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Merge pull request #686 from monarch-initiative/_main_data-build-11No…
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…v2024

data build files on main
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@twhetzel
twhetzel authored Nov 12, 2024
2 parents eceb06a + 271d64b commit 7216182
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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/2024-11-09/doid.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-11-11/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/2024-11-09/gard.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-11-11/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/2024-11-09/icd10cm.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-11-11/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/2024-11-09/icd10who.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-11-11/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/2024-11-09/icd11foundation.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-11-11/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/2024-11-09/ncit.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-11-11/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/2024-11-09/omim.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-11-11/omim.owl

### Entities and axioms

| Metric | Value |
| ------ | ----- |
| Annotation properties | 21 |
| Axioms | 356115 |
| Logical axioms | 26262 |
| Classes | 23005 |
| Axioms | 356172 |
| Logical axioms | 26272 |
| Classes | 23008 |
| Object properties | 7 |
| Data properties | 0 |
| Individuals | 0 |
Expand All @@ -32,17 +32,17 @@

| Metric | Value |
| ------ | ----- |
| AnnotationAssertion | 306822 |
| AnnotationAssertion | 306866 |
| SubAnnotationPropertyOf | 2 |
| Declaration | 23029 |
| SubClassOf | 26262 |
| Declaration | 23032 |
| SubClassOf | 26272 |


#### Entity namespaces: axiom counts by namespace

| Metric | Value |
| ------ | ----- |
| prefix_unknown | 21566 |
| prefix_unknown | 21569 |
| oboInOwl | 4 |
| owl | 2 |
| xsd | 1 |
Expand All @@ -62,8 +62,8 @@

| Metric | Value |
| ------ | ----- |
| Class | 75522 |
| ObjectSomeValuesFrom | 21301 |
| Class | 75545 |
| ObjectSomeValuesFrom | 21308 |


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/2024-11-09/ordo.owl
**Version IRI:** http://purl.obolibrary.org/obo/mondo/sources/2024-11-11/ordo.owl

### Entities and axioms

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6 changes: 3 additions & 3 deletions docs/reports/migrate_omim.md
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| MONDO:0975810 | short stature with nonspecific skeletal abnormalities | OMIMPS:616255 | MONDO:equivalentTo | Short stature with nonspecific skeletal abnormalities | | |
| MONDO:0975826 | arthrogryposis multiplex congenita 7, x-linked | OMIM:301127 | MONDO:equivalentTo | arthrogryposis multiplex congenita 7, X-linked | | MONDO:0015168 |
| MONDO:0975827 | orofaciodigital syndrome 21 | OMIM:301132 | MONDO:equivalentTo | orofaciodigital syndrome 21 | | MONDO:0015375 |
| MONDO:0975828 | intellectual developmental disorder, x-linked 114 | OMIM:301134 | MONDO:equivalentTo | intellectual developmental disorder, X-linked 114 | | |
| MONDO:0975828 | intellectual developmental disorder, x-linked 114 | OMIM:301134 | MONDO:equivalentTo | intellectual developmental disorder, X-linked 114 | | MONDO:0019181 |
| MONDO:0975829 | anemia, congenital dyserythropoietic, type ivb | OMIM:620969 | MONDO:equivalentTo | anemia, congenital dyserythropoietic, type ivb | | MONDO:0019403 |
| MONDO:0975830 | myopathy with myalgia, increased serum creatine kinase, and with or without episodic rhabdomyolysis 2 | OMIM:620971 | MONDO:equivalentTo | myopathy with myalgia, increased serum creatine kinase, and with or without episodic rhabdomyolysis 2 | | |
| MONDO:0975831 | blood group, anton system | OMIM:620975 | MONDO:equivalentTo | blood group, anton system | | |
Expand All @@ -36,6 +36,6 @@
| MONDO:0975839 | pancreatic agenesis 3 | OMIM:620991 | MONDO:equivalentTo | pancreatic agenesis 3 | | MONDO:0009832 |
| MONDO:0975840 | retinitis pigmentosa 98 | OMIM:620996 | MONDO:equivalentTo | retinitis pigmentosa 98 | | MONDO:0019200 |
| 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:0975843 | premature ovarian failure 25 | OMIM:621002 | MONDO:equivalentTo | premature ovarian failure 25 | | |
| 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 | | |
2 changes: 1 addition & 1 deletion docs/reports/unmapped.md
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| [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) | 29,532 | 19,371 | 1,367 | 1,324 | 8,795 | 8,758 | 37 | 0.4% |
| [OMIM](./unmapped_omim.md) | 29,537 | 19,376 | 1,367 | 1,324 | 8,795 | 8,758 | 37 | 0.4% |

`Ontology`: Name of ontology
`Tot terms`: Total terms in ontology
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2 changes: 1 addition & 1 deletion src/mappings/gard.sssom.tsv
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# skos: http://www.w3.org/2004/02/skos/core#
# sssom: https://w3id.org/sssom/
# license: https://w3id.org/sssom/license/unspecified
# mapping_set_id: https://w3id.org/sssom/mappings/638c7360-1045-42e9-ad3f-2b89da705226
# mapping_set_id: https://w3id.org/sssom/mappings/0a81d7f9-31b9-4e12-90ac-b2ec378b7e3f
subject_id subject_label predicate_id object_id mapping_justification
obo:GARD_1 GRACILE syndrome skos:exactMatch Orphanet:53693 semapv:UnspecifiedMatching
obo:GARD_1 GRACILE syndrome skos:narrowMatch OMIM:603358 semapv:UnspecifiedMatching
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2 changes: 1 addition & 1 deletion src/mappings/icd10cm.sssom.tsv
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# skos: http://www.w3.org/2004/02/skos/core#
# sssom: https://w3id.org/sssom/
# license: https://w3id.org/sssom/license/unspecified
# mapping_set_id: https://w3id.org/sssom/mappings/2c109aa8-08fe-4f70-97c2-e0e898d430d4
# mapping_set_id: https://w3id.org/sssom/mappings/7181634f-e0fd-4df0-9134-98884172d804


2 changes: 1 addition & 1 deletion src/mappings/icd10who.sssom.tsv
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# skos: http://www.w3.org/2004/02/skos/core#
# sssom: https://w3id.org/sssom/
# license: https://w3id.org/sssom/license/unspecified
# mapping_set_id: https://w3id.org/sssom/mappings/56361ca8-483d-42a3-9992-233a0ac947f2
# mapping_set_id: https://w3id.org/sssom/mappings/e2665dc1-fe61-42ee-ac4e-439aeededd13


2 changes: 1 addition & 1 deletion src/mappings/icd11foundation.sssom.tsv
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# skos: http://www.w3.org/2004/02/skos/core#
# sssom: https://w3id.org/sssom/
# license: https://w3id.org/sssom/license/unspecified
# mapping_set_id: https://w3id.org/sssom/mappings/bb416a7b-9ff4-4ca8-aad4-3e284ffaf6cb
# mapping_set_id: https://w3id.org/sssom/mappings/5e66dbb7-0a1c-4e91-96ee-a5672357651f


2 changes: 1 addition & 1 deletion src/mappings/mondo-nando.sssom.tsv
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# mapping_provider: MONDO:NANDO
# mapping_set_description: This mapping set is manually curated by the NANDO team at
# nanbyodata.jp.
# mapping_set_id: https://w3id.org/sssom/mappings/7ee7aad3-4c30-4d6f-b5b6-bf7df88adc74
# mapping_set_id: https://w3id.org/sssom/mappings/edb09e28-49e0-4b78-af29-dcec3ac5763f
# mapping_set_title: NANDO - Mondo mappings provided by nanbyodata.jp
subject_id subject_label predicate_id object_id object_label mapping_justification
MONDO:0000050 isolated congenital growth hormone deficiency skos:closeMatch NANDO:2200317 Congenital growth hormone deficiency semapv:MappingInversion
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2 changes: 1 addition & 1 deletion src/mappings/ncit.sssom.tsv
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# skos: http://www.w3.org/2004/02/skos/core#
# sssom: https://w3id.org/sssom/
# license: https://w3id.org/sssom/license/unspecified
# mapping_set_id: https://w3id.org/sssom/mappings/67925cc6-35a2-4a81-ba84-68743f1a17b3
# mapping_set_id: https://w3id.org/sssom/mappings/08db7978-fe7e-439d-af53-934ffa8a7c9d
subject_id subject_label predicate_id object_id mapping_justification
NCIT:C103222 Popliteal Fossa oboInOwl:hasDbXref UBERON:0013069 semapv:UnspecifiedMatching
NCIT:C103384 Common Iliac Lymph Node oboInOwl:hasDbXref UBERON:0015878 semapv:UnspecifiedMatching
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12 changes: 12 additions & 0 deletions src/mappings/omim.sssom.tsv
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Expand Up @@ -26236,6 +26236,9 @@ OMIM:301130 RTL3 skos:exactMatch ncbigene:203430 semapv:UnspecifiedMatching
OMIM:301131 RTL4 skos:exactMatch hgnc.symbol:25214 semapv:UnspecifiedMatching
OMIM:301131 RTL4 skos:exactMatch hgnc.symbol:RTL4 semapv:UnspecifiedMatching
OMIM:301131 RTL4 skos:exactMatch ncbigene:340595 semapv:UnspecifiedMatching
OMIM:301135 RTL5 skos:exactMatch hgnc.symbol:29430 semapv:UnspecifiedMatching
OMIM:301135 RTL5 skos:exactMatch hgnc.symbol:RTL5 semapv:UnspecifiedMatching
OMIM:301135 RTL5 skos:exactMatch ncbigene:340526 semapv:UnspecifiedMatching
OMIM:301200 amelogenesis imperfecta, type 1e skos:exactMatch MONDO:0010521 semapv:UnspecifiedMatching
OMIM:301201 amelogenesis imperfecta, hypoplastic/hypomaturation, X-linked 2 skos:exactMatch MONDO:0010522 semapv:UnspecifiedMatching
OMIM:301201 amelogenesis imperfecta, hypoplastic/hypomaturation, X-linked 2 skos:exactMatch hgnc.symbol:AIH3 semapv:UnspecifiedMatching
Expand Down Expand Up @@ -81866,6 +81869,15 @@ OMIM:620998 ZNF230 skos:exactMatch ncbigene:7773 semapv:UnspecifiedMatching
OMIM:621000 SNX18 skos:exactMatch hgnc.symbol:19245 semapv:UnspecifiedMatching
OMIM:621000 SNX18 skos:exactMatch hgnc.symbol:SNX18 semapv:UnspecifiedMatching
OMIM:621000 SNX18 skos:exactMatch ncbigene:112574 semapv:UnspecifiedMatching
OMIM:621003 SP9 skos:exactMatch hgnc.symbol:30690 semapv:UnspecifiedMatching
OMIM:621003 SP9 skos:exactMatch hgnc.symbol:SP9 semapv:UnspecifiedMatching
OMIM:621003 SP9 skos:exactMatch ncbigene:100131390 semapv:UnspecifiedMatching
OMIM:621005 SBSPON skos:exactMatch hgnc.symbol:30362 semapv:UnspecifiedMatching
OMIM:621005 SBSPON skos:exactMatch hgnc.symbol:SBSPON semapv:UnspecifiedMatching
OMIM:621005 SBSPON skos:exactMatch ncbigene:157869 semapv:UnspecifiedMatching
OMIM:621006 RTL6 skos:exactMatch hgnc.symbol:13343 semapv:UnspecifiedMatching
OMIM:621006 RTL6 skos:exactMatch hgnc.symbol:RTL6 semapv:UnspecifiedMatching
OMIM:621006 RTL6 skos:exactMatch ncbigene:84247 semapv:UnspecifiedMatching
OMIMPS:100070 Aortic aneurysm, familial abdominal skos:exactMatch MONDO:0007031 semapv:UnspecifiedMatching
OMIMPS:100300 Adams-Oliver syndrome skos:exactMatch MONDO:0007034 semapv:UnspecifiedMatching
OMIMPS:101800 Acrodysostosis skos:exactMatch MONDO:0019797 semapv:UnspecifiedMatching
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2 changes: 1 addition & 1 deletion src/ontology/external/mondo-omim-genes.robot.owl
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xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/mondo/external/nord.robot.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mondo/external/2024-11-09/nord.robot.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mondo/external/2024-11-12/nord.robot.owl"/>
</owl:Ontology>


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2 changes: 1 addition & 1 deletion src/ontology/external/nando-mappings.robot.owl
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xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/mondo/external/nord.robot.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mondo/external/2024-11-09/nord.robot.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mondo/external/2024-11-12/nord.robot.owl"/>
</owl:Ontology>


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16 changes: 15 additions & 1 deletion src/ontology/external/nord.robot.owl
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xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/mondo/external/nord.robot.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mondo/external/2024-11-09/nord.robot.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mondo/external/2024-11-12/nord.robot.owl"/>
</owl:Ontology>


Expand Down Expand Up @@ -6120,6 +6120,20 @@



<!-- http://purl.obolibrary.org/obo/MONDO_0005149 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/MONDO_0005149">
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/mondo#nord_rare"/>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/MONDO_0005149"/>
<owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#inSubset"/>
<owl:annotatedTarget rdf:resource="http://purl.obolibrary.org/obo/mondo#nord_rare"/>
<oboInOwl:source>MONDO:NORD</oboInOwl:source>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/MONDO_0005153 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/MONDO_0005153">
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1 change: 1 addition & 0 deletions src/ontology/external/nord.robot.tsv
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Expand Up @@ -9712,6 +9712,7 @@ MONDO:0005198 http://purl.obolibrary.org/obo/mondo#NORD_LABEL http://purl.ob
MONDO:0005197 http://purl.obolibrary.org/obo/mondo#NORD_LABEL http://purl.obolibrary.org/obo/mondo#nord_rare MONDO:NORD
MONDO:0005164 http://purl.obolibrary.org/obo/mondo#NORD_LABEL http://purl.obolibrary.org/obo/mondo#nord_rare MONDO:NORD
MONDO:0005153 http://purl.obolibrary.org/obo/mondo#NORD_LABEL http://purl.obolibrary.org/obo/mondo#nord_rare MONDO:NORD
MONDO:0005149 http://purl.obolibrary.org/obo/mondo#NORD_LABEL http://purl.obolibrary.org/obo/mondo#nord_rare MONDO:NORD
MONDO:0005144 http://purl.obolibrary.org/obo/mondo#NORD_LABEL http://purl.obolibrary.org/obo/mondo#nord_rare MONDO:NORD
MONDO:0005145 http://purl.obolibrary.org/obo/mondo#NORD_LABEL http://purl.obolibrary.org/obo/mondo#nord_rare MONDO:NORD
MONDO:0005136 NORD:1395 MONDO:NORD NORD:1395 http://purl.obolibrary.org/obo/mondo#NORD_LABEL http://purl.obolibrary.org/obo/mondo#nord_rare NORD:1395 MONDO:NORD
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2 changes: 1 addition & 1 deletion src/ontology/external/ordo-subsets.robot.owl
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xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/mondo/external/nord.robot.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mondo/external/2024-11-09/nord.robot.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mondo/external/2024-11-12/nord.robot.owl"/>
</owl:Ontology>


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4 changes: 2 additions & 2 deletions src/ontology/imports/omo_import.owl
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Expand Up @@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)


Ontology(<http://purl.obolibrary.org/obo/mondo-ingest/imports/omo_import.owl>
<http://purl.obolibrary.org/obo/mondo-ingest/releases/2024-11-09/imports/omo_import.owl>
<http://purl.obolibrary.org/obo/mondo-ingest/releases/2024-11-11/imports/omo_import.owl>
Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/omo/releases/2023-11-02/omo.owl>)
Annotation(owl:versionInfo "2024-11-09")
Annotation(owl:versionInfo "2024-11-11")

Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000031>))
Declaration(Class(<http://purl.obolibrary.org/obo/IAO_0000027>))
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4 changes: 2 additions & 2 deletions src/ontology/imports/ro_import.owl
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Expand Up @@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)


Ontology(<http://purl.obolibrary.org/obo/mondo-ingest/imports/ro_import.owl>
<http://purl.obolibrary.org/obo/mondo-ingest/releases/2024-11-09/imports/ro_import.owl>
<http://purl.obolibrary.org/obo/mondo-ingest/releases/2024-11-11/imports/ro_import.owl>
Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/ro/releases/2024-04-24/ro.owl>)
Annotation(owl:versionInfo "2024-11-09")
Annotation(owl:versionInfo "2024-11-11")

Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000002>))
Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000003>))
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