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pnrobinson committed Nov 26, 2023
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3 changes: 3 additions & 0 deletions docs/collections.md
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Expand Up @@ -25,6 +25,9 @@ were mainly created using the Python library [pyphetools](https://github.com/mon
| [SLC45A2](https://github.com/monarch-initiative/phenopacket-store/blob/main/notebooks/SLC45A2/SLC45A2_Moreno2022PMID_36553465.ipynb){:target="_blank"} | 30 phenopackets; [Albinism, oculocutaneous, type IV](https://omim.org/entry/606574){:target="_blank"} |
| [SMARCB1](https://github.com/monarch-initiative/phenopacket-store/tree/main/notebooks/SMARCB1){:target="_blank"} | 17 phenopackets; [Coffin-Siris syndrome 3](https://omim.org/entry/614608){:target="_blank"}, [Rhabdoid tumor predisposition syndrome-1](https://omim.org/entry/609322){:target="_blank"} |
| [SMARCC2](https://github.com/monarch-initiative/phenopacket-store/blob/main/notebooks/SMARCC2/SMARCC2_Bosch_2023_PMID_37551667.ipynb){:target="_blank"}| 60 phenopackets; [Coffin-Siris syndrome 8](https://omim.org/entry/618362){:target="_blank"} |
| [SON](https://github.com/monarch-initiative/phenopacket-store/blob/main/notebooks/SON/Dingemans_2022_SON_PMID_34521999.ipynb){:target="_blank"} | 52 phenopackets; [ZTTK syndrome](https://omim.org/entry/617140){:target="_blank"} |





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1,016 changes: 146 additions & 870 deletions notebooks/SON/Dingemans_2022_SON_PMID_34521999.ipynb
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363 changes: 363 additions & 0 deletions notebooks/SON/phenopackets/PMID_34521999_1.json
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{
"id": "PMID_34521999_1",
"subject": {
"id": "1",
"timeAtLastEncounter": {
"age": {
"iso8601duration": "P5Y"
}
},
"sex": "MALE"
},
"phenotypicFeatures": [
{
"type": {
"id": "HP:0004325",
"label": "Decreased body weight"
}
},
{
"type": {
"id": "HP:0000750",
"label": "Delayed speech and language development"
}
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{
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"label": "Hypotonia"
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"label": "Sleep abnormality"
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"type": {
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"type": {
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"type": {
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"interpretations": [
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"progressStatus": "SOLVED",
"diagnosis": {
"disease": {
"id": "OMIM:617140",
"label": "ZTTK SYNDROME"
},
"genomicInterpretations": [
{
"subjectOrBiosampleId": "1",
"interpretationStatus": "CAUSATIVE",
"variantInterpretation": {
"variationDescriptor": {
"id": "var_yVGlRbtOoClCTLhHNwEvGyCVD",
"geneContext": {
"valueId": "HGNC:11183",
"symbol": "SON"
},
"expressions": [
{
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"value": "NM_138927.2:c.5753_5756del"
},
{
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},
"moleculeContext": "genomic",
"allelicState": {
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"label": "heterozygous"
}
}
}
}
]
}
}
],
"metaData": {
"created": "2023-11-26T07:16:28.574844837Z",
"createdBy": "ORCID:0000-0002-5648-2155",
"resources": [
{
"id": "geno",
"name": "Genotype Ontology",
"url": "http://purl.obolibrary.org/obo/geno.owl",
"version": "2022-03-05",
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},
{
"id": "hgnc",
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"version": "06/01/23",
"namespacePrefix": "HGNC",
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},
{
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"version": "January 4, 2023",
"namespacePrefix": "OMIM",
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},
{
"id": "so",
"name": "Sequence types and features ontology",
"url": "http://purl.obolibrary.org/obo/so.obo",
"version": "2021-11-22",
"namespacePrefix": "SO",
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},
{
"id": "hp",
"name": "human phenotype ontology",
"url": "http://purl.obolibrary.org/obo/hp.owl",
"version": "2023-10-09",
"namespacePrefix": "HP",
"iriPrefix": "http://purl.obolibrary.org/obo/HP_"
}
],
"phenopacketSchemaVersion": "2.0",
"externalReferences": [
{
"id": "PMID:34521999",
"reference": "https://pubmed.ncbi.nlm.nih.gov/34521999",
"description": "Establishing the phenotypic spectrum of ZTTK syndrome by analysis of 52 individuals with variants in SON"
}
]
}
}
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