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CMPK2
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pnrobinson committed Dec 23, 2024
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174 changes: 174 additions & 0 deletions notebooks/CMPK2/CMPK2_IBGC10_individuals.ipynb
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{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# CMPK2\n",
"[autosomal recessive idiopathic basal ganglia calcification-10 (IBGC10)](https://omim.org/entry/621018) is caused by homozygous or compound heterozygous mutation in the mitochondrial cytidine monophosphate (UMP-CMP) kinase-2 gene (CMPK2)."
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Using pyphetools version 0.9.115\n"
]
}
],
"source": [
"from pyphetools.creation import TemplateImporter, Moi\n",
"from pyphetools.visualization import IndividualTable, QcVisualizer\n",
"from IPython.display import display, HTML\n",
"import pyphetools\n",
"print(f\"Using pyphetools version {pyphetools.__version__}\")"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"template = \"input/CMPK2_IBGC10_individuals.xlsx\"\n",
"created_by = \"0000-0002-0736-9199\""
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"HPO version 2024-12-12\n",
"Created encoders for 32 fields\n",
"Importing OMIM:621018, Basal ganglia calcification, idiopathic, 10, autosomal recessive, HGNC:27015, CMPK2, NM_207315.4\n",
"[INFO] encoding variant \"c.1241A>G\"\n",
"https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_207315.4%3Ac.1241A>G/NM_207315.4?content-type=application%2Fjson\n",
"[INFO] encoding variant \"c.1A>C\"\n",
"https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_207315.4%3Ac.1A>C/NM_207315.4?content-type=application%2Fjson\n",
"[INFO] encoding variant \"c.2T>C\"\n",
"https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_207315.4%3Ac.2T>C/NM_207315.4?content-type=application%2Fjson\n",
"We output 3 GA4GH phenopackets to the directory phenopackets\n"
]
}
],
"source": [
"timporter = TemplateImporter(template=template, created_by=created_by)\n",
"individual_list, cvalidator = timporter.import_phenopackets_from_template()"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<h2>Cohort validation</h2>\n",
"<p>No errors found for the cohort with 3 individuals</p>"
],
"text/plain": [
"<IPython.core.display.HTML object>"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"qc = QcVisualizer(cohort_validator=cvalidator)\n",
"display(HTML(qc.to_summary_html()))"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<table style=\"border: 2px solid black; align: \"left\">\n",
"<caption>3 phenopackets - PMID:36443312 (n=3)</caption>\n",
"<tr><th style=\"text-align: left;font-weight: bold;\">Individual</th><th style=\"text-align: left;font-weight: bold;\">Disease</th><th style=\"text-align: left;font-weight: bold;\">Genotype</th><th style=\"text-align: left;font-weight: bold;\">Phenotypic features</th></tr>\n",
"<tr><td style=\"text-align: left;\">Family 1 II-3 (MALE; P44Y)</td><td style=\"text-align: left;\">Basal ganglia calcification, idiopathic, 10, autosomal recessive (OMIM:621018)</td><td style=\"text-align: left;\">NM_207315.4:c.2T>C (homozygous)</td><td style=\"text-align: left;\">Globus pallidus calcification (HP:0031627): onset ; Thalamic calcification (HP:0025041): onset ; Cerebellar calcifications (HP:0007352): onset ; excluded: Cognitive impairment (HP:0100543): onset ; excluded: Ataxia (HP:0001251): onset ; excluded: Dysarthria (HP:0001260): onset ; excluded: Seizure (HP:0001250): onset ; excluded: Headache (HP:0002315): onset ; excluded: Intracerebral periventricular calcifications (HP:0007229): onset ; excluded: Stroke-like episode (HP:0002401): onset ; excluded: Antinuclear antibody positivity (HP:0003493): onset ; excluded: Abnormal circulating calcium concentration (HP:0004363): onset ; excluded: Abnormal blood phosphate concentration (HP:0100529): onset </td></tr>\n",
"<tr><td style=\"text-align: left;\">Family 1 II-5 (FEMALE; P42Y)</td><td style=\"text-align: left;\">Basal ganglia calcification, idiopathic, 10, autosomal recessive (OMIM:621018)</td><td style=\"text-align: left;\">NM_207315.4:c.2T>C (homozygous)</td><td style=\"text-align: left;\">Cognitive impairment (HP:0100543): onset ; Ataxia (HP:0001251): onset ; Dysarthria (HP:0001260): onset ; Globus pallidus calcification (HP:0031627): onset ; Thalamic calcification (HP:0025041): onset ; Cerebellar calcifications (HP:0007352): onset ; Intracerebral periventricular calcifications (HP:0007229): onset ; CSF pleocytosis (HP:0012229): onset ; excluded: Seizure (HP:0001250): onset ; excluded: Headache (HP:0002315): onset ; excluded: Stroke-like episode (HP:0002401): onset ; excluded: Antinuclear antibody positivity (HP:0003493): onset ; excluded: Abnormal circulating calcium concentration (HP:0004363): onset ; excluded: Abnormal blood phosphate concentration (HP:0100529): onset ; excluded: Elevated circulating parathyroid hormone level (HP:0003165): onset </td></tr>\n",
"<tr><td style=\"text-align: left;\">Family 2 II-1 (FEMALE; P39Y)</td><td style=\"text-align: left;\">Basal ganglia calcification, idiopathic, 10, autosomal recessive (OMIM:621018)</td><td style=\"text-align: left;\"><ul> <li>NM_207315.4:c.1A>C (heterozygous)</li> <li>NM_207315.4:c.1241A>G (heterozygous)</li> </ul></td><td style=\"text-align: left;\">Ataxia (HP:0001251): onset ; Globus pallidus calcification (HP:0031627): onset ; Thalamic calcification (HP:0025041): onset ; Cerebellar calcifications (HP:0007352): onset ; Intracerebral periventricular calcifications (HP:0007229): onset ; Antinuclear antibody positivity (HP:0003493): onset ; excluded: Seizure (HP:0001250): onset ; excluded: Headache (HP:0002315): onset ; excluded: Stroke-like episode (HP:0002401): onset ; excluded: Abnormal circulating calcium concentration (HP:0004363): onset ; excluded: Abnormal blood phosphate concentration (HP:0100529): onset ; excluded: Elevated circulating parathyroid hormone level (HP:0003165): onset <br/><b>TimeElement(element=Age(iso8601duration=P32Y))</b>: Cognitive impairment (HP:0100543): onset age {\n",
" iso8601duration: \"P32Y\"\n",
"}\n",
"; Dysarthria (HP:0001260): onset age {\n",
" iso8601duration: \"P32Y\"\n",
"}\n",
"</td></tr>\n",
"</table>"
],
"text/plain": [
"<IPython.core.display.HTML object>"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"table = IndividualTable(cvalidator.get_error_free_individual_list())\n",
"display(HTML(table.to_html()))"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"[pyphetools] Ingested 3 GA4GH phenopackets.\n",
"[INFO] Extracted 3 from 3 phenopackets with OMIM:621018\n",
"\n",
"\tBasal ganglia calcification, idiopathic, 10, autosomal recessive (OMIM:621018): n=3\n",
"We found a total of 15 unique HPO terms\n",
"Extracted disease: Basal ganglia calcification, idiopathic, 10, autosomal recessive (OMIM:621018)\n",
"Wrote HPOA disease file to OMIM-621018.tab\n"
]
}
],
"source": [
"pmid = \"PMID:36443312\"\n",
"df = timporter.create_hpoa_from_phenopackets(pmid=pmid, mode_of_inheritance=Moi.AR, target=\"OMIM:621018\")"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "ps24venv",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.4"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
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221 changes: 221 additions & 0 deletions notebooks/CMPK2/phenopackets/PMID_36443312_Family1II-3.json
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{
"id": "PMID_36443312_Family_1_II_3",
"subject": {
"id": "Family 1 II-3",
"timeAtLastEncounter": {
"age": {
"iso8601duration": "P44Y"
}
},
"vitalStatus": {
"status": "ALIVE"
},
"sex": "MALE"
},
"phenotypicFeatures": [
{
"type": {
"id": "HP:0031627",
"label": "Globus pallidus calcification"
}
},
{
"type": {
"id": "HP:0025041",
"label": "Thalamic calcification"
}
},
{
"type": {
"id": "HP:0007352",
"label": "Cerebellar calcifications"
}
},
{
"type": {
"id": "HP:0100543",
"label": "Cognitive impairment"
},
"excluded": true
},
{
"type": {
"id": "HP:0001251",
"label": "Ataxia"
},
"excluded": true
},
{
"type": {
"id": "HP:0001260",
"label": "Dysarthria"
},
"excluded": true
},
{
"type": {
"id": "HP:0001250",
"label": "Seizure"
},
"excluded": true
},
{
"type": {
"id": "HP:0002315",
"label": "Headache"
},
"excluded": true
},
{
"type": {
"id": "HP:0007229",
"label": "Intracerebral periventricular calcifications"
},
"excluded": true
},
{
"type": {
"id": "HP:0002401",
"label": "Stroke-like episode"
},
"excluded": true
},
{
"type": {
"id": "HP:0003493",
"label": "Antinuclear antibody positivity"
},
"excluded": true
},
{
"type": {
"id": "HP:0004363",
"label": "Abnormal circulating calcium concentration"
},
"excluded": true
},
{
"type": {
"id": "HP:0100529",
"label": "Abnormal blood phosphate concentration"
},
"excluded": true
}
],
"interpretations": [
{
"id": "Family 1 II-3",
"progressStatus": "SOLVED",
"diagnosis": {
"disease": {
"id": "OMIM:621018",
"label": "Basal ganglia calcification, idiopathic, 10, autosomal recessive"
},
"genomicInterpretations": [
{
"subjectOrBiosampleId": "Family 1 II-3",
"interpretationStatus": "CAUSATIVE",
"variantInterpretation": {
"variationDescriptor": {
"id": "var_RPQzArmzQzmMDeQBeajQzAcHS",
"geneContext": {
"valueId": "HGNC:27015",
"symbol": "CMPK2"
},
"expressions": [
{
"syntax": "hgvs.c",
"value": "NM_207315.4:c.2T>C"
},
{
"syntax": "hgvs.g",
"value": "NC_000002.12:g.6865695A>G"
}
],
"vcfRecord": {
"genomeAssembly": "hg38",
"chrom": "chr2",
"pos": "6865695",
"ref": "A",
"alt": "G"
},
"moleculeContext": "genomic",
"allelicState": {
"id": "GENO:0000136",
"label": "homozygous"
}
}
}
}
]
}
}
],
"diseases": [
{
"term": {
"id": "OMIM:621018",
"label": "Basal ganglia calcification, idiopathic, 10, autosomal recessive"
},
"onset": {
"age": {
"iso8601duration": "P44Y"
}
}
}
],
"metaData": {
"created": "2024-12-23T12:51:29.646223068Z",
"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": "2024-12-12",
"namespacePrefix": "HP",
"iriPrefix": "http://purl.obolibrary.org/obo/HP_"
}
],
"phenopacketSchemaVersion": "2.0",
"externalReferences": [
{
"id": "PMID:36443312",
"reference": "https://pubmed.ncbi.nlm.nih.gov/36443312",
"description": "Loss of function of CMPK2 causes mitochondria deficiency and brain calcification"
}
]
}
}
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