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LIRICAL phenopacket data
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pnrobinson committed Nov 5, 2023
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542 changes: 542 additions & 0 deletions notebooks/LIRICAL/LIRICAL.ipynb
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162 changes: 162 additions & 0 deletions notebooks/LIRICAL/v1phenopackets/Abdul_Wahab-2016-GCDH-Patient_5.json
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{
"id": "PMID:27672653-Abdul_Wahab-2016-GCDH-Patient_5",
"subject": {
"id": "Patient 5",
"ageAtCollection": {
"age": "P14Y"
},
"sex": "FEMALE",
"taxonomy": {
"id": "NCBITaxon:9606",
"label": "Homo sapiens"
}
},
"phenotypicFeatures": [{
"type": {
"id": "HP:0000256",
"label": "Macrocephaly"
},
"evidence": [{
"evidenceCode": {
"id": "ECO:0000033",
"label": "author statement supported by traceable reference"
},
"reference": {
"id": "PMID:27672653",
"description": "Clinical and Mutational Analysis of the GCDH Gene in Malaysian Patients with Glutaric Aciduria Type 1"
}
}]
}, {
"type": {
"id": "HP:0002059",
"label": "Cerebral atrophy"
},
"evidence": [{
"evidenceCode": {
"id": "ECO:0000033",
"label": "author statement supported by traceable reference"
},
"reference": {
"id": "PMID:27672653",
"description": "Clinical and Mutational Analysis of the GCDH Gene in Malaysian Patients with Glutaric Aciduria Type 1"
}
}]
}, {
"type": {
"id": "HP:0100309",
"label": "Subdural hemorrhage"
},
"evidence": [{
"evidenceCode": {
"id": "ECO:0000033",
"label": "author statement supported by traceable reference"
},
"reference": {
"id": "PMID:27672653",
"description": "Clinical and Mutational Analysis of the GCDH Gene in Malaysian Patients with Glutaric Aciduria Type 1"
}
}]
}, {
"type": {
"id": "HP:0003150",
"label": "Glutaric aciduria"
},
"evidence": [{
"evidenceCode": {
"id": "ECO:0000033",
"label": "author statement supported by traceable reference"
},
"reference": {
"id": "PMID:27672653",
"description": "Clinical and Mutational Analysis of the GCDH Gene in Malaysian Patients with Glutaric Aciduria Type 1"
}
}]
}, {
"type": {
"id": "HP:0001332",
"label": "Dystonia"
},
"evidence": [{
"evidenceCode": {
"id": "ECO:0000033",
"label": "author statement supported by traceable reference"
},
"reference": {
"id": "PMID:27672653",
"description": "Clinical and Mutational Analysis of the GCDH Gene in Malaysian Patients with Glutaric Aciduria Type 1"
}
}]
}],
"genes": [{
"id": "NCBIGene:2639",
"symbol": "GCDH"
}],
"variants": [{
"vcfAllele": {
"genomeAssembly": "GRCh37",
"chr": "19",
"pos": 13007113,
"ref": "G",
"alt": "A"
},
"zygosity": {
"id": "GENO:0000136",
"label": "homozygous"
}
}],
"diseases": [{
"term": {
"id": "OMIM:231670",
"label": "GLUTARIC ACIDEMIA I"
}
}],
"metaData": {
"createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
"submittedBy": "HPO:probinson",
"resources": [{
"id": "hp",
"name": "human phenotype ontology",
"url": "http://purl.obolibrary.org/obo/hp.owl",
"version": "2018-03-08",
"namespacePrefix": "HP",
"iriPrefix": "http://purl.obolibrary.org/obo/HP_"
}, {
"id": "pato",
"name": "Phenotype And Trait Ontology",
"url": "http://purl.obolibrary.org/obo/pato.owl",
"version": "2018-03-28",
"namespacePrefix": "PATO",
"iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
}, {
"id": "geno",
"name": "Genotype Ontology",
"url": "http://purl.obolibrary.org/obo/geno.owl",
"version": "19-03-2018",
"namespacePrefix": "GENO",
"iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
}, {
"id": "ncbitaxon",
"name": "NCBI organismal classification",
"url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
"version": "2018-03-02",
"namespacePrefix": "NCBITaxon"
}, {
"id": "eco",
"name": "Evidence and Conclusion Ontology",
"url": "http://purl.obolibrary.org/obo/eco.owl",
"version": "2018-11-10",
"namespacePrefix": "ECO",
"iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
}, {
"id": "omim",
"name": "Online Mendelian Inheritance in Man",
"url": "https://www.omim.org",
"namespacePrefix": "OMIM"
}],
"phenopacketSchemaVersion": "1.0.0-RC3",
"externalReferences": [{
"id": "PMID:27672653",
"description": "Clinical and Mutational Analysis of the GCDH Gene in Malaysian Patients with Glutaric Aciduria Type 1"
}]
}
}
191 changes: 191 additions & 0 deletions notebooks/LIRICAL/v1phenopackets/Ajmal-2013-BBS1-IV-5_family_A.json
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{
"id": "PMID:23559858-Ajmal-2013-BBS1-IV-5/family_A",
"subject": {
"id": "IV-5/family A",
"ageAtCollection": {
"age": "26Y"
},
"sex": "MALE",
"taxonomy": {
"id": "NCBITaxon:9606",
"label": "Homo sapiens"
}
},
"phenotypicFeatures": [{
"type": {
"id": "HP:0007843",
"label": "Attenuation of retinal blood vessels"
},
"evidence": [{
"evidenceCode": {
"id": "ECO:0000033",
"label": "author statement supported by traceable reference"
},
"reference": {
"id": "PMID:23559858",
"description": "Exome sequencing identifies a novel and a recurrent BBS1 mutation in Pakistani families with Bardet-Biedl syndrome"
}
}]
}, {
"type": {
"id": "HP:0001513",
"label": "Obesity"
},
"evidence": [{
"evidenceCode": {
"id": "ECO:0000033",
"label": "author statement supported by traceable reference"
},
"reference": {
"id": "PMID:23559858",
"description": "Exome sequencing identifies a novel and a recurrent BBS1 mutation in Pakistani families with Bardet-Biedl syndrome"
}
}]
}, {
"type": {
"id": "HP:0000608",
"label": "Macular degeneration"
},
"evidence": [{
"evidenceCode": {
"id": "ECO:0000033",
"label": "author statement supported by traceable reference"
},
"reference": {
"id": "PMID:23559858",
"description": "Exome sequencing identifies a novel and a recurrent BBS1 mutation in Pakistani families with Bardet-Biedl syndrome"
}
}]
}, {
"type": {
"id": "HP:0000486",
"label": "Strabismus"
},
"evidence": [{
"evidenceCode": {
"id": "ECO:0000033",
"label": "author statement supported by traceable reference"
},
"reference": {
"id": "PMID:23559858",
"description": "Exome sequencing identifies a novel and a recurrent BBS1 mutation in Pakistani families with Bardet-Biedl syndrome"
}
}]
}, {
"type": {
"id": "HP:0001328",
"label": "Specific learning disability"
},
"evidence": [{
"evidenceCode": {
"id": "ECO:0000033",
"label": "author statement supported by traceable reference"
},
"reference": {
"id": "PMID:23559858",
"description": "Exome sequencing identifies a novel and a recurrent BBS1 mutation in Pakistani families with Bardet-Biedl syndrome"
}
}]
}, {
"type": {
"id": "HP:0000510",
"label": "Rod-cone dystrophy"
},
"evidence": [{
"evidenceCode": {
"id": "ECO:0000033",
"label": "author statement supported by traceable reference"
},
"reference": {
"id": "PMID:23559858",
"description": "Exome sequencing identifies a novel and a recurrent BBS1 mutation in Pakistani families with Bardet-Biedl syndrome"
}
}]
}, {
"type": {
"id": "HP:0001263",
"label": "Global developmental delay"
},
"evidence": [{
"evidenceCode": {
"id": "ECO:0000033",
"label": "author statement supported by traceable reference"
},
"reference": {
"id": "PMID:23559858",
"description": "Exome sequencing identifies a novel and a recurrent BBS1 mutation in Pakistani families with Bardet-Biedl syndrome"
}
}]
}],
"genes": [{
"id": "NCBIGene:582",
"symbol": "BBS1"
}],
"variants": [{
"vcfAllele": {
"genomeAssembly": "GRCh37",
"chr": "11",
"pos": 66278178,
"ref": "G",
"alt": "T"
},
"zygosity": {
"id": "GENO:0000136",
"label": "homozygous"
}
}],
"diseases": [{
"term": {
"id": "OMIM:209900",
"label": "BARDET-BIEDL SYNDROME 1; BBS1"
}
}],
"metaData": {
"submittedBy": "HPO:probinson",
"resources": [{
"id": "hp",
"name": "human phenotype ontology",
"url": "http://purl.obolibrary.org/obo/hp.owl",
"version": "2018-03-08",
"namespacePrefix": "HP",
"iriPrefix": "http://purl.obolibrary.org/obo/HP_"
}, {
"id": "pato",
"name": "Phenotype And Trait Ontology",
"url": "http://purl.obolibrary.org/obo/pato.owl",
"version": "2018-03-28",
"namespacePrefix": "PATO",
"iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
}, {
"id": "geno",
"name": "Genotype Ontology",
"url": "http://purl.obolibrary.org/obo/geno.owl",
"version": "19-03-2018",
"namespacePrefix": "GENO",
"iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
}, {
"id": "ncbitaxon",
"name": "NCBI organismal classification",
"url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
"version": "2018-03-02",
"namespacePrefix": "NCBITaxon"
}, {
"id": "eco",
"name": "Evidence and Conclusion Ontology",
"url": "http://purl.obolibrary.org/obo/eco.owl",
"version": "2018-11-10",
"namespacePrefix": "ECO",
"iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
}, {
"id": "omim",
"name": "Online Mendelian Inheritance in Man",
"url": "https://www.omim.org",
"namespacePrefix": "OMIM"
}],
"phenopacketSchemaVersion": "1.0.0-RC3",
"externalReferences": [{
"id": "PMID:23559858",
"description": "Exome sequencing identifies a novel and a recurrent BBS1 mutation in Pakistani families with Bardet-Biedl syndrome"
}]
}
}
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