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339 add synthetic corpus #340

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2843d0b
Create corpus.yml
yaseminbridges Jun 12, 2024
2d5c2e7
add synthetic patient phenopackets based on hpoa
yaseminbridges Jun 12, 2024
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159 changes: 159 additions & 0 deletions ...ic_based_on_hpoa/default/phenopackets/2_4_dienoyl_CoA_reductase_deficiency_patient_1.json
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{
"id": "2,4-dienoyl-coa_reductase_deficiency",
"subject": {
"id": "patient1"
},
"phenotypicFeatures": [
{
"type": {
"id": "HP:0002188",
"label": "Delayed CNS myelination"
}
},
{
"type": {
"id": "HP:0002421",
"label": "Poor head control"
}
},
{
"type": {
"id": "HP:0002311",
"label": "Incoordination"
}
},
{
"type": {
"id": "HP:0033994",
"label": "Dependency on parenteral nutrition"
}
},
{
"type": {
"id": "HP:0000540",
"label": "Hypermetropia"
}
},
{
"type": {
"id": "HP:0006829",
"label": "Severe muscular hypotonia"
},
"onset": {
"ontologyClass": {
"id": "HP:0003623",
"label": "Neonatal onset"
}
}
},
{
"type": {
"id": "HP:0012638",
"label": "Abnormal nervous system physiology"
}
},
{
"type": {
"id": "HP:0001996",
"label": "Chronic metabolic acidosis"
}
},
{
"type": {
"id": "HP:0012389",
"label": "Appendicular hypotonia"
}
},
{
"type": {
"id": "HP:0034919",
"label": "Reduced liver 2,4-dienoyl-CoA reductase activity"
}
},
{
"type": {
"id": "HP:0012547",
"label": "Abnormal involuntary eye movements"
}
},
{
"type": {
"id": "HP:0011408",
"label": "Moderate intrauterine growth retardation"
}
},
{
"type": {
"id": "HP:0003112",
"label": "Abnormal circulating amino acid concentration"
}
},
{
"type": {
"id": "HP:0007034",
"label": "Generalized hyperreflexia"
}
},
{
"type": {
"id": "HP:0002179",
"label": "Opisthotonus"
}
},
{
"type": {
"id": "HP:0002118",
"label": "Abnormal cerebral ventricle morphology"
}
},
{
"type": {
"id": "HP:0012372",
"label": "Abnormal eye morphology"
}
},
{
"type": {
"id": "HP:0100704",
"label": "Cerebral visual impairment"
}
},
{
"type": {
"id": "HP:0003297",
"label": "Hyperlysinuria"
}
}
],
"diseases": [
{
"term": {
"id": "OMIM:616034",
"label": "2,4-dienoyl-CoA reductase deficiency"
}
}
],
"metaData": {
"created": "2024-06-11T22:16:14.617257Z",
"createdBy": "phenotype2phenopacket",
"resources": [
{
"id": "hp",
"name": "human phenotype ontology",
"url": "http://purl.obolibrary.org/obo/hp.owl",
"version": "hp/releases/2024-04-24",
"namespacePrefix": "HP",
"iriPrefix": "http://purl.obolibrary.org/obo/HP_"
},
{
"id": "omim",
"name": "Online Mendelian Inheritance in Man",
"url": "https://www.omim.org",
"version": "hp/releases/2023-04-18",
"namespacePrefix": "OMIM",
"iriPrefix": "https://omim.org/entry/"
}
],
"phenopacketSchemaVersion": "2.0"
}
}
63 changes: 63 additions & 0 deletions ..._on_hpoa/default/phenopackets/2_Methylbutyryl_Coa_dehydrogenase_deficiency_patient_1.json
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{
"id": "2-methylbutyryl-coa_dehydrogenase_deficiency",
"subject": {
"id": "patient1"
},
"phenotypicFeatures": [
{
"type": {
"id": "HP:0012389",
"label": "Appendicular hypotonia"
}
},
{
"type": {
"id": "HP:0040156",
"label": "Elevated urinary carboxylic acid"
}
},
{
"type": {
"id": "HP:0010862",
"label": "Delayed fine motor development"
}
},
{
"type": {
"id": "HP:0005964",
"label": "Intermittent hypothermia"
}
}
],
"diseases": [
{
"term": {
"id": "OMIM:610006",
"label": "2-Methylbutyryl-Coa dehydrogenase deficiency"
}
}
],
"metaData": {
"created": "2024-06-11T17:50:02.748292Z",
"createdBy": "phenotype2phenopacket",
"resources": [
{
"id": "hp",
"name": "human phenotype ontology",
"url": "http://purl.obolibrary.org/obo/hp.owl",
"version": "hp/releases/2024-04-24",
"namespacePrefix": "HP",
"iriPrefix": "http://purl.obolibrary.org/obo/HP_"
},
{
"id": "omim",
"name": "Online Mendelian Inheritance in Man",
"url": "https://www.omim.org",
"version": "hp/releases/2023-04-18",
"namespacePrefix": "OMIM",
"iriPrefix": "https://omim.org/entry/"
}
],
"phenopacketSchemaVersion": "2.0"
}
}
99 changes: 99 additions & 0 deletions corpora/synthetic_based_on_hpoa/default/phenopackets/3MC_syndrome_1_patient_1.json
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{
"id": "3mc_syndrome_1",
"subject": {
"id": "patient1"
},
"phenotypicFeatures": [
{
"type": {
"id": "HP:0001631",
"label": "Atrial septal defect"
}
},
{
"type": {
"id": "HP:0000496",
"label": "Abnormality of eye movement"
}
},
{
"type": {
"id": "HP:0000501",
"label": "Glaucoma"
}
},
{
"type": {
"id": "HP:0001773",
"label": "Short foot"
}
},
{
"type": {
"id": "HP:0001256",
"label": "Intellectual disability, mild"
}
},
{
"type": {
"id": "HP:0004227",
"label": "Short distal phalanx of the 5th finger"
}
},
{
"type": {
"id": "HP:0007838",
"label": "Progressive ptosis"
}
},
{
"type": {
"id": "HP:0011321",
"label": "Left unilambdoid synostosis"
}
},
{
"type": {
"id": "HP:0010944",
"label": "Abnormal renal pelvis morphology"
}
},
{
"type": {
"id": "HP:0002553",
"label": "Highly arched eyebrow"
}
}
],
"diseases": [
{
"term": {
"id": "OMIM:257920",
"label": "3MC syndrome 1"
}
}
],
"metaData": {
"created": "2024-06-11T21:55:42.580395Z",
"createdBy": "phenotype2phenopacket",
"resources": [
{
"id": "hp",
"name": "human phenotype ontology",
"url": "http://purl.obolibrary.org/obo/hp.owl",
"version": "hp/releases/2024-04-24",
"namespacePrefix": "HP",
"iriPrefix": "http://purl.obolibrary.org/obo/HP_"
},
{
"id": "omim",
"name": "Online Mendelian Inheritance in Man",
"url": "https://www.omim.org",
"version": "hp/releases/2023-04-18",
"namespacePrefix": "OMIM",
"iriPrefix": "https://omim.org/entry/"
}
],
"phenopacketSchemaVersion": "2.0"
}
}
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