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fixing obs/exp error with EZH1
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@pnrobinson
pnrobinson committed Nov 29, 2023
1 parent dc041a0 commit 81060b0
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Showing 23 changed files with 323 additions and 743 deletions.
52 changes: 0 additions & 52 deletions data/count_cases.py
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9 changes: 1 addition & 8 deletions docs/collections.md
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Expand Up @@ -32,14 +32,7 @@ were mainly created using the Python library [pyphetools](https://github.com/mon
| [TRAF7](){:target="_blank"} | 45 phenopackets; [Cardiac, facial, and digital anomalies with developmental delay](https://omim.org/entry/618164){:target="_blank"} |
| [WFS1](https://github.com/monarch-initiative/phenopacket-store/tree/main/notebooks/WFS1){:target="_blank"} | 16 phenopackets; [Wolfram syndrome 1](https://omim.org/entry/222300){:target="_blank"}, [Deafness, autosomal dominant 6](https://omim.org/entry/600965){:target="_blank"} |
| [WWOX](https://github.com/monarch-initiative/phenopacket-store/tree/main/notebooks/WWOX){:target="_blank"} | 9 phenopackets; [Developmental and epileptic encephalopathy 28](https://omim.org/entry/616211){:target="_blank"}, [Spinocerebellar ataxia, autosomal recessive 12](https://omim.org/entry/614322){:target="_blank"} |
| [ZSWIN6](https://github.com/monarch-initiative/phenopacket-store/tree/main/notebooks/ZSWIM6){:target="_blank"} |?? phenopackets; [Acromelic frontonasal dysostosis](https://omim.org/entry/603671){:target="_blank"}, [Neurodevelopmental disorder with movement abnormalities, abnormal gait, and autistic features](https://omim.org/entry/617865){:target="_blank"}







| [ZSWIN6](https://github.com/monarch-initiative/phenopacket-store/tree/main/notebooks/ZSWIM6){:target="_blank"} | 16 phenopackets; [Acromelic frontonasal dysostosis](https://omim.org/entry/603671){:target="_blank"}, [Neurodevelopmental disorder with movement abnormalities, abnormal gait, and autistic features](https://omim.org/entry/617865){:target="_blank"}



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215 changes: 98 additions & 117 deletions notebooks/EZH1/GraciaDiaz_EZH1_PMID_37433783.ipynb
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63 changes: 28 additions & 35 deletions notebooks/EZH1/phenopackets/PMID_37433783_P1.json
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Expand Up @@ -77,13 +77,6 @@
"label": "Scoliosis"
}
},
{
"type": {
"id": "HP:0030834",
"label": "Shoulder pain"
},
"excluded": true
},
{
"type": {
"id": "HP:0000717",
Expand All @@ -93,92 +86,92 @@
},
{
"type": {
"id": "HP:0002376",
"label": "Developmental regression"
"id": "HP:0001252",
"label": "Hypotonia"
},
"excluded": true
},
{
"type": {
"id": "HP:0001276",
"label": "Hypertonia"
"id": "HP:0002172",
"label": "Postural instability"
},
"excluded": true
},
{
"type": {
"id": "HP:0001252",
"label": "Hypotonia"
"id": "HP:0002376",
"label": "Developmental regression"
},
"excluded": true
},
{
"type": {
"id": "HP:0001332",
"label": "Dystonia"
"id": "HP:0000648",
"label": "Optic atrophy"
},
"excluded": true
},
{
"type": {
"id": "HP:0031826",
"label": "Abnormal reflex"
"id": "HP:0000365",
"label": "Hearing impairment"
},
"excluded": true
},
{
"type": {
"id": "HP:0002172",
"label": "Postural instability"
"id": "HP:0001310",
"label": "Dysmetria"
},
"excluded": true
},
{
"type": {
"id": "HP:0001310",
"label": "Dysmetria"
"id": "HP:0001332",
"label": "Dystonia"
},
"excluded": true
},
{
"type": {
"id": "HP:0001288",
"label": "Gait disturbance"
"id": "HP:0031826",
"label": "Abnormal reflex"
},
"excluded": true
},
{
"type": {
"id": "HP:0003202",
"label": "Skeletal muscle atrophy"
"id": "HP:0000639",
"label": "Nystagmus"
},
"excluded": true
},
{
"type": {
"id": "HP:0100704",
"label": "Cerebral visual impairment"
"id": "HP:0003202",
"label": "Skeletal muscle atrophy"
},
"excluded": true
},
{
"type": {
"id": "HP:0000648",
"label": "Optic atrophy"
"id": "HP:0001288",
"label": "Gait disturbance"
},
"excluded": true
},
{
"type": {
"id": "HP:0000639",
"label": "Nystagmus"
"id": "HP:0100704",
"label": "Cerebral visual impairment"
},
"excluded": true
},
{
"type": {
"id": "HP:0000365",
"label": "Hearing impairment"
"id": "HP:0001276",
"label": "Hypertonia"
},
"excluded": true
}
Expand All @@ -198,7 +191,7 @@
"interpretationStatus": "CAUSATIVE",
"variantInterpretation": {
"variationDescriptor": {
"id": "var_prvDFILOPxkMRZLzsRJsNGqYu",
"id": "var_nBucyHGKWGljUqcxQZwrMDfll",
"geneContext": {
"valueId": "HGNC:3526",
"symbol": "EZH1"
Expand Down Expand Up @@ -233,7 +226,7 @@
}
],
"metaData": {
"created": "2023-11-25T07:14:09.439437150Z",
"created": "2023-11-29T09:30:58.387803792Z",
"createdBy": "ORCID:0000-0002-0736-9199",
"resources": [
{
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71 changes: 32 additions & 39 deletions notebooks/EZH1/phenopackets/PMID_37433783_P10.json
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Expand Up @@ -13,92 +13,92 @@
},
{
"type": {
"id": "HP:0002194",
"label": "Delayed gross motor development"
"id": "HP:0002172",
"label": "Postural instability"
}
},
{
"type": {
"id": "HP:0010862",
"label": "Delayed fine motor development"
"id": "HP:0002194",
"label": "Delayed gross motor development"
}
},
{
"type": {
"id": "HP:0000750",
"label": "Delayed speech and language development"
"id": "HP:0005274",
"label": "Prominent nasal tip"
}
},
{
"type": {
"id": "HP:0012434",
"label": "Delayed early-childhood social milestone development"
"id": "HP:0000276",
"label": "Long face"
}
},
{
"type": {
"id": "HP:0001249",
"label": "Intellectual disability"
"id": "HP:0002136",
"label": "Broad-based gait"
}
},
{
"type": {
"id": "HP:0002172",
"label": "Postural instability"
"id": "HP:0003202",
"label": "Skeletal muscle atrophy"
}
},
{
"type": {
"id": "HP:0001310",
"label": "Dysmetria"
"id": "HP:0008551",
"label": "Microtia"
}
},
{
"type": {
"id": "HP:0002136",
"label": "Broad-based gait"
"id": "HP:0000252",
"label": "Microcephaly"
}
},
{
"type": {
"id": "HP:0003202",
"label": "Skeletal muscle atrophy"
"id": "HP:0001310",
"label": "Dysmetria"
}
},
{
"type": {
"id": "HP:0000252",
"label": "Microcephaly"
"id": "HP:0000768",
"label": "Pectus carinatum"
}
},
{
"type": {
"id": "HP:0000276",
"label": "Long face"
"id": "HP:0010862",
"label": "Delayed fine motor development"
}
},
{
"type": {
"id": "HP:0012471",
"label": "Thick vermilion border"
"id": "HP:0001249",
"label": "Intellectual disability"
}
},
{
"type": {
"id": "HP:0008551",
"label": "Microtia"
"id": "HP:0000750",
"label": "Delayed speech and language development"
}
},
{
"type": {
"id": "HP:0005274",
"label": "Prominent nasal tip"
"id": "HP:0012471",
"label": "Thick vermilion border"
}
},
{
"type": {
"id": "HP:0000768",
"label": "Pectus carinatum"
"id": "HP:0012434",
"label": "Delayed early-childhood social milestone development"
}
},
{
Expand Down Expand Up @@ -143,13 +143,6 @@
},
"excluded": true
},
{
"type": {
"id": "HP:0031826",
"label": "Abnormal reflex"
},
"excluded": true
},
{
"type": {
"id": "HP:0100704",
Expand Down Expand Up @@ -187,7 +180,7 @@
"interpretationStatus": "CAUSATIVE",
"variantInterpretation": {
"variationDescriptor": {
"id": "var_vZnmVYitTIxtswOmndqBKqymO",
"id": "var_qmErmLbkTxxsXstlBRdbTUFQW",
"geneContext": {
"valueId": "HGNC:3526",
"symbol": "EZH1"
Expand Down Expand Up @@ -222,7 +215,7 @@
}
],
"metaData": {
"created": "2023-11-25T07:14:09.500533103Z",
"created": "2023-11-29T09:30:58.457184076Z",
"createdBy": "ORCID:0000-0002-0736-9199",
"resources": [
{
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