From d2e5af31558697a4716b1e7a42a4553f4ca809ea Mon Sep 17 00:00:00 2001 From: Peter Robinson Date: Fri, 10 Jan 2025 08:11:07 +0100 Subject: [PATCH] AMT --- notebooks/AMT/AMT_GCE2_individuals.ipynb | 160 +++++++++++ notebooks/AMT/input/AMT_GCE2_individuals.xlsx | Bin 0 -> 10562 bytes .../phenopackets/PMID_33791923_Patient6.json | 248 ++++++++++++++++++ .../phenopackets/PMID_33791923_Patient7.json | 234 +++++++++++++++++ .../phenopackets/PMID_8005589_patientA.json | 146 +++++++++++ .../phenopackets/PMID_8005589_patientB.json | 193 ++++++++++++++ .../PMID_9600239_propositusVII-7.json | 162 ++++++++++++ 7 files changed, 1143 insertions(+) create mode 100644 notebooks/AMT/AMT_GCE2_individuals.ipynb create mode 100644 notebooks/AMT/input/AMT_GCE2_individuals.xlsx create mode 100644 notebooks/AMT/phenopackets/PMID_33791923_Patient6.json create mode 100644 notebooks/AMT/phenopackets/PMID_33791923_Patient7.json create mode 100644 notebooks/AMT/phenopackets/PMID_8005589_patientA.json create mode 100644 notebooks/AMT/phenopackets/PMID_8005589_patientB.json create mode 100644 notebooks/AMT/phenopackets/PMID_9600239_propositusVII-7.json diff --git a/notebooks/AMT/AMT_GCE2_individuals.ipynb b/notebooks/AMT/AMT_GCE2_individuals.ipynb new file mode 100644 index 00000000..9e8f891f --- /dev/null +++ b/notebooks/AMT/AMT_GCE2_individuals.ipynb @@ -0,0 +1,160 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# AMT\n", + "[glycine encephalopathy-2 (GCE2)](https://omim.org/entry/620398) is caused by homozygous or compound heterozygous mutation in the AMT gene." + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "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": 13, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "HPO version 2024-12-12\n", + "Created encoders for 38 fields\n", + "Importing OMIM:620398, Glycine encephalopathy 2, HGNC:473, AMT, NM_000481.4\n", + "We output 5 GA4GH phenopackets to the directory phenopackets\n" + ] + } + ], + "source": [ + "template = \"input/AMT_GCE2_individuals.xlsx\"\n", + "created_by = \"0000-0002-0736-9199\"\n", + "deletions = {\"DEL:Total AMT gene deletion\"}\n", + "timporter = TemplateImporter(template=template, created_by=created_by)\n", + "individual_list, cvalidator = timporter.import_phenopackets_from_template(deletions=deletions)" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "

Cohort validation

\n", + "

No errors found for the cohort with 5 individuals

" + ], + "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": 15, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "
5 phenopackets - PMID:8005589 (n=2); PMID:9600239 (n=1); PMID:33791923 (n=2)
IndividualDiseaseGenotypePhenotypic features
patient A (FEMALE; P19Y)Glycine encephalopathy 2 (OMIM:620398)NM_000481.4:c.806G>A (homozygous)Global developmental delay (HP:0001263): onset ; Hyperglycinuria (HP:0003108): onset ; Intellectual disability, severe (HP:0010864): onset
patient B (FEMALE; P9Y)Glycine encephalopathy 2 (OMIM:620398)
  • NM_000481.4:c.139G>A (heterozygous)
  • NM_000481.4:c.959G>A (heterozygous)
Global developmental delay (HP:0001263): onset ; Seizure (HP:0001250): onset ; Cerebral atrophy (HP:0002059): onset ; Hyperglycinuria (HP:0003108): onset ; Intellectual disability, severe (HP:0010864): onset
propositus VII-7 (MALE; P2D)Glycine encephalopathy 2 (OMIM:620398)NM_000481.4:c.125A>G (homozygous)EEG with burst suppression (HP:0010851): onset ; Increased CSF glycine concentration (HP:0500230): onset ; Hyperglycinemia (HP:0002154): onset
TimeElement(element=Age(iso8601duration=P2D)): Seizure (HP:0001250): onset age {\n", + " iso8601duration: \"P2D\"\n", + "}\n", + "
Patient 6 (FEMALE; P5D)Glycine encephalopathy 2 (OMIM:620398)NM_000481.4:c.434A>T (homozygous)Global developmental delay (HP:0001263): onset ; Seizure (HP:0001250): onset ; EEG with burst suppression (HP:0010851): onset ; Increased CSF glycine concentration (HP:0500230): onset ; Hyperglycinemia (HP:0002154): onset ; Respiratory failure requiring assisted ventilation (HP:0004887): onset ; Patent foramen ovale (HP:0001655): onset ; Microcephaly (HP:0000252): onset ; Hypotonia (HP:0001252): onset ; Vomiting (HP:0002013): onset ; Pyloric stenosis (HP:0002021): onset ; Micrognathia (HP:0000347): onset ; Hyperreflexia (HP:0001347): onset ; Poor suck (HP:0002033): onset ; Dysplastic corpus callosum (HP:0006989): onset ; Cerebral hypomyelination (HP:0006808): onset ; excluded: Hydrocephalus (HP:0000238): onset ; excluded: Ventriculomegaly (HP:0002119): onset
Patient 7 (MALE; P7Y5M)Glycine encephalopathy 2 (OMIM:620398)DEL:Total AMT gene deletion: chromosomal_deletion (SO:1000029)Global developmental delay (HP:0001263): onset ; Seizure (HP:0001250): onset ; EEG with burst suppression (HP:0010851): onset ; Increased CSF glycine concentration (HP:0500230): onset ; Hyperglycinemia (HP:0002154): onset ; Respiratory failure requiring assisted ventilation (HP:0004887): onset ; Microcephaly (HP:0000252): onset ; Hypotonia (HP:0001252): onset ; Micrognathia (HP:0000347): onset ; Hyperreflexia (HP:0001347): onset ; Poor suck (HP:0002033): onset ; Dysplastic corpus callosum (HP:0006989): onset ; Hydrocephalus (HP:0000238): onset ; excluded: Patent foramen ovale (HP:0001655): onset ; excluded: Vomiting (HP:0002013): onset ; excluded: Pyloric stenosis (HP:0002021): onset ; excluded: Cerebral hypomyelination (HP:0006808): onset ; excluded: Ventriculomegaly (HP:0002119): onset
" + ], + "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": 16, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[pyphetools] Ingested 5 GA4GH phenopackets.\n", + "[INFO] Extracted 5 from 5 phenopackets with OMIM:620398\n", + "\n", + "\tGlycine encephalopathy 2 (OMIM:620398): n=5\n", + "We found a total of 21 unique HPO terms\n", + "Extracted disease: Glycine encephalopathy 2 (OMIM:620398)\n", + "Wrote HPOA disease file to OMIM-620398.tab\n" + ] + } + ], + "source": [ + "pmid = \"PMID:8005589\"\n", + "df = timporter.create_hpoa_from_phenopackets(pmid=pmid, mode_of_inheritance=Moi.AR, target=\"OMIM:620398\")" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "ps24venv", + "language": "python", + "name": 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