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{ | ||
"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": [ | ||
"<h2>Cohort validation</h2>\n", | ||
"<p>Errors found with 1 of 6 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;\">1</td></tr>\n", | ||
"</table>\n", | ||
"<p>A total of 1 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": 5, | ||
"metadata": {}, | ||
"outputs": [ | ||
{ | ||
"data": { | ||
"text/html": [ | ||
"<table style=\"border: 2px solid black; align: \"left\">\n", | ||
"<caption>6 phenopackets - PMID:27738187 (n=5); PMID:30569521 (n=1)</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;\">Patient 1 (MALE; P21Y)</td><td style=\"text-align: left;\">Chitayat syndrome (OMIM:617180)</td><td style=\"text-align: left;\">NM_006494.4:c.266A>G (heterozygous)</td><td style=\"text-align: left;\">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)</td></tr>\n", | ||
"<tr><td style=\"text-align: left;\">Patient 2 (FEMALE; P5Y6M)</td><td style=\"text-align: left;\">Chitayat syndrome (OMIM:617180)</td><td style=\"text-align: left;\">NM_006494.4:c.266A>G (heterozygous)</td><td style=\"text-align: left;\"><b>P2M</b>: 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)<br/><b>P5Y6M</b>: Pectus excavatum (HP:0000767)<br/>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)</td></tr>\n", | ||
"<tr><td style=\"text-align: left;\">Patient 3 (MALE; P6Y)</td><td style=\"text-align: left;\">Chitayat syndrome (OMIM:617180)</td><td style=\"text-align: left;\">NM_006494.4:c.266A>G (heterozygous)</td><td style=\"text-align: left;\"><b>P19D</b>: 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)<br/>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)</td></tr>\n", | ||
"<tr><td style=\"text-align: left;\">Patient 4 (MALE; P4Y)</td><td style=\"text-align: left;\">Chitayat syndrome (OMIM:617180)</td><td style=\"text-align: left;\">NM_006494.4:c.266A>G (heterozygous)</td><td style=\"text-align: left;\">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)</td></tr>\n", | ||
"<tr><td style=\"text-align: left;\">Patient 5 (MALE; P40Y)</td><td style=\"text-align: left;\">Chitayat syndrome (OMIM:617180)</td><td style=\"text-align: left;\">NM_006494.4:c.266A>G (heterozygous)</td><td style=\"text-align: left;\">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)</td></tr>\n", | ||
"<tr><td style=\"text-align: left;\">proband (MALE; P3Y)</td><td style=\"text-align: left;\">Chitayat syndrome (OMIM:617180)</td><td style=\"text-align: left;\">NM_006494.4:c.266A>G (heterozygous)</td><td style=\"text-align: left;\"><b>P2Y8M</b>: 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)<br/>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)</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 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" | ||
}, | ||
"language_info": { | ||
"codemirror_mode": { | ||
"name": "ipython", | ||
"version": 3 | ||
}, | ||
"file_extension": ".py", | ||
"mimetype": "text/x-python", | ||
"name": "python", | ||
"nbconvert_exporter": "python", | ||
"pygments_lexer": "ipython3", | ||
"version": "3.9.6" | ||
} | ||
}, | ||
"nbformat": 4, | ||
"nbformat_minor": 2 | ||
} |
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