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Removing redundant phenopacket generation code #116

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Dec 18, 2023
Merged

Removing redundant phenopacket generation code #116

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1,330 changes: 0 additions & 1,330 deletions notebooks/KBG/KBG_Martinez_PMID_36446582_CreatePhenopackets.ipynb
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Binary file removed notebooks/KBG/input/Martinez-KBG-SupplTable-340-v2.xlsx
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50 changes: 23 additions & 27 deletions ...henopackets/PMID_36446582_Alves_2019.json → ...phenopackets/PMID_36446582_Alves2019.json
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
{
"id": "Alves, 2019",
"id": "PMID_36446582_Alves,_2019",
"subject": {
"id": "Alves, 2019",
"timeAtLastEncounter": {
Expand All @@ -12,46 +12,26 @@
"phenotypicFeatures": [
{
"type": {
"id": "HP:0006482",
"label": "Abnormality of dental morphology"
},
"onset": {
"age": {
"iso8601duration": "P2Y"
}
"id": "HP:0001572",
"label": "Macrodontia"
}
},
{
"type": {
"id": "HP:0001155",
"label": "Abnormality of the hand"
},
"onset": {
"age": {
"iso8601duration": "P2Y"
}
}
},
{
"type": {
"id": "HP:0004322",
"label": "Short stature"
},
"onset": {
"age": {
"iso8601duration": "P2Y"
}
}
},
{
"type": {
"id": "HP:0000365",
"label": "Hearing impairment"
},
"onset": {
"age": {
"iso8601duration": "P2Y"
}
}
}
],
Expand All @@ -70,6 +50,7 @@
"interpretationStatus": "CAUSATIVE",
"variantInterpretation": {
"variationDescriptor": {
"id": "var_rINdzLNehXDQccIlUhmVIRVBW",
"geneContext": {
"valueId": "HGNC:21316",
"symbol": "ANKRD11"
Expand Down Expand Up @@ -104,8 +85,8 @@
}
],
"metaData": {
"created": "2023-09-15T19:23:49.837050914Z",
"createdBy": "ORCID:0000-0003-2598-6622",
"created": "2023-11-25T12:07:35.880573034Z",
"createdBy": "ORCID:0000-0002-0736-9199",
"resources": [
{
"id": "geno",
Expand All @@ -131,15 +112,30 @@
"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": "2023-01-27",
"version": "2023-10-09",
"namespacePrefix": "HP",
"iriPrefix": "http://purl.obolibrary.org/obo/HP_"
}
],
"phenopacketSchemaVersion": "2.0"
"phenopacketSchemaVersion": "2.0",
"externalReferences": [
{
"id": "PMID:36446582",
"reference": "https://pubmed.ncbi.nlm.nih.gov/36446582",
"description": "Clinical description, molecular delineation and genotype-phenotype correlation in 340 patients with KBG syndrome: addition of 67 new patients"
}
]
}
}
173 changes: 173 additions & 0 deletions notebooks/KBG/phenopackets/PMID_36446582_Behnert2018.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,173 @@
{
"id": "PMID_36446582_Behnert,_2018",
"subject": {
"id": "Behnert, 2018",
"timeAtLastEncounter": {
"age": {
"iso8601duration": "P2Y"
}
},
"sex": "MALE"
},
"phenotypicFeatures": [
{
"type": {
"id": "HP:0001249",
"label": "Intellectual disability"
}
},
{
"type": {
"id": "HP:0001572",
"label": "Macrodontia"
}
},
{
"type": {
"id": "HP:0010938",
"label": "Abnormal external nose morphology"
}
},
{
"type": {
"id": "HP:0000325",
"label": "Triangular face"
}
},
{
"type": {
"id": "HP:0000574",
"label": "Thick eyebrow"
}
},
{
"type": {
"id": "HP:0000356",
"label": "Abnormality of the outer ear"
}
},
{
"type": {
"id": "HP:0001155",
"label": "Abnormality of the hand"
}
},
{
"type": {
"id": "HP:0004322",
"label": "Short stature"
}
},
{
"type": {
"id": "HP:0000365",
"label": "Hearing impairment"
}
},
{
"type": {
"id": "HP:0000729",
"label": "Autistic behavior"
},
"excluded": true
},
{
"type": {
"id": "HP:0007018",
"label": "Attention deficit hyperactivity disorder"
},
"excluded": true
}
],
"interpretations": [
{
"id": "Behnert, 2018",
"progressStatus": "SOLVED",
"diagnosis": {
"disease": {
"id": "OMIM:148050",
"label": "KBG syndrome"
},
"genomicInterpretations": [
{
"subjectOrBiosampleId": "Behnert, 2018",
"interpretationStatus": "CAUSATIVE",
"variantInterpretation": {
"variationDescriptor": {
"id": "var_GntpvqcrHznGBFoutpNQVGWmu",
"label": "16q24.3(88854757_89577705)x1 (hg19)",
"geneContext": {
"valueId": "HGNC:21316",
"symbol": "ANKRD11"
},
"moleculeContext": "genomic",
"structuralType": {
"id": "SO:1000029",
"label": "chromosomal_deletion"
},
"allelicState": {
"id": "GENO:0000135",
"label": "heterozygous"
}
}
}
}
]
}
}
],
"metaData": {
"created": "2023-11-25T12:07:35.892725944Z",
"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": "2023-10-09",
"namespacePrefix": "HP",
"iriPrefix": "http://purl.obolibrary.org/obo/HP_"
}
],
"phenopacketSchemaVersion": "2.0",
"externalReferences": [
{
"id": "PMID:36446582",
"reference": "https://pubmed.ncbi.nlm.nih.gov/36446582",
"description": "Clinical description, molecular delineation and genotype-phenotype correlation in 340 patients with KBG syndrome: addition of 67 new patients"
}
]
}
}
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