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DO NOT MERGE - Build for Updated bugfix icd11 generated synonyms #757

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DO NOT MERGE - Build for Updated bugfix icd11 generated synonyms #757

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40dd2fa
icd11 specific synonym sparql query fix
twhetzel Jan 16, 2025
cc128cd
add icd11 specific query to makefile for icd11 processing
twhetzel Jan 16, 2025
5736e96
build files
twhetzel Jan 17, 2025
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14 changes: 7 additions & 7 deletions docs/metrics/doid.md
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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/2024-12-23/doid.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2025-01-16/doid.owl

### Entities and axioms

| Metric | Value |
| ------ | ----- |
| Annotation properties | 28 |
| Axioms | 134288 |
| Axioms | 134297 |
| Logical axioms | 16444 |
| Classes | 13297 |
| Classes | 13298 |
| Object properties | 0 |
| Data properties | 0 |
| Individuals | 0 |
Expand All @@ -32,10 +32,10 @@

| Metric | Value |
| ------ | ----- |
| AnnotationAssertion | 104518 |
| AnnotationAssertion | 104526 |
| SubAnnotationPropertyOf | 2 |
| DisjointClasses | 26 |
| Declaration | 13324 |
| Declaration | 13325 |
| SubClassOf | 16418 |


Expand All @@ -62,7 +62,7 @@
| IAO | 2 |
| UBERON | 414 |
| SO | 18 |
| obo | 191 |
| obo | 192 |
| GENO | 10 |
| dc | 1 |

Expand All @@ -71,7 +71,7 @@

| Metric | Value |
| ------ | ----- |
| Class | 46345 |
| Class | 46346 |


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/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/2024-12-23/icd10cm.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2025-01-16/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/2024-12-23/icd10who.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2025-01-16/icd10who.owl

### Entities and axioms

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14 changes: 6 additions & 8 deletions 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/2024-12-23/icd11foundation.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2025-01-16/icd11foundation.owl

### Entities and axioms

| Metric | Value |
| ------ | ----- |
| Annotation properties | 12 |
| Axioms | 309765 |
| Annotation properties | 9 |
| Axioms | 305291 |
| Logical axioms | 65391 |
| Classes | 57711 |
| Object properties | 0 |
Expand All @@ -32,9 +32,8 @@

| Metric | Value |
| ------ | ----- |
| AnnotationAssertion | 186651 |
| SubAnnotationPropertyOf | 1 |
| Declaration | 57722 |
| AnnotationAssertion | 182181 |
| Declaration | 57719 |
| SubClassOf | 65391 |


Expand All @@ -43,13 +42,12 @@
| Metric | Value |
| ------ | ----- |
| prefix_unknown | 57713 |
| oboInOwl | 3 |
| oboInOwl | 1 |
| owl | 2 |
| rdf | 1 |
| IAO | 1 |
| xsd | 1 |
| rdfs | 2 |
| obo | 1 |
| dc | 1 |


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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/2024-12-23/ncit.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2025-01-16/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/2024-12-23/omim.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2025-01-16/omim.owl

### Entities and axioms

| Metric | Value |
| ------ | ----- |
| Annotation properties | 23 |
| Axioms | 373337 |
| Logical axioms | 28245 |
| Classes | 23610 |
| Axioms | 373426 |
| Logical axioms | 28264 |
| Classes | 23624 |
| Object properties | 7 |
| Data properties | 0 |
| Individuals | 0 |
Expand All @@ -32,17 +32,17 @@

| Metric | Value |
| ------ | ----- |
| AnnotationAssertion | 321454 |
| AnnotationAssertion | 321510 |
| SubAnnotationPropertyOf | 2 |
| Declaration | 23636 |
| SubClassOf | 28245 |
| Declaration | 23650 |
| SubClassOf | 28264 |


#### Entity namespaces: axiom counts by namespace

| Metric | Value |
| ------ | ----- |
| prefix_unknown | 22171 |
| prefix_unknown | 22185 |
| oboInOwl | 6 |
| owl | 2 |
| xsd | 1 |
Expand All @@ -62,8 +62,8 @@

| Metric | Value |
| ------ | ----- |
| Class | 80095 |
| ObjectSomeValuesFrom | 23263 |
| Class | 80147 |
| ObjectSomeValuesFrom | 23280 |


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/2024-12-23/ordo.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2025-01-16/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) | 48 |
| [DOID](./mapped_deprecated_doid.md) | 2 |
| [ORDO](./mapped_deprecated_ordo.md) | 190 |
| [OMIM](./mapped_deprecated_omim.md) | 45 |
| [ORDO](./mapped_deprecated_ordo.md) | 171 |
| [DOID](./mapped_deprecated_doid.md) | 1 |
| [ICD11FOUNDATION](./mapped_deprecated_icd11foundation.md) | 0 |
| [ICD10CM](./mapped_deprecated_icd10cm.md) | 0 |
| [ICD10WHO](./mapped_deprecated_icd10who.md) | 0 |
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3 changes: 1 addition & 2 deletions docs/reports/mapped_deprecated_doid.md
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| mondo_id | source_id | source |
|:--------------|:---------------------|:-------------------------|
| ID | A oboInOwl:hasDbXref | >A oboInOwl:source |
| MONDO:0011893 | DOID:0110578 | MONDO:equivalentObsolete |
| MONDO:0013209 | DOID:0080546 | MONDO:equivalentObsolete |
| MONDO:0011893 | DOID:0110578 | MONDO:equivalentObsolete |
3 changes: 0 additions & 3 deletions docs/reports/mapped_deprecated_omim.md
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| ID | A oboInOwl:hasDbXref | >A oboInOwl:source |
| MONDO:0000911 | OMIM:613740 | MONDO:equivalentObsolete |
| MONDO:0007061 | OMIM:102590 | MONDO:equivalentObsolete |
| MONDO:0007066 | OMIM:102800 | MONDO:equivalentObsolete |
| MONDO:0007602 | OMIM:134700 | MONDO:equivalentObsolete |
| MONDO:0007659 | OMIM:137560 | MONDO:equivalentObsolete |
| MONDO:0007779 | OMIM:145410 | MONDO:equivalentObsolete |
Expand All @@ -31,10 +30,8 @@
| 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:0010996 | OMIM:601101 | MONDO:equivalentObsolete |
| MONDO:0011111 | OMIM:601563 | MONDO:equivalentObsolete |
| MONDO:0011543 | OMIM:605365 | MONDO:equivalentObsolete |
| MONDO:0011893 | OMIM:607683 | MONDO:equivalentObsolete |
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19 changes: 0 additions & 19 deletions docs/reports/mapped_deprecated_ordo.md
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Expand Up @@ -7,26 +7,18 @@
| ID | A oboInOwl:hasDbXref | >A oboInOwl:source |
| MONDO:0001153 | Orphanet:459690 | MONDO:equivalentObsolete |
| MONDO:0001807 | Orphanet:79211 | MONDO:equivalentObsolete |
| MONDO:0001971 | Orphanet:99906 | MONDO:equivalentObsolete |
| MONDO:0005668 | Orphanet:99908 | MONDO:equivalentObsolete |
| MONDO:0007744 | Orphanet:79506 | MONDO:equivalentObsolete |
| MONDO:0007761 | Orphanet:413 | MONDO:equivalentObsolete |
| MONDO:0007779 | Orphanet:306588 | MONDO:equivalentObsolete |
| MONDO:0008401 | Orphanet:454821 | MONDO:equivalentObsolete |
| MONDO:0009317 | Orphanet:1245 | MONDO:equivalentObsolete |
| MONDO:0009971 | Orphanet:70587 | MONDO:equivalentObsolete |
| MONDO:0010045 | Orphanet:2823 | MONDO:equivalentObsolete |
| MONDO:0010994 | Orphanet:2641 | MONDO:equivalentObsolete |
| MONDO:0011054 | Orphanet:1027 | MONDO:equivalentObsolete |
| MONDO:0011910 | Orphanet:265 | MONDO:equivalentObsolete |
| MONDO:0012839 | Orphanet:183713 | MONDO:equivalentObsolete |
| MONDO:0015120 | Orphanet:101949 | MONDO:equivalentObsolete |
| MONDO:0015163 | Orphanet:102373 | MONDO:equivalentObsolete |
| MONDO:0015172 | Orphanet:103912 | MONDO:equivalentObsolete |
| MONDO:0015173 | Orphanet:103916 | MONDO:equivalentObsolete |
| MONDO:0015217 | Orphanet:108985 | MONDO:equivalentObsolete |
| MONDO:0015218 | Orphanet:108987 | MONDO:equivalentObsolete |
| MONDO:0015238 | Orphanet:1135 | MONDO:equivalentObsolete |
| MONDO:0015255 | Orphanet:1256 | MONDO:equivalentObsolete |
| MONDO:0015297 | Orphanet:137653 | MONDO:equivalentObsolete |
| MONDO:0015343 | Orphanet:139420 | MONDO:equivalentObsolete |
Expand All @@ -37,17 +29,13 @@
| MONDO:0015593 | Orphanet:163914 | MONDO:equivalentObsolete |
| MONDO:0015594 | Orphanet:163918 | MONDO:equivalentObsolete |
| MONDO:0015602 | Orphanet:163988 | MONDO:equivalentObsolete |
| MONDO:0015637 | Orphanet:166295 | MONDO:equivalentObsolete |
| MONDO:0015638 | Orphanet:166299 | MONDO:equivalentObsolete |
| MONDO:0015639 | Orphanet:166302 | MONDO:equivalentObsolete |
| MONDO:0015902 | Orphanet:181425 | MONDO:equivalentObsolete |
| MONDO:0015919 | Orphanet:182073 | MONDO:equivalentObsolete |
| MONDO:0015920 | Orphanet:182076 | MONDO:equivalentObsolete |
| 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:0016022 | Orphanet:1935 | MONDO:equivalentObsolete |
| MONDO:0016082 | Orphanet:2042 | MONDO:equivalentObsolete |
| MONDO:0016111 | Orphanet:206659 | MONDO:equivalentObsolete |
| MONDO:0016124 | Orphanet:206985 | MONDO:equivalentObsolete |
Expand All @@ -59,7 +47,6 @@
| MONDO:0016997 | Orphanet:263676 | MONDO:equivalentObsolete |
| MONDO:0017036 | Orphanet:264955 | MONDO:equivalentObsolete |
| MONDO:0017083 | Orphanet:268832 | MONDO:equivalentObsolete |
| MONDO:0017199 | Orphanet:2787 | MONDO:equivalentObsolete |
| MONDO:0017240 | Orphanet:280651 | MONDO:equivalentObsolete |
| MONDO:0017336 | Orphanet:289527 | MONDO:equivalentObsolete |
| MONDO:0017378 | Orphanet:2925 | MONDO:equivalentObsolete |
Expand All @@ -86,7 +73,6 @@
| MONDO:0018110 | Orphanet:35064 | MONDO:equivalentObsolete |
| MONDO:0018113 | Orphanet:35098 | MONDO:equivalentObsolete |
| MONDO:0018138 | Orphanet:352740 | MONDO:equivalentObsolete |
| MONDO:0018212 | Orphanet:36382 | MONDO:equivalentObsolete |
| MONDO:0018239 | Orphanet:364817 | MONDO:equivalentObsolete |
| MONDO:0018285 | Orphanet:371054 | MONDO:equivalentObsolete |
| MONDO:0018286 | Orphanet:371064 | MONDO:equivalentObsolete |
Expand All @@ -95,8 +81,6 @@
| MONDO:0018665 | Orphanet:448348 | MONDO:equivalentObsolete |
| MONDO:0018718 | Orphanet:458827 | MONDO:equivalentObsolete |
| MONDO:0018722 | Orphanet:458841 | MONDO:equivalentObsolete |
| MONDO:0018932 | Orphanet:57777 | MONDO:equivalentObsolete |
| MONDO:0018981 | Orphanet:64545 | MONDO:equivalentObsolete |
| MONDO:0019116 | Orphanet:717 | MONDO:equivalentObsolete |
| MONDO:0019348 | Orphanet:82004 | MONDO:equivalentObsolete |
| MONDO:0019389 | Orphanet:83648 | MONDO:equivalentObsolete |
Expand Down Expand Up @@ -182,16 +166,13 @@
| MONDO:0020282 | Orphanet:98714 | MONDO:equivalentObsolete |
| MONDO:0020489 | Orphanet:99763 | MONDO:equivalentObsolete |
| MONDO:0020524 | Orphanet:99878 | MONDO:equivalentObsolete |
| MONDO:0020535 | Orphanet:99907 | MONDO:equivalentObsolete |
| MONDO:0020537 | Orphanet:99909 | MONDO:equivalentObsolete |
| MONDO:0020742 | Orphanet:1317 | MONDO:equivalentObsolete |
| MONDO:0020871 | Orphanet:623 | MONDO:equivalentObsolete |
| MONDO:0021062 | Orphanet:306539 | MONDO:equivalentObsolete |
| MONDO:0022414 | Orphanet:1526 | MONDO:equivalentObsolete |
| MONDO:0022921 | Orphanet:2861 | MONDO:equivalentObsolete |
| MONDO:0023072 | Orphanet:1939 | MONDO:equivalentObsolete |
| MONDO:0033672 | Orphanet:50817 | MONDO:equivalentObsolete |
| MONDO:0043007 | Orphanet:330197 | MONDO:equivalentObsolete |
| MONDO:0044683 | Orphanet:498700 | MONDO:equivalentObsolete |
| MONDO:0044740 | Orphanet:500481 | MONDO:equivalentObsolete |
| MONDO:0100343 | Orphanet:93604 | MONDO:equivalentObsolete |
6 changes: 3 additions & 3 deletions docs/reports/migrate.md
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@@ -1,11 +1,11 @@
# Migratable terms
| Ontology | Tot |
|:------------------------------------------------|:------|
| [DOID](./migrate_doid.md) | 94 |
| [DOID](./migrate_doid.md) | 95 |
| [ORDO](./migrate_ordo.md) | 62 |
| [OMIM](./migrate_omim.md) | 45 |
| [OMIM](./migrate_omim.md) | 50 |
| [ICD11FOUNDATION](./migrate_icd11foundation.md) | 4,593 |
| [NCIT](./migrate_ncit.md) | 2,211 |
| [NCIT](./migrate_ncit.md) | 2,228 |
| [ICD10WHO](./migrate_icd10who.md) | 119 |
| [ICD10CM](./migrate_icd10cm.md) | 1,894 |

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3 changes: 2 additions & 1 deletion docs/reports/migrate_doid.md
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Expand Up @@ -98,4 +98,5 @@
| MONDO:0975946 | combined pituitary hormone deficiency 3 | DOID:0061021 | MONDO:equivalentTo | combined pituitary hormone deficiency 3 | | MONDO:0019591,MONDO:0006025 |
| MONDO:0975947 | combined pituitary hormone deficiency 6 | DOID:0061022 | MONDO:equivalentTo | combined pituitary hormone deficiency 6 | | MONDO:0019591,MONDO:0000426 |
| MONDO:0975948 | nonphotosensitive trichothiodystrophy 8 | DOID:0061023 | MONDO:equivalentTo | nonphotosensitive trichothiodystrophy 8 | | MONDO:0009317,MONDO:0006025 |
| MONDO:0975949 | nonphotosensitive trichothiodystrophy 9 | DOID:0061024 | MONDO:equivalentTo | nonphotosensitive trichothiodystrophy 9 | | MONDO:0009317,MONDO:0006025 |
| MONDO:0975949 | nonphotosensitive trichothiodystrophy 9 | DOID:0061024 | MONDO:equivalentTo | nonphotosensitive trichothiodystrophy 9 | | MONDO:0009317,MONDO:0006025 |
| MONDO:0976003 | variable age at onset electroclinical syndrome | DOID:0050706 | MONDO:equivalentTo | variable age at onset electroclinical syndrome | An electroclinial syndrome that is characterized by development of seizures later in life with a variable age of onset and duration. | MONDO:0000411 |
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