Skip to content

Commit

Permalink
Merge pull request #673 from monarch-initiative/_develop_data-build-2…
Browse files Browse the repository at this point in the history 
…7Sep2024

Data build to merge into main
  • Loading branch information
@twhetzel
twhetzel authored Oct 4, 2024
2 parents 1fc274b + 2105513 commit 0f7fe00
Show file tree
Hide file tree
Showing 138 changed files with 92,115 additions and 13,297 deletions.
13 changes: 4 additions & 9 deletions .gitignore
View file
Original file line number Diff line number Diff line change
Expand Up @@ -41,15 +41,6 @@ src/mappings/mondo-sources-all-lexical-2.sssom.tsv

# src/ontology/
src/ontology/.template.db
src/ontology/mirror
src/ontology/mirror/*
src/ontology/reports/*.ttl
!src/ontology/reports/README.md
!src/ontology/reports/*excluded_terms_in_mondo_xrefs.tsv
!src/ontology/reports/*exclusion_reasons.robot.template.tsv
!src/ontology/reports/*excluded_terms.txt
src/ontology/reports/mondo-ingest-edit.owl-obo-report.tsv

src/ontology/mondo-ingest.owl
src/ontology/mondo-ingest.obo
src/ontology/mondo-ingest.json
Expand Down Expand Up @@ -85,6 +76,10 @@ src/ontology/mirror/*
src/ontology/reports/*.ttl
src/ontology/reports/*.subclass.direct-in-mondo-only.tsv
src/ontology/reports/mondo-ingest-edit.owl-obo-report.tsv
!src/ontology/reports/README.md
!src/ontology/reports/*excluded_terms_in_mondo_xrefs.tsv
!src/ontology/reports/*exclusion_reasons.robot.template.tsv
!src/ontology/reports/*excluded_terms.txt
# todo: These ! patterns don't seem to be an exception to anything that would currently be ignoring them, so I don't think they're needed. Commented out. - Joe 2023/11/16
#!src/ontology/reports/README.md
#!src/ontology/reports/*excluded_terms_in_mondo_xrefs.tsv
Expand Down
23 changes: 12 additions & 11 deletions docs/metrics/doid.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,16 +2,16 @@

**IRI:** http://purl.obolibrary.org/obo/mondo/sources/doid.owl

**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-09-12/doid.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-09-27/doid.owl

### Entities and axioms

| Metric | Value |
| ------ | ----- |
| Annotation properties | 27 |
| Axioms | 129444 |
| Logical axioms | 16297 |
| Classes | 13204 |
| Annotation properties | 28 |
| Axioms | 133598 |
| Logical axioms | 16341 |
| Classes | 13230 |
| Object properties | 0 |
| Data properties | 0 |
| Individuals | 0 |
Expand All @@ -32,11 +32,11 @@

| Metric | Value |
| ------ | ----- |
| AnnotationAssertion | 99916 |
| SubAnnotationPropertyOf | 1 |
| AnnotationAssertion | 103998 |
| SubAnnotationPropertyOf | 2 |
| DisjointClasses | 26 |
| Declaration | 13230 |
| SubClassOf | 16271 |
| Declaration | 13257 |
| SubClassOf | 16315 |


#### Entity namespaces: axiom counts by namespace
Expand All @@ -45,7 +45,7 @@
| ------ | ----- |
| oboInOwl | 12 |
| owl | 2 |
| DOID | 11646 |
| DOID | 11672 |
| HP | 114 |
| xsd | 1 |
| CL | 62 |
Expand All @@ -55,6 +55,7 @@
| NCBITaxon | 322 |
| TRANS | 13 |
| SYMP | 306 |
| OMO | 1 |
| dc11 | 2 |
| rdf | 1 |
| CHEBI | 90 |
Expand All @@ -70,7 +71,7 @@

| Metric | Value |
| ------ | ----- |
| Class | 45958 |
| Class | 46072 |


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).
Expand Down
2 changes: 1 addition & 1 deletion docs/metrics/gard.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@

**IRI:** http://purl.obolibrary.org/obo/mondo/sources/gard.owl

**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-09-12/gard.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-09-27/gard.owl

### Entities and axioms

Expand Down
2 changes: 1 addition & 1 deletion docs/metrics/icd10cm.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@

**IRI:** http://purl.obolibrary.org/obo/mondo/sources/icd10cm.owl

**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-09-12/icd10cm.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-09-27/icd10cm.owl

### Entities and axioms

Expand Down
2 changes: 1 addition & 1 deletion docs/metrics/icd10who.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@

**IRI:** http://purl.obolibrary.org/obo/mondo/sources/icd10who.owl

**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-09-12/icd10who.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-09-27/icd10who.owl

### Entities and axioms

Expand Down
2 changes: 1 addition & 1 deletion docs/metrics/icd11foundation.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@

**IRI:** http://purl.obolibrary.org/obo/mondo/sources/icd11foundation.owl

**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-09-12/icd11foundation.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-09-27/icd11foundation.owl

### Entities and axioms

Expand Down
6 changes: 3 additions & 3 deletions docs/metrics/ncit.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,14 +2,14 @@

**IRI:** http://purl.obolibrary.org/obo/mondo/sources/ncit.owl

**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-09-12/ncit.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-09-27/ncit.owl

### Entities and axioms

| Metric | Value |
| ------ | ----- |
| Annotation properties | 12 |
| Axioms | 623839 |
| Axioms | 1328208 |
| Logical axioms | 33655 |
| Classes | 15971 |
| Object properties | 0 |
Expand All @@ -32,7 +32,7 @@

| Metric | Value |
| ------ | ----- |
| AnnotationAssertion | 574182 |
| AnnotationAssertion | 1278551 |
| EquivalentClasses | 6260 |
| DatatypeDefinition | 19 |
| AnnotationPropertyRangeOf | 1 |
Expand Down
26 changes: 13 additions & 13 deletions docs/metrics/omim.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,16 +2,16 @@

**IRI:** http://purl.obolibrary.org/obo/mondo/sources/omim.owl

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

### Entities and axioms

| Metric | Value |
| ------ | ----- |
| Annotation properties | 19 |
| Axioms | 355487 |
| Logical axioms | 26217 |
| Classes | 22957 |
| Annotation properties | 20 |
| Axioms | 355637 |
| Logical axioms | 26237 |
| Classes | 22971 |
| Object properties | 7 |
| Data properties | 0 |
| Individuals | 0 |
Expand All @@ -32,17 +32,17 @@

| Metric | Value |
| ------ | ----- |
| AnnotationAssertion | 306290 |
| SubAnnotationPropertyOf | 1 |
| Declaration | 22979 |
| SubClassOf | 26217 |
| AnnotationAssertion | 306404 |
| SubAnnotationPropertyOf | 2 |
| Declaration | 22994 |
| SubClassOf | 26237 |


#### Entity namespaces: axiom counts by namespace

| Metric | Value |
| ------ | ----- |
| prefix_unknown | 21515 |
| prefix_unknown | 21529 |
| oboInOwl | 4 |
| owl | 2 |
| xsd | 1 |
Expand All @@ -54,15 +54,15 @@
| IAO | 2 |
| biolink | 2 |
| RO | 7 |
| obo | 2 |
| obo | 3 |


#### Class expressions used

| Metric | Value |
| ------ | ----- |
| Class | 75381 |
| ObjectSomeValuesFrom | 21262 |
| Class | 75435 |
| ObjectSomeValuesFrom | 21274 |


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).
Expand Down
2 changes: 1 addition & 1 deletion docs/metrics/ordo.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@

**IRI:** http://purl.obolibrary.org/obo/mondo/sources/ordo.owl

**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-09-12/ordo.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-09-27/ordo.owl

### Entities and axioms

Expand Down
2 changes: 1 addition & 1 deletion docs/reports/mapped_deprecated.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3,11 +3,11 @@
|:----------------------------------------------------------|--------------------------:|
| [NCIT](./mapped_deprecated_ncit.md) | 5 |
| [OMIM](./mapped_deprecated_omim.md) | 42 |
| [DOID](./mapped_deprecated_doid.md) | 3 |
| [ORDO](./mapped_deprecated_ordo.md) | 167 |
| [GARD](./mapped_deprecated_gard.md) | 0 |
| [ICD11FOUNDATION](./mapped_deprecated_icd11foundation.md) | 0 |
| [ICD10CM](./mapped_deprecated_icd10cm.md) | 0 |
| [DOID](./mapped_deprecated_doid.md) | 0 |
| [ICD10WHO](./mapped_deprecated_icd10who.md) | 0 |

`Ontology`: Name of ontology
Expand Down
9 changes: 3 additions & 6 deletions docs/reports/mapped_deprecated_doid.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,9 +2,6 @@
[Interactive FlatGithub table](https://flatgithub.com/monarch-initiative/mondo-ingest?filename=src/ontology/reports/doid_mapped_deprecated_terms.robot.template.tsv)

### Mapped deprecated terms
| mondo_id | source_id | source |
|:--------------|:---------------------|:-------------------------|
| ID | A oboInOwl:hasDbXref | >A oboInOwl:source |
| MONDO:0010542 | DOID:0081164 | MONDO:equivalentObsolete |
| MONDO:0011893 | DOID:0110578 | MONDO:equivalentObsolete |
| MONDO:0015701 | DOID:0060015 | MONDO:equivalentObsolete |
| mondo_id | source_id | source |
|:-----------|:---------------------|:-------------------|
| ID | A oboInOwl:hasDbXref | >A oboInOwl:source |
10 changes: 5 additions & 5 deletions docs/reports/migrate.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,13 +2,13 @@
| Ontology | Tot |
|:------------------------------------------------|:------|
| [GARD](./migrate_gard.md) | 9,370 |
| [DOID](./migrate_doid.md) | 53 |
| [ICD11FOUNDATION](./migrate_icd11foundation.md) | 4,594 |
| [NCIT](./migrate_ncit.md) | 2,209 |
| [OMIM](./migrate_omim.md) | 9 |
| [ICD11FOUNDATION](./migrate_icd11foundation.md) | 4,593 |
| [DOID](./migrate_doid.md) | 37 |
| [NCIT](./migrate_ncit.md) | 2,211 |
| [ORDO](./migrate_ordo.md) | 13 |
| [ICD10WHO](./migrate_icd10who.md) | 119 |
| [ICD10CM](./migrate_icd10cm.md) | 1,892 |
| [OMIM](./migrate_omim.md) | 1 |
| [ICD10CM](./migrate_icd10cm.md) | 1,894 |

### Codebook
`Ontology`: Name of ontology
Expand Down
Loading

0 comments on commit 0f7fe00

Please sign in to comment.