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Merge pull request #436 from monarch-initiative/data-release-09092024
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Data release files 09.02.2024
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sabrinatoro authored Feb 9, 2024
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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/2024-02-04/doid.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-02-09/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/2024-02-04/gard.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-02-09/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/2024-02-04/icd10cm.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-02-09/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/2024-02-04/icd10who.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-02-09/icd10who.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/2024-02-04/ncit.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-02-09/ncit.owl

### Entities and axioms

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26 changes: 13 additions & 13 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/2024-02-04/omim.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-02-09/omim.owl

### Entities and axioms

| Metric | Value |
| ------ | ----- |
| Annotation properties | 13 |
| Axioms | 320535 |
| Logical axioms | 19160 |
| Classes | 19392 |
| Object properties | 6 |
| Annotation properties | 16 |
| Axioms | 344611 |
| Logical axioms | 22561 |
| Classes | 19399 |
| Object properties | 7 |
| Data properties | 0 |
| Individuals | 0 |

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| Metric | Value |
| ------ | ----- |
| AnnotationAssertion | 281968 |
| Declaration | 19407 |
| SubClassOf | 19160 |
| AnnotationAssertion | 302632 |
| Declaration | 19418 |
| SubClassOf | 22561 |


#### Entity namespaces: axiom counts by namespace

| Metric | Value |
| ------ | ----- |
| prefix_unknown | 17946 |
| prefix_unknown | 17956 |
| MONDO | 1 |
| oboInOwl | 3 |
| owl | 2 |
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| rdfs | 2 |
| CHR | 1446 |
| biolink | 2 |
| RO | 6 |
| RO | 7 |


#### Class expressions used

| Metric | Value |
| ------ | ----- |
| Class | 57706 |
| ObjectSomeValuesFrom | 14306 |
| Class | 64513 |
| ObjectSomeValuesFrom | 17706 |


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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6 changes: 3 additions & 3 deletions 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/2024-02-04/ordo.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-02-09/ordo.owl

### Entities and axioms

| Metric | Value |
| ------ | ----- |
| Annotation properties | 8 |
| Axioms | 155842 |
| Axioms | 162312 |
| Logical axioms | 42481 |
| Classes | 14917 |
| Object properties | 3 |
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| Metric | Value |
| ------ | ----- |
| AnnotationAssertion | 98435 |
| AnnotationAssertion | 104905 |
| Declaration | 14926 |
| SubClassOf | 42481 |

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2 changes: 1 addition & 1 deletion docs/reports/mapped_deprecated.md
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| [DOID](./mapped_deprecated_doid.md) | 3 |
| [ORDO](./mapped_deprecated_ordo.md) | 225 |
| [NCIT](./mapped_deprecated_ncit.md) | 12 |
| [GARD](./mapped_deprecated_gard.md) | 0 |
| [ICD10CM](./mapped_deprecated_icd10cm.md) | 0 |
| [ICD10WHO](./mapped_deprecated_icd10who.md) | 0 |
| [GARD](./mapped_deprecated_gard.md) | 0 |

`Ontology`: Name of ontology
`Tot deprecated in Mondo`: Total terms that the ontology source itself has deprecated which have existing xrefs in Mondo
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2 changes: 1 addition & 1 deletion docs/reports/migrate.md
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|:----------------------------------|:------|
| [ORDO](./migrate_ordo.md) | 97 |
| [GARD](./migrate_gard.md) | 9,370 |
| [OMIM](./migrate_omim.md) | 32 |
| [OMIM](./migrate_omim.md) | 8 |
| [NCIT](./migrate_ncit.md) | 2,179 |
| [DOID](./migrate_doid.md) | 188 |
| [ICD10WHO](./migrate_icd10who.md) | 119 |
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46 changes: 11 additions & 35 deletions docs/reports/migrate_omim.md
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[Interactive FlatGithub table](https://flatgithub.com/monarch-initiative/mondo-ingest?filename=src/ontology/slurp/omim.tsv)

### Migratable terms
| mondo_id | mondo_label | xref | xref_source | original_label | definition | parents |
|:--------------|:-----------------------------------------------------------------------|:---------------------|:---------------------------|:-----------------------------------------------------------------------|:--------------|:----------------------------|
| ID | LABEL | A oboInOwl:hasDbXref | >A oboInOwl:source SPLIT=| | | A IAO:0000115 | SC % |
| MONDO:0957597 | li-fraumeni syndrome | OMIMPS:151623 | MONDO:equivalentTo | Li-Fraumeni syndrome | | |
| MONDO:0958027 | fg syndrome | OMIMPS:305450 | MONDO:equivalentTo | FG syndrome | | |
| MONDO:0958030 | immunodeficiency 118 | OMIM:301115 | MONDO:equivalentTo | immunodeficiency 118 | | MONDO:0021094 |
| MONDO:0958034 | lipodystrophy, familial partial, iia 9 | OMIM:620683 | MONDO:equivalentTo | lipodystrophy, familial partial, iia 9 | | |
| MONDO:0958035 | premature ovarian failure 23 | OMIM:620686 | MONDO:equivalentTo | premature ovarian failure 23 | | MONDO:0019852 |
| MONDO:0958037 | developmental dysplasia of the hip 3 | OMIM:620690 | MONDO:equivalentTo | developmental dysplasia of the hip 3 | | |
| MONDO:0958039 | myoclonic epilepsy of lafora | OMIMPS:254780 | MONDO:equivalentTo | Myoclonic epilepsy of Lafora | | |
| MONDO:0958040 | supranuclear palsy, progressive | OMIMPS:601104 | MONDO:equivalentTo | Supranuclear palsy, progressive | | |
| MONDO:0958174 | basal cell nevus syndrome 1 | OMIM:109400 | MONDO:equivalentTo | basal cell nevus syndrome 1 | | MONDO:0007187 |
| MONDO:0958175 | craniofacial microsomia 1 | OMIM:164210 | MONDO:equivalentTo | craniofacial microsomia 1 | | MONDO:0015397 |
| MONDO:0958176 | oculopharyngeal muscular dystrophy 1 | OMIM:164300 | MONDO:equivalentTo | oculopharyngeal muscular dystrophy 1 | | MONDO:0008116 |
| MONDO:0958177 | chronic recurrent multifocal osteomyelitis 3 | OMIM:259680 | MONDO:equivalentTo | chronic recurrent multifocal osteomyelitis 3 | | MONDO:0009813 |
| MONDO:0958178 | cataracts, hearing impairment, nephrotic syndrome, and enterocolitis 1 | OMIM:301108 | MONDO:equivalentTo | cataracts, hearing impairment, nephrotic syndrome, and enterocolitis 1 | | MONDO:0957400 |
| MONDO:0958179 | glycine encephalopathy 1 | OMIM:605899 | MONDO:equivalentTo | glycine encephalopathy 1 | | MONDO:0011612 |
| MONDO:0958180 | prolonged electroretinal response suppression 1 | OMIM:608415 | MONDO:equivalentTo | prolonged electroretinal response suppression 1 | | MONDO:0012033 |
| MONDO:0958181 | mitochondrial trifunctional protein deficiency 1 | OMIM:609015 | MONDO:equivalentTo | mitochondrial trifunctional protein deficiency 1 | | MONDO:0012172 |
| MONDO:0958182 | c1q deficiency 1 | OMIM:613652 | MONDO:equivalentTo | c1q deficiency 1 | | MONDO:0013343 |
| MONDO:0958183 | leber-like hereditary optic neuropathy, autosomal recessive 1 | OMIM:619382 | MONDO:equivalentTo | leber-like hereditary optic neuropathy, autosomal recessive 1 | | MONDO:0030309|MONDO:0100223 |
| MONDO:0958184 | epidermolytic hyperkeratosis 2 | OMIM:620150 | MONDO:equivalentTo | epidermolytic hyperkeratosis 2 | | MONDO:0957316 |
| MONDO:0958185 | mitochondrial trifunctional protein deficiency 2 | OMIM:620300 | MONDO:equivalentTo | mitochondrial trifunctional protein deficiency 2 | | MONDO:0012172 |
| MONDO:0958186 | hematuria, benign familial, 2 | OMIM:620320 | MONDO:equivalentTo | hematuria, benign familial, 2 | | MONDO:0957317 |
| MONDO:0958187 | c1q deficiency 2 | OMIM:620321 | MONDO:equivalentTo | c1q deficiency 2 | | MONDO:0013343 |
| MONDO:0958188 | c1q deficiency 3 | OMIM:620322 | MONDO:equivalentTo | c1q deficiency 3 | | MONDO:0013343 |
| MONDO:0958189 | basal cell nevus syndrome 2 | OMIM:620343 | MONDO:equivalentTo | basal cell nevus syndrome 2 | | MONDO:0007187 |
| MONDO:0958190 | prolonged electroretinal response suppression 2 | OMIM:620344 | MONDO:equivalentTo | prolonged electroretinal response suppression 2 | | MONDO:0012033 |
| MONDO:0958191 | nephrolithiasis, calcium oxalate, 2, with or without nephrocalcinosis | OMIM:620374 | MONDO:equivalentTo | nephrolithiasis, calcium oxalate, 2, with or without nephrocalcinosis | | MONDO:0957318 |
| MONDO:0958192 | glycine encephalopathy 2 | OMIM:620398 | MONDO:equivalentTo | glycine encephalopathy 2 | | MONDO:0011612 |
| MONDO:0958193 | cataracts, hearing impairment, nephrotic syndrome, and enterocolitis 2 | OMIM:620425 | MONDO:equivalentTo | cataracts, hearing impairment, nephrotic syndrome, and enterocolitis 2 | | MONDO:0957400 |
| MONDO:0958194 | craniofacial microsomia 2 | OMIM:620444 | MONDO:equivalentTo | craniofacial microsomia 2 | | MONDO:0015397 |
| MONDO:0958195 | oculopharyngeal muscular dystrophy 2 | OMIM:620460 | MONDO:equivalentTo | oculopharyngeal muscular dystrophy 2 | | MONDO:0008116 |
| MONDO:0958196 | epilepsy, early-onset, 3, with or without developmental delay | OMIM:620465 | MONDO:equivalentTo | epilepsy, early-onset, 3, with or without developmental delay | | MONDO:0957599 |
| MONDO:0958197 | leber-like hereditary optic neuropathy, autosomal recessive 2 | OMIM:620569 | MONDO:equivalentTo | leber-like hereditary optic neuropathy, autosomal recessive 2 | | MONDO:0030309 |
| mondo_id | mondo_label | xref | xref_source | original_label | definition | parents |
|:--------------|:------------------------------------------------------------|:---------------------|:---------------------------|:------------------------------------------------------------|:--------------|:----------|
| ID | LABEL | A oboInOwl:hasDbXref | >A oboInOwl:source SPLIT=| | | A IAO:0000115 | SC % |
| MONDO:0958199 | myoclonic epilepsy of lafora 1 | OMIM:254780 | MONDO:equivalentTo | myoclonic epilepsy of lafora 1 | | |
| MONDO:0958200 | intellectual developmental disorder, x-linked 113 | OMIM:301116 | MONDO:equivalentTo | intellectual developmental disorder, X-linked 113 | | |
| MONDO:0958201 | myoclonic epilepsy of lafora 2 | OMIM:620681 | MONDO:equivalentTo | myoclonic epilepsy of lafora 2 | | |
| MONDO:0958202 | moyamoya disease 7 | OMIM:620687 | MONDO:equivalentTo | moyamoya disease 7 | | |
| MONDO:0958203 | intellectual developmental disorder, autosomal dominant 74 | OMIM:620688 | MONDO:equivalentTo | intellectual developmental disorder, autosomal dominant 74 | | |
| MONDO:0958204 | intellectual developmental disorder, autosomal recessive 81 | OMIM:620700 | MONDO:equivalentTo | intellectual developmental disorder, autosomal recessive 81 | | |
| MONDO:0958205 | yuksel-vogel-bauer syndrome | OMIM:620703 | MONDO:equivalentTo | yuksel-vogel-bauer syndrome | | |
| MONDO:0958206 | spermatogenic failure 89 | OMIM:620705 | MONDO:equivalentTo | spermatogenic failure 89 | | |
2 changes: 1 addition & 1 deletion docs/reports/unmapped.md
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| [DOID](./unmapped_doid.md) | 13,982 | 2,646 | 2,481 | 2,468 | 11,334 | 11,084 | 250 | 2.2% |
| [GARD](./unmapped_gard.md) | 12,004 | 0 | 0 | 0 | 12,004 | 0 | 12,004 | 100.0% |
| [ORDO](./unmapped_ordo.md) | 10,915 | 1,724 | 1,391 | 1,166 | 9,191 | 9,025 | 166 | 1.8% |
| [OMIM](./unmapped_omim.md) | 29,176 | 19,174 | 1,359 | 1,316 | 8,644 | 8,611 | 33 | 0.4% |
| [OMIM](./unmapped_omim.md) | 29,200 | 19,185 | 1,359 | 1,316 | 8,657 | 8,648 | 9 | 0.1% |

`Ontology`: Name of ontology
`Tot terms`: Total terms in ontology
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