-
Notifications
You must be signed in to change notification settings - Fork 4
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
1 parent
c174eeb
commit a0b2fe0
Showing
22 changed files
with
3,587 additions
and
0 deletions.
There are no files selected for viewing
Large diffs are not rendered by default.
Oops, something went wrong.
Binary file not shown.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,215 @@ | ||
{ | ||
"id": "PMID_36215968_patient", | ||
"subject": { | ||
"id": "patient", | ||
"timeAtLastEncounter": { | ||
"age": { | ||
"iso8601duration": "P2M" | ||
} | ||
}, | ||
"vitalStatus": { | ||
"status": "ALIVE" | ||
}, | ||
"sex": "MALE" | ||
}, | ||
"phenotypicFeatures": [ | ||
{ | ||
"type": { | ||
"id": "HP:0000822", | ||
"label": "Hypertension" | ||
}, | ||
"onset": { | ||
"age": { | ||
"iso8601duration": "P2M" | ||
} | ||
} | ||
}, | ||
{ | ||
"type": { | ||
"id": "HP:0000083", | ||
"label": "Renal insufficiency" | ||
}, | ||
"onset": { | ||
"age": { | ||
"iso8601duration": "P1M" | ||
} | ||
} | ||
}, | ||
{ | ||
"type": { | ||
"id": "HP:0000103", | ||
"label": "Polyuria" | ||
}, | ||
"onset": { | ||
"age": { | ||
"iso8601duration": "P1M" | ||
} | ||
} | ||
}, | ||
{ | ||
"type": { | ||
"id": "HP:0001959", | ||
"label": "Polydipsia" | ||
}, | ||
"onset": { | ||
"age": { | ||
"iso8601duration": "P1M" | ||
} | ||
} | ||
}, | ||
{ | ||
"type": { | ||
"id": "HP:0004719", | ||
"label": "Hyperechogenic kidneys" | ||
}, | ||
"onset": { | ||
"age": { | ||
"iso8601duration": "P1M" | ||
} | ||
} | ||
}, | ||
{ | ||
"type": { | ||
"id": "HP:0000105", | ||
"label": "Enlarged kidney" | ||
} | ||
}, | ||
{ | ||
"type": { | ||
"id": "HP:0000090", | ||
"label": "Nephronophthisis" | ||
}, | ||
"excluded": true | ||
}, | ||
{ | ||
"type": { | ||
"id": "HP:0001407", | ||
"label": "Hepatic cysts" | ||
}, | ||
"excluded": true | ||
}, | ||
{ | ||
"type": { | ||
"id": "HP:0003774", | ||
"label": "Stage 5 chronic kidney disease" | ||
}, | ||
"excluded": true | ||
} | ||
], | ||
"interpretations": [ | ||
{ | ||
"id": "patient", | ||
"progressStatus": "SOLVED", | ||
"diagnosis": { | ||
"disease": { | ||
"id": "OMIM:620903", | ||
"label": "Polycystic kidney disease 8" | ||
}, | ||
"genomicInterpretations": [ | ||
{ | ||
"subjectOrBiosampleId": "patient", | ||
"interpretationStatus": "CAUSATIVE", | ||
"variantInterpretation": { | ||
"variationDescriptor": { | ||
"id": "var_ijqBhHWjJVXNhuqEeuODDUGwW", | ||
"geneContext": { | ||
"valueId": "HGNC:13387", | ||
"symbol": "NEK8" | ||
}, | ||
"expressions": [ | ||
{ | ||
"syntax": "hgvs.c", | ||
"value": "NM_178170.3:c.133C>T" | ||
}, | ||
{ | ||
"syntax": "hgvs.g", | ||
"value": "NC_000017.11:g.28734068C>T" | ||
} | ||
], | ||
"vcfRecord": { | ||
"genomeAssembly": "hg38", | ||
"chrom": "chr17", | ||
"pos": "28734068", | ||
"ref": "C", | ||
"alt": "T" | ||
}, | ||
"moleculeContext": "genomic", | ||
"allelicState": { | ||
"id": "GENO:0000135", | ||
"label": "heterozygous" | ||
} | ||
} | ||
} | ||
} | ||
] | ||
} | ||
} | ||
], | ||
"diseases": [ | ||
{ | ||
"term": { | ||
"id": "OMIM:620903", | ||
"label": "Polycystic kidney disease 8" | ||
}, | ||
"onset": { | ||
"age": { | ||
"iso8601duration": "P1M" | ||
} | ||
} | ||
} | ||
], | ||
"metaData": { | ||
"created": "2024-12-27T09:44:46.088234901Z", | ||
"createdBy": "ORCID:0000-0002-0736-9199", | ||
"resources": [ | ||
{ | ||
"id": "geno", | ||
"name": "Genotype Ontology", | ||
"url": "http://purl.obolibrary.org/obo/geno.owl", | ||
"version": "2022-03-05", | ||
"namespacePrefix": "GENO", | ||
"iriPrefix": "http://purl.obolibrary.org/obo/GENO_" | ||
}, | ||
{ | ||
"id": "hgnc", | ||
"name": "HUGO Gene Nomenclature Committee", | ||
"url": "https://www.genenames.org", | ||
"version": "06/01/23", | ||
"namespacePrefix": "HGNC", | ||
"iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" | ||
}, | ||
{ | ||
"id": "omim", | ||
"name": "An Online Catalog of Human Genes and Genetic Disorders", | ||
"url": "https://www.omim.org", | ||
"version": "January 4, 2023", | ||
"namespacePrefix": "OMIM", | ||
"iriPrefix": "https://www.omim.org/entry/" | ||
}, | ||
{ | ||
"id": "so", | ||
"name": "Sequence types and features ontology", | ||
"url": "http://purl.obolibrary.org/obo/so.obo", | ||
"version": "2021-11-22", | ||
"namespacePrefix": "SO", | ||
"iriPrefix": "http://purl.obolibrary.org/obo/SO_" | ||
}, | ||
{ | ||
"id": "hp", | ||
"name": "human phenotype ontology", | ||
"url": "http://purl.obolibrary.org/obo/hp.owl", | ||
"version": "2024-12-12", | ||
"namespacePrefix": "HP", | ||
"iriPrefix": "http://purl.obolibrary.org/obo/HP_" | ||
} | ||
], | ||
"phenopacketSchemaVersion": "2.0", | ||
"externalReferences": [ | ||
{ | ||
"id": "PMID:36215968", | ||
"reference": "https://pubmed.ncbi.nlm.nih.gov/36215968", | ||
"description": "NEK8-Associated Nephropathies: Do Autosomal Dominant Forms Exist?" | ||
} | ||
] | ||
} | ||
} |
160 changes: 160 additions & 0 deletions
160
notebooks/NEK8/phenopackets/PMID_37598857_Family10individual.json
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,160 @@ | ||
{ | ||
"id": "PMID_37598857_Family_10_individual", | ||
"subject": { | ||
"id": "Family 10 individual", | ||
"vitalStatus": { | ||
"status": "ALIVE" | ||
}, | ||
"sex": "FEMALE" | ||
}, | ||
"phenotypicFeatures": [ | ||
{ | ||
"type": { | ||
"id": "HP:0000105", | ||
"label": "Enlarged kidney" | ||
} | ||
}, | ||
{ | ||
"type": { | ||
"id": "HP:0000090", | ||
"label": "Nephronophthisis" | ||
} | ||
}, | ||
{ | ||
"type": { | ||
"id": "HP:0000822", | ||
"label": "Hypertension" | ||
} | ||
}, | ||
{ | ||
"type": { | ||
"id": "HP:0001407", | ||
"label": "Hepatic cysts" | ||
}, | ||
"excluded": true | ||
}, | ||
{ | ||
"type": { | ||
"id": "HP:0004322", | ||
"label": "Short stature" | ||
}, | ||
"excluded": true | ||
} | ||
], | ||
"interpretations": [ | ||
{ | ||
"id": "Family 10 individual", | ||
"progressStatus": "SOLVED", | ||
"diagnosis": { | ||
"disease": { | ||
"id": "OMIM:620903", | ||
"label": "Polycystic kidney disease 8" | ||
}, | ||
"genomicInterpretations": [ | ||
{ | ||
"subjectOrBiosampleId": "Family 10 individual", | ||
"interpretationStatus": "CAUSATIVE", | ||
"variantInterpretation": { | ||
"variationDescriptor": { | ||
"id": "var_ijqBhHWjJVXNhuqEeuODDUGwW", | ||
"geneContext": { | ||
"valueId": "HGNC:13387", | ||
"symbol": "NEK8" | ||
}, | ||
"expressions": [ | ||
{ | ||
"syntax": "hgvs.c", | ||
"value": "NM_178170.3:c.133C>T" | ||
}, | ||
{ | ||
"syntax": "hgvs.g", | ||
"value": "NC_000017.11:g.28734068C>T" | ||
} | ||
], | ||
"vcfRecord": { | ||
"genomeAssembly": "hg38", | ||
"chrom": "chr17", | ||
"pos": "28734068", | ||
"ref": "C", | ||
"alt": "T" | ||
}, | ||
"moleculeContext": "genomic", | ||
"allelicState": { | ||
"id": "GENO:0000135", | ||
"label": "heterozygous" | ||
} | ||
} | ||
} | ||
} | ||
] | ||
} | ||
} | ||
], | ||
"diseases": [ | ||
{ | ||
"term": { | ||
"id": "OMIM:620903", | ||
"label": "Polycystic kidney disease 8" | ||
}, | ||
"onset": { | ||
"age": { | ||
"iso8601duration": "P3Y" | ||
} | ||
} | ||
} | ||
], | ||
"metaData": { | ||
"created": "2024-12-27T09:44:46.085093021Z", | ||
"createdBy": "ORCID:0000-0002-0736-9199", | ||
"resources": [ | ||
{ | ||
"id": "geno", | ||
"name": "Genotype Ontology", | ||
"url": "http://purl.obolibrary.org/obo/geno.owl", | ||
"version": "2022-03-05", | ||
"namespacePrefix": "GENO", | ||
"iriPrefix": "http://purl.obolibrary.org/obo/GENO_" | ||
}, | ||
{ | ||
"id": "hgnc", | ||
"name": "HUGO Gene Nomenclature Committee", | ||
"url": "https://www.genenames.org", | ||
"version": "06/01/23", | ||
"namespacePrefix": "HGNC", | ||
"iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" | ||
}, | ||
{ | ||
"id": "omim", | ||
"name": "An Online Catalog of Human Genes and Genetic Disorders", | ||
"url": "https://www.omim.org", | ||
"version": "January 4, 2023", | ||
"namespacePrefix": "OMIM", | ||
"iriPrefix": "https://www.omim.org/entry/" | ||
}, | ||
{ | ||
"id": "so", | ||
"name": "Sequence types and features ontology", | ||
"url": "http://purl.obolibrary.org/obo/so.obo", | ||
"version": "2021-11-22", | ||
"namespacePrefix": "SO", | ||
"iriPrefix": "http://purl.obolibrary.org/obo/SO_" | ||
}, | ||
{ | ||
"id": "hp", | ||
"name": "human phenotype ontology", | ||
"url": "http://purl.obolibrary.org/obo/hp.owl", | ||
"version": "2024-12-12", | ||
"namespacePrefix": "HP", | ||
"iriPrefix": "http://purl.obolibrary.org/obo/HP_" | ||
} | ||
], | ||
"phenopacketSchemaVersion": "2.0", | ||
"externalReferences": [ | ||
{ | ||
"id": "PMID:37598857", | ||
"reference": "https://pubmed.ncbi.nlm.nih.gov/37598857", | ||
"description": "Certain heterozygous variants in the kinase domain of the serine/threonine kinase NEK8 can cause an autosomal dominant form of polycystic kidney disease" | ||
} | ||
] | ||
} | ||
} |
Oops, something went wrong.