From 7335935da632448f44f8edb81624c70fe3ca062d Mon Sep 17 00:00:00 2001 From: Peter Robinson Date: Mon, 6 Jan 2025 22:12:27 +0100 Subject: [PATCH] HROB --- notebooks/HROB/HROB_ODG11_individuals.ipynb | 336 ++++++++++++++++++ .../HROB/input/HROB_ODG11_individuals.xlsx | Bin 0 -> 9657 bytes .../HROB/phenopackets/PMID_34707299_nan.json | 165 +++++++++ .../HROB/phenopackets/PMID_38105698_nan.json | 205 +++++++++++ .../phenopackets/PMID_38105698_proband.json | 205 +++++++++++ 5 files changed, 911 insertions(+) create mode 100644 notebooks/HROB/HROB_ODG11_individuals.ipynb create mode 100644 notebooks/HROB/input/HROB_ODG11_individuals.xlsx create mode 100644 notebooks/HROB/phenopackets/PMID_34707299_nan.json create mode 100644 notebooks/HROB/phenopackets/PMID_38105698_nan.json create mode 100644 notebooks/HROB/phenopackets/PMID_38105698_proband.json diff --git a/notebooks/HROB/HROB_ODG11_individuals.ipynb b/notebooks/HROB/HROB_ODG11_individuals.ipynb new file mode 100644 index 00000000..d6e95fde --- /dev/null +++ b/notebooks/HROB/HROB_ODG11_individuals.ipynb @@ -0,0 +1,336 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# HROB\n", + "[ovarian dysgenesis-11 (ODG11)](https://omim.org/entry/620897) is caused by homozygous or compound heterozygous mutation in the HROB 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": 2, + "metadata": {}, + "outputs": [], + "source": [ + "template = \"input/HROB_ODG11_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 2024-12-12\n", + "Created encoders for 25 fields\n", + "Importing OMIM:620897, Ovarian dysgenesis 11, HGNC:28460, HROB, NM_001171251.3\n", + "[INFO] encoding variant \"c.421del\"\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001171251.3%3Ac.421del/NM_001171251.3?content-type=application%2Fjson\n", + "[INFO] encoding variant \"c.1351C>T\"\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001171251.3%3Ac.1351C>T/NM_001171251.3?content-type=application%2Fjson\n", + "[INFO] encoding variant \"c.718C>T\"\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001171251.3%3Ac.718C>T/NM_001171251.3?content-type=application%2Fjson\n", + "We output 3 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 2 of 3 phenopackets.

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Error counts
LevelError categoryCount
WARNINGREDUNDANT2
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A total of 2 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", + "
3 phenopackets - PMID:34707299 (n=1); PMID:38105698 (n=2)
IndividualDiseaseGenotypePhenotypic features
nan (FEMALE; P33Y)Ovarian dysgenesis 11 (OMIM:620897)NM_001171251.3:c.421del (homozygous)Delayed puberty (HP:0000823): onset ; Primary amenorrhea (HP:0000786): onset ; Elevated circulating follicle stimulating hormone level (HP:0008232): onset ; Decreased serum estradiol (HP:0008214): onset ; excluded: Delayed menarche (HP:0012569): onset
proband (FEMALE; P13Y6M)Ovarian dysgenesis 11 (OMIM:620897)
  • NM_001171251.3:c.718C>T (heterozygous)
  • NM_001171251.3:c.1351C>T (heterozygous)
Delayed menarche (HP:0012569): onset ; Elevated circulating luteinizing hormone level (HP:0011969): onset ; Elevated circulating follicle stimulating hormone level (HP:0008232): onset ; Decreased circulating antimullerian hormone circulation (HP:0031103): onset ; Aplasia of the ovary (HP:0010463): onset ; excluded: Primary amenorrhea (HP:0000786): onset
nan (FEMALE; P11Y6M)Ovarian dysgenesis 11 (OMIM:620897)
  • NM_001171251.3:c.718C>T (heterozygous)
  • NM_001171251.3:c.1351C>T (heterozygous)
Delayed menarche (HP:0012569): onset ; Elevated circulating luteinizing hormone level (HP:0011969): onset ; Elevated circulating follicle stimulating hormone level (HP:0008232): onset ; Decreased circulating antimullerian hormone circulation (HP:0031103): onset ; Aplasia of the ovary (HP:0010463): onset ; excluded: Primary amenorrhea (HP:0000786): 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": 6, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[pyphetools] Ingested 3 GA4GH phenopackets.\n", + "[INFO] Extracted 3 from 3 phenopackets with OMIM:620897\n", + "\n", + "\tOvarian dysgenesis 11 (OMIM:620897): n=3\n", + "We found a total of 8 unique HPO terms\n", + "Extracted disease: Ovarian dysgenesis 11 (OMIM:620897)\n", + "Wrote HPOA disease file to OMIM-620897.tab\n" + ] + }, + { + "data": { + "text/html": [ + "
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#diseaseIDdiseaseNamephenotypeIDphenotypeNameonsetIDonsetNamefrequencysexnegationmodifierdescriptionpublicationevidencebiocuration
0OMIM:620897Ovarian dysgenesis 11HP:0000823Delayed puberty1/1PMID:34707299PCSORCID:0000-0002-0736-9199[2025-01-06]
1OMIM:620897Ovarian dysgenesis 11HP:0000786Primary amenorrhea1/1PMID:34707299PCSORCID:0000-0002-0736-9199[2025-01-06]
2OMIM:620897Ovarian dysgenesis 11HP:0008232Elevated circulating follicle stimulating horm...1/1PMID:34707299PCSORCID:0000-0002-0736-9199[2025-01-06]
3OMIM:620897Ovarian dysgenesis 11HP:0008214Decreased serum estradiol1/1PMID:34707299PCSORCID:0000-0002-0736-9199[2025-01-06]
4OMIM:620897Ovarian dysgenesis 11HP:0012569Delayed menarche0/1PMID:34707299PCSORCID:0000-0002-0736-9199[2025-01-06]
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" + ], + "text/plain": [ + " #diseaseID diseaseName phenotypeID \\\n", + "0 OMIM:620897 Ovarian dysgenesis 11 HP:0000823 \n", + "1 OMIM:620897 Ovarian dysgenesis 11 HP:0000786 \n", + "2 OMIM:620897 Ovarian dysgenesis 11 HP:0008232 \n", + "3 OMIM:620897 Ovarian dysgenesis 11 HP:0008214 \n", + "4 OMIM:620897 Ovarian dysgenesis 11 HP:0012569 \n", + "\n", + " phenotypeName onsetID onsetName \\\n", + "0 Delayed puberty \n", + "1 Primary amenorrhea \n", + "2 Elevated circulating follicle stimulating horm... \n", + "3 Decreased serum estradiol \n", + "4 Delayed menarche \n", + "\n", + " frequency sex negation modifier description publication evidence \\\n", + "0 1/1 PMID:34707299 PCS \n", + "1 1/1 PMID:34707299 PCS \n", + "2 1/1 PMID:34707299 PCS \n", + "3 1/1 PMID:34707299 PCS \n", + "4 0/1 PMID:34707299 PCS \n", + "\n", + " biocuration \n", + "0 ORCID:0000-0002-0736-9199[2025-01-06] \n", + "1 ORCID:0000-0002-0736-9199[2025-01-06] \n", + "2 ORCID:0000-0002-0736-9199[2025-01-06] \n", + "3 ORCID:0000-0002-0736-9199[2025-01-06] \n", + "4 ORCID:0000-0002-0736-9199[2025-01-06] " + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "pmid = \"PMID:34707299\"\n", + "df = timporter.create_hpoa_from_phenopackets(pmid=pmid, mode_of_inheritance=Moi.AR, target=\"OMIM:620897\")\n", + "df.head()" + ] + } + ], + "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": "3.12.8" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/notebooks/HROB/input/HROB_ODG11_individuals.xlsx b/notebooks/HROB/input/HROB_ODG11_individuals.xlsx new file mode 100644 index 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