Update

monarch-initiative · Dec 27, 2024 · 2dc726b · 2dc726b
1 parent a0b2fe0
commit 2dc726b
Show file tree

Hide file tree

Showing 6 changed files with 1,399 additions and 0 deletions.
diff --git a/notebooks/TBK1/TBK1_AIARV_individuals.ipynb 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": [
+       "<h2>Cohort validation</h2>\n",
+       "<p>Errors found with 3 of 4 phenopackets.</p>\n",
+       "<table style=\"border: 2px solid black; align: \"left\">\n",
+       "<caption>Error counts</caption>\n",
+       "<tr><th style=\"text-align: left;font-weight: bold;\">Level</th><th style=\"text-align: left;font-weight: bold;\">Error category</th><th style=\"text-align: left;font-weight: bold;\">Count</th></tr>\n",
+       "<tr><td style=\"text-align: left;\">WARNING</td><td style=\"text-align: left;\">REDUNDANT</td><td style=\"text-align: left;\">4</td></tr>\n",
+       "</table>\n",
+       "<p>A total of 4 issues were fixed and no individual was removed from the cohort.</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": 6,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<table style=\"border: 2px solid black; align: \"left\">\n",
+       "<caption>4 phenopackets - PMID:34363755 (n=4)</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 individual P1 (FEMALE; P32Y)</td><td style=\"text-align: left;\">Autoinflammation with arthritis and vasculitis (OMIM:620880)</td><td style=\"text-align: left;\">NM_013254.4:c.1857G>A (homozygous)</td><td style=\"text-align: left;\">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 <br/><b>TimeElement(element=OntologyClass(id=HP:0003593, label=Infantile onset))</b>: 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",
+       "<br/><b>TimeElement(element=Age(iso8601duration=P5Y))</b>: Villous atrophy (HP:0011473): onset age {\n",
+       "  iso8601duration: \"P5Y\"\n",
+       "}\n",
+       "<br/><b>TimeElement(element=OntologyClass(id=HP:0011462, label=Young adult onset))</b>: Recurrent urinary tract infections (HP:0000010): onset ontology_class {\n",
+       "  id: \"HP:0011462\"\n",
+       "  label: \"Young adult onset\"\n",
+       "}\n",
+       "<br/><b>TimeElement(element=Age(iso8601duration=P22Y))</b>: Osteomyelitis (HP:0002754): onset age {\n",
+       "  iso8601duration: \"P22Y\"\n",
+       "}\n",
+       "<br/><b>TimeElement(element=Age(iso8601duration=P28Y))</b>: Cerebral infarct (HP:0025722): onset age {\n",
+       "  iso8601duration: \"P28Y\"\n",
+       "}\n",
+       "</td></tr>\n",
+       "<tr><td style=\"text-align: left;\">Family 1 individual P2 (MALE; P26Y)</td><td style=\"text-align: left;\">Autoinflammation with arthritis and vasculitis (OMIM:620880)</td><td style=\"text-align: left;\">NM_013254.4:c.1857G>A (homozygous)</td><td style=\"text-align: left;\">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 <br/><b>TimeElement(element=OntologyClass(id=HP:0003593, label=Infantile onset))</b>: 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",
+       "<br/><b>TimeElement(element=Age(iso8601duration=P1Y))</b>: Seizure (HP:0001250): onset age {\n",
+       "  iso8601duration: \"P1Y\"\n",
+       "}\n",
+       "<br/><b>TimeElement(element=Age(iso8601duration=P1Y6M))</b>: Vasculitis in the skin (HP:0200029): onset age {\n",
+       "  iso8601duration: \"P1Y6M\"\n",
+       "}\n",
+       "; Leukocytoclastic vasculitis (HP:0034786): onset age {\n",
+       "  iso8601duration: \"P1Y6M\"\n",
+       "}\n",
+       "</td></tr>\n",
+       "<tr><td style=\"text-align: left;\">Family 2 individual P3 (MALE; P7Y)</td><td style=\"text-align: left;\">Autoinflammation with arthritis and vasculitis (OMIM:620880)</td><td style=\"text-align: left;\">NM_013254.4:c.634T>G (homozygous)</td><td style=\"text-align: left;\">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 <br/><b>TimeElement(element=OntologyClass(id=HP:0003593, label=Infantile onset))</b>: Arthritis (HP:0001369): onset ontology_class {\n",
+       "  id: \"HP:0003593\"\n",
+       "  label: \"Infantile onset\"\n",
+       "}\n",
+       "<br/><b>TimeElement(element=Age(iso8601duration=P7Y9M))</b>: Nephrotic syndrome (HP:0000100): onset age {\n",
+       "  iso8601duration: \"P7Y9M\"\n",
+       "}\n",
+       "</td></tr>\n",
+       "<tr><td style=\"text-align: left;\">Family 3 individual P4 (FEMALE; P8Y)</td><td style=\"text-align: left;\">Autoinflammation with arthritis and vasculitis (OMIM:620880)</td><td style=\"text-align: left;\">NM_013254.4:c.1318C>T (homozygous)</td><td style=\"text-align: left;\">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 <br/><b>TimeElement(element=Age(iso8601duration=P3Y))</b>: Seizure (HP:0001250): onset age {\n",
+       "  iso8601duration: \"P3Y\"\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": 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": "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
+}
diff --git a/notebooks/TBK1/input/TBK1_AIARV_individuals.xlsx b/notebooks/TBK1/input/TBK1_AIARV_individuals.xlsx