From aed7f6bef5109f680f6ffbfa86cccf19759dac8f Mon Sep 17 00:00:00 2001 From: Peter Robinson Date: Tue, 28 May 2024 10:47:25 +0200 Subject: [PATCH] ERF --- notebooks/ERF/ERF_CHYTS_individuals.ipynb | 179 ++++++++ .../ERF/input/ERF_CHYTS_individuals.xlsx | Bin 0 -> 11167 bytes .../phenopackets/PMID_27738187_Patient1.json | 359 ++++++++++++++++ .../phenopackets/PMID_27738187_Patient2.json | 342 +++++++++++++++ .../phenopackets/PMID_27738187_Patient3.json | 341 +++++++++++++++ .../phenopackets/PMID_27738187_Patient4.json | 352 +++++++++++++++ .../phenopackets/PMID_27738187_Patient5.json | 300 +++++++++++++ .../phenopackets/PMID_30569521_proband.json | 351 +++++++++++++++ .../Caro-Contreras-2019-ERF-proband.json | 343 --------------- ...69521-Caro-Contreras-2019-ERF-proband.json | 403 ------------------ 10 files changed, 2224 insertions(+), 746 deletions(-) create mode 100644 notebooks/ERF/ERF_CHYTS_individuals.ipynb create mode 100644 notebooks/ERF/input/ERF_CHYTS_individuals.xlsx create mode 100644 notebooks/ERF/phenopackets/PMID_27738187_Patient1.json create mode 100644 notebooks/ERF/phenopackets/PMID_27738187_Patient2.json create mode 100644 notebooks/ERF/phenopackets/PMID_27738187_Patient3.json create mode 100644 notebooks/ERF/phenopackets/PMID_27738187_Patient4.json create mode 100644 notebooks/ERF/phenopackets/PMID_27738187_Patient5.json create mode 100644 notebooks/ERF/phenopackets/PMID_30569521_proband.json delete mode 100644 notebooks/LIRICAL/v1ppkts/Caro-Contreras-2019-ERF-proband.json delete mode 100644 notebooks/LIRICAL/v2phenopackets/PMID_30569521-Caro-Contreras-2019-ERF-proband.json diff --git a/notebooks/ERF/ERF_CHYTS_individuals.ipynb b/notebooks/ERF/ERF_CHYTS_individuals.ipynb new file mode 100644 index 00000000..f9e1c6df --- /dev/null +++ b/notebooks/ERF/ERF_CHYTS_individuals.ipynb @@ -0,0 +1,179 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# ERF\n", + "[Chitayat syndrome (CHYTS)](https://omim.org/entry/617180) is caused by heterozygous mutation in the ERF gene." + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Using pyphetools version 0.9.88\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/Users/robin/GIT/phenopacket-store/ps24venv/lib/python3.9/site-packages/urllib3/__init__.py:35: NotOpenSSLWarning: urllib3 v2 only supports OpenSSL 1.1.1+, currently the 'ssl' module is compiled with 'LibreSSL 2.8.3'. See: https://github.com/urllib3/urllib3/issues/3020\n", + " warnings.warn(\n" + ] + } + ], + "source": [ + "from pyphetools.creation import TemplateImporter\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/ERF_CHYTS_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 2024-04-26\n", + "Created encoders for 49 fields\n", + "Importing OMIM:617180, Chitayat syndrome, HGNC:3444, ERF, NM_006494.4\n", + "We output 6 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": [ + "

Cohort validation

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Errors found with 1 of 6 phenopackets.

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Error counts
LevelError categoryCount
WARNINGREDUNDANT1
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A total of 1 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": 5, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "
6 phenopackets - PMID:27738187 (n=5); PMID:30569521 (n=1)
IndividualDiseaseGenotypePhenotypic features
Patient 1 (MALE; P21Y)Chitayat syndrome (OMIM:617180)NM_006494.4:c.266A>G (heterozygous)Diaphragmatic eventration (HP:0009110); Bronchomalacia (HP:0002780); Thick vermilion border (HP:0012471); Long philtrum (HP:0000343); Anteverted nares (HP:0000463); Depressed nasal bridge (HP:0005280); Hallux valgus (HP:0001822); Finger hyperphalangy (HP:0030367); Hypertelorism (HP:0000316); Proptosis (HP:0000520); Respiratory distress (HP:0002098); Motor delay (HP:0001270); Recurrent respiratory infections (HP:0002205); excluded: Global developmental delay (HP:0001263); excluded: Polyhydramnios (HP:0001561); excluded: Patent ductus arteriosus (HP:0001643); excluded: Tracheomalacia (HP:0002779); excluded: Overfolded helix (HP:0000396); excluded: Wide nasal bridge (HP:0000431); excluded: Flat occiput (HP:0005469); excluded: Narrow forehead (HP:0000341); excluded: Pectus excavatum (HP:0000767); excluded: Hypotonia (HP:0001252); excluded: Interstitial emphysema (HP:0032965); excluded: Gastroesophageal reflux (HP:0002020)
Patient 2 (FEMALE; P5Y6M)Chitayat syndrome (OMIM:617180)NM_006494.4:c.266A>G (heterozygous)P2M: Anteverted nares (HP:0000463); Depressed nasal bridge (HP:0005280); Hallux valgus (HP:0001822); Short 2nd finger (HP:0009536); Hypertelorism (HP:0000316); Interstitial emphysema (HP:0032965)
P5Y6M: Pectus excavatum (HP:0000767)
Polyhydramnios (HP:0001561); Respiratory distress (HP:0002098); Patent ductus arteriosus (HP:0001643); Recurrent respiratory infections (HP:0002205); excluded: Diaphragmatic eventration (HP:0009110); excluded: Motor delay (HP:0001270); excluded: Global developmental delay (HP:0001263); excluded: Tracheomalacia (HP:0002779); excluded: Bronchomalacia (HP:0002780); excluded: Long philtrum (HP:0000343); excluded: Overfolded helix (HP:0000396); excluded: Wide nasal bridge (HP:0000431); excluded: Flat occiput (HP:0005469); excluded: Narrow forehead (HP:0000341); excluded: Finger hyperphalangy (HP:0030367); excluded: Hypotonia (HP:0001252); excluded: Proptosis (HP:0000520); excluded: Gastroesophageal reflux (HP:0002020)
Patient 3 (MALE; P6Y)Chitayat syndrome (OMIM:617180)NM_006494.4:c.266A>G (heterozygous)P19D: Anteverted nares (HP:0000463); Depressed nasal bridge (HP:0005280); Pectus excavatum (HP:0000767); Hallux valgus (HP:0001822); Short 2nd finger (HP:0009536); Hypotonia (HP:0001252); Hypertelorism (HP:0000316)
Polyhydramnios (HP:0001561); Respiratory distress (HP:0002098); Motor delay (HP:0001270); Patent ductus arteriosus (HP:0001643); Finger hyperphalangy (HP:0030367); excluded: Diaphragmatic eventration (HP:0009110); excluded: Global developmental delay (HP:0001263); excluded: Tracheomalacia (HP:0002779); excluded: Recurrent respiratory infections (HP:0002205); excluded: Bronchomalacia (HP:0002780); excluded: Long philtrum (HP:0000343); excluded: Overfolded helix (HP:0000396); excluded: Wide nasal bridge (HP:0000431); excluded: Flat occiput (HP:0005469); excluded: Narrow forehead (HP:0000341); excluded: Proptosis (HP:0000520); excluded: Interstitial emphysema (HP:0032965); excluded: Gastroesophageal reflux (HP:0002020)
Patient 4 (MALE; P4Y)Chitayat syndrome (OMIM:617180)NM_006494.4:c.266A>G (heterozygous)Polyhydramnios (HP:0001561); Respiratory distress (HP:0002098); Overfolded helix (HP:0000396); Wide nasal bridge (HP:0000431); Pectus excavatum (HP:0000767); Hallux valgus (HP:0001822); Clinodactyly of the 5th finger (HP:0004209); Hypertelorism (HP:0000316); Motor delay (HP:0001270); Global developmental delay (HP:0001263); Tracheomalacia (HP:0002779); Recurrent respiratory infections (HP:0002205); Bronchomalacia (HP:0002780); Short middle phalanx of the 2nd finger (HP:0009577); Short middle phalanx of the 5th finger (HP:0004220); Short proximal phalanx of hallux (HP:0010107); excluded: Diaphragmatic eventration (HP:0009110); excluded: Patent ductus arteriosus (HP:0001643); excluded: Long philtrum (HP:0000343); excluded: Anteverted nares (HP:0000463); excluded: Flat occiput (HP:0005469); excluded: Narrow forehead (HP:0000341); excluded: Finger hyperphalangy (HP:0030367); excluded: Hypotonia (HP:0001252); excluded: Proptosis (HP:0000520); excluded: Interstitial emphysema (HP:0032965); excluded: Gastroesophageal reflux (HP:0002020)
Patient 5 (MALE; P40Y)Chitayat syndrome (OMIM:617180)NM_006494.4:c.266A>G (heterozygous)Respiratory distress (HP:0002098); Pectus excavatum (HP:0000767); Hallux valgus (HP:0001822); Short middle phalanx of the 2nd finger (HP:0009577); Short middle phalanx of the 5th finger (HP:0004220); Short proximal phalanx of hallux (HP:0010107); excluded: Diaphragmatic eventration (HP:0009110); excluded: Motor delay (HP:0001270); excluded: Global developmental delay (HP:0001263); excluded: Polyhydramnios (HP:0001561); excluded: Patent ductus arteriosus (HP:0001643); excluded: Tracheomalacia (HP:0002779); excluded: Recurrent respiratory infections (HP:0002205); excluded: Bronchomalacia (HP:0002780); excluded: Long philtrum (HP:0000343); excluded: Overfolded helix (HP:0000396); excluded: Anteverted nares (HP:0000463); excluded: Wide nasal bridge (HP:0000431); excluded: Flat occiput (HP:0005469); excluded: Narrow forehead (HP:0000341); excluded: Finger hyperphalangy (HP:0030367); excluded: Hypotonia (HP:0001252); excluded: Proptosis (HP:0000520); excluded: Interstitial emphysema (HP:0032965); excluded: Gastroesophageal reflux (HP:0002020)
proband (MALE; P3Y)Chitayat syndrome (OMIM:617180)NM_006494.4:c.266A>G (heterozygous)P2Y8M: Wide nasal bridge (HP:0000431); Depressed nasal bridge (HP:0005280); Flat occiput (HP:0005469); Narrow forehead (HP:0000341); Short middle phalanx of the 2nd finger (HP:0009577); Short middle phalanx of the 5th finger (HP:0004220); Clinodactyly of the 5th finger (HP:0004209); Hypertelorism (HP:0000316); Proptosis (HP:0000520)
Respiratory distress (HP:0002098); Motor delay (HP:0001270); Global developmental delay (HP:0001263); Gastroesophageal reflux (HP:0002020); excluded: Diaphragmatic eventration (HP:0009110); excluded: Polyhydramnios (HP:0001561); excluded: Patent ductus arteriosus (HP:0001643); excluded: Tracheomalacia (HP:0002779); excluded: Recurrent respiratory infections (HP:0002205); excluded: Bronchomalacia (HP:0002780); excluded: Long philtrum (HP:0000343); excluded: Overfolded helix (HP:0000396); excluded: Anteverted nares (HP:0000463); excluded: Pectus excavatum (HP:0000767); excluded: Finger hyperphalangy (HP:0030367); excluded: Hypotonia (HP:0001252); excluded: Interstitial emphysema (HP:0032965)
" + ], + "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": 6, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[pyphetools] Ingested 6 GA4GH phenopackets.\n", + "[INFO] Extracted 6 from 6 phenopackets with OMIM:617180\n", + "\n", + "\tChitayat syndrome (OMIM:617180): n=6\n", + "We found a total of 30 unique HPO terms\n", + "Extracted disease: Chitayat syndrome (OMIM:617180)\n", + "Wrote HPOA disease file to OMIM-617180.tab\n" + ] + } + ], + "source": [ + "pmid = \"PMID:27738187\"\n", + "df = timporter.create_hpoa_from_phenopackets(pmid=pmid, moi=\"Autosomal dominant\", target=\"OMIM:617180\")" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "ps24venv", + "language": "python", + "name": "python3" + }, + 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