From 2dc726b9d01c73fc849e6c92cc3252d1f25351c9 Mon Sep 17 00:00:00 2001 From: Peter Robinson Date: Fri, 27 Dec 2024 12:30:26 +0100 Subject: [PATCH] Update --- notebooks/TBK1/TBK1_AIARV_individuals.ipynb | 219 +++++++++++ .../TBK1/input/TBK1_AIARV_individuals.xlsx | Bin 0 -> 11107 bytes .../PMID_34363755_Family1individualP1.json | 344 ++++++++++++++++++ .../PMID_34363755_Family1individualP2.json | 288 +++++++++++++++ .../PMID_34363755_Family2individualP3.json | 283 ++++++++++++++ .../PMID_34363755_Family3individualP4.json | 265 ++++++++++++++ 6 files changed, 1399 insertions(+) create mode 100644 notebooks/TBK1/TBK1_AIARV_individuals.ipynb create mode 100644 notebooks/TBK1/input/TBK1_AIARV_individuals.xlsx create mode 100644 notebooks/TBK1/phenopackets/PMID_34363755_Family1individualP1.json create mode 100644 notebooks/TBK1/phenopackets/PMID_34363755_Family1individualP2.json create mode 100644 notebooks/TBK1/phenopackets/PMID_34363755_Family2individualP3.json create mode 100644 notebooks/TBK1/phenopackets/PMID_34363755_Family3individualP4.json diff --git a/notebooks/TBK1/TBK1_AIARV_individuals.ipynb b/notebooks/TBK1/TBK1_AIARV_individuals.ipynb new file mode 100644 index 00000000..d492d494 --- /dev/null +++ b/notebooks/TBK1/TBK1_AIARV_individuals.ipynb @@ -0,0 +1,219 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# TBK1\n", + "[Autoinflammation with arthritis and vasculitis (AIARV)](https://omim.org/entry/620880) is caused by homozygous mutation in the TBK1 gene." + ] + }, + { + "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": 4, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "HPO version 2024-12-12\n", + "Created encoders for 57 fields\n", + "Importing OMIM:620880, Autoinflammation with arthritis and vasculitis, HGNC:11584, TBK1, NM_013254.4\n", + "[INFO] encoding variant \"c.1318C>T\"\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_013254.4%3Ac.1318C>T/NM_013254.4?content-type=application%2Fjson\n", + "[INFO] encoding variant \"c.634T>G\"\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_013254.4%3Ac.634T>G/NM_013254.4?content-type=application%2Fjson\n", + "[INFO] encoding variant \"c.1857G>A\"\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_013254.4%3Ac.1857G>A/NM_013254.4?content-type=application%2Fjson\n", + "We output 4 GA4GH phenopackets to the directory phenopackets\n" + ] + } + ], + "source": [ + "template = \"input/TBK1_AIARV_individuals.xlsx\"\n", + "created_by = \"0000-0002-0736-9199\"\n", + "timporter = TemplateImporter(template=template, created_by=created_by)\n", + "individual_list, cvalidator = timporter.import_phenopackets_from_template()" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "

Cohort validation

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Errors found with 3 of 4 phenopackets.

\n", + "\n", + "\n", + "\n", + "\n", + "
Error counts
LevelError categoryCount
WARNINGREDUNDANT4
\n", + "

A total of 4 issues were fixed and no individual was removed from the cohort.

" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "qc = QcVisualizer(cohort_validator=cvalidator)\n", + "display(HTML(qc.to_summary_html()))" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "
4 phenopackets - PMID:34363755 (n=4)
IndividualDiseaseGenotypePhenotypic features
Family 1 individual P1 (FEMALE; P32Y)Autoinflammation with arthritis and vasculitis (OMIM:620880)NM_013254.4:c.1857G>A (homozygous)Motor delay (HP:0001270): onset ; Global developmental delay (HP:0001263): onset ; Intellectual disability, mild (HP:0001256): onset ; Seizure (HP:0001250): onset ; Vasculitis (HP:0002633): onset ; Microcytic anemia (HP:0001935): onset ; Recurrent fever (HP:0001954): onset ; Celiac disease (HP:0002608): onset ; Disproportionate short-limb short stature (HP:0008873): onset ; Autoimmunity (HP:0002960): onset ; Recurrent sinusitis (HP:0011108): onset ; excluded: Delayed speech and language development (HP:0000750): onset ; excluded: Status epilepticus (HP:0002133): onset ; excluded: Thrombocytosis (HP:0001894): onset ; excluded: Conjunctivitis (HP:0000509): onset ; excluded: Immunodeficiency (HP:0002721): onset ; excluded: Visceromegaly (HP:0003271): onset ; excluded: Recurrent tonsillitis (HP:0011110): onset ; excluded: Abdominal pain (HP:0002027): onset ; excluded: Herpes simplex encephalitis (HP:0012302): onset
TimeElement(element=OntologyClass(id=HP:0003593, label=Infantile onset)): Arthritis (HP:0001369): onset ontology_class {\n", + " id: \"HP:0003593\"\n", + " label: \"Infantile onset\"\n", + "}\n", + "; Feeding difficulties (HP:0011968): onset ontology_class {\n", + " id: \"HP:0003593\"\n", + " label: \"Infantile onset\"\n", + "}\n", + "; Exanthem (HP:4000054): onset ontology_class {\n", + " id: \"HP:0003593\"\n", + " label: \"Infantile onset\"\n", + "}\n", + "
TimeElement(element=Age(iso8601duration=P5Y)): Villous atrophy (HP:0011473): onset age {\n", + " iso8601duration: \"P5Y\"\n", + "}\n", + "
TimeElement(element=OntologyClass(id=HP:0011462, label=Young adult onset)): Recurrent urinary tract infections (HP:0000010): onset ontology_class {\n", + " id: \"HP:0011462\"\n", + " label: \"Young adult onset\"\n", + "}\n", + "
TimeElement(element=Age(iso8601duration=P22Y)): Osteomyelitis (HP:0002754): onset age {\n", + " iso8601duration: \"P22Y\"\n", + "}\n", + "
TimeElement(element=Age(iso8601duration=P28Y)): Cerebral infarct (HP:0025722): onset age {\n", + " iso8601duration: \"P28Y\"\n", + "}\n", + "
Family 1 individual P2 (MALE; P26Y)Autoinflammation with arthritis and vasculitis (OMIM:620880)NM_013254.4:c.1857G>A (homozygous)Global developmental delay (HP:0001263): onset ; Intellectual disability, mild (HP:0001256): onset ; Microcytic anemia (HP:0001935): onset ; Recurrent fever (HP:0001954): onset ; Disproportionate short-limb short stature (HP:0008873): onset ; Recurrent tonsillitis (HP:0011110): onset ; Autoimmunity (HP:0002960): onset ; Abdominal pain (HP:0002027): onset ; excluded: Status epilepticus (HP:0002133): onset ; excluded: Thrombocytosis (HP:0001894): onset ; excluded: Celiac disease (HP:0002608): onset ; excluded: Conjunctivitis (HP:0000509): onset ; excluded: Immunodeficiency (HP:0002721): onset ; excluded: Visceromegaly (HP:0003271): onset ; excluded: Villous atrophy (HP:0011473): onset
TimeElement(element=OntologyClass(id=HP:0003593, label=Infantile onset)): Arthritis (HP:0001369): onset ontology_class {\n", + " id: \"HP:0003593\"\n", + " label: \"Infantile onset\"\n", + "}\n", + "; Feeding difficulties (HP:0011968): onset ontology_class {\n", + " id: \"HP:0003593\"\n", + " label: \"Infantile onset\"\n", + "}\n", + "
TimeElement(element=Age(iso8601duration=P1Y)): Seizure (HP:0001250): onset age {\n", + " iso8601duration: \"P1Y\"\n", + "}\n", + "
TimeElement(element=Age(iso8601duration=P1Y6M)): Vasculitis in the skin (HP:0200029): onset age {\n", + " iso8601duration: \"P1Y6M\"\n", + "}\n", + "; Leukocytoclastic vasculitis (HP:0034786): onset age {\n", + " iso8601duration: \"P1Y6M\"\n", + "}\n", + "
Family 2 individual P3 (MALE; P7Y)Autoinflammation with arthritis and vasculitis (OMIM:620880)NM_013254.4:c.634T>G (homozygous)Status epilepticus (HP:0002133): onset ; Thrombocytosis (HP:0001894): onset ; Microcytic anemia (HP:0001935): onset ; Conjunctivitis (HP:0000509): onset ; Short stature (HP:0004322): onset ; Inflammatory abnormality of the skin (HP:0011123): onset ; Autoimmunity (HP:0002960): onset ; excluded: Lymphadenopathy (HP:0002716): onset ; excluded: Brain atrophy (HP:0012444): onset ; excluded: Global developmental delay (HP:0001263): onset ; excluded: Intellectual disability, mild (HP:0001256): onset ; excluded: Vasculitis (HP:0002633): onset ; excluded: Feeding difficulties (HP:0011968): onset ; excluded: Recurrent fever (HP:0001954): onset ; excluded: Celiac disease (HP:0002608): onset ; excluded: Immunodeficiency (HP:0002721): onset ; excluded: Visceromegaly (HP:0003271): onset ; excluded: Recurrent tonsillitis (HP:0011110): onset ; excluded: Abdominal pain (HP:0002027): onset
TimeElement(element=OntologyClass(id=HP:0003593, label=Infantile onset)): Arthritis (HP:0001369): onset ontology_class {\n", + " id: \"HP:0003593\"\n", + " label: \"Infantile onset\"\n", + "}\n", + "
TimeElement(element=Age(iso8601duration=P7Y9M)): Nephrotic syndrome (HP:0000100): onset age {\n", + " iso8601duration: \"P7Y9M\"\n", + "}\n", + "
Family 3 individual P4 (FEMALE; P8Y)Autoinflammation with arthritis and vasculitis (OMIM:620880)NM_013254.4:c.1318C>T (homozygous)Lymphadenopathy (HP:0002716): onset ; Recurrent fever (HP:0001954): onset ; Ventriculomegaly (HP:0002119): onset ; Recurrent tonsillitis (HP:0011110): onset ; Autoimmunity (HP:0002960): onset ; excluded: Global developmental delay (HP:0001263): onset ; excluded: Intellectual disability, mild (HP:0001256): onset ; excluded: Status epilepticus (HP:0002133): onset ; excluded: Vasculitis (HP:0002633): onset ; excluded: Thrombocytosis (HP:0001894): onset ; excluded: Microcytic anemia (HP:0001935): onset ; excluded: Feeding difficulties (HP:0011968): onset ; excluded: Celiac disease (HP:0002608): onset ; excluded: Conjunctivitis (HP:0000509): onset ; excluded: Short stature (HP:0004322): onset ; excluded: Immunodeficiency (HP:0002721): onset ; excluded: Visceromegaly (HP:0003271): onset ; excluded: Abdominal pain (HP:0002027): onset
TimeElement(element=Age(iso8601duration=P3Y)): Seizure (HP:0001250): onset age {\n", + " iso8601duration: \"P3Y\"\n", + "}\n", + "
" + ], + "text/plain": [ + "" + ] + }, + "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": 7, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[pyphetools] Ingested 4 GA4GH phenopackets.\n", + "[INFO] Extracted 4 from 4 phenopackets with OMIM:620880\n", + "\n", + "\tAutoinflammation with arthritis and vasculitis (OMIM:620880): n=4\n", + "We found a total of 35 unique HPO terms\n", + "Extracted disease: Autoinflammation with arthritis and vasculitis (OMIM:620880)\n", + "Wrote HPOA disease file to OMIM-620880.tab\n" + ] + } + ], + "source": [ + "pmid = \"PMID:34363755\"\n", + "df = timporter.create_hpoa_from_phenopackets(pmid=pmid, mode_of_inheritance=Moi.AR, target=\"OMIM:620880\")" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": 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difficulties" + }, + "onset": { + "ontologyClass": { + "id": "HP:0003593", + "label": "Infantile onset" + } + } + }, + { + "type": { + "id": "HP:4000054", + "label": "Exanthem" + }, + "onset": { + "ontologyClass": { + "id": "HP:0003593", + "label": "Infantile onset" + } + } + }, + { + "type": { + "id": "HP:0011473", + "label": "Villous atrophy" + }, + "onset": { + "age": { + "iso8601duration": "P5Y" + } + } + }, + { + "type": { + "id": "HP:0002754", + "label": "Osteomyelitis" + }, + "onset": { + "age": { + "iso8601duration": "P22Y" + } + } + }, + { + "type": { + "id": "HP:0000010", + "label": "Recurrent urinary tract infections" + }, + "onset": { + "ontologyClass": { + "id": "HP:0011462", + "label": "Young adult onset" + } + } + }, + { + "type": { + "id": "HP:0025722", + "label": "Cerebral infarct" + }, + "onset": { + "age": { + "iso8601duration": "P28Y" + } + } + }, + { + "type": { + "id": "HP:0001270", + "label": "Motor delay" + } + }, + { + "type": { + "id": "HP:0001263", + "label": 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"namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + } + ], + "phenopacketSchemaVersion": "2.0", + "externalReferences": [ + { + "id": "PMID:34363755", + "reference": "https://pubmed.ncbi.nlm.nih.gov/34363755", + "description": "Human TBK1 deficiency leads to autoinflammation driven by TNF-induced cell death" + } + ] + } +} \ No newline at end of file diff --git a/notebooks/TBK1/phenopackets/PMID_34363755_Family1individualP2.json b/notebooks/TBK1/phenopackets/PMID_34363755_Family1individualP2.json new file mode 100644 index 00000000..bdeaa40f --- /dev/null +++ b/notebooks/TBK1/phenopackets/PMID_34363755_Family1individualP2.json @@ -0,0 +1,288 @@ +{ + "id": "PMID_34363755_Family_1_individual_P2", + "subject": { + "id": "Family 1 individual P2", + "timeAtLastEncounter": { + "age": { + "iso8601duration": "P26Y" + } + }, + "vitalStatus": { + "status": "ALIVE" + }, + "sex": "MALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0001369", + "label": 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