build #552

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b2e8975
Create mondo-nando.sssom.tsv
matentzn May 16, 2024
3162499
Update mondo-nando.sssom.tsv
matentzn May 16, 2024
f73e752
Update mondo-ingest.Makefile
matentzn May 16, 2024
10bf971
NanDO mappings
joeflack4 May 16, 2024
7db4fe2
Update mondo-nando.sssom.tsv
matentzn May 17, 2024
7b02948
Merge branch 'nando-mapping-set' of https://github.com/monarch-initia…
matentzn May 17, 2024
5776667
Update mapping set pipeline
matentzn May 17, 2024
11ee478
Update goal: $(EXTERNAL_CONTENT_DIR)/nando-mappings.robot.tsv
joeflack4 May 17, 2024
4e03662
Update src/scripts/sssom_to_robot_template.py
joeflack4 May 17, 2024
5ce6083
Update src/scripts/sssom_to_robot_template.py
joeflack4 May 17, 2024
227d5c7
SSSOMtoROBOT & NanDO mappings
joeflack4 May 17, 2024
8bad880
Update goal $(MAPPINGSDIR)/%.sssom.tsv:
joeflack4 May 19, 2024
02a07f5
Update sssom_to_robot_template
joeflack4 May 19, 2024
33601ae
Update nando-mondo.sssom.tsv
matentzn May 31, 2024
92e439f
Merge branch 'main' into nando-mapping-set
matentzn May 31, 2024
1d2ca97
Fixed the remaining issues of the pipeline
matentzn May 31, 2024
e1d16e0
NanDO mapping set - build
joeflack4 Jun 1, 2024
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21 changes: 10 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/2024-05-28/doid.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-01/doid.owl

### Entities and axioms

| Metric | Value |
| ------ | ----- |
| Annotation properties | 27 |
| Axioms | 115971 |
| Logical axioms | 16110 |
| Classes | 13099 |
| Object properties | 2 |
| Axioms | 110948 |
| Logical axioms | 16161 |
| Classes | 13124 |
| Object properties | 0 |
| Data properties | 0 |
| Individuals | 0 |

Expand All @@ -32,11 +32,11 @@

| Metric | Value |
| ------ | ----- |
| AnnotationAssertion | 86733 |
| AnnotationAssertion | 81636 |
| SubAnnotationPropertyOf | 1 |
| DisjointClasses | 26 |
| Declaration | 13127 |
| SubClassOf | 16084 |
| Declaration | 13150 |
| SubClassOf | 16135 |


#### Entity namespaces: axiom counts by namespace
Expand All @@ -45,12 +45,11 @@
| ------ | ----- |
| oboInOwl | 12 |
| owl | 2 |
| DOID | 11552 |
| DOID | 11577 |
| HP | 118 |
| xsd | 1 |
| CL | 63 |
| skos | 5 |
| BFO | 2 |
| rdfs | 2 |
| FOODON | 24 |
| NCBITaxon | 322 |
Expand All @@ -71,7 +70,7 @@

| Metric | Value |
| ------ | ----- |
| Class | 45479 |
| Class | 45606 |


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/2024-05-28/gard.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-01/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/2024-05-28/icd10cm.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-01/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/2024-05-28/icd10who.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-01/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/2024-05-28/icd11foundation.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-01/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/2024-05-28/ncit.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-01/ncit.owl

### Entities and axioms

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2 changes: 1 addition & 1 deletion 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/2024-05-28/omim.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-01/omim.owl

### Entities and axioms

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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/2024-05-28/ordo.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-06-01/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 |
| [DOID](./migrate_doid.md) | 8 |
| [DOID](./migrate_doid.md) | 34 |
| [NCIT](./migrate_ncit.md) | 2,209 |
| [OMIM](./migrate_omim.md) | 13 |
| [ICD11FOUNDATION](./migrate_icd11foundation.md) | 12,409 |
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48 changes: 37 additions & 11 deletions docs/reports/migrate_doid.md
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2 changes: 1 addition & 1 deletion docs/reports/migrate_ncit.md
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| MONDO:0856703 | eyelid vascular disorder | NCIT:C35198 | MONDO:equivalentTo | Eyelid Vascular Disorder | | |
| MONDO:0856706 | placental polyp | NCIT:C3521 | MONDO:equivalentTo | Placental Polyp | | MONDO:0021498|MONDO:0005079 |
| MONDO:0856715 | chondromatosis | NCIT:C35259 | MONDO:equivalentTo | Chondromatosis | | MONDO:0024470 |
| MONDO:0856716 | malignant submandibular gland neoplasm | NCIT:C3526 | MONDO:equivalentTo | Malignant Submandibular Gland Neoplasm | | MONDO:0044743|MONDO:0021244 |
| MONDO:0856716 | malignant submandibular gland neoplasm | NCIT:C3526 | MONDO:equivalentTo | Malignant Submandibular Gland Neoplasm | | MONDO:0021244|MONDO:0044743 |
| MONDO:0856723 | malignant palate neoplasm | NCIT:C3530 | MONDO:equivalentTo | Malignant Palate Neoplasm | | MONDO:0005515|MONDO:0005286 |
| MONDO:0856758 | malignant neoplasm of multiple primary sites | NCIT:C35427 | MONDO:equivalentTo | Malignant Neoplasm of Multiple Primary Sites | | MONDO:0004992 |
| MONDO:0856764 | behavioral disorder | NCIT:C35470 | MONDO:equivalentTo | Behavioral Disorder | | |
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2 changes: 1 addition & 1 deletion docs/reports/unmapped.md
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| [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% |
| [DOID](./unmapped_doid.md) | 14,058 | 2,655 | 2,483 | 2,468 | 11,401 | 11,367 | 34 | 0.3% |
| [OMIM](./unmapped_omim.md) | 29,346 | 19,253 | 1,364 | 1,317 | 8,730 | 8,712 | 18 | 0.2% |
| [DOID](./unmapped_doid.md) | 14,033 | 2,655 | 2,483 | 2,468 | 11,376 | 11,368 | 8 | 0.1% |

`Ontology`: Name of ontology
`Tot terms`: Total terms in ontology
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46 changes: 36 additions & 10 deletions docs/reports/unmapped_doid.md
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[Interactive FlatGithub table](https://flatgithub.com/monarch-initiative/mondo-ingest?filename=src/ontology/reports/doid_mapping_status.tsv)

### Unmapped mappable terms _(!excluded, !deprecated)_
| subject_id | subject_label |
|:-------------|:-----------------------------------------------------------------|
| DOID:2934 | aleutian mink disease |
| DOID:5154 | borna disease |
| DOID:0060160 | childhood spinal muscular atrophy |
| DOID:0111368 | cholesterol-ester transfer protein deficiency |
| DOID:2536 | chronic inflammatory demyelinating polyneuritis |
| DOID:4668 | congenital kyphosis |
| DOID:0060333 | mitochondrial complex V (ATP synthase) deficiency nuclear type 4 |
| DOID:9373 | postural kyphosis |
| subject_id | subject_label |
|:-------------|:-------------------------------------------------------------------------------------|
| DOID:0070541 | 3-hydroxy-3-methylglutaryl-CoA lyase deficiency |
| DOID:0060949 | 3-hydroxyisobutryl-CoA hydrolase deficiency |
| DOID:0060970 | Cornelia de Lange syndrome 6 |
| DOID:0081453 | Dent disease 1 |
| DOID:0081454 | Dent disease 2 |
| DOID:0060954 | Holoprosencephaly 13, X-linked |
| DOID:0060964 | Loeys-Dietz syndrome 6 |
| DOID:0060948 | Ullrich congenital muscular dystrophy 2 |
| DOID:0060953 | ZTTK syndrome |
| DOID:2934 | aleutian mink disease |
| DOID:5154 | borna disease |
| DOID:0060160 | childhood spinal muscular atrophy |
| DOID:0111368 | cholesterol-ester transfer protein deficiency |
| DOID:2536 | chronic inflammatory demyelinating polyneuritis |
| DOID:0070544 | congenital glutamine deficiency |
| DOID:4668 | congenital kyphosis |
| DOID:0070545 | developmental and epileptic encephalopathy 116 |
| DOID:0060965 | episodic ataxia type 9 |
| DOID:0060969 | galactosemia 4 |
| DOID:0060950 | hypervalinemia and hyperleucine-isoleucinemia |
| DOID:0060968 | hypotrichosis 15 |
| DOID:0060333 | mitochondrial complex V (ATP synthase) deficiency nuclear type 4 |
| DOID:0070540 | mitochondrial short-chain enoyl-CoA hydratase 1 deficiency |
| DOID:0070543 | neurodevelopmental disorder with cardiomyopathy, spasticity, and brain abnormalities |
| DOID:0070542 | neurodevelopmental disorder with spastic paraplegia and microcephaly |
| DOID:0060959 | orofaciodigital syndrome II |
| DOID:0060958 | orofaciodigital syndrome XIV |
| DOID:0060960 | orofaciodigital syndrome XIX |
| DOID:0060961 | orofaciodigital syndrome XVIII |
| DOID:0060962 | orofaciodigital syndrome XX |
| DOID:146 | papilledema |
| DOID:0060951 | polycystic kidney disease 6 |
| DOID:0060952 | polycystic kidney disease 7 |
| DOID:9373 | postural kyphosis |
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