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Merge pull request #704 from monarch-initiative/develop-data21112024
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Data build 21 Nov 2023 (develop)
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@matentzn
matentzn authored Nov 21, 2024
2 parents 7216182 + 3e65b80 commit 595da7f
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4 changes: 3 additions & 1 deletion .gitignore
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Expand Up @@ -13,6 +13,7 @@ semantic.cache/
*.tmp.owl
*.tmp.json
*.db
!/tests/input/**/*.db
.vscode/*

# - static
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src/scripts/mondo_unmapped.tsv

# Test
tests/output/
tests/output/*
!tests/output/.gitkeep
src/scripts/dataframes/*
src/ontology/reports/gard.subclass.added-obsolete.robot.tsv
src/ontology/reports/gard.subclass.added.robot.tsv
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12 changes: 12 additions & 0 deletions docs/developer/workflows.md
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Expand Up @@ -70,6 +70,7 @@ These workflows will help with excluding certain terms from integration into Mon
## Synchronization
These workflows help synchronize Mondo with source ontologies.

### Sub-class of
#### Makefile goals
1. `generate-synchronization-files`: Runs synchronization pipeline.
2. `sync-subclassof`: Runs 'sync-subclassof' part of synchronization pipeline, generating set of outputs for all ontologies.
Expand All @@ -80,3 +81,14 @@ These workflows help synchronize Mondo with source ontologies.
7. `reports/%.subclass.direct-in-mondo-only.tsv`: Path to create file for relations for given ontology where direct subclass relation exists only in Mondo and not in the source. Running this also runs / generates `reports/%.subclass.added.robot.tsv`, `reports/%.subclass.added-obsolete.robot.tsv`, and `reports/%.subclass.confirmed.robot.tsv`.
8. `reports/sync-subClassOf.direct-in-mondo-only.tsv`: For all subclass relationships in Mondo, shows which sources do not have it and whether no source has it. Combination of all `--outpath-direct-in-mondo-only` outputs for all sources, using those as inputs, and then deletes them after.
9. `reports/sync-subClassOf.confirmed.tsv`: For all subclass relationships in Mondo, by source, a robot template containing showing what is in Mondo and are confirmed to also exist in the source. Combination of all `--outpath-confirmed` outputs for all sources.

### Synonyms
#### Makefile goals
1. `sync-synonyms`: Runs 'sync-synonyms' part of synchronization pipeline, creating outputs for all sources for each of the 4 cases - 'added', 'confirmed', 'updated', and 'deleted'.
2. `reports/%.subclass.added.robot.tsv`: ROBOT template TSV to create which will contain synonyms that aren't yet integrated into Mondo for all mapped source terms.
3. `reports/%.subclass.confirmed.robot.tsv`: ROBOT template TSV to create which will contain synonym confirmations; combination of synonym scope predicate and synonym string exists in both source and Mondo for a given mapping.
4. `reports/%.subclass.deleted.robot.tsv`: ROBOT template TSV to create which will contain synonym deletions; exists in Mondo but not in source(s) for a given mapping.
5. `reports/%.subclass.updated.robot.tsv`: ROBOT template TSV to create which will contain updates to synonym scope predicate; cases where the synonym exists in Mondo and on the mapped source term, but the scope predicate is different.
6. `reports/sync-synonyms.added.tsv`: Combination of all 'added' synonym outputs for all sources.
7. `reports/sync-synonyms.confirmed.tsv`: Combination of all 'confirmed' synonym outputs for all sources.
8. `reports/sync-synonyms.updated.tsv`: Combination of all 'updated' synonym outputs for all sources.
6 changes: 3 additions & 3 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/2024-11-11/doid.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-11-21/doid.owl

### Entities and axioms

| Metric | Value |
| ------ | ----- |
| Annotation properties | 28 |
| Axioms | 133759 |
| Axioms | 133761 |
| Logical axioms | 16363 |
| Classes | 13250 |
| Object properties | 0 |
Expand All @@ -32,7 +32,7 @@

| Metric | Value |
| ------ | ----- |
| AnnotationAssertion | 104117 |
| AnnotationAssertion | 104119 |
| SubAnnotationPropertyOf | 2 |
| DisjointClasses | 26 |
| Declaration | 13277 |
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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/2024-11-11/gard.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-11-21/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/2024-11-11/icd10cm.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-11-21/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/2024-11-11/icd10who.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-11-21/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/2024-11-11/icd11foundation.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-11-21/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/2024-11-11/ncit.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-11-21/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/2024-11-11/omim.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-11-21/omim.owl

### Entities and axioms

| Metric | Value |
| ------ | ----- |
| Annotation properties | 21 |
| Axioms | 356172 |
| Logical axioms | 26272 |
| Classes | 23008 |
| Axioms | 358729 |
| Logical axioms | 28206 |
| Classes | 23591 |
| Object properties | 7 |
| Data properties | 0 |
| Individuals | 0 |
Expand All @@ -32,17 +32,17 @@

| Metric | Value |
| ------ | ----- |
| AnnotationAssertion | 306866 |
| AnnotationAssertion | 306906 |
| SubAnnotationPropertyOf | 2 |
| Declaration | 23032 |
| SubClassOf | 26272 |
| Declaration | 23615 |
| SubClassOf | 28206 |


#### Entity namespaces: axiom counts by namespace

| Metric | Value |
| ------ | ----- |
| prefix_unknown | 21569 |
| prefix_unknown | 22152 |
| oboInOwl | 4 |
| owl | 2 |
| xsd | 1 |
Expand All @@ -62,8 +62,8 @@

| Metric | Value |
| ------ | ----- |
| Class | 75545 |
| ObjectSomeValuesFrom | 21308 |
| Class | 79998 |
| ObjectSomeValuesFrom | 23242 |


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/2024-11-11/ordo.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-11-21/ordo.owl

### Entities and axioms

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6 changes: 3 additions & 3 deletions docs/reports/mapped_deprecated.md
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| Ontology | Tot deprecated in Mondo |
|:----------------------------------------------------------|--------------------------:|
| [NCIT](./mapped_deprecated_ncit.md) | 5 |
| [OMIM](./mapped_deprecated_omim.md) | 43 |
| [ORDO](./mapped_deprecated_ordo.md) | 168 |
| [OMIM](./mapped_deprecated_omim.md) | 46 |
| [ORDO](./mapped_deprecated_ordo.md) | 169 |
| [DOID](./mapped_deprecated_doid.md) | 1 |
| [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
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7 changes: 4 additions & 3 deletions docs/reports/mapped_deprecated_doid.md
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Expand Up @@ -2,6 +2,7 @@
[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_id | source_id | source |
|:--------------|:---------------------|:-------------------------|
| ID | A oboInOwl:hasDbXref | >A oboInOwl:source |
| MONDO:0011893 | DOID:0110578 | MONDO:equivalentObsolete |
3 changes: 3 additions & 0 deletions docs/reports/mapped_deprecated_omim.md
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Expand Up @@ -17,6 +17,7 @@
| MONDO:0008126 | OMIM:164891 | MONDO:equivalentObsolete |
| MONDO:0008204 | OMIM:168850 | MONDO:equivalentObsolete |
| MONDO:0008415 | OMIM:181515 | MONDO:equivalentObsolete |
| MONDO:0009455 | OMIM:242870 | MONDO:equivalentObsolete |
| MONDO:0009535 | OMIM:247440 | MONDO:equivalentObsolete |
| MONDO:0009654 | OMIM:252700 | MONDO:equivalentObsolete |
| MONDO:0010045 | OMIM:270710 | MONDO:equivalentObsolete |
Expand All @@ -29,10 +30,12 @@
| MONDO:0010527 | OMIM:301590 | MONDO:equivalentObsolete |
| MONDO:0010601 | OMIM:306500 | MONDO:equivalentObsolete |
| MONDO:0010666 | OMIM:309605 | MONDO:equivalentObsolete |
| MONDO:0010760 | OMIM:314800 | MONDO:equivalentObsolete |
| MONDO:0010804 | OMIM:600048 | MONDO:equivalentObsolete |
| MONDO:0010859 | OMIM:600309 | MONDO:equivalentObsolete |
| MONDO:0011111 | OMIM:601563 | MONDO:equivalentObsolete |
| MONDO:0011543 | OMIM:605365 | MONDO:equivalentObsolete |
| MONDO:0011893 | OMIM:607683 | MONDO:equivalentObsolete |
| MONDO:0011910 | OMIM:607801 | MONDO:equivalentObsolete |
| MONDO:0012461 | OMIM:610269 | MONDO:equivalentObsolete |
| MONDO:0012560 | OMIM:610799 | MONDO:equivalentObsolete |
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1 change: 1 addition & 0 deletions docs/reports/mapped_deprecated_ordo.md
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Expand Up @@ -35,6 +35,7 @@
| MONDO:0015937 | Orphanet:182214 | MONDO:equivalentObsolete |
| MONDO:0015964 | Orphanet:183598 | MONDO:equivalentObsolete |
| MONDO:0015965 | Orphanet:183601 | MONDO:equivalentObsolete |
| MONDO:0015985 | Orphanet:1844 | MONDO:equivalentObsolete |
| MONDO:0016082 | Orphanet:2042 | MONDO:equivalentObsolete |
| MONDO:0016111 | Orphanet:206659 | MONDO:equivalentObsolete |
| MONDO:0016124 | Orphanet:206985 | 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) | 50 |
| [ICD11FOUNDATION](./migrate_icd11foundation.md) | 4,593 |
| [OMIM](./migrate_omim.md) | 34 |
| [OMIM](./migrate_omim.md) | 37 |
| [NCIT](./migrate_ncit.md) | 2,211 |
| [ORDO](./migrate_ordo.md) | 13 |
| [ICD10WHO](./migrate_icd10who.md) | 119 |
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5 changes: 4 additions & 1 deletion docs/reports/migrate_omim.md
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Expand Up @@ -38,4 +38,7 @@
| MONDO:0975841 | fibromatosis, gingival, 6 | OMIM:620999 | MONDO:equivalentTo | fibromatosis, gingival, 6 | | MONDO:0016070 |
| MONDO:0975842 | spermatogenic failure 96 | OMIM:621001 | MONDO:equivalentTo | spermatogenic failure 96 | | MONDO:0004983 |
| MONDO:0975843 | premature ovarian failure 25 | OMIM:621002 | MONDO:equivalentTo | premature ovarian failure 25 | | MONDO:0019852 |
| MONDO:0975844 | acth-independent macronodular adrenal hyperplasia | OMIMPS:219080 | MONDO:equivalentTo | ACTH-independent macronodular adrenal hyperplasia | | |
| MONDO:0975844 | acth-independent macronodular adrenal hyperplasia | OMIMPS:219080 | MONDO:equivalentTo | ACTH-independent macronodular adrenal hyperplasia | | |
| MONDO:0975846 | congenital disorder of glycosylation, type 1dd | OMIM:301133 | MONDO:equivalentTo | congenital disorder of glycosylation, type 1dd | | |
| MONDO:0975847 | autoimmune disease with susceptibility to mycobacterium tuberculosis | OMIM:621004 | MONDO:equivalentTo | autoimmune disease with susceptibility to mycobacterium tuberculosis | | |
| MONDO:0975848 | morimoto-ryu-malicdan neuromuscular syndrome | OMIM:621010 | MONDO:equivalentTo | morimoto-ryu-malicdan neuromuscular syndrome | | |
8 changes: 4 additions & 4 deletions docs/reports/unmapped.md
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| Ontology | Tot terms | Tot excluded | Tot deprecated | Tot deprecated unmapped | Tot mappable _(!excluded, !deprecated)_ | Tot mapped _(mappable)_ | Tot unmapped _(mappable)_ | % unmapped _(mappable)_ |
|:-------------------------------------------------|:------------|:---------------|:-----------------|:--------------------------|:------------------------------------------|:--------------------------|:----------------------------|:--------------------------|
| [ICD10WHO](./unmapped_icd10who.md) | 12,542 | 0 | 0 | 0 | 12,542 | 18 | 12,524 | 99.9% |
| [ICD10CM](./unmapped_icd10cm.md) | 95,847 | 15,452 | 0 | 0 | 80,395 | 1,165 | 79,230 | 98.6% |
| [ICD10CM](./unmapped_icd10cm.md) | 95,847 | 15,452 | 0 | 0 | 80,395 | 1,166 | 79,229 | 98.5% |
| [ICD11FOUNDATION](./unmapped_icd11foundation.md) | 57,713 | 0 | 5,594 | 5,594 | 52,119 | 4,108 | 48,011 | 92.1% |
| [NCIT](./unmapped_ncit.md) | 191,123 | 169,937 | 5,221 | 5,216 | 15,965 | 3,676 | 12,289 | 77.0% |
| [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 | 1,256 | 9,291 | 9,214 | 77 | 0.8% |
| [DOID](./unmapped_doid.md) | 14,172 | 2,660 | 2,488 | 2,478 | 11,510 | 11,457 | 53 | 0.5% |
| [OMIM](./unmapped_omim.md) | 29,537 | 19,376 | 1,367 | 1,324 | 8,795 | 8,758 | 37 | 0.4% |
| [ORDO](./unmapped_ordo.md) | 15,561 | 6,270 | 1,424 | 1,255 | 9,291 | 9,214 | 77 | 0.8% |
| [DOID](./unmapped_doid.md) | 14,172 | 2,660 | 2,488 | 2,477 | 11,510 | 11,457 | 53 | 0.5% |
| [OMIM](./unmapped_omim.md) | 29,542 | 19,377 | 1,368 | 1,322 | 8,798 | 8,758 | 40 | 0.5% |

`Ontology`: Name of ontology
`Tot terms`: Total terms in ontology
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1 change: 0 additions & 1 deletion docs/reports/unmapped_icd10cm.md
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| ICD10CM:D12.9 | Benign neoplasm of anus and anal canal |
| ICD10CM:D35.6 | Benign neoplasm of aortic body and other paraganglia |
| ICD10CM:D12.2 | Benign neoplasm of ascending colon |
| ICD10CM:D30.3 | Benign neoplasm of bladder |
| ICD10CM:D16 | Benign neoplasm of bone and articular cartilage |
| ICD10CM:D16.9 | Benign neoplasm of bone and articular cartilage, unspecified |
| ICD10CM:D16.4 | Benign neoplasm of bones of skull and face |
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