diff --git a/notebooks/NEK8/NEK8_PKD8_individuals.ipynb b/notebooks/NEK8/NEK8_PKD8_individuals.ipynb new file mode 100644 index 00000000..eea0d735 --- /dev/null +++ b/notebooks/NEK8/NEK8_PKD8_individuals.ipynb @@ -0,0 +1,245 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# NEK8\n", + "[polycystic kidney disease-8 (PKD8)](https://omim.org/entry/620903) is caused by heterozygous mutation in the NEK8 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/NEK8_PKD8_individuals.xlsx\"\n", + "created_by = \"0000-0002-0736-9199\"" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "HPO version 2024-12-12\n", + "Created encoders for 29 fields\n", + "Importing OMIM:620903, Polycystic kidney disease 8, HGNC:13387, NEK8, NM_178170.3\n", + "[INFO] encoding variant \"c.133C>T\"\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_178170.3%3Ac.133C>T/NM_178170.3?content-type=application%2Fjson\n", + "[INFO] encoding variant \"c.469A>G\"\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_178170.3%3Ac.469A>G/NM_178170.3?content-type=application%2Fjson\n", + "[INFO] encoding variant \"c.450C>G\"\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_178170.3%3Ac.450C>G/NM_178170.3?content-type=application%2Fjson\n", + "We output 20 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": 6, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "

Cohort validation

\n", + "

No errors found for the cohort with 20 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": 7, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "
20 phenopackets - PMID:37598857 (n=19); PMID:36215968 (n=1)
IndividualDiseaseGenotypePhenotypic features
Family 1 individual (MALE)Polycystic kidney disease 8 (OMIM:620903)NM_178170.3:c.133C>T (heterozygous)Enlarged kidney (HP:0000105): onset ; Nephronophthisis (HP:0000090): onset ; Hypertension (HP:0000822): onset ; excluded: Hepatic cysts (HP:0001407): onset ; excluded: Short stature (HP:0004322): onset
TimeElement(element=Age(iso8601duration=P11Y)): Stage 5 chronic kidney disease (HP:0003774): onset age {\n", + " iso8601duration: \"P11Y\"\n", + "}\n", + "
Family 2 individual (FEMALE)Polycystic kidney disease 8 (OMIM:620903)NM_178170.3:c.133C>T (heterozygous)Enlarged kidney (HP:0000105): onset ; Hypertension (HP:0000822): onset ; excluded: Hepatic cysts (HP:0001407): onset ; excluded: Short stature (HP:0004322): onset
TimeElement(element=Age(iso8601duration=P4Y)): Stage 5 chronic kidney disease (HP:0003774): onset age {\n", + " iso8601duration: \"P4Y\"\n", + "}\n", + "
Family 3 individual (MALE)Polycystic kidney disease 8 (OMIM:620903)NM_178170.3:c.133C>T (heterozygous)Enlarged kidney (HP:0000105): onset ; Hypertension (HP:0000822): onset ; excluded: Hepatic cysts (HP:0001407): onset ; excluded: Short stature (HP:0004322): onset
TimeElement(element=Age(iso8601duration=P19Y)): Stage 5 chronic kidney disease (HP:0003774): onset age {\n", + " iso8601duration: \"P19Y\"\n", + "}\n", + "
Family 4 individual (MALE)Polycystic kidney disease 8 (OMIM:620903)NM_178170.3:c.133C>T (heterozygous)Enlarged kidney (HP:0000105): onset ; Hypertension (HP:0000822): onset ; excluded: Hepatic cysts (HP:0001407): onset ; excluded: Short stature (HP:0004322): onset
TimeElement(element=Age(iso8601duration=P5Y)): Stage 5 chronic kidney disease (HP:0003774): onset age {\n", + " iso8601duration: \"P5Y\"\n", + "}\n", + "
Family 5 individual (MALE)Polycystic kidney disease 8 (OMIM:620903)NM_178170.3:c.133C>T (heterozygous)Enlarged kidney (HP:0000105): onset ; Hypertension (HP:0000822): onset ; Left ventricular hypertrophy (HP:0001712): onset ; excluded: Hepatic cysts (HP:0001407): onset ; excluded: Short stature (HP:0004322): onset
TimeElement(element=Age(iso8601duration=P12Y)): Stage 5 chronic kidney disease (HP:0003774): onset age {\n", + " iso8601duration: \"P12Y\"\n", + "}\n", + "
Family 6 individual (FEMALE)Polycystic kidney disease 8 (OMIM:620903)NM_178170.3:c.133C>T (heterozygous)Hypertension (HP:0000822): onset ; excluded: Enlarged kidney (HP:0000105): onset ; excluded: Hepatic cysts (HP:0001407): onset ; excluded: Short stature (HP:0004322): onset
TimeElement(element=Age(iso8601duration=P11Y)): Stage 5 chronic kidney disease (HP:0003774): onset age {\n", + " iso8601duration: \"P11Y\"\n", + "}\n", + "
Family 7 individual III-3 (MALE)Polycystic kidney disease 8 (OMIM:620903)NM_178170.3:c.133C>T (heterozygous)Enlarged kidney (HP:0000105): onset ; Hypertension (HP:0000822): onset ; Short stature (HP:0004322): onset ; excluded: Hepatic cysts (HP:0001407): onset
TimeElement(element=Age(iso8601duration=P14Y)): Stage 5 chronic kidney disease (HP:0003774): onset age {\n", + " iso8601duration: \"P14Y\"\n", + "}\n", + "
Family 7 individual III-4 (MALE)Polycystic kidney disease 8 (OMIM:620903)NM_178170.3:c.133C>T (heterozygous)Enlarged kidney (HP:0000105): onset ; Hypertension (HP:0000822): onset ; Short stature (HP:0004322): onset ; excluded: Hepatic cysts (HP:0001407): onset
TimeElement(element=Age(iso8601duration=P15Y)): Stage 5 chronic kidney disease (HP:0003774): onset age {\n", + " iso8601duration: \"P15Y\"\n", + "}\n", + "
Family 8 individual (MALE)Polycystic kidney disease 8 (OMIM:620903)NM_178170.3:c.133C>T (heterozygous)Enlarged kidney (HP:0000105): onset ; Hypertension (HP:0000822): onset ; Left ventricular hypertrophy (HP:0001712): onset ; excluded: Hepatic cysts (HP:0001407): onset ; excluded: Short stature (HP:0004322): onset
TimeElement(element=Age(iso8601duration=P7Y)): Stage 5 chronic kidney disease (HP:0003774): onset age {\n", + " iso8601duration: \"P7Y\"\n", + "}\n", + "
Family 9 individual III-1 (FEMALE)Polycystic kidney disease 8 (OMIM:620903)NM_178170.3:c.133C>T (heterozygous)Enlarged kidney (HP:0000105): onset ; Hypertension (HP:0000822): onset ; excluded: Hepatic cysts (HP:0001407): onset ; excluded: Short stature (HP:0004322): onset
TimeElement(element=Age(iso8601duration=P1Y)): Stage 5 chronic kidney disease (HP:0003774): onset age {\n", + " iso8601duration: \"P1Y\"\n", + "}\n", + "
Family 9 individual IV-1 (FEMALE)Polycystic kidney disease 8 (OMIM:620903)NM_178170.3:c.133C>T (heterozygous)Enlarged kidney (HP:0000105): onset ; Hypertension (HP:0000822): onset ; excluded: Hepatic cysts (HP:0001407): onset ; excluded: Short stature (HP:0004322): onset
TimeElement(element=Age(iso8601duration=P6Y)): Stage 5 chronic kidney disease (HP:0003774): onset age {\n", + " iso8601duration: \"P6Y\"\n", + "}\n", + "
Family 10 individual (FEMALE)Polycystic kidney disease 8 (OMIM:620903)NM_178170.3:c.133C>T (heterozygous)Enlarged kidney (HP:0000105): onset ; Nephronophthisis (HP:0000090): onset ; Hypertension (HP:0000822): onset ; excluded: Hepatic cysts (HP:0001407): onset ; excluded: Short stature (HP:0004322): onset
Family 11 individual II-1 (FEMALE)Polycystic kidney disease 8 (OMIM:620903)NM_178170.3:c.450C>G (heterozygous)Hypertension (HP:0000822): onset ; excluded: Enlarged kidney (HP:0000105): onset ; excluded: Hepatic cysts (HP:0001407): onset ; excluded: Short stature (HP:0004322): onset
TimeElement(element=Age(iso8601duration=P70Y)): Stage 5 chronic kidney disease (HP:0003774): onset age {\n", + " iso8601duration: \"P70Y\"\n", + "}\n", + "
Family 11 individual III-1 (FEMALE)Polycystic kidney disease 8 (OMIM:620903)NM_178170.3:c.450C>G (heterozygous)excluded: Enlarged kidney (HP:0000105): onset ; excluded: Hypertension (HP:0000822): onset ; excluded: Short stature (HP:0004322): onset
TimeElement(element=Age(iso8601duration=P52Y)): Hepatic cysts (HP:0001407): onset age {\n", + " iso8601duration: \"P52Y\"\n", + "}\n", + "
Family 11 individual III-2 (MALE)Polycystic kidney disease 8 (OMIM:620903)NM_178170.3:c.450C>G (heterozygous)Enlarged kidney (HP:0000105): onset ; Hypertension (HP:0000822): onset ; excluded: Hepatic cysts (HP:0001407): onset ; excluded: Short stature (HP:0004322): onset
Family 11 individual III-3 (FEMALE)Polycystic kidney disease 8 (OMIM:620903)NM_178170.3:c.450C>G (heterozygous)excluded: Enlarged kidney (HP:0000105): onset ; excluded: Hepatic cysts (HP:0001407): onset ; excluded: Hypertension (HP:0000822): onset ; excluded: Short stature (HP:0004322): onset
Family 11 11 individual IV-3 (MALE)Polycystic kidney disease 8 (OMIM:620903)NM_178170.3:c.450C>G (heterozygous)Focal segmental glomerulosclerosis (HP:0000097): onset ; excluded: Enlarged kidney (HP:0000105): onset ; excluded: Hepatic cysts (HP:0001407): onset ; excluded: Hypertension (HP:0000822): onset ; excluded: Short stature (HP:0004322): onset
Family 11 individual IV-4 (FEMALE)Polycystic kidney disease 8 (OMIM:620903)NM_178170.3:c.450C>G (heterozygous)Focal segmental glomerulosclerosis (HP:0000097): onset ; excluded: Enlarged kidney (HP:0000105): onset ; excluded: Hypertension (HP:0000822): onset ; excluded: Short stature (HP:0004322): onset
TimeElement(element=Age(iso8601duration=P18Y)): Hepatic cysts (HP:0001407): onset age {\n", + " iso8601duration: \"P18Y\"\n", + "}\n", + "
Family 12 individual (MALE)Polycystic kidney disease 8 (OMIM:620903)NM_178170.3:c.469A>G (heterozygous)Enlarged kidney (HP:0000105): onset ; Hypertension (HP:0000822): onset ; excluded: Hepatic cysts (HP:0001407): onset ; excluded: Short stature (HP:0004322): onset
TimeElement(element=Age(iso8601duration=P4Y)): Stage 5 chronic kidney disease (HP:0003774): onset age {\n", + " iso8601duration: \"P4Y\"\n", + "}\n", + "
patient (MALE; P2M)Polycystic kidney disease 8 (OMIM:620903)NM_178170.3:c.133C>T (heterozygous)Enlarged kidney (HP:0000105): onset ; excluded: Nephronophthisis (HP:0000090): onset ; excluded: Hepatic cysts (HP:0001407): onset ; excluded: Stage 5 chronic kidney disease (HP:0003774): onset
TimeElement(element=Age(iso8601duration=P1M)): Renal insufficiency (HP:0000083): onset age {\n", + " iso8601duration: \"P1M\"\n", + "}\n", + "; Polyuria (HP:0000103): onset age {\n", + " iso8601duration: \"P1M\"\n", + "}\n", + "; Polydipsia (HP:0001959): onset age {\n", + " iso8601duration: \"P1M\"\n", + "}\n", + "; Hyperechogenic kidneys (HP:0004719): onset age {\n", + " iso8601duration: \"P1M\"\n", + "}\n", + "
TimeElement(element=Age(iso8601duration=P2M)): Hypertension (HP:0000822): onset age {\n", + " iso8601duration: \"P2M\"\n", + "}\n", + "
" + ], + "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": 8, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[pyphetools] Ingested 20 GA4GH phenopackets.\n", + "[INFO] Extracted 20 from 20 phenopackets with OMIM:620903\n", + "\n", + "\tPolycystic kidney disease 8 (OMIM:620903): n=20\n", + "We found a total of 12 unique HPO terms\n", + "Extracted disease: Polycystic kidney disease 8 (OMIM:620903)\n", + "Wrote HPOA disease file to OMIM-620903.tab\n" + ] + } + ], + "source": [ + "pmid = \"PMID:37598857\"\n", + "df = timporter.create_hpoa_from_phenopackets(pmid=pmid, mode_of_inheritance=Moi.AD, target=\"OMIM:620903\")" + ] + } + ], + "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": "3.12.4" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/notebooks/NEK8/input/NEK8_PKD8_individuals.xlsx b/notebooks/NEK8/input/NEK8_PKD8_individuals.xlsx new file mode 100644 index 00000000..e0f55fc1 Binary files /dev/null and b/notebooks/NEK8/input/NEK8_PKD8_individuals.xlsx differ diff --git a/notebooks/NEK8/phenopackets/PMID_36215968_patient.json b/notebooks/NEK8/phenopackets/PMID_36215968_patient.json new file mode 100644 index 00000000..7296e729 --- /dev/null +++ b/notebooks/NEK8/phenopackets/PMID_36215968_patient.json @@ -0,0 +1,215 @@ +{ + "id": "PMID_36215968_patient", + "subject": { + "id": "patient", + "timeAtLastEncounter": { + "age": { + "iso8601duration": "P2M" + } + }, + "vitalStatus": { + "status": "ALIVE" + }, + "sex": "MALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0000822", + "label": "Hypertension" + }, + "onset": { + "age": { + "iso8601duration": "P2M" + } + } + }, + { + "type": { + "id": "HP:0000083", + "label": "Renal insufficiency" + }, + "onset": { + "age": { + "iso8601duration": "P1M" + } + } + }, + { + "type": { + "id": "HP:0000103", + "label": "Polyuria" + }, + "onset": { + "age": { + "iso8601duration": "P1M" + } + } + }, + { + "type": { + "id": "HP:0001959", + "label": "Polydipsia" + }, + "onset": { + "age": { + "iso8601duration": "P1M" + } + } + }, + { + "type": { + "id": "HP:0004719", + "label": "Hyperechogenic kidneys" + }, + "onset": { + "age": { + "iso8601duration": "P1M" + } + } + }, + { + "type": { + "id": "HP:0000105", + "label": "Enlarged kidney" + } + }, + { + "type": { + "id": "HP:0000090", + "label": "Nephronophthisis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001407", + "label": "Hepatic cysts" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0003774", + "label": "Stage 5 chronic kidney disease" + }, + "excluded": true + } + ], + "interpretations": [ + { + "id": "patient", + "progressStatus": "SOLVED", + "diagnosis": { + "disease": { + "id": "OMIM:620903", + "label": "Polycystic kidney disease 8" + }, + "genomicInterpretations": [ + { + "subjectOrBiosampleId": "patient", + "interpretationStatus": "CAUSATIVE", + "variantInterpretation": { + "variationDescriptor": { + "id": "var_ijqBhHWjJVXNhuqEeuODDUGwW", + "geneContext": { + "valueId": "HGNC:13387", + "symbol": "NEK8" + }, + "expressions": [ + { + "syntax": "hgvs.c", + "value": "NM_178170.3:c.133C>T" + }, + { + "syntax": "hgvs.g", + "value": "NC_000017.11:g.28734068C>T" + } + ], + "vcfRecord": { + "genomeAssembly": "hg38", + "chrom": "chr17", + "pos": "28734068", + "ref": "C", + "alt": "T" + }, + "moleculeContext": "genomic", + "allelicState": { + "id": "GENO:0000135", + "label": "heterozygous" + } + } + } + } + ] + } + } + ], + "diseases": [ + { + "term": { + "id": "OMIM:620903", + "label": "Polycystic kidney disease 8" + }, + "onset": { + "age": { + "iso8601duration": "P1M" + } + } + } + ], + "metaData": { + "created": "2024-12-27T09:44:46.088234901Z", + "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:36215968", + "reference": "https://pubmed.ncbi.nlm.nih.gov/36215968", + "description": "NEK8-Associated Nephropathies: Do Autosomal Dominant Forms Exist?" + } + ] + } +} \ No newline at end of file diff --git a/notebooks/NEK8/phenopackets/PMID_37598857_Family10individual.json b/notebooks/NEK8/phenopackets/PMID_37598857_Family10individual.json new file mode 100644 index 00000000..d69f2651 --- /dev/null +++ b/notebooks/NEK8/phenopackets/PMID_37598857_Family10individual.json @@ -0,0 +1,160 @@ +{ + "id": "PMID_37598857_Family_10_individual", + "subject": { + "id": "Family 10 individual", + "vitalStatus": { + "status": "ALIVE" + }, + "sex": "FEMALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0000105", + "label": "Enlarged kidney" + } + }, + { + "type": { + "id": "HP:0000090", + "label": "Nephronophthisis" + } + }, + { + "type": { + "id": "HP:0000822", + "label": "Hypertension" + } + }, + { + "type": { + "id": "HP:0001407", + "label": "Hepatic cysts" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0004322", + "label": "Short stature" + }, + "excluded": true + } + ], + "interpretations": [ + { + "id": "Family 10 individual", + "progressStatus": "SOLVED", + "diagnosis": { + "disease": { + "id": "OMIM:620903", + "label": "Polycystic kidney disease 8" + }, + "genomicInterpretations": [ + { + "subjectOrBiosampleId": "Family 10 individual", + "interpretationStatus": "CAUSATIVE", + "variantInterpretation": { + "variationDescriptor": { + "id": "var_ijqBhHWjJVXNhuqEeuODDUGwW", + "geneContext": { + "valueId": "HGNC:13387", + "symbol": "NEK8" + }, + "expressions": [ + { + "syntax": "hgvs.c", + "value": "NM_178170.3:c.133C>T" + }, + { + "syntax": "hgvs.g", + "value": "NC_000017.11:g.28734068C>T" + } + ], + "vcfRecord": { + "genomeAssembly": "hg38", + "chrom": "chr17", + "pos": "28734068", + "ref": "C", + "alt": "T" + }, + "moleculeContext": "genomic", + "allelicState": { + "id": "GENO:0000135", + "label": "heterozygous" + } + } + } + } + ] + } + } + ], + "diseases": [ + { + "term": { + "id": "OMIM:620903", + "label": "Polycystic kidney disease 8" + }, + "onset": { + "age": { + "iso8601duration": "P3Y" + } + } + } + ], + "metaData": { + "created": "2024-12-27T09:44:46.085093021Z", + "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": 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