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Update EMC data files
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@matentzn
matentzn committed Nov 22, 2024
1 parent 5af8a11 commit 1103f92
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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/204f6b4a-3c0d-47c7-998e-1668ceaa99da
# mapping_set_id: https://w3id.org/sssom/mappings/056ce54c-b213-4c8b-80e2-1f9d7add42e0
# 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/ontology/external/gard.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/2024-08-22/nord.robot.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mondo/external/2024-11-22/nord.robot.owl"/>
</owl:Ontology>


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2 changes: 1 addition & 1 deletion src/ontology/external/mondo-clingen.robot.owl
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xmlns:mondo="http://purl.obolibrary.org/obo/mondo#"
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/2024-08-22/nord.robot.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mondo/external/2024-11-22/nord.robot.owl"/>
</owl:Ontology>


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2 changes: 1 addition & 1 deletion src/ontology/external/mondo-efo.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/2024-08-22/nord.robot.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mondo/external/2024-11-22/nord.robot.owl"/>
</owl:Ontology>


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1,278 changes: 1,131 additions & 147 deletions src/ontology/external/mondo-medgen.robot.owl
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118 changes: 100 additions & 18 deletions src/ontology/external/mondo-medgen.robot.tsv
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4 changes: 1 addition & 3 deletions src/ontology/external/mondo-omim-genes-qc-failures.md
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# QC Report for mondo-omim-genes

| mondo_id | hgnc_id | omim_disease_xref | omim_gene | Source | Check |
|:-----------|:----------|:--------------------|:------------|:-----------------|:--------------------------|
| {} | {} | {} | {} | mondo-omim-genes | MONDO:MONDO_pattern (IRI) |
No QC failures found.
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/2024-11-21/nord.robot.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mondo/external/2024-11-22/nord.robot.owl"/>
</owl:Ontology>


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2 changes: 1 addition & 1 deletion src/ontology/external/mondo-otar-subset.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/2024-08-22/nord.robot.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mondo/external/2024-11-22/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/2024-11-21/nord.robot.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mondo/external/2024-11-22/nord.robot.owl"/>
</owl:Ontology>


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22 changes: 11 additions & 11 deletions src/ontology/external/nord-qc-failures.md
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# QC Report for nord

| mondo_id | report_ref | report_ref_source | preferred_name | preferred_name_source | synonym_type | subset | subset_source | subset_source2 | Source | Check |
|:---------------------------|:-------------|:--------------------|:---------------------------|:------------------------|:-------------------------------------------------------|:------------------------------------------------------|:----------------|:------------------|:---------|:----------------------------------------------------|
| MONDO:0001280 | | | Posterior Uveitis | | | | | | nord | duplicate_scoped_synonym (oboInOwl:hasExactSynonym) |
| MONDO:0002119 | | | Juvenile Ossifying Fibroma | | | | | | nord | duplicate_scoped_synonym (oboInOwl:hasExactSynonym) |
| MONDO:0005731 | | | Acanthocheilonemiasis | | | | | | nord | duplicate_scoped_synonym (oboInOwl:hasExactSynonym) |
| MONDO:0005761 | | | Elephantiasis | | | | | | nord | duplicate_scoped_synonym (oboInOwl:hasBroadSynonym) |
| MONDO:0007030 | | | Aarskog Syndrome | | | | | | nord | duplicate_scoped_synonym (oboInOwl:hasExactSynonym) |
| MONDO:0007306 | | | Klippel-Feil Syndrome | | | | | | nord | duplicate_scoped_synonym (oboInOwl:hasBroadSynonym) |
| MONDO:0007389 | | | Spondylothoracic Dysplasia | | | | | | nord | duplicate_scoped_synonym (oboInOwl:hasExactSynonym) |
| MONDO:0005676 | | | | | | http://purl.obolibrary.org/obo/mondo#nord_rare | | | nord | qc-animal-disease-rare (oboInOwl:inSubset) |
| {3: 'MONDO:MONDO:0859214'} | {3: nan} | {3: nan} | {3: nan} | {3: nan} | {3: 'http://purl.obolibrary.org/obo/mondo#NORD_LABEL'} | {3: 'http://purl.obolibrary.org/obo/mondo#nord_rare'} | {3: nan} | {3: 'MONDO:NORD'} | nord | MONDO:MONDO_pattern (IRI) |
| mondo_id | report_ref | report_ref_source | preferred_name | preferred_name_source | synonym_type | subset | subset_source | subset_source2 | Source | Check |
|:--------------------|:-------------|:--------------------|:---------------------------|:------------------------|:------------------------------------------------|:-----------------------------------------------|:----------------|:-----------------|:---------|:----------------------------------------------------|
| MONDO:0001280 | | | Posterior Uveitis | | | | | | nord | duplicate_scoped_synonym (oboInOwl:hasExactSynonym) |
| MONDO:0002119 | | | Juvenile Ossifying Fibroma | | | | | | nord | duplicate_scoped_synonym (oboInOwl:hasExactSynonym) |
| MONDO:0005731 | | | Acanthocheilonemiasis | | | | | | nord | duplicate_scoped_synonym (oboInOwl:hasExactSynonym) |
| MONDO:0005761 | | | Elephantiasis | | | | | | nord | duplicate_scoped_synonym (oboInOwl:hasBroadSynonym) |
| MONDO:0007030 | | | Aarskog Syndrome | | | | | | nord | duplicate_scoped_synonym (oboInOwl:hasExactSynonym) |
| MONDO:0007306 | | | Klippel-Feil Syndrome | | | | | | nord | duplicate_scoped_synonym (oboInOwl:hasBroadSynonym) |
| MONDO:0007389 | | | Spondylothoracic Dysplasia | | | | | | nord | duplicate_scoped_synonym (oboInOwl:hasExactSynonym) |
| MONDO:0005676 | | | | | | http://purl.obolibrary.org/obo/mondo#nord_rare | | | nord | qc-animal-disease-rare (oboInOwl:inSubset) |
| MONDO:MONDO:0859214 | | | | | http://purl.obolibrary.org/obo/mondo#NORD_LABEL | http://purl.obolibrary.org/obo/mondo#nord_rare | | MONDO:NORD | nord | MONDO:MONDO_pattern (IRI) |
2 changes: 1 addition & 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/2024-11-21/nord.robot.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mondo/external/2024-11-22/nord.robot.owl"/>
</owl:Ontology>


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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/2024-11-21/nord.robot.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mondo/external/2024-11-22/nord.robot.owl"/>
</owl:Ontology>


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2 changes: 1 addition & 1 deletion src/ontology/external/processed-gard.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/2024-11-21/nord.robot.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mondo/external/2024-11-22/nord.robot.owl"/>
</owl:Ontology>


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