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 00000000..9c5714b7 Binary files /dev/null and b/notebooks/HROB/input/HROB_ODG11_individuals.xlsx differ diff --git a/notebooks/HROB/phenopackets/PMID_34707299_nan.json b/notebooks/HROB/phenopackets/PMID_34707299_nan.json new file mode 100644 index 00000000..3b0728c7 --- /dev/null +++ b/notebooks/HROB/phenopackets/PMID_34707299_nan.json @@ -0,0 +1,165 @@ +{ + "id": "PMID_34707299_nan", + "subject": { + "id": "nan", + "timeAtLastEncounter": { + "age": { + "iso8601duration": "P33Y" + } + }, + "vitalStatus": { + "status": "ALIVE" + }, + "sex": "FEMALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0000823", + "label": "Delayed puberty" + } + }, + { + "type": { + "id": "HP:0000786", + "label": "Primary amenorrhea" + } + }, + { + "type": { + "id": "HP:0008232", + "label": "Elevated circulating follicle stimulating hormone level" + } + }, + { + "type": { + "id": "HP:0008214", + "label": "Decreased serum estradiol" + } + }, + { + "type": { + "id": "HP:0012569", + "label": "Delayed menarche" + }, + "excluded": true + } + ], + "interpretations": [ + { + "id": "nan", + "progressStatus": "SOLVED", + "diagnosis": { + "disease": { + "id": "OMIM:620897", + "label": "Ovarian dysgenesis 11" + }, + "genomicInterpretations": [ + { + "subjectOrBiosampleId": "nan", + "interpretationStatus": "CAUSATIVE", + "variantInterpretation": { + "variationDescriptor": { + "id": "var_WfVeQFiUvOWrKzUmDoXEuuIqj", + "geneContext": { + "valueId": "HGNC:28460", + "symbol": "HROB" + }, + "expressions": [ + { + "syntax": "hgvs.c", + "value": "NM_001171251.3:c.421del" + }, + { + "syntax": "hgvs.g", + "value": "NC_000017.11:g.44148224del" + } + ], + "vcfRecord": { + "genomeAssembly": "hg38", + "chrom": "chr17", + "pos": "44148223", + "ref": "TG", + "alt": "T" + }, + "moleculeContext": "genomic", + "allelicState": { + "id": "GENO:0000136", + "label": "homozygous" + } + } + } + } + ] + } + } + ], + "diseases": [ + { + "term": { + "id": "OMIM:620897", + "label": "Ovarian dysgenesis 11" + }, + "onset": { + "ontologyClass": { + "id": "HP:0025708", + "label": "Early young adult onset" + } + } + } + ], + "metaData": { + "created": "2025-01-06T21:10:29.681088924Z", + "createdBy": "ORCID:0000-0002-0736-9199", + "resources": [ + { + "id": "geno", + "name": "Genotype Ontology", + "url": "http://purl.obolibrary.org/obo/geno.owl", + "version": "2022-03-05", + "namespacePrefix": "GENO", + "iriPrefix": "http://purl.obolibrary.org/obo/GENO_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "06/01/23", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "omim", + "name": "An Online Catalog of Human Genes and Genetic Disorders", + "url": "https://www.omim.org", + "version": "January 4, 2023", + "namespacePrefix": "OMIM", + "iriPrefix": "https://www.omim.org/entry/" + }, + { + "id": "so", + "name": "Sequence types and features ontology", + "url": "http://purl.obolibrary.org/obo/so.obo", + "version": "2021-11-22", + "namespacePrefix": "SO", + "iriPrefix": "http://purl.obolibrary.org/obo/SO_" + }, + { + "id": "hp", + "name": "human phenotype ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2024-12-12", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + } + ], + "phenopacketSchemaVersion": "2.0", + "externalReferences": [ + { + "id": "PMID:34707299", + "reference": "https://pubmed.ncbi.nlm.nih.gov/34707299", + "description": "Meiotic genes in premature ovarian insufficiency: variants in HROB and REC8 as likely genetic causes" + } + ] + } +} \ No newline at end of file diff --git a/notebooks/HROB/phenopackets/PMID_38105698_nan.json b/notebooks/HROB/phenopackets/PMID_38105698_nan.json new file mode 100644 index 00000000..33e3582c --- /dev/null +++ b/notebooks/HROB/phenopackets/PMID_38105698_nan.json @@ -0,0 +1,205 @@ +{ + "id": "PMID_38105698_nan", + "subject": { + "id": "nan", + "timeAtLastEncounter": { + "age": { + "iso8601duration": "P11Y6M" + } + }, + "vitalStatus": { + "status": "ALIVE" + }, + "sex": "FEMALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0012569", + "label": "Delayed menarche" + } + }, + { + "type": { + "id": "HP:0011969", + "label": "Elevated circulating luteinizing hormone level" + } + }, + { + "type": { + "id": "HP:0008232", + "label": "Elevated circulating follicle stimulating hormone level" + } + }, + { + "type": { + "id": "HP:0031103", + "label": "Decreased circulating antimullerian hormone circulation" + } + }, + { + "type": { + "id": "HP:0010463", + "label": "Aplasia of the ovary" + } + }, + { + "type": { + "id": "HP:0000786", + "label": "Primary amenorrhea" + }, + "excluded": true + } + ], + "interpretations": [ + { + "id": "nan", + "progressStatus": "SOLVED", + "diagnosis": { + "disease": { + "id": "OMIM:620897", + "label": "Ovarian dysgenesis 11" + }, + "genomicInterpretations": [ + { + "subjectOrBiosampleId": "nan", + "interpretationStatus": "CAUSATIVE", + "variantInterpretation": { + "variationDescriptor": { + "id": "var_FKVBPZPqmvtuEmYhJUasDxXdd", + "geneContext": { + "valueId": "HGNC:28460", + "symbol": "HROB" + }, + "expressions": [ + { + "syntax": "hgvs.c", + "value": "NM_001171251.3:c.718C>T" + }, + { + "syntax": "hgvs.g", + "value": "NC_000017.11:g.44148521C>T" + } + ], + "vcfRecord": { + "genomeAssembly": "hg38", + "chrom": "chr17", + "pos": "44148521", + "ref": "C", + "alt": "T" + }, + "moleculeContext": "genomic", + "allelicState": { + "id": "GENO:0000135", + "label": "heterozygous" + } + } + } + }, + { + "subjectOrBiosampleId": "nan", + "interpretationStatus": "CAUSATIVE", + "variantInterpretation": { + "variationDescriptor": { + "id": "var_aPOhTbcVuZzoJRIEfzVmVpxFL", + "geneContext": { + "valueId": "HGNC:28460", + "symbol": "HROB" + }, + "expressions": [ + { + "syntax": "hgvs.c", + "value": "NM_001171251.3:c.1351C>T" + }, + { + "syntax": "hgvs.g", + "value": "NC_000017.11:g.44152679C>T" + } + ], + "vcfRecord": { + "genomeAssembly": "hg38", + "chrom": "chr17", + "pos": "44152679", + "ref": "C", + "alt": "T" + }, + "moleculeContext": "genomic", + "allelicState": { + "id": "GENO:0000135", + "label": "heterozygous" + } + } + } + } + ] + } + } + ], + "diseases": [ + { + "term": { + "id": "OMIM:620897", + "label": "Ovarian dysgenesis 11" + }, + "onset": { + "age": { + "iso8601duration": "P11Y6M" + } + } + } + ], + "metaData": { + "created": "2025-01-06T21:10:29.684844970Z", + "createdBy": "ORCID:0000-0002-0736-9199", + "resources": [ + { + "id": "geno", + "name": "Genotype Ontology", + "url": "http://purl.obolibrary.org/obo/geno.owl", + "version": "2022-03-05", + "namespacePrefix": "GENO", + "iriPrefix": "http://purl.obolibrary.org/obo/GENO_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "06/01/23", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "omim", + "name": "An Online Catalog of Human Genes and Genetic Disorders", + "url": "https://www.omim.org", + "version": "January 4, 2023", + "namespacePrefix": "OMIM", + "iriPrefix": "https://www.omim.org/entry/" + }, + { + "id": "so", + "name": "Sequence types and features ontology", + "url": "http://purl.obolibrary.org/obo/so.obo", + "version": "2021-11-22", + "namespacePrefix": "SO", + "iriPrefix": "http://purl.obolibrary.org/obo/SO_" + }, + { + "id": "hp", + "name": "human phenotype ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2024-12-12", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + } + ], + "phenopacketSchemaVersion": "2.0", + "externalReferences": [ + { + "id": "PMID:38105698", + "reference": "https://pubmed.ncbi.nlm.nih.gov/38105698", + "description": "Genetic analysis of novel pathogenic gene HROB in a family with primary ovarian insufficiency" + } + ] + } +} \ No newline at end of file diff --git a/notebooks/HROB/phenopackets/PMID_38105698_proband.json b/notebooks/HROB/phenopackets/PMID_38105698_proband.json new file mode 100644 index 00000000..908c548f --- /dev/null +++ b/notebooks/HROB/phenopackets/PMID_38105698_proband.json @@ -0,0 +1,205 @@ +{ + "id": "PMID_38105698_proband", + "subject": { + "id": "proband", + "timeAtLastEncounter": { + "age": { + "iso8601duration": "P13Y6M" + } + }, + "vitalStatus": { + "status": "ALIVE" + }, + "sex": "FEMALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0012569", + "label": "Delayed menarche" + } + }, + { + "type": { + "id": "HP:0011969", + "label": "Elevated circulating luteinizing hormone level" + } + }, + { + "type": { + "id": "HP:0008232", + "label": "Elevated circulating follicle stimulating hormone level" + } + }, + { + "type": { + "id": "HP:0031103", + "label": "Decreased circulating antimullerian hormone circulation" + } + }, + { + "type": { + "id": "HP:0010463", + "label": "Aplasia of the ovary" + } + }, + { + "type": { + "id": "HP:0000786", + "label": "Primary amenorrhea" + }, + "excluded": true + } + ], + "interpretations": [ + { + "id": "proband", + "progressStatus": "SOLVED", + "diagnosis": { + "disease": { + "id": "OMIM:620897", + "label": "Ovarian dysgenesis 11" + }, + "genomicInterpretations": [ + { + "subjectOrBiosampleId": "proband", + "interpretationStatus": "CAUSATIVE", + "variantInterpretation": { + "variationDescriptor": { + "id": "var_FKVBPZPqmvtuEmYhJUasDxXdd", + "geneContext": { + "valueId": "HGNC:28460", + "symbol": "HROB" + }, + "expressions": [ + { + "syntax": "hgvs.c", + "value": "NM_001171251.3:c.718C>T" + }, + { + "syntax": "hgvs.g", + "value": "NC_000017.11:g.44148521C>T" + } + ], + "vcfRecord": { + "genomeAssembly": "hg38", + "chrom": "chr17", + "pos": "44148521", + "ref": "C", + "alt": "T" + }, + "moleculeContext": "genomic", + "allelicState": { + "id": "GENO:0000135", + "label": "heterozygous" + } + } + } + }, + { + "subjectOrBiosampleId": "proband", + "interpretationStatus": "CAUSATIVE", + "variantInterpretation": { + "variationDescriptor": { + "id": "var_aPOhTbcVuZzoJRIEfzVmVpxFL", + "geneContext": { + "valueId": "HGNC:28460", + "symbol": "HROB" + }, + "expressions": [ + { + "syntax": "hgvs.c", + "value": "NM_001171251.3:c.1351C>T" + }, + { + "syntax": "hgvs.g", + "value": "NC_000017.11:g.44152679C>T" + } + ], + "vcfRecord": { + "genomeAssembly": "hg38", + "chrom": "chr17", + "pos": "44152679", + "ref": "C", + "alt": "T" + }, + "moleculeContext": "genomic", + "allelicState": { + "id": "GENO:0000135", + "label": "heterozygous" + } + } + } + } + ] + } + } + ], + "diseases": [ + { + "term": { + "id": "OMIM:620897", + "label": "Ovarian dysgenesis 11" + }, + "onset": { + "age": { + "iso8601duration": "P13Y6M" + } + } + } + ], + "metaData": { + "created": "2025-01-06T21:10:29.683621883Z", + "createdBy": "ORCID:0000-0002-0736-9199", + "resources": [ + { + "id": "geno", + "name": 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