diff --git a/notebooks/POLR1A/POLR1A_AFDCIN_individuals.ipynb b/notebooks/POLR1A/POLR1A_AFDCIN_individuals.ipynb new file mode 100644 index 000000000..27fcf71ef --- /dev/null +++ b/notebooks/POLR1A/POLR1A_AFDCIN_individuals.ipynb @@ -0,0 +1,167 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# POLR1A \n", + "\n", + "[Acrofacial dysostosis, Cincinnati type](https://omim.org/entry/616462) is caused by variants in the POLR1A gene." + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Using pyphetools version 0.9.113\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": 20, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "HPO version 2024-08-13\n", + "Created encoders for 94 fields\n", + "Importing OMIM:616462, Acrofacial dysostosis, Cincinnati type, HGNC:17264, POLR1A, NM_015425.6\n", + "We output 18 GA4GH phenopackets to the directory phenopackets\n" + ] + } + ], + "source": [ + "template = \"input/POLR1A_AFDCIN_individuals.xlsx\"\n", + "created_by = \"0000-0002-0736-9199\"\n", + "timporter = TemplateImporter(template=template, created_by=created_by)\n", + "individual_list, cvalidator = timporter.import_phenopackets_from_template()" + ] + }, + { + "cell_type": "code", + "execution_count": 21, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "

Cohort validation

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Errors found with 16 of 18 phenopackets.

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Error counts
LevelError categoryCount
ERRORCONFLICT1
WARNINGREDUNDANT26
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A total of 27 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": 22, + "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", + "
18 phenopackets - PMID:37075751 (n=18)
IndividualDiseaseGenotypePhenotypic features
Individual 1 (MALE; P3M)Acrofacial dysostosis, Cincinnati type (OMIM:616462)NM_015425.6:c.176A>T (heterozygous)Cleft palate (HP:0000175): onset ; Cleft upper lip (HP:0000204): onset ; Metopic synostosis (HP:0011330): onset ; excluded: Epicanthus (HP:0000286): onset ; excluded: Upslanted palpebral fissure (HP:0000582): onset ; excluded: Long palpebral fissure (HP:0000637): onset ; excluded: Patent foramen ovale (HP:0001655): onset ; excluded: Ventricular septal defect (HP:0001629): onset ; excluded: Feeding difficulties (HP:0011968): onset ; excluded: Hypertelorism (HP:0000316): onset ; excluded: Facial asymmetry (HP:0000324): onset ; excluded: Underdeveloped nasal alae (HP:0000430): onset ; excluded: Choanal atresia (HP:0000453): onset ; excluded: Infantile spasms (HP:0012469): onset ; excluded: Atonic seizure (HP:0010819): onset ; excluded: Myoclonus (HP:0001336): onset ; excluded: Epileptic encephalopathy (HP:0200134): onset ; excluded: Global developmental delay (HP:0001263): onset ; excluded: Developmental regression (HP:0002376): onset ; excluded: High palate (HP:0000218): onset ; excluded: Low-set ears (HP:0000369): onset ; excluded: Anteverted nares (HP:0000463): onset ; excluded: Micrognathia (HP:0000347): onset ; excluded: Duane anomaly (HP:0009921): onset ; excluded: Deeply set eye (HP:0000490): onset ; excluded: Scoliosis (HP:0002650): onset ; excluded: Vocal cord paralysis (HP:0001605): onset ; excluded: Clinodactyly of the 5th finger (HP:0004209): onset ; excluded: Eyelid coloboma (HP:0000625): onset ; excluded: Hypotonia (HP:0001252): onset ; excluded: Depressed nasal bridge (HP:0005280): onset ; excluded: Ptosis (HP:0000508): onset ; excluded: Hearing impairment (HP:0000365): onset ; excluded: Microtia (HP:0008551): onset ; excluded: Intrauterine growth retardation (HP:0001511): onset ; excluded: Single transverse palmar crease (HP:0000954): onset ; excluded: Cryptorchidism (HP:0000028): onset ; excluded: Inguinal hernia (HP:0000023): onset
Individual 2 (MALE; P5Y)Acrofacial dysostosis, Cincinnati type (OMIM:616462)NM_015425.6:c.176A>T (heterozygous)Cleft palate (HP:0000175): onset ; Cleft upper lip (HP:0000204): onset ; Metopic synostosis (HP:0011330): onset ; excluded: Epicanthus (HP:0000286): onset ; excluded: Upslanted palpebral fissure (HP:0000582): onset ; excluded: Long palpebral fissure (HP:0000637): onset ; excluded: Patent foramen ovale (HP:0001655): onset ; excluded: Ventricular septal defect (HP:0001629): onset ; excluded: Feeding difficulties (HP:0011968): onset ; excluded: Hypertelorism (HP:0000316): onset ; excluded: Facial asymmetry (HP:0000324): onset ; excluded: Underdeveloped nasal alae (HP:0000430): onset ; excluded: Choanal atresia (HP:0000453): onset ; excluded: Infantile spasms (HP:0012469): onset ; excluded: Atonic seizure (HP:0010819): onset ; excluded: Myoclonus (HP:0001336): onset ; excluded: Epileptic encephalopathy (HP:0200134): onset ; excluded: Global developmental delay (HP:0001263): onset ; excluded: Developmental regression (HP:0002376): onset ; excluded: High palate (HP:0000218): onset ; excluded: Low-set ears (HP:0000369): onset ; excluded: Anteverted nares (HP:0000463): onset ; excluded: Micrognathia (HP:0000347): onset ; excluded: Duane anomaly (HP:0009921): onset ; excluded: Deeply set eye (HP:0000490): onset ; excluded: Scoliosis (HP:0002650): onset ; excluded: Vocal cord paralysis (HP:0001605): onset ; excluded: Clinodactyly of the 5th finger (HP:0004209): onset ; excluded: Eyelid coloboma (HP:0000625): onset ; excluded: Hypotonia (HP:0001252): onset ; excluded: Depressed nasal bridge (HP:0005280): onset ; excluded: Ptosis (HP:0000508): onset ; excluded: Hearing impairment (HP:0000365): onset ; excluded: Microtia (HP:0008551): onset ; excluded: Intrauterine growth retardation (HP:0001511): onset ; excluded: Single transverse palmar crease (HP:0000954): onset ; excluded: Cryptorchidism (HP:0000028): onset ; excluded: Inguinal hernia (HP:0000023): onset
Individual 3 (FEMALE; P8W)Acrofacial dysostosis, Cincinnati type (OMIM:616462)NM_015425.6:c.190del (heterozygous)Global developmental delay (HP:0001263): onset ; Hypotonia (HP:0001252): onset ; Microcephaly (HP:0000252): onset ; excluded: Epicanthus (HP:0000286): onset ; excluded: Upslanted palpebral fissure (HP:0000582): onset ; excluded: Long palpebral fissure (HP:0000637): onset ; excluded: Patent foramen ovale (HP:0001655): onset ; excluded: Ventricular septal defect (HP:0001629): onset ; excluded: Feeding difficulties (HP:0011968): onset ; excluded: Hypertelorism (HP:0000316): onset ; excluded: Facial asymmetry (HP:0000324): onset ; excluded: Underdeveloped nasal alae (HP:0000430): onset ; excluded: Choanal atresia (HP:0000453): onset ; excluded: Infantile spasms (HP:0012469): onset ; excluded: Atonic seizure (HP:0010819): onset ; excluded: Myoclonus (HP:0001336): onset ; excluded: Epileptic encephalopathy (HP:0200134): onset ; excluded: Developmental regression (HP:0002376): onset ; excluded: High palate (HP:0000218): onset ; excluded: Cleft palate (HP:0000175): onset ; excluded: Cleft upper lip (HP:0000204): onset ; excluded: Low-set ears (HP:0000369): onset ; excluded: Anteverted nares (HP:0000463): onset ; excluded: Micrognathia (HP:0000347): onset ; excluded: Duane anomaly (HP:0009921): onset ; excluded: Deeply set eye (HP:0000490): onset ; excluded: Scoliosis (HP:0002650): onset ; excluded: Vocal cord paralysis (HP:0001605): onset ; excluded: Clinodactyly of the 5th finger (HP:0004209): onset ; excluded: Eyelid coloboma (HP:0000625): onset ; excluded: Depressed nasal bridge (HP:0005280): onset ; excluded: Metopic synostosis (HP:0011330): onset ; excluded: Ptosis (HP:0000508): onset ; excluded: Microtia (HP:0008551): onset ; excluded: Macrocephaly (HP:0000256): onset ; excluded: Ventriculomegaly (HP:0002119): onset ; excluded: Intrauterine growth retardation (HP:0001511): onset ; excluded: Single transverse palmar crease (HP:0000954): onset ; excluded: Inguinal hernia (HP:0000023): onset ; excluded: Hydrocephalus (HP:0000238): onset
TimeElement(element=OntologyClass(id=HP:0003577, label=Congenital onset)): Hearing impairment (HP:0000365): onset ontology_class {\n", + " id: \"HP:0003577\"\n", + " label: \"Congenital onset\"\n", + "}\n", + "
Individual 4 (MALE; P11M)Acrofacial dysostosis, Cincinnati type (OMIM:616462)NM_015425.6:c.1178G>A (heterozygous)Long palpebral fissure (HP:0000637): onset ; Low-set ears (HP:0000369): onset ; Anteverted nares (HP:0000463): onset ; Vocal cord paralysis (HP:0001605): onset ; Clinodactyly of the 5th finger (HP:0004209): onset ; Short stature (HP:0004322): onset ; Hypotonia (HP:0001252): onset ; Single transverse palmar crease (HP:0000954): onset ; excluded: Epicanthus (HP:0000286): onset ; excluded: Upslanted palpebral fissure (HP:0000582): onset ; excluded: Patent foramen ovale (HP:0001655): onset ; excluded: Ventricular septal defect (HP:0001629): onset ; excluded: Feeding difficulties (HP:0011968): onset ; excluded: Hypertelorism (HP:0000316): onset ; excluded: Facial asymmetry (HP:0000324): onset ; excluded: Underdeveloped nasal alae (HP:0000430): onset ; excluded: Choanal atresia (HP:0000453): onset ; excluded: Infantile spasms (HP:0012469): onset ; excluded: Atonic seizure (HP:0010819): onset ; excluded: Myoclonus (HP:0001336): onset ; excluded: Epileptic encephalopathy (HP:0200134): onset ; excluded: High palate (HP:0000218): onset ; excluded: Cleft palate (HP:0000175): onset ; excluded: Cleft upper lip (HP:0000204): onset ; excluded: Micrognathia (HP:0000347): onset ; excluded: Duane anomaly (HP:0009921): onset ; excluded: Deeply set eye (HP:0000490): onset ; excluded: Scoliosis (HP:0002650): onset ; excluded: Eyelid coloboma (HP:0000625): onset ; excluded: Depressed nasal bridge (HP:0005280): onset ; excluded: Metopic synostosis (HP:0011330): onset ; excluded: Ptosis (HP:0000508): onset ; excluded: Hearing impairment (HP:0000365): onset ; excluded: Microtia (HP:0008551): onset ; excluded: Microcephaly (HP:0000252): onset ; excluded: Macrocephaly (HP:0000256): onset ; excluded: Intrauterine growth retardation (HP:0001511): onset ; excluded: Cryptorchidism (HP:0000028): onset ; excluded: Inguinal hernia (HP:0000023): onset
Individual 5 (FEMALE)Acrofacial dysostosis, Cincinnati type (OMIM:616462)NM_015425.6:c.1178G>A (heterozygous)Ventricular septal defect (HP:0001629): onset ; Vocal cord paralysis (HP:0001605): onset ; Short stature (HP:0004322): onset ; Hypotonia (HP:0001252): onset ; Ptosis (HP:0000508): onset ; excluded: Epicanthus (HP:0000286): onset ; excluded: Upslanted palpebral fissure (HP:0000582): onset ; excluded: Long palpebral fissure (HP:0000637): onset ; excluded: Patent foramen ovale (HP:0001655): onset ; excluded: Feeding difficulties (HP:0011968): onset ; excluded: Hypertelorism (HP:0000316): onset ; excluded: Facial asymmetry (HP:0000324): onset ; excluded: Underdeveloped nasal alae (HP:0000430): onset ; excluded: Choanal atresia (HP:0000453): onset ; excluded: Infantile spasms (HP:0012469): onset ; excluded: Atonic seizure (HP:0010819): onset ; excluded: Myoclonus (HP:0001336): onset ; excluded: Epileptic encephalopathy (HP:0200134): onset ; excluded: High palate (HP:0000218): onset ; excluded: Cleft palate (HP:0000175): onset ; excluded: Cleft upper lip (HP:0000204): onset ; excluded: Low-set ears (HP:0000369): onset ; excluded: Anteverted nares (HP:0000463): onset ; excluded: Micrognathia (HP:0000347): onset ; excluded: Duane anomaly (HP:0009921): onset ; excluded: Deeply set eye (HP:0000490): onset ; excluded: Scoliosis (HP:0002650): onset ; excluded: Clinodactyly of the 5th finger (HP:0004209): onset ; excluded: Eyelid coloboma (HP:0000625): onset ; excluded: Depressed nasal bridge (HP:0005280): onset ; excluded: Metopic synostosis (HP:0011330): onset ; excluded: Hearing impairment (HP:0000365): onset ; excluded: Microtia (HP:0008551): onset ; excluded: Single transverse palmar crease (HP:0000954): onset ; excluded: Inguinal hernia (HP:0000023): onset
Individual 6 (FEMALE; P10Y4M)Acrofacial dysostosis, Cincinnati type (OMIM:616462)NM_015425.6:c.1442G>A (heterozygous)Hypertelorism (HP:0000316): onset ; Facial asymmetry (HP:0000324): onset ; Hypodontia (HP:0000668): onset ; Choanal atresia (HP:0000453): onset ; Cleft palate (HP:0000175): onset ; Low-set ears (HP:0000369): onset ; Micrognathia (HP:0000347): onset ; Ventriculomegaly (HP:0002119): onset ; Intrauterine growth retardation (HP:0001511): onset ; Hydrocephalus (HP:0000238): onset ; excluded: Epicanthus (HP:0000286): onset ; excluded: Upslanted palpebral fissure (HP:0000582): onset ; excluded: Long palpebral fissure (HP:0000637): onset ; excluded: Patent foramen ovale (HP:0001655): onset ; excluded: Ventricular septal defect (HP:0001629): onset ; excluded: Feeding difficulties (HP:0011968): onset ; excluded: Underdeveloped nasal alae (HP:0000430): onset ; excluded: Infantile spasms (HP:0012469): onset ; excluded: Atonic seizure (HP:0010819): onset ; excluded: Myoclonus (HP:0001336): onset ; excluded: Epileptic encephalopathy (HP:0200134): onset ; excluded: Global developmental delay (HP:0001263): onset ; excluded: Developmental regression (HP:0002376): onset ; excluded: High palate (HP:0000218): onset ; excluded: Cleft upper lip (HP:0000204): onset ; excluded: Anteverted nares (HP:0000463): onset ; excluded: Duane anomaly (HP:0009921): onset ; excluded: Deeply set eye (HP:0000490): onset ; excluded: Scoliosis (HP:0002650): onset ; excluded: Vocal cord paralysis (HP:0001605): onset ; excluded: Clinodactyly of the 5th finger (HP:0004209): onset ; excluded: Short stature (HP:0004322): onset ; excluded: Eyelid coloboma (HP:0000625): onset ; excluded: Hypotonia (HP:0001252): onset ; excluded: Depressed nasal bridge (HP:0005280): onset ; excluded: Metopic synostosis (HP:0011330): onset ; excluded: Ptosis (HP:0000508): onset ; excluded: Hearing impairment (HP:0000365): onset ; excluded: Microtia (HP:0008551): onset ; excluded: Microcephaly (HP:0000252): onset ; excluded: Macrocephaly (HP:0000256): onset ; excluded: Single transverse palmar crease (HP:0000954): onset ; excluded: Inguinal hernia (HP:0000023): onset
Individual 7 (FEMALE; P44Y)Acrofacial dysostosis, Cincinnati type (OMIM:616462)NM_015425.6:c.1442G>A (heterozygous)Hypertelorism (HP:0000316): onset ; Cleft palate (HP:0000175): onset ; Low-set ears (HP:0000369): onset ; Micrognathia (HP:0000347): onset ; excluded: Epicanthus (HP:0000286): onset ; excluded: Upslanted palpebral fissure (HP:0000582): onset ; excluded: Long palpebral fissure (HP:0000637): onset ; excluded: Patent foramen ovale (HP:0001655): onset ; excluded: Ventricular septal defect (HP:0001629): onset ; excluded: Feeding difficulties (HP:0011968): onset ; excluded: Facial asymmetry (HP:0000324): onset ; excluded: Hypodontia (HP:0000668): onset ; excluded: Underdeveloped nasal alae (HP:0000430): onset ; excluded: Choanal atresia (HP:0000453): onset ; excluded: Infantile spasms (HP:0012469): onset ; excluded: Atonic seizure (HP:0010819): onset ; excluded: Myoclonus (HP:0001336): onset ; excluded: Epileptic encephalopathy (HP:0200134): onset ; excluded: Global developmental delay (HP:0001263): onset ; excluded: Developmental regression (HP:0002376): onset ; excluded: High palate (HP:0000218): onset ; excluded: Cleft upper lip (HP:0000204): onset ; excluded: Anteverted nares (HP:0000463): onset ; excluded: Duane anomaly (HP:0009921): onset ; excluded: Deeply set eye (HP:0000490): onset ; excluded: Scoliosis (HP:0002650): onset ; excluded: Vocal cord paralysis (HP:0001605): onset ; excluded: Clinodactyly of the 5th finger (HP:0004209): onset ; excluded: Eyelid coloboma (HP:0000625): onset ; excluded: Hypotonia (HP:0001252): onset ; excluded: Depressed nasal bridge (HP:0005280): onset ; excluded: Metopic synostosis (HP:0011330): onset ; excluded: Ptosis (HP:0000508): onset ; excluded: Hearing impairment (HP:0000365): onset ; excluded: Microtia (HP:0008551): onset ; excluded: Microcephaly (HP:0000252): onset ; excluded: Macrocephaly (HP:0000256): onset ; excluded: Ventriculomegaly (HP:0002119): onset ; excluded: Single transverse palmar crease (HP:0000954): onset ; excluded: Inguinal hernia (HP:0000023): onset ; excluded: Hydrocephalus (HP:0000238): onset
Individual 8 (MALE; P2Y)Acrofacial dysostosis, Cincinnati type (OMIM:616462)NM_015425.6:c.1488G>T (heterozygous)Patent foramen ovale (HP:0001655): onset ; Hypertelorism (HP:0000316): onset ; Seizure (HP:0001250): onset ; Global developmental delay (HP:0001263): onset ; Low-set ears (HP:0000369): onset ; Micrognathia (HP:0000347): onset ; Eyelid coloboma (HP:0000625): onset ; Hypotonia (HP:0001252): onset ; Microtia (HP:0008551): onset ; Microcephaly (HP:0000252): onset ; Cryptorchidism (HP:0000028): onset ; excluded: Epicanthus (HP:0000286): onset ; excluded: Upslanted palpebral fissure (HP:0000582): onset ; excluded: Long palpebral fissure (HP:0000637): onset ; excluded: Ventricular septal defect (HP:0001629): onset ; excluded: Feeding difficulties (HP:0011968): onset ; excluded: Facial asymmetry (HP:0000324): onset ; excluded: Underdeveloped nasal alae (HP:0000430): onset ; excluded: Choanal atresia (HP:0000453): onset ; excluded: Infantile spasms (HP:0012469): onset ; excluded: Atonic seizure (HP:0010819): onset ; excluded: Myoclonus (HP:0001336): onset ; excluded: Epileptic encephalopathy (HP:0200134): onset ; excluded: Developmental regression (HP:0002376): onset ; excluded: High palate (HP:0000218): onset ; excluded: Cleft palate (HP:0000175): onset ; excluded: Cleft upper lip (HP:0000204): onset ; excluded: Anteverted nares (HP:0000463): onset ; excluded: Duane anomaly (HP:0009921): onset ; excluded: Deeply set eye (HP:0000490): onset ; excluded: Scoliosis (HP:0002650): onset ; excluded: Vocal cord paralysis (HP:0001605): onset ; excluded: Clinodactyly of the 5th finger (HP:0004209): onset ; excluded: Short stature (HP:0004322): onset ; excluded: Depressed nasal bridge (HP:0005280): onset ; excluded: Metopic synostosis (HP:0011330): onset ; excluded: Ptosis (HP:0000508): onset ; excluded: Hearing impairment (HP:0000365): onset ; excluded: Macrocephaly (HP:0000256): onset ; excluded: Ventriculomegaly (HP:0002119): onset ; excluded: Intrauterine growth retardation (HP:0001511): onset ; excluded: Single transverse palmar crease (HP:0000954): onset ; excluded: Inguinal hernia (HP:0000023): onset ; excluded: Hydrocephalus (HP:0000238): onset
Individual 9 (MALE; P4Y)Acrofacial dysostosis, Cincinnati type (OMIM:616462)NM_015425.6:c.2583_2586del (heterozygous)Epicanthus (HP:0000286): onset ; Upslanted palpebral fissure (HP:0000582): onset ; Hypertelorism (HP:0000316): onset ; Underdeveloped nasal alae (HP:0000430): onset ; Atonic seizure (HP:0010819): onset ; Myoclonus (HP:0001336): onset ; Epileptic encephalopathy (HP:0200134): onset ; Developmental regression (HP:0002376): onset ; Anteverted nares (HP:0000463): onset ; Deeply set eye (HP:0000490): onset ; Short stature (HP:0004322): onset ; Depressed nasal bridge (HP:0005280): onset ; Microtia (HP:0008551): onset ; excluded: Long palpebral fissure (HP:0000637): onset ; excluded: Facial asymmetry (HP:0000324): onset ; excluded: Hypodontia (HP:0000668): onset ; excluded: Choanal atresia (HP:0000453): onset ; excluded: Infantile spasms (HP:0012469): onset ; excluded: Global developmental delay (HP:0001263): onset ; excluded: High palate (HP:0000218): onset ; excluded: Cleft palate (HP:0000175): onset ; excluded: Cleft upper lip (HP:0000204): onset ; excluded: Low-set ears (HP:0000369): onset ; excluded: Micrognathia (HP:0000347): onset ; excluded: Duane anomaly (HP:0009921): onset ; excluded: Scoliosis (HP:0002650): onset ; excluded: Vocal cord paralysis (HP:0001605): onset ; excluded: Clinodactyly of the 5th finger (HP:0004209): onset ; excluded: Eyelid coloboma (HP:0000625): onset ; excluded: Hypotonia (HP:0001252): onset ; excluded: Metopic synostosis (HP:0011330): onset ; excluded: Ptosis (HP:0000508): onset ; excluded: Hearing impairment (HP:0000365): onset ; excluded: Microcephaly (HP:0000252): onset ; excluded: Macrocephaly (HP:0000256): onset ; excluded: Ventriculomegaly (HP:0002119): onset ; excluded: Intrauterine growth retardation (HP:0001511): onset ; excluded: Single transverse palmar crease (HP:0000954): onset ; excluded: Cryptorchidism (HP:0000028): onset ; excluded: Inguinal hernia (HP:0000023): onset ; excluded: Hydrocephalus (HP:0000238): onset
Individual 10 (FEMALE; P7Y7M)Acrofacial dysostosis, Cincinnati type (OMIM:616462)NM_015425.6:c.3649del (heterozygous)Hypertelorism (HP:0000316): onset ; Hypodontia (HP:0000668): onset ; Cleft palate (HP:0000175): onset ; Micrognathia (HP:0000347): onset ; Duane anomaly (HP:0009921): onset ; Ptosis (HP:0000508): onset ; excluded: Epicanthus (HP:0000286): onset ; excluded: Upslanted palpebral fissure (HP:0000582): onset ; excluded: Long palpebral fissure (HP:0000637): onset ; excluded: Patent foramen ovale (HP:0001655): onset ; excluded: Ventricular septal defect (HP:0001629): onset ; excluded: Feeding difficulties (HP:0011968): onset ; excluded: Facial asymmetry (HP:0000324): onset ; excluded: Underdeveloped nasal alae (HP:0000430): onset ; excluded: Choanal atresia (HP:0000453): onset ; excluded: Infantile spasms (HP:0012469): onset ; excluded: Atonic seizure (HP:0010819): onset ; excluded: Myoclonus (HP:0001336): onset ; excluded: Epileptic encephalopathy (HP:0200134): onset ; excluded: Global developmental delay (HP:0001263): onset ; excluded: Developmental regression (HP:0002376): onset ; excluded: High palate (HP:0000218): onset ; excluded: Cleft upper lip (HP:0000204): onset ; excluded: Low-set ears (HP:0000369): onset ; excluded: Anteverted nares (HP:0000463): onset ; excluded: Deeply set eye (HP:0000490): onset ; excluded: Scoliosis (HP:0002650): onset ; excluded: Vocal cord paralysis (HP:0001605): onset ; excluded: Clinodactyly of the 5th finger (HP:0004209): onset ; excluded: Eyelid coloboma (HP:0000625): onset ; excluded: Hypotonia (HP:0001252): onset ; excluded: Depressed nasal bridge (HP:0005280): onset ; excluded: Metopic synostosis (HP:0011330): onset ; excluded: Hearing impairment (HP:0000365): onset ; excluded: Microtia (HP:0008551): onset ; excluded: Microcephaly (HP:0000252): onset ; excluded: Macrocephaly (HP:0000256): onset ; excluded: Ventriculomegaly (HP:0002119): onset ; excluded: Intrauterine growth retardation (HP:0001511): onset ; excluded: Single transverse palmar crease (HP:0000954): onset ; excluded: Inguinal hernia (HP:0000023): onset ; excluded: Hydrocephalus (HP:0000238): onset
Individual 11 (MALE; P11Y)Acrofacial dysostosis, Cincinnati type (OMIM:616462)NM_015425.6:c.3721G>A (heterozygous)Hypertelorism (HP:0000316): onset ; Hypotonia (HP:0001252): onset ; excluded: Epicanthus (HP:0000286): onset ; excluded: Upslanted palpebral fissure (HP:0000582): onset ; excluded: Long palpebral fissure (HP:0000637): onset ; excluded: Feeding difficulties (HP:0011968): onset ; excluded: Facial asymmetry (HP:0000324): onset ; excluded: Hypodontia (HP:0000668): onset ; excluded: Underdeveloped nasal alae (HP:0000430): onset ; excluded: Choanal atresia (HP:0000453): onset ; excluded: Infantile spasms (HP:0012469): onset ; excluded: Atonic seizure (HP:0010819): onset ; excluded: Myoclonus (HP:0001336): onset ; excluded: Epileptic encephalopathy (HP:0200134): onset ; excluded: Global developmental delay (HP:0001263): onset ; excluded: Developmental regression (HP:0002376): onset ; excluded: High palate (HP:0000218): onset ; excluded: Cleft palate (HP:0000175): onset ; excluded: Cleft upper lip (HP:0000204): onset ; excluded: Low-set ears (HP:0000369): onset ; excluded: Anteverted nares (HP:0000463): onset ; excluded: Micrognathia (HP:0000347): onset ; excluded: Duane anomaly (HP:0009921): onset ; excluded: Deeply set eye (HP:0000490): onset ; excluded: Scoliosis (HP:0002650): onset ; excluded: Vocal cord paralysis (HP:0001605): onset ; excluded: Clinodactyly of the 5th finger (HP:0004209): onset ; excluded: Eyelid coloboma (HP:0000625): onset ; excluded: Depressed nasal bridge (HP:0005280): onset ; excluded: Metopic synostosis (HP:0011330): onset ; excluded: Ptosis (HP:0000508): onset ; excluded: Hearing impairment (HP:0000365): onset ; excluded: Microtia (HP:0008551): onset ; excluded: Microcephaly (HP:0000252): onset ; excluded: Macrocephaly (HP:0000256): onset ; excluded: Ventriculomegaly (HP:0002119): onset ; excluded: Intrauterine growth retardation (HP:0001511): onset ; excluded: Single transverse palmar crease (HP:0000954): onset ; excluded: Cryptorchidism (HP:0000028): onset ; excluded: Inguinal hernia (HP:0000023): onset ; excluded: Hydrocephalus (HP:0000238): onset
Individual 12 (MALE; P4Y3M)Acrofacial dysostosis, Cincinnati type (OMIM:616462)NM_015425.6:c.3850C>T (heterozygous)Decreased body weight (HP:0004325): onset ; Ventricular septal defect (HP:0001629): onset ; Facial asymmetry (HP:0000324): onset ; Deeply set eye (HP:0000490): onset ; Ptosis (HP:0000508): onset ; Microtia (HP:0008551): onset ; Microcephaly (HP:0000252): onset ; Intrauterine growth retardation (HP:0001511): onset ; excluded: Epicanthus (HP:0000286): onset ; excluded: Upslanted palpebral fissure (HP:0000582): onset ; excluded: Long palpebral fissure (HP:0000637): onset ; excluded: Patent foramen ovale (HP:0001655): onset ; excluded: Feeding difficulties (HP:0011968): onset ; excluded: Hypertelorism (HP:0000316): onset ; excluded: Hypodontia (HP:0000668): onset ; excluded: Underdeveloped nasal alae (HP:0000430): onset ; excluded: Choanal atresia (HP:0000453): onset ; excluded: Infantile spasms (HP:0012469): onset ; excluded: Atonic seizure (HP:0010819): onset ; excluded: Myoclonus (HP:0001336): onset ; excluded: Epileptic encephalopathy (HP:0200134): onset ; excluded: Global developmental delay (HP:0001263): onset ; excluded: Developmental regression (HP:0002376): onset ; excluded: High palate (HP:0000218): onset ; excluded: Cleft palate (HP:0000175): onset ; excluded: Cleft upper lip (HP:0000204): onset ; excluded: Low-set ears (HP:0000369): onset ; excluded: Anteverted nares (HP:0000463): onset ; excluded: Micrognathia (HP:0000347): onset ; excluded: Duane anomaly (HP:0009921): onset ; excluded: Scoliosis (HP:0002650): onset ; excluded: Vocal cord paralysis (HP:0001605): onset ; excluded: Clinodactyly of the 5th finger (HP:0004209): onset ; excluded: Short stature (HP:0004322): onset ; excluded: Eyelid coloboma (HP:0000625): onset ; excluded: Hypotonia (HP:0001252): onset ; excluded: Depressed nasal bridge (HP:0005280): onset ; excluded: Metopic synostosis (HP:0011330): onset ; excluded: Hearing impairment (HP:0000365): onset ; excluded: Macrocephaly (HP:0000256): onset ; excluded: Single transverse palmar crease (HP:0000954): onset ; excluded: Cryptorchidism (HP:0000028): onset ; excluded: Inguinal hernia (HP:0000023): onset
Individual 13 (MALE; P24Y)Acrofacial dysostosis, Cincinnati type (OMIM:616462)NM_015425.6:c.3988_3990del (heterozygous)Seizure (HP:0001250): onset ; Global developmental delay (HP:0001263): onset ; Low-set ears (HP:0000369): onset ; Hypotonia (HP:0001252): onset ; Ptosis (HP:0000508): onset ; excluded: Epicanthus (HP:0000286): onset ; excluded: Upslanted palpebral fissure (HP:0000582): onset ; excluded: Long palpebral fissure (HP:0000637): onset ; excluded: Feeding difficulties (HP:0011968): onset ; excluded: Hypertelorism (HP:0000316): onset ; excluded: Facial asymmetry (HP:0000324): onset ; excluded: Hypodontia (HP:0000668): onset ; excluded: Underdeveloped nasal alae (HP:0000430): onset ; excluded: Choanal atresia (HP:0000453): onset ; excluded: Infantile spasms (HP:0012469): onset ; excluded: Atonic seizure (HP:0010819): onset ; excluded: Myoclonus (HP:0001336): onset ; excluded: Epileptic encephalopathy (HP:0200134): onset ; excluded: Developmental regression (HP:0002376): onset ; excluded: High palate (HP:0000218): onset ; excluded: Cleft palate (HP:0000175): onset ; excluded: Cleft upper lip (HP:0000204): onset ; excluded: Anteverted nares (HP:0000463): onset ; excluded: Micrognathia (HP:0000347): onset ; excluded: Duane anomaly (HP:0009921): onset ; excluded: Deeply set eye (HP:0000490): onset ; excluded: Scoliosis (HP:0002650): onset ; excluded: Vocal cord paralysis (HP:0001605): onset ; excluded: Clinodactyly of the 5th finger (HP:0004209): onset ; excluded: Eyelid coloboma (HP:0000625): onset ; excluded: Depressed nasal bridge (HP:0005280): onset ; excluded: Metopic synostosis (HP:0011330): onset ; excluded: Hearing impairment (HP:0000365): onset ; excluded: Microtia (HP:0008551): onset ; excluded: Ventriculomegaly (HP:0002119): onset ; excluded: Single transverse palmar crease (HP:0000954): onset ; excluded: Cryptorchidism (HP:0000028): onset ; excluded: Inguinal hernia (HP:0000023): onset ; excluded: Hydrocephalus (HP:0000238): onset
Individual 14 (MALE; P6M)Acrofacial dysostosis, Cincinnati type (OMIM:616462)NM_015425.6:c.3988_3990del (heterozygous)Epicanthus (HP:0000286): onset ; Upslanted palpebral fissure (HP:0000582): onset ; Hypertelorism (HP:0000316): onset ; Underdeveloped nasal alae (HP:0000430): onset ; Seizure (HP:0001250): onset ; Global developmental delay (HP:0001263): onset ; Low-set ears (HP:0000369): onset ; Anteverted nares (HP:0000463): onset ; Micrognathia (HP:0000347): onset ; Short stature (HP:0004322): onset ; Hypotonia (HP:0001252): onset ; Depressed nasal bridge (HP:0005280): onset ; Metopic synostosis (HP:0011330): onset ; Cryptorchidism (HP:0000028): onset ; Inguinal hernia (HP:0000023): onset ; excluded: Long palpebral fissure (HP:0000637): onset ; excluded: Patent foramen ovale (HP:0001655): onset ; excluded: Ventricular septal defect (HP:0001629): onset ; excluded: Feeding difficulties (HP:0011968): onset ; excluded: Facial asymmetry (HP:0000324): onset ; excluded: Choanal atresia (HP:0000453): onset ; excluded: Infantile spasms (HP:0012469): onset ; excluded: Atonic seizure (HP:0010819): onset ; excluded: Myoclonus (HP:0001336): onset ; excluded: Epileptic encephalopathy (HP:0200134): onset ; excluded: Developmental regression (HP:0002376): onset ; excluded: High palate (HP:0000218): onset ; excluded: Cleft palate (HP:0000175): onset ; excluded: Cleft upper lip (HP:0000204): onset ; excluded: Duane anomaly (HP:0009921): onset ; excluded: Deeply set eye (HP:0000490): onset ; excluded: Scoliosis (HP:0002650): onset ; excluded: Vocal cord paralysis (HP:0001605): onset ; excluded: Clinodactyly of the 5th finger (HP:0004209): onset ; excluded: Eyelid coloboma (HP:0000625): onset ; excluded: Ptosis (HP:0000508): onset ; excluded: Hearing impairment (HP:0000365): onset ; excluded: Microtia (HP:0008551): onset ; excluded: Microcephaly (HP:0000252): onset ; excluded: Macrocephaly (HP:0000256): onset ; excluded: Ventriculomegaly (HP:0002119): onset ; excluded: Intrauterine growth retardation (HP:0001511): onset ; excluded: Single transverse palmar crease (HP:0000954): onset ; excluded: Hydrocephalus (HP:0000238): onset
Individual 15 (MALE; P6Y)Acrofacial dysostosis, Cincinnati type (OMIM:616462)NM_015425.6:c.4685G>T (heterozygous)Patent foramen ovale (HP:0001655): onset ; Hypertelorism (HP:0000316): onset ; Infantile spasms (HP:0012469): onset ; Global developmental delay (HP:0001263): onset ; Hypotonia (HP:0001252): onset ; Microcephaly (HP:0000252): onset ; excluded: Epicanthus (HP:0000286): onset ; excluded: Upslanted palpebral fissure (HP:0000582): onset ; excluded: Long palpebral fissure (HP:0000637): onset ; excluded: Ventricular septal defect (HP:0001629): onset ; excluded: Feeding difficulties (HP:0011968): onset ; excluded: Facial asymmetry (HP:0000324): onset ; excluded: Underdeveloped nasal alae (HP:0000430): onset ; excluded: Choanal atresia (HP:0000453): onset ; excluded: Atonic seizure (HP:0010819): onset ; excluded: Myoclonus (HP:0001336): onset ; excluded: Epileptic encephalopathy (HP:0200134): onset ; excluded: Developmental regression (HP:0002376): onset ; excluded: High palate (HP:0000218): onset ; excluded: Cleft palate (HP:0000175): onset ; excluded: Cleft upper lip (HP:0000204): onset ; excluded: Low-set ears (HP:0000369): onset ; excluded: Anteverted nares (HP:0000463): onset ; excluded: Micrognathia (HP:0000347): onset ; excluded: Duane anomaly (HP:0009921): onset ; excluded: Deeply set eye (HP:0000490): onset ; excluded: Scoliosis (HP:0002650): onset ; excluded: Vocal cord paralysis (HP:0001605): onset ; excluded: Clinodactyly of the 5th finger (HP:0004209): onset ; excluded: Short stature (HP:0004322): onset ; excluded: Eyelid coloboma (HP:0000625): onset ; excluded: Depressed nasal bridge (HP:0005280): onset ; excluded: Metopic synostosis (HP:0011330): onset ; excluded: Ptosis (HP:0000508): onset ; excluded: Hearing impairment (HP:0000365): onset ; excluded: Microtia (HP:0008551): onset ; excluded: Macrocephaly (HP:0000256): onset ; excluded: Ventriculomegaly (HP:0002119): onset ; excluded: Intrauterine growth retardation (HP:0001511): onset ; excluded: Single transverse palmar crease (HP:0000954): onset ; excluded: Cryptorchidism (HP:0000028): onset ; excluded: Inguinal hernia (HP:0000023): onset ; excluded: Hydrocephalus (HP:0000238): onset
Individual 16 (MALE; P3Y)Acrofacial dysostosis, Cincinnati type (OMIM:616462)NM_015425.6:c.4685G>T (heterozygous)Feeding difficulties (HP:0011968): onset ; Hypertelorism (HP:0000316): onset ; Seizure (HP:0001250): onset ; Global developmental delay (HP:0001263): onset ; Short stature (HP:0004322): onset ; Hypotonia (HP:0001252): onset ; Microcephaly (HP:0000252): onset ; excluded: Epicanthus (HP:0000286): onset ; excluded: Upslanted palpebral fissure (HP:0000582): onset ; excluded: Long palpebral fissure (HP:0000637): onset ; excluded: Facial asymmetry (HP:0000324): onset ; excluded: Underdeveloped nasal alae (HP:0000430): onset ; excluded: Choanal atresia (HP:0000453): onset ; excluded: Infantile spasms (HP:0012469): onset ; excluded: Atonic seizure (HP:0010819): onset ; excluded: Myoclonus (HP:0001336): onset ; excluded: Epileptic encephalopathy (HP:0200134): onset ; excluded: Developmental regression (HP:0002376): onset ; excluded: High palate (HP:0000218): onset ; excluded: Cleft palate (HP:0000175): onset ; excluded: Cleft upper lip (HP:0000204): onset ; excluded: Low-set ears (HP:0000369): onset ; excluded: Anteverted nares (HP:0000463): onset ; excluded: Micrognathia (HP:0000347): onset ; excluded: Duane anomaly (HP:0009921): onset ; excluded: Deeply set eye (HP:0000490): onset ; excluded: Scoliosis (HP:0002650): onset ; excluded: Vocal cord paralysis (HP:0001605): onset ; excluded: Clinodactyly of the 5th finger (HP:0004209): onset ; excluded: Eyelid coloboma (HP:0000625): onset ; excluded: Depressed nasal bridge (HP:0005280): onset ; excluded: Metopic synostosis (HP:0011330): onset ; excluded: Ptosis (HP:0000508): onset ; excluded: Hearing impairment (HP:0000365): onset ; excluded: Microtia (HP:0008551): onset ; excluded: Macrocephaly (HP:0000256): onset ; excluded: Ventriculomegaly (HP:0002119): onset ; excluded: Intrauterine growth retardation (HP:0001511): onset ; excluded: Single transverse palmar crease (HP:0000954): onset ; excluded: Cryptorchidism (HP:0000028): onset ; excluded: Inguinal hernia (HP:0000023): onset ; excluded: Hydrocephalus (HP:0000238): onset
Individual 17 (FEMALE; P7Y)Acrofacial dysostosis, Cincinnati type (OMIM:616462)NM_015425.6:c.4891G>A (heterozygous)Patent foramen ovale (HP:0001655): onset ; Feeding difficulties (HP:0011968): onset ; Facial asymmetry (HP:0000324): onset ; Seizure (HP:0001250): onset ; Global developmental delay (HP:0001263): onset ; High palate (HP:0000218): onset ; Micrognathia (HP:0000347): onset ; Scoliosis (HP:0002650): onset ; Hearing impairment (HP:0000365): onset ; Microtia (HP:0008551): onset ; Ventriculomegaly (HP:0002119): onset ; Intrauterine growth retardation (HP:0001511): onset ; excluded: Epicanthus (HP:0000286): onset ; excluded: Upslanted palpebral fissure (HP:0000582): onset ; excluded: Long palpebral fissure (HP:0000637): onset ; excluded: Ventricular septal defect (HP:0001629): onset ; excluded: Underdeveloped nasal alae (HP:0000430): onset ; excluded: Choanal atresia (HP:0000453): onset ; excluded: Infantile spasms (HP:0012469): onset ; excluded: Atonic seizure (HP:0010819): onset ; excluded: Myoclonus (HP:0001336): onset ; excluded: Epileptic encephalopathy (HP:0200134): onset ; excluded: Developmental regression (HP:0002376): onset ; excluded: Cleft palate (HP:0000175): onset ; excluded: Cleft upper lip (HP:0000204): onset ; excluded: Anteverted nares (HP:0000463): onset ; excluded: Duane anomaly (HP:0009921): onset ; excluded: Deeply set eye (HP:0000490): onset ; excluded: Vocal cord paralysis (HP:0001605): onset ; excluded: Clinodactyly of the 5th finger (HP:0004209): onset ; excluded: Short stature (HP:0004322): onset ; excluded: Eyelid coloboma (HP:0000625): onset ; excluded: Depressed nasal bridge (HP:0005280): onset ; excluded: Metopic synostosis (HP:0011330): onset ; excluded: Ptosis (HP:0000508): onset ; excluded: Microcephaly (HP:0000252): onset ; excluded: Macrocephaly (HP:0000256): onset ; excluded: Single transverse palmar crease (HP:0000954): onset ; excluded: Inguinal hernia (HP:0000023): onset ; excluded: Hydrocephalus (HP:0000238): onset
Individual 18 (FEMALE; P11Y)Acrofacial dysostosis, Cincinnati type (OMIM:616462)NM_015425.6:c.4913C>T (heterozygous)Patent foramen ovale (HP:0001655): onset ; Ventricular septal defect (HP:0001629): onset ; Global developmental delay (HP:0001263): onset ; Micrognathia (HP:0000347): onset ; Short stature (HP:0004322): onset ; Hypotonia (HP:0001252): onset ; Ptosis (HP:0000508): onset ; excluded: Epicanthus (HP:0000286): onset ; excluded: Upslanted palpebral fissure (HP:0000582): onset ; excluded: Long palpebral fissure (HP:0000637): onset ; excluded: Feeding difficulties (HP:0011968): onset ; excluded: Facial asymmetry (HP:0000324): onset ; excluded: Underdeveloped nasal alae (HP:0000430): onset ; excluded: Choanal atresia (HP:0000453): onset ; excluded: Infantile spasms (HP:0012469): onset ; excluded: Atonic seizure (HP:0010819): onset ; excluded: Myoclonus (HP:0001336): onset ; excluded: Epileptic encephalopathy (HP:0200134): onset ; excluded: Developmental regression (HP:0002376): onset ; excluded: High palate (HP:0000218): onset ; excluded: Cleft palate (HP:0000175): onset ; excluded: Cleft upper lip (HP:0000204): onset ; excluded: Low-set ears (HP:0000369): onset ; excluded: Anteverted nares (HP:0000463): onset ; excluded: Duane anomaly (HP:0009921): onset ; excluded: Deeply set eye (HP:0000490): onset ; excluded: Scoliosis (HP:0002650): onset ; excluded: Vocal cord paralysis (HP:0001605): onset ; excluded: Clinodactyly of the 5th finger (HP:0004209): onset ; excluded: Eyelid coloboma (HP:0000625): onset ; excluded: Depressed nasal bridge (HP:0005280): onset ; excluded: Metopic synostosis (HP:0011330): onset ; excluded: Hearing impairment (HP:0000365): onset ; excluded: Microtia (HP:0008551): onset ; excluded: Single transverse palmar crease (HP:0000954): onset ; excluded: Inguinal hernia (HP:0000023): 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": 23, + "metadata": {}, + "outputs": [], + "source": [ + "pmid = \"PMID:37075751\"\n", + "#df = timporter.create_hpoa_from_phenopackets(pmid=pmid, mode_of_inheritance=Moi.AD, target=\"OMIM:616462\")" + ] + } + ], + "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/POLR1A/POLR1A_HLD27_individuals.ipynb b/notebooks/POLR1A/POLR1A_HLD27_individuals.ipynb index 46cd59577..f96456857 100644 --- a/notebooks/POLR1A/POLR1A_HLD27_individuals.ipynb +++ b/notebooks/POLR1A/POLR1A_HLD27_individuals.ipynb @@ -10,27 +10,19 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": 7, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "Using pyphetools version 0.9.84\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" + "Using pyphetools version 0.9.113\n" ] } ], "source": [ - "from pyphetools.creation import TemplateImporter\n", + "from pyphetools.creation import TemplateImporter, Moi\n", "from pyphetools.visualization import IndividualTable, QcVisualizer\n", "from IPython.display import display, HTML\n", "import pyphetools\n", @@ -39,7 +31,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": 8, "metadata": {}, "outputs": [], "source": [ @@ -49,14 +41,14 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 9, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "HPO version 2024-04-26\n", + "HPO version 2024-08-13\n", "Created encoders for 56 fields\n", "Importing OMIM:620675, Leukodystrophy, hypomyelinating, 27, HGNC:17264, POLR1A, NM_015425.6\n", "We output 4 GA4GH phenopackets to the directory phenopackets\n" @@ -70,7 +62,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 10, "metadata": {}, "outputs": [ { @@ -100,7 +92,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 11, "metadata": {}, "outputs": [ { @@ -109,10 +101,81 @@ "\n", "\n", "\n", - "\n", - "\n", - "\n", - "\n", + "\n", + "\n", + "\n", + "\n", "
4 phenopackets - PMID:28051070 (n=2); PMID:36917474 (n=2)
IndividualDiseaseGenotypePhenotypic features
Brother 1 (203) (MALE; P11Y)Leukodystrophy, hypomyelinating, 27 (OMIM:620675)NM_015425.6:c.2801C>T (homozygous)P5Y: Gait ataxia (HP:0002066)
P9Y6M: Loss of ambulation (HP:0002505)
Small for gestational age (HP:0001518); Babinski sign (HP:0003487); Leukodystrophy (HP:0002415); Ventriculomegaly (HP:0002119); Global developmental delay (HP:0001263); Intellectual disability (HP:0001249); Developmental regression (HP:0002376); Head titubation (HP:0002599); Delayed ability to walk (HP:0031936); Dystonia (HP:0001332); Hyperreflexia (HP:0001347); Cerebellar atrophy (HP:0001272); Cerebral atrophy (HP:0002059); Truncal ataxia (HP:0002078); Thin corpus callosum (HP:0033725); Spasticity (HP:0001257); Joint hypermobility (HP:0001382); Pes cavus (HP:0001761); Optic atrophy (HP:0000648); Supranuclear gaze palsy (HP:0000605); Relative macrocephaly (HP:0004482); excluded: Feeding difficulties (HP:0011968); excluded: Seizure (HP:0001250); excluded: Atrophy/Degeneration affecting the brainstem (HP:0007366); excluded: Irritability (HP:0000737); excluded: Hypotonia (HP:0001252); excluded: Short stature (HP:0004322); excluded: Strabismus (HP:0000486); excluded: Cataract (HP:0000518); excluded: Nystagmus (HP:0000639); excluded: Neonatal hypoglycemia (HP:0001998)
Brother 2 (204) (MALE; P6Y6M)Leukodystrophy, hypomyelinating, 27 (OMIM:620675)NM_015425.6:c.2801C>T (homozygous)P6Y: Seizure (HP:0001250)
P6Y6M: Absent speech (HP:0001344)
Poor head control (HP:0002421); Small for gestational age (HP:0001518); Neonatal hypoglycemia (HP:0001998); Babinski sign (HP:0003487); Leukodystrophy (HP:0002415); Ventriculomegaly (HP:0002119); Global developmental delay (HP:0001263); Intellectual disability (HP:0001249); Head titubation (HP:0002599); Delayed ability to walk (HP:0031936); Dystonia (HP:0001332); Hyperreflexia (HP:0001347); Cerebellar atrophy (HP:0001272); Cerebral atrophy (HP:0002059); Truncal ataxia (HP:0002078); Thin corpus callosum (HP:0033725); Spasticity (HP:0001257); Joint hypermobility (HP:0001382); Short stature (HP:0004322); Optic atrophy (HP:0000648); Supranuclear gaze palsy (HP:0000605); Relative macrocephaly (HP:0004482); excluded: Feeding difficulties (HP:0011968); excluded: Developmental regression (HP:0002376); excluded: Atrophy/Degeneration affecting the brainstem (HP:0007366); excluded: Irritability (HP:0000737); excluded: Gait ataxia (HP:0002066); excluded: Hypotonia (HP:0001252); excluded: Pes cavus (HP:0001761); excluded: Strabismus (HP:0000486); excluded: Cataract (HP:0000518); excluded: Nystagmus (HP:0000639)
Patient 1 (MALE; P16Y6M)Leukodystrophy, hypomyelinating, 27 (OMIM:620675)NM_015425.6:c.1925C>A (homozygous)P1Y1M: Strabismus (HP:0000486)
P5Y: Developmental regression (HP:0002376)
P7Y: Dystonia (HP:0001332); Scoliosis (HP:0002650)
P8Y: Seizure (HP:0001250)
P11Y: Cataract (HP:0000518)
Hyperreflexia (HP:0001347); Irritability (HP:0000737); Hypertonia (HP:0001276); Leukodystrophy (HP:0002415); Ventriculomegaly (HP:0002119); Global developmental delay (HP:0001263); Intellectual disability (HP:0001249); Atrophy/Degeneration affecting the brainstem (HP:0007366); CNS hypomyelination (HP:0003429); Cerebellar atrophy (HP:0001272); Cerebral atrophy (HP:0002059); Truncal ataxia (HP:0002078); Thin corpus callosum (HP:0033725); Nystagmus (HP:0000639); excluded: Feeding difficulties (HP:0011968); excluded: Absent speech (HP:0001344); excluded: Head titubation (HP:0002599); excluded: Gait ataxia (HP:0002066); excluded: Hypotonia (HP:0001252); excluded: Short stature (HP:0004322); excluded: Optic atrophy (HP:0000648); excluded: Supranuclear gaze palsy (HP:0000605); excluded: Small for gestational age (HP:0001518); excluded: Neonatal hypoglycemia (HP:0001998); excluded: Relative macrocephaly (HP:0004482)
Patient 2 (FEMALE; P2Y10M)Leukodystrophy, hypomyelinating, 27 (OMIM:620675)NM_015425.6:c.1925C>A (homozygous)P2Y10M: Dystonia (HP:0001332); Hyperreflexia (HP:0001347); Spasticity (HP:0001257)
Feeding difficulties (HP:0011968); Leukodystrophy (HP:0002415); Global developmental delay (HP:0001263); CNS hypomyelination (HP:0003429); Cerebellar atrophy (HP:0001272); Thin corpus callosum (HP:0033725); Hypotonia (HP:0001252); Short stature (HP:0004322); Nystagmus (HP:0000639); excluded: Ventriculomegaly (HP:0002119); excluded: Seizure (HP:0001250); excluded: Developmental regression (HP:0002376); excluded: Absent speech (HP:0001344); excluded: Atrophy/Degeneration affecting the brainstem (HP:0007366); excluded: Head titubation (HP:0002599); excluded: Irritability (HP:0000737); excluded: Gait ataxia (HP:0002066); excluded: Scoliosis (HP:0002650); excluded: Strabismus (HP:0000486); excluded: Cataract (HP:0000518); excluded: Optic atrophy (HP:0000648); excluded: Supranuclear gaze palsy (HP:0000605); excluded: Small for gestational age (HP:0001518); excluded: Neonatal hypoglycemia (HP:0001998); excluded: Relative macrocephaly (HP:0004482)
Brother 1 (203) (MALE; P11Y)Leukodystrophy, hypomyelinating, 27 (OMIM:620675)NM_015425.6:c.2801C>T (homozygous)Babinski sign (HP:0003487): onset ; Leukodystrophy (HP:0002415): onset ; Ventriculomegaly (HP:0002119): onset ; Global developmental delay (HP:0001263): onset ; Intellectual disability (HP:0001249): onset ; Developmental regression (HP:0002376): onset ; Head titubation (HP:0002599): onset ; Delayed ability to walk (HP:0031936): onset ; Dystonia (HP:0001332): onset ; Hyperreflexia (HP:0001347): onset ; Cerebellar atrophy (HP:0001272): onset ; Cerebral atrophy (HP:0002059): onset ; Truncal ataxia (HP:0002078): onset ; Thin corpus callosum (HP:0033725): onset ; Spasticity (HP:0001257): onset ; Joint hypermobility (HP:0001382): onset ; Pes cavus (HP:0001761): onset ; Optic atrophy (HP:0000648): onset ; Supranuclear gaze palsy (HP:0000605): onset ; Relative macrocephaly (HP:0004482): onset ; excluded: Feeding difficulties (HP:0011968): onset ; excluded: Seizure (HP:0001250): onset ; excluded: Atrophy/Degeneration affecting the brainstem (HP:0007366): onset ; excluded: Irritability (HP:0000737): onset ; excluded: Hypotonia (HP:0001252): onset ; excluded: Short stature (HP:0004322): onset ; excluded: Strabismus (HP:0000486): onset ; excluded: Cataract (HP:0000518): onset ; excluded: Nystagmus (HP:0000639): onset ; excluded: Neonatal hypoglycemia (HP:0001998): onset
TimeElement(element=OntologyClass(id=HP:0003577, label=Congenital onset)): Small for gestational age (HP:0001518): onset ontology_class {\n", + " id: \"HP:0003577\"\n", + " label: \"Congenital onset\"\n", + "}\n", + "
TimeElement(element=Age(iso8601duration=P5Y)): Gait ataxia (HP:0002066): onset age {\n", + " iso8601duration: \"P5Y\"\n", + "}\n", + "
TimeElement(element=Age(iso8601duration=P9Y6M)): Loss of ambulation (HP:0002505): onset age {\n", + " iso8601duration: \"P9Y6M\"\n", + "}\n", + "
Brother 2 (204) (MALE; P6Y6M)Leukodystrophy, hypomyelinating, 27 (OMIM:620675)NM_015425.6:c.2801C>T (homozygous)Babinski sign (HP:0003487): onset ; Leukodystrophy (HP:0002415): onset ; Ventriculomegaly (HP:0002119): onset ; Global developmental delay (HP:0001263): onset ; Intellectual disability (HP:0001249): onset ; Head titubation (HP:0002599): onset ; Delayed ability to walk (HP:0031936): onset ; Dystonia (HP:0001332): onset ; Hyperreflexia (HP:0001347): onset ; Cerebellar atrophy (HP:0001272): onset ; Cerebral atrophy (HP:0002059): onset ; Truncal ataxia (HP:0002078): onset ; Thin corpus callosum (HP:0033725): onset ; Spasticity (HP:0001257): onset ; Joint hypermobility (HP:0001382): onset ; Short stature (HP:0004322): onset ; Optic atrophy (HP:0000648): onset ; Supranuclear gaze palsy (HP:0000605): onset ; Relative macrocephaly (HP:0004482): onset ; excluded: Feeding difficulties (HP:0011968): onset ; excluded: Developmental regression (HP:0002376): onset ; excluded: Atrophy/Degeneration affecting the brainstem (HP:0007366): onset ; excluded: Irritability (HP:0000737): onset ; excluded: Gait ataxia (HP:0002066): onset ; excluded: Hypotonia (HP:0001252): onset ; excluded: Pes cavus (HP:0001761): onset ; excluded: Strabismus (HP:0000486): onset ; excluded: Cataract (HP:0000518): onset ; excluded: Nystagmus (HP:0000639): onset
TimeElement(element=OntologyClass(id=HP:0003577, label=Congenital onset)): Small for gestational age (HP:0001518): onset ontology_class {\n", + " id: \"HP:0003577\"\n", + " label: \"Congenital onset\"\n", + "}\n", + "
TimeElement(element=OntologyClass(id=HP:0003623, label=Neonatal onset)): Neonatal hypoglycemia (HP:0001998): onset ontology_class {\n", + " id: \"HP:0003623\"\n", + " label: \"Neonatal onset\"\n", + "}\n", + "
TimeElement(element=OntologyClass(id=HP:0003593, label=Infantile onset)): Poor head control (HP:0002421): onset ontology_class {\n", + " id: \"HP:0003593\"\n", + " label: \"Infantile onset\"\n", + "}\n", + "
TimeElement(element=Age(iso8601duration=P6Y)): Seizure (HP:0001250): onset age {\n", + " iso8601duration: \"P6Y\"\n", + "}\n", + "
TimeElement(element=Age(iso8601duration=P6Y6M)): Absent speech (HP:0001344): onset age {\n", + " iso8601duration: \"P6Y6M\"\n", + "}\n", + "
Patient 1 (MALE; P16Y6M)Leukodystrophy, hypomyelinating, 27 (OMIM:620675)NM_015425.6:c.1925C>A (homozygous)Leukodystrophy (HP:0002415): onset ; Ventriculomegaly (HP:0002119): onset ; Global developmental delay (HP:0001263): onset ; Intellectual disability (HP:0001249): onset ; Atrophy/Degeneration affecting the brainstem (HP:0007366): onset ; CNS hypomyelination (HP:0003429): onset ; Cerebellar atrophy (HP:0001272): onset ; Cerebral atrophy (HP:0002059): onset ; Truncal ataxia (HP:0002078): onset ; Thin corpus callosum (HP:0033725): onset ; Nystagmus (HP:0000639): onset ; excluded: Feeding difficulties (HP:0011968): onset ; excluded: Absent speech (HP:0001344): onset ; excluded: Head titubation (HP:0002599): onset ; excluded: Gait ataxia (HP:0002066): onset ; excluded: Hypotonia (HP:0001252): onset ; excluded: Short stature (HP:0004322): onset ; excluded: Optic atrophy (HP:0000648): onset ; excluded: Supranuclear gaze palsy (HP:0000605): onset ; excluded: Small for gestational age (HP:0001518): onset ; excluded: Neonatal hypoglycemia (HP:0001998): onset ; excluded: Relative macrocephaly (HP:0004482): onset
TimeElement(element=OntologyClass(id=HP:0003577, label=Congenital onset)): Hyperreflexia (HP:0001347): onset ontology_class {\n", + " id: \"HP:0003577\"\n", + " label: \"Congenital onset\"\n", + "}\n", + "; Irritability (HP:0000737): onset ontology_class {\n", + " id: \"HP:0003577\"\n", + " label: \"Congenital onset\"\n", + "}\n", + "; Hypertonia (HP:0001276): onset ontology_class {\n", + " id: \"HP:0003577\"\n", + " label: \"Congenital onset\"\n", + "}\n", + "
TimeElement(element=Age(iso8601duration=P1Y1M)): Strabismus (HP:0000486): onset age {\n", + " iso8601duration: \"P1Y1M\"\n", + "}\n", + "
TimeElement(element=Age(iso8601duration=P5Y)): Developmental regression (HP:0002376): onset age {\n", + " iso8601duration: \"P5Y\"\n", + "}\n", + "
TimeElement(element=Age(iso8601duration=P7Y)): Dystonia (HP:0001332): onset age {\n", + " iso8601duration: \"P7Y\"\n", + "}\n", + "; Scoliosis (HP:0002650): onset age {\n", + " iso8601duration: \"P7Y\"\n", + "}\n", + "
TimeElement(element=Age(iso8601duration=P8Y)): Seizure (HP:0001250): onset age {\n", + " iso8601duration: \"P8Y\"\n", + "}\n", + "
TimeElement(element=Age(iso8601duration=P11Y)): Cataract (HP:0000518): onset age {\n", + " iso8601duration: \"P11Y\"\n", + "}\n", + "
Patient 2 (FEMALE; P2Y10M)Leukodystrophy, hypomyelinating, 27 (OMIM:620675)NM_015425.6:c.1925C>A (homozygous)Leukodystrophy (HP:0002415): onset ; Global developmental delay (HP:0001263): onset ; CNS hypomyelination (HP:0003429): onset ; Cerebellar atrophy (HP:0001272): onset ; Thin corpus callosum (HP:0033725): onset ; Hypotonia (HP:0001252): onset ; Short stature (HP:0004322): onset ; Nystagmus (HP:0000639): onset ; excluded: Ventriculomegaly (HP:0002119): onset ; excluded: Seizure (HP:0001250): onset ; excluded: Developmental regression (HP:0002376): onset ; excluded: Absent speech (HP:0001344): onset ; excluded: Atrophy/Degeneration affecting the brainstem (HP:0007366): onset ; excluded: Head titubation (HP:0002599): onset ; excluded: Irritability (HP:0000737): onset ; excluded: Gait ataxia (HP:0002066): onset ; excluded: Scoliosis (HP:0002650): onset ; excluded: Strabismus (HP:0000486): onset ; excluded: Cataract (HP:0000518): onset ; excluded: Optic atrophy (HP:0000648): onset ; excluded: Supranuclear gaze palsy (HP:0000605): onset ; excluded: Small for gestational age (HP:0001518): onset ; excluded: Neonatal hypoglycemia (HP:0001998): onset ; excluded: Relative macrocephaly (HP:0004482): onset
TimeElement(element=OntologyClass(id=HP:0003593, label=Infantile onset)): Feeding difficulties (HP:0011968): onset ontology_class {\n", + " id: \"HP:0003593\"\n", + " label: \"Infantile onset\"\n", + "}\n", + "
TimeElement(element=Age(iso8601duration=P2Y10M)): Dystonia (HP:0001332): onset age {\n", + " iso8601duration: \"P2Y10M\"\n", + "}\n", + "; Hyperreflexia (HP:0001347): onset age {\n", + " iso8601duration: \"P2Y10M\"\n", + "}\n", + "; Spasticity (HP:0001257): onset age {\n", + " iso8601duration: \"P2Y10M\"\n", + "}\n", + "
" ], "text/plain": [ @@ -130,7 +193,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 12, "metadata": {}, "outputs": [ { @@ -199,7 +262,7 @@ " \n", " PMID:36917474\n", " PCS\n", - " ORCID:0000-0002-0736-9199[2024-05-08]\n", + " ORCID:0000-0002-0736-9199[2024-11-30]\n", " \n", " \n", " 1\n", @@ -216,7 +279,7 @@ " \n", " PMID:36917474\n", " PCS\n", - " ORCID:0000-0002-0736-9199[2024-05-08]\n", + " ORCID:0000-0002-0736-9199[2024-11-30]\n", " \n", " \n", " 2\n", @@ -233,7 +296,7 @@ " \n", " PMID:36917474\n", " PCS\n", - " ORCID:0000-0002-0736-9199[2024-05-08]\n", + " ORCID:0000-0002-0736-9199[2024-11-30]\n", " \n", " \n", " 3\n", @@ -250,7 +313,7 @@ " \n", " PMID:36917474\n", " PCS\n", - " ORCID:0000-0002-0736-9199[2024-05-08]\n", + " ORCID:0000-0002-0736-9199[2024-11-30]\n", " \n", " \n", " 4\n", @@ -267,7 +330,7 @@ " \n", " PMID:36917474\n", " PCS\n", - " ORCID:0000-0002-0736-9199[2024-05-08]\n", + " ORCID:0000-0002-0736-9199[2024-11-30]\n", " \n", " \n", " ...\n", @@ -301,7 +364,7 @@ " \n", " PMID:28051070\n", " PCS\n", - " ORCID:0000-0002-0736-9199[2024-05-08]\n", + " ORCID:0000-0002-0736-9199[2024-11-30]\n", " \n", " \n", " 67\n", @@ -318,7 +381,7 @@ " \n", " PMID:36917474\n", " PCS\n", - " ORCID:0000-0002-0736-9199[2024-05-08]\n", + " ORCID:0000-0002-0736-9199[2024-11-30]\n", " \n", " \n", " 68\n", @@ -335,7 +398,7 @@ " \n", " PMID:36917474\n", " PCS\n", - " ORCID:0000-0002-0736-9199[2024-05-08]\n", + " ORCID:0000-0002-0736-9199[2024-11-30]\n", " \n", " \n", " 69\n", @@ -352,7 +415,7 @@ " \n", " PMID:28051070\n", " PCS\n", - " ORCID:0000-0002-0736-9199[2024-05-08]\n", + " ORCID:0000-0002-0736-9199[2024-11-30]\n", " \n", " \n", " 70\n", @@ -369,7 +432,7 @@ " \n", " PMID:28051070\n", " PCS\n", - " ORCID:0000-0002-0736-9199[2024-05-08]\n", + " ORCID:0000-0002-0736-9199[2024-11-30]\n", " \n", " \n", "\n", @@ -417,29 +480,29 @@ "70 PMID:28051070 PCS \n", "\n", " biocuration \n", - "0 ORCID:0000-0002-0736-9199[2024-05-08] \n", - "1 ORCID:0000-0002-0736-9199[2024-05-08] \n", - "2 ORCID:0000-0002-0736-9199[2024-05-08] \n", - "3 ORCID:0000-0002-0736-9199[2024-05-08] \n", - "4 ORCID:0000-0002-0736-9199[2024-05-08] \n", + "0 ORCID:0000-0002-0736-9199[2024-11-30] \n", + "1 ORCID:0000-0002-0736-9199[2024-11-30] \n", + "2 ORCID:0000-0002-0736-9199[2024-11-30] \n", + "3 ORCID:0000-0002-0736-9199[2024-11-30] \n", + "4 ORCID:0000-0002-0736-9199[2024-11-30] \n", ".. ... \n", - "66 ORCID:0000-0002-0736-9199[2024-05-08] \n", - "67 ORCID:0000-0002-0736-9199[2024-05-08] \n", - "68 ORCID:0000-0002-0736-9199[2024-05-08] \n", - "69 ORCID:0000-0002-0736-9199[2024-05-08] \n", - "70 ORCID:0000-0002-0736-9199[2024-05-08] \n", + "66 ORCID:0000-0002-0736-9199[2024-11-30] \n", + "67 ORCID:0000-0002-0736-9199[2024-11-30] \n", + "68 ORCID:0000-0002-0736-9199[2024-11-30] \n", + "69 ORCID:0000-0002-0736-9199[2024-11-30] \n", + "70 ORCID:0000-0002-0736-9199[2024-11-30] \n", "\n", "[71 rows x 14 columns]" ] }, - "execution_count": 6, + "execution_count": 12, "metadata": {}, "output_type": "execute_result" } ], "source": [ "pmid = \"PMID:28051070\"\n", - "timporter.create_hpoa_from_phenopackets(pmid=pmid, moi=\"Autosomal recessive\", target=\"OMIM:620675\")" + "timporter.create_hpoa_from_phenopackets(pmid=pmid, mode_of_inheritance=Moi.AR, target=\"OMIM:620675\")" ] } ], diff --git a/notebooks/POLR1A/POLR1A_Smallwood_2023.ipynb b/notebooks/POLR1A/POLR1A_Smallwood_2023.ipynb deleted file mode 100644 index 81df949c7..000000000 --- a/notebooks/POLR1A/POLR1A_Smallwood_2023.ipynb +++ /dev/null @@ -1,2851 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "id": "293e1b5d-78a6-4880-9788-2fc635ac255e", - "metadata": {}, - "source": [ - " ### POLR1A \n", - "\n", - "[Acrofacial dysostosis, Cincinnati type - OMIM:616462](https://omim.org/entry/616462) is caused by variants in the POLR1A gene.\n", - "\n", - "Data is extracted from [Smallwood K, et al. POLR1A variants underlie phenotypic heterogeneity in craniofacial, neural, and cardiac anomalies. Am J Hum Genet. 2023;110(5):809-825](https://pubmed.ncbi.nlm.nih.gov/37075751/)." - ] - }, - { - "cell_type": "code", - "execution_count": 1, - "id": "cb845a0f-adf2-4fcd-957f-2176b752372a", - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Using pyphetools version 0.9.66\n" - ] - } - ], - "source": [ - "import pandas as pd\n", - "pd.set_option('display.max_colwidth', None) # show entire column contents, important!\n", - "from IPython.display import display, HTML\n", - "from pyphetools.creation import *\n", - "from pyphetools.visualization import *\n", - "from pyphetools.validation import *\n", - "import pyphetools\n", - "print(f\"Using pyphetools version {pyphetools.__version__}\")" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "id": "a3972a01-7149-4c6f-ad1b-292bc5489821", - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "HPO version 2024-03-06\n" - ] - } - ], - "source": [ - "PMID = \"PMID:37075751\"\n", - "title = \"POLR1A variants underlie phenotypic heterogeneity in craniofacial, neural, and cardiac anomalies\"\n", - "cite = Citation(pmid=PMID, title=title)\n", - "parser = HpoParser(hpo_json_file=\"../hp.json\")\n", - "hpo_cr = parser.get_hpo_concept_recognizer()\n", - "hpo_version = parser.get_version()\n", - "hpo_ontology = parser.get_ontology()\n", - "metadata = MetaData(created_by=\"ORCID:0000-0001-7941-2961\", citation=cite)\n", - "metadata.default_versions_with_hpo(version=hpo_version)\n", - "print(f\"HPO version {hpo_version}\")" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "id": "b9270778-a3f5-4d04-a957-e9e8937f429b", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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individual_idTestNM_015425.6SexOnsetAge (at most recent assessment)DeceasedProteinInheritanceACMG classificationACMG criteria...IUGRNaNhead circumference (cm)length (cm)weight (kg)Any other featuresAbbreviations: U/L unilateral; B/L bilateral; n/a not available; VUS variant of uncertain significance; BP4 lack of segregation in affected members of a family; PM2 absent from controls; PP3 computational evidence supports deleterious effect; PS2 de novo; PP5 reputable source reports variant as pathogenic; PM4 protein length changes due to in frame deletion in a non-repeat regionSD calculated using CDC growth chartspersonperson_id
1Targeted variantc.176A>TmaleCongenital onsetP3Myesp.(Asp59Val)paternalVUSPM2, PP3...noNaNNaNNaNNaNNaNNaNNaN1Individual 1
2Exome trioc.176A>TmaleCongenital onsetP5Ynop.(Asp59Val)paternalVUSPM2, PP3...noNaNNaNNaNNaNNaNNaNNaN2Individual 2
\n", - "

2 rows × 49 columns

\n", - "
" - ], - "text/plain": [ - "individual_id Test NM_015425.6 Sex Onset \\\n", - "1 Targeted variant c.176A>T male Congenital onset \n", - "2 Exome trio c.176A>T male Congenital onset \n", - "\n", - "individual_id Age (at most recent assessment) Deceased Protein \\\n", - "1 P3M yes p.(Asp59Val) \n", - "2 P5Y no p.(Asp59Val) \n", - "\n", - "individual_id Inheritance ACMG classification ACMG criteria ... IUGR NaN \\\n", - "1 paternal VUS PM2, PP3 ... no NaN \n", - "2 paternal VUS PM2, PP3 ... no NaN \n", - "\n", - "individual_id head circumference (cm) length (cm) weight (kg) \\\n", - "1 NaN NaN NaN \n", - "2 NaN NaN NaN \n", - "\n", - "individual_id Any other features \\\n", - "1 NaN \n", - "2 NaN \n", - "\n", - "individual_id Abbreviations: U/L unilateral; B/L bilateral; n/a not available; VUS variant of uncertain significance; BP4 lack of segregation in affected members of a family; PM2 absent from controls; PP3 computational evidence supports deleterious effect; PS2 de novo; PP5 reputable source reports variant as pathogenic; PM4 protein length changes due to in frame deletion in a non-repeat region \\\n", - "1 NaN \n", - "2 NaN \n", - "\n", - "individual_id SD calculated using CDC growth charts person person_id \n", - "1 NaN 1 Individual 1 \n", - "2 NaN 2 Individual 2 \n", - "\n", - "[2 rows x 49 columns]" - ] - }, - "execution_count": 3, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "df = pd.read_excel(\"input/POLR1A_Smallwood_2023.xlsx\")\n", - "dft = df.transpose()\n", - "dft.columns = dft.iloc[0] \n", - "dft.drop(dft.index[0], inplace=True)\n", - "dft['person'] = dft.index\n", - "dft['person_id'] = dft['person'].apply(lambda x: f\"Individual {x}\")\n", - "dft.head(2)" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "id": "1e158836-4ee1-468f-9c68-ea653a27cd73", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - "\n", - " \n", - " \n", - " \n", - " \n", - "\n", - "\n", - "
ResultColumns
MappedMacrocephaly; Microcephaly; Craniosynostosis; Ptosis; Hypertelorism; Cleft lip; Cleft palate; Micrognathia; Facial Asymmetry; Hypodontia; Ventriculomegaly; Hypotonia; Infantile spasms; Epilepsy; Developmental delay
UnmappedTest; NM_015425.6; Sex; Onset; Age (at most recent assessment); Deceased; Protein; Inheritance; ACMG classification; ACMG criteria; gnomAD allele count (homozygotes); Ears-low set; Microtia (unilateral or bilateral); Other craniofacial; Brain imaging (CT, MRI, Ultrasound); Structural Brain anomaly; Contractures; Regression; Other neuro; Limb defects; Echocardiogram (Y/N); PFO/ASD; VSD; Other structural heart; IUGR; nan; head circumference (cm); length (cm); weight (kg); Any other features; Abbreviations: U/L unilateral; B/L bilateral; n/a not available; VUS variant of uncertain significance; BP4 lack of segregation in affected members of a family; PM2 absent from controls; PP3 computational evidence supports deleterious effect; PS2 de novo; PP5 reputable source reports variant as pathogenic; PM4 protein length changes due to in frame deletion in a non-repeat region ; SD calculated using CDC growth charts; person; person_id
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mappingcount
0Macrocephaly (HP:0000256) (excluded)13
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mappingcount
0Microcephaly (HP:0000252) (observed)5
1Microcephaly (HP:0000252) (excluded)8
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mappingcount
0Metopic synostosis (HP:0011330) (observed)3
1Metopic synostosis (HP:0011330) (excluded)15
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mappingcount
0Ptosis (HP:0000508) (excluded)13
1Ptosis (HP:0000508) (observed)5
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mappingcount
0Hypertelorism (HP:0000316) (excluded)7
1Hypertelorism (HP:0000316) (observed)9
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mappingcount
0Cleft lip (HP:0410030) (observed)2
1Cleft lip (HP:0410030) (excluded)16
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mappingcount
0Cleft palate (HP:0000175) (observed)5
1Cleft palate (HP:0000175) (excluded)12
2High palate (HP:0000218) (observed)1
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mappingcount
0Micrognathia (HP:0000347) (excluded)11
1Micrognathia (HP:0000347) (observed)7
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mappingcount
0Low-set ears (HP:0000369) (excluded)11
1Low-set ears (HP:0000369) (observed)6
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" - ], - "text/plain": [ - " mapping count\n", - "0 Low-set ears (HP:0000369) (excluded) 11\n", - "1 Low-set ears (HP:0000369) (observed) 6" - ] - }, - "execution_count": 14, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "ears_low_set_d = {'yes': 'Low-set ears',}\n", - "excluded = {'no': 'Low-set ears'}\n", - "ears_low_setMapper = OptionColumnMapper(column_name=\"Ears-low set\", concept_recognizer=hpo_cr, option_d=ears_low_set_d, excluded_d=excluded)\n", - "column_mapper_list.append(ears_low_setMapper)\n", - "ears_low_setMapper.preview_column(dft)" - ] - }, - { - "cell_type": "code", - "execution_count": 15, - "id": "5be0741e-9d2d-4255-acc4-dbe2bcdf76df", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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mappingcount
0Microtia (HP:0008551) (excluded)14
1Microtia (HP:0008551) (observed)4
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" - ], - "text/plain": [ - " mapping count\n", - "0 Microtia (HP:0008551) (excluded) 14\n", - "1 Microtia (HP:0008551) (observed) 4" - ] - }, - "execution_count": 15, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "microtia_d = {\n", - " 'yes': 'Microtia',\n", - " 'small ears': 'Microtia',\n", - " 'U/L': 'Microtia',\n", - " 'unilateral': 'Microtia'}\n", - "excluded = {'no': 'Microtia'}\n", - "microtiaMapper = OptionColumnMapper(column_name=\"Microtia (unilateral or bilateral)\", concept_recognizer=hpo_cr, option_d=microtia_d, excluded_d=excluded)\n", - "column_mapper_list.append(microtiaMapper)\n", - "microtiaMapper.preview_column(dft)" - ] - }, - { - "cell_type": "code", - "execution_count": 16, - "id": "c6359953-61b0-4d5d-b9d6-6c0dd1d77b98", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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mappingcount
0Facial asymmetry (HP:0000324) (excluded)15
1Facial asymmetry (HP:0000324) (observed)3
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" - ], - "text/plain": [ - " mapping count\n", - "0 Facial asymmetry (HP:0000324) (excluded) 15\n", - "1 Facial asymmetry (HP:0000324) (observed) 3" - ] - }, - "execution_count": 16, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "facial_asymmetry_d = {'yes': 'Facial asymmetry'}\n", - "excluded = {'no': 'Facial asymmetry'}\n", - "facial_asymmetryMapper = OptionColumnMapper(column_name=\"Facial Asymmetry\", concept_recognizer=hpo_cr, option_d=facial_asymmetry_d, excluded_d=excluded)\n", - "column_mapper_list.append(facial_asymmetryMapper)\n", - "facial_asymmetryMapper.preview_column(dft)" - ] - }, - { - "cell_type": "code", - "execution_count": 17, - "id": "17bb438e-6b01-486f-ba0e-18e269758524", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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mappingcount
0Hypodontia (HP:0000668) (observed)2
1Hypodontia (HP:0000668) (excluded)5
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" - ], - "text/plain": [ - " mapping count\n", - "0 Hypodontia (HP:0000668) (observed) 2\n", - "1 Hypodontia (HP:0000668) (excluded) 5" - ] - }, - "execution_count": 17, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "hypodontia_d = {'yes': 'Hypodontia',}\n", - "excluded = {'no': 'Hypodontia'}\n", - "hypodontiaMapper = OptionColumnMapper(column_name=\"Hypodontia\", concept_recognizer=hpo_cr, option_d=hypodontia_d, excluded_d=excluded)\n", - "column_mapper_list.append(hypodontiaMapper)\n", - "hypodontiaMapper.preview_column(dft)" - ] - }, - { - "cell_type": "code", - "execution_count": 18, - "id": "da5594f6-7ff6-434c-9053-d6443b14492b", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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mappingcount
0Abnormality of the face (HP:0000271) (excluded)6
1Hearing impairment (HP:0000365) (observed)3
2Vocal cord paralysis (HP:0001605) (observed)2
3Short nose (HP:0003196) (observed)1
4Long palpebral fissure (HP:0000637) (observed)1
5Bilateral choanal atresia (HP:0004502) (observed)1
6Upper eyelid coloboma (HP:0000636) (observed)1
7Calvarial skull defect (HP:0001362) (observed)1
8Broad forehead (HP:0000337) (observed)1
9Thick eyebrow (HP:0000574) (observed)1
10Deeply set eye (HP:0000490) (observed)2
11Duane anomaly (HP:0009921) (observed)1
12Ptosis (HP:0000508) (observed)1
13Mild hearing impairment (HP:0012712) (observed)1
14Epicanthus (HP:0000286) (observed)1
15Depressed nasal bridge (HP:0005280) (observed)1
16Anteverted nares (HP:0000463) (observed)1
17Upslanted palpebral fissure (HP:0000582) (observed)1
18Median pseudocleft lip (HP:0034185) (observed)1
19Tracheobronchomalacia (HP:0002786) (observed)1
20Laryngomalacia (HP:0001601) (observed)1
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" - ], - "text/plain": [ - " mapping count\n", - "0 Abnormality of the face (HP:0000271) (excluded) 6\n", - "1 Hearing impairment (HP:0000365) (observed) 3\n", - "2 Vocal cord paralysis (HP:0001605) (observed) 2\n", - "3 Short nose (HP:0003196) (observed) 1\n", - "4 Long palpebral fissure (HP:0000637) (observed) 1\n", - "5 Bilateral choanal atresia (HP:0004502) (observed) 1\n", - "6 Upper eyelid coloboma (HP:0000636) (observed) 1\n", - "7 Calvarial skull defect (HP:0001362) (observed) 1\n", - "8 Broad forehead (HP:0000337) (observed) 1\n", - "9 Thick eyebrow (HP:0000574) (observed) 1\n", - "10 Deeply set eye (HP:0000490) (observed) 2\n", - "11 Duane anomaly (HP:0009921) (observed) 1\n", - "12 Ptosis (HP:0000508) (observed) 1\n", - "13 Mild hearing impairment (HP:0012712) (observed) 1\n", - "14 Epicanthus (HP:0000286) (observed) 1\n", - "15 Depressed nasal bridge (HP:0005280) (observed) 1\n", - "16 Anteverted nares (HP:0000463) (observed) 1\n", - "17 Upslanted palpebral fissure (HP:0000582) (observed) 1\n", - "18 Median pseudocleft lip (HP:0034185) (observed) 1\n", - "19 Tracheobronchomalacia (HP:0002786) (observed) 1\n", - "20 Laryngomalacia (HP:0001601) (observed) 1" - ] - }, - "execution_count": 18, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "other_craniofacial_d = {\n", - " 'Congenital hearing loss': 'Hearing impairment',\n", - " 'B/L vocal cord paralysis. Tall and wide palpebral fissures. Short nose with upturned tip.': ['Vocal cord paralysis', 'Long palpebral fissure', 'Anteverted nares'],\n", - " 'U/L vocal cord paralysis': 'Vocal cord paralysis',\n", - " 'bilateral choanal atresia': 'Bilateral choanal atresia',\n", - " 'partial acalvaria, bilateral upper eyelid colobomas': ['Upper eyelid coloboma', 'Calvarial skull defect'],\n", - " 'wide forehead, full eyebrows, deep set eyes': ['Broad forehead', 'Thick eyebrow', 'Deeply set eye'],\n", - " 'strabismus (Duane anomaly)': 'Duane anomaly',\n", - " 'L enophthalmia with ptosis. L partial hearing loss': ['Deeply set eye', 'Hearing impairment', 'Ptosis', 'Mild hearing impairment'],\n", - " 'B/l epicanthal folds': 'Epicanthus',\n", - " 'broad, flat nasal bridge, mild ala nasi deficiency': ['Depressed nasal bridge', 'Underdeveloped nasal alae'],\n", - " 'short upturned nose': 'Anteverted nares',\n", - " 'upslanting palpebral fissures': 'Upslanted palpebral fissure',\n", - " 'midline pseudocleft of upper lip': 'Median pseudocleft lip',\n", - " 'airway malacia, hearing loss': ['Tracheobronchomalacia','Hearing impairment'],\n", - " 's/p Md distraction': 'Abnormal mandible morphology', ##NOT SURE OF THE CORRECT TERM\n", - " 'laryngomalacia': 'Laryngomalacia'}\n", - "excluded = {'no': 'Abnormality of the face'}\n", - "other_craniofacialMapper = OptionColumnMapper(column_name=\"Other craniofacial\", concept_recognizer=hpo_cr, option_d=other_craniofacial_d, excluded_d=excluded)\n", - "column_mapper_list.append(other_craniofacialMapper)\n", - "other_craniofacialMapper.preview_column(dft)" - ] - }, - { - "cell_type": "code", - "execution_count": 19, - "id": "38ad6792-6af0-4923-a7be-327e48bd10bc", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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mappingcount
0Brain imaging abnormality (HP:0410263) (excluded)7
1Hydrocephalus (HP:0000238) (observed)1
2Syringomyelia (HP:0003396) (observed)1
3Brain imaging abnormality (HP:0410263) (observed)5
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" - ], - "text/plain": [ - " mapping count\n", - "0 Brain imaging abnormality (HP:0410263) (excluded) 7\n", - "1 Hydrocephalus (HP:0000238) (observed) 1\n", - "2 Syringomyelia (HP:0003396) (observed) 1\n", - "3 Brain imaging abnormality (HP:0410263) (observed) 5" - ] - }, - "execution_count": 19, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "#NOTE: LEAST CONFIDENT OF THIS SECTION\n", - "brain_imaging_d = {\n", - " #'MRI': 'PLACEHOLDER',\n", - " 'MRI: hydrocephaly with junctional stenosis C0-C1 and syringomyelia':['Hydrocephalus', 'Syringomyelia'], \n", - " ##NOT SURE IF HYDROCEPHALUS IS THE CORRECT TERM OR IF A CHILD TERM WOULD BE MORE APPROPRIATE\n", - " 'MRI Punctate restricted diffusion in the right parietal white matter and periatrial white matter representing ischemia or infarctions with minimal petechial hemorrhage':['Brain ischemia', 'Encephalomalacia', 'Cerebral contusions'],\n", - " #'CT': 'PLACEHOLDER',\n", - " 'yes': 'Brain imaging abnormality'}\n", - "excluded = {'no': 'Brain imaging abnormality','normal': 'Brain imaging abnormality',}\n", - "brain_imagingMapper = OptionColumnMapper(column_name=\"Brain imaging (CT, MRI, Ultrasound)\", concept_recognizer=hpo_cr, option_d=brain_imaging_d, excluded_d=excluded)\n", - "column_mapper_list.append(brain_imagingMapper)\n", - "brain_imagingMapper.preview_column(dft)" - ] - }, - { - "cell_type": "code", - "execution_count": 20, - "id": "acaeedb5-e165-4385-a5aa-fc84fcafc1f5", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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mappingcount
0Ventriculomegaly (HP:0002119) (excluded)9
1Ventriculomegaly (HP:0002119) (observed)1
2Dandy-Walker malformation (HP:0001305) (observed)1
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" - ], - "text/plain": [ - " mapping count\n", - "0 Ventriculomegaly (HP:0002119) (excluded) 9\n", - "1 Ventriculomegaly (HP:0002119) (observed) 1\n", - "2 Dandy-Walker malformation (HP:0001305) (observed) 1" - ] - }, - "execution_count": 20, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "ventriculomegaly_d = { \n", - " 'yes': 'Ventriculomegaly',\n", - " 'mild prominent 4th ventricle and infracerebellar space': 'Dandy-Walker malformation',\n", - "}\n", - "excluded = {'no': 'Ventriculomegaly',}\n", - "ventriculomegalyMapper = OptionColumnMapper(column_name=\"Ventriculomegaly\", concept_recognizer=hpo_cr, option_d=ventriculomegaly_d, excluded_d=excluded)\n", - "column_mapper_list.append(ventriculomegalyMapper)\n", - "ventriculomegalyMapper.preview_column(dft)" - ] - }, - { - "cell_type": "code", - "execution_count": 21, - "id": "234c3c9c-8a33-4e89-bb8c-0fbdc21e5a8a", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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mappingcount
0Abnormal brain morphology (HP:0012443) (excluded)8
1Cavum septum pellucidum (HP:0002389) (observed)1
2Aqueductal stenosis (HP:0002410) (observed)1
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" - ], - "text/plain": [ - " mapping count\n", - "0 Abnormal brain morphology (HP:0012443) (excluded) 8\n", - "1 Cavum septum pellucidum (HP:0002389) (observed) 1\n", - "2 Aqueductal stenosis (HP:0002410) (observed) 1" - ] - }, - "execution_count": 21, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "structural_brain_anomaly_d = { #'nan': 'PLACEHOLDER',\n", - " 'cavum septum pellucidum': 'Cavum septum pellucidum',\n", - " 'aqueductal stenosis': 'Aqueductal stenosis'}\n", - "excluded = { 'no': 'Abnormal brain morphology',}\n", - "structural_brain_anomalyMapper = OptionColumnMapper(column_name=\"Structural Brain anomaly\", concept_recognizer=hpo_cr, option_d=structural_brain_anomaly_d, excluded_d=excluded)\n", - "column_mapper_list.append(structural_brain_anomalyMapper)\n", - "structural_brain_anomalyMapper.preview_column(dft)" - ] - }, - { - "cell_type": "code", - "execution_count": 22, - "id": "110d0a40-5107-4133-9c5c-d4de2714f298", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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mappingcount
0Hypotonia (HP:0001252) (excluded)7
1Hypotonia (HP:0001252) (observed)10
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" - ], - "text/plain": [ - " mapping count\n", - "0 Hypotonia (HP:0001252) (excluded) 7\n", - "1 Hypotonia (HP:0001252) (observed) 10" - ] - }, - "execution_count": 22, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "hypotonia_d = {'yes': 'Hypotonia'}\n", - "excluded = {'no': 'Hypotonia',}\n", - "hypotoniaMapper = OptionColumnMapper(column_name=\"Hypotonia\", concept_recognizer=hpo_cr, option_d=hypotonia_d, excluded_d=excluded)\n", - "column_mapper_list.append(hypotoniaMapper)\n", - "hypotoniaMapper.preview_column(dft)" - ] - }, - { - "cell_type": "code", - "execution_count": 23, - "id": "2da06742-62ef-4b56-ab71-37be8d1308f0", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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mappingcount
0Joint contracture (HP:0034392) (excluded)14
1Joint contracture (HP:0034392) (observed)2
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" - ], - "text/plain": [ - " mapping count\n", - "0 Joint contracture (HP:0034392) (excluded) 14\n", - "1 Joint contracture (HP:0034392) (observed) 2" - ] - }, - "execution_count": 23, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "contractures_d = {'yes': 'Joint contracture'}\n", - "excluded = {'no': 'Joint contracture',}\n", - "contracturesMapper = OptionColumnMapper(column_name=\"Contractures\", concept_recognizer=hpo_cr, option_d=contractures_d, excluded_d=excluded)\n", - "column_mapper_list.append(contracturesMapper)\n", - "contracturesMapper.preview_column(dft)" - ] - }, - { - "cell_type": "code", - "execution_count": 24, - "id": "3c22a815-df58-4c86-84bd-b89705e81bc9", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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mappingcount
0Infantile spasms (HP:0012469) (excluded)17
1Infantile spasms (HP:0012469) (observed)1
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" - ], - "text/plain": [ - " mapping count\n", - "0 Infantile spasms (HP:0012469) (excluded) 17\n", - "1 Infantile spasms (HP:0012469) (observed) 1" - ] - }, - "execution_count": 24, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "infantile_spasms_d = {'yes': 'Infantile spasms'}\n", - "excluded = {'no': 'Infantile spasms',}\n", - "infantile_spasmsMapper = OptionColumnMapper(column_name=\"Infantile spasms\", concept_recognizer=hpo_cr, option_d=infantile_spasms_d, excluded_d=excluded)\n", - "column_mapper_list.append(infantile_spasmsMapper)\n", - "infantile_spasmsMapper.preview_column(dft)" - ] - }, - { - "cell_type": "code", - "execution_count": 25, - "id": "7ed542a4-d15a-49c7-b78c-c0ec42e7dba0", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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mappingcount
0Seizure (HP:0001250) (excluded)11
1Seizure (HP:0001250) (observed)6
2Epileptic encephalopathy (HP:0200134) (observed)1
3Myoclonus (HP:0001336) (observed)1
4Atonic seizure (HP:0010819) (observed)1
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" - ], - "text/plain": [ - " mapping count\n", - "0 Seizure (HP:0001250) (excluded) 11\n", - "1 Seizure (HP:0001250) (observed) 6\n", - "2 Epileptic encephalopathy (HP:0200134) (observed) 1\n", - "3 Myoclonus (HP:0001336) (observed) 1\n", - "4 Atonic seizure (HP:0010819) (observed) 1" - ] - }, - "execution_count": 25, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "epilepsy_d = {\n", - " 'yes': 'Seizure',\n", - " 'yes, epileptic encephalopathy, myoclonia, atonic seizures': ['Epileptic encephalopathy', 'Myoclonus', 'Atonic seizure'],\n", - "}\n", - "excluded = {'no': 'Seizure',}\n", - "epilepsyMapper = OptionColumnMapper(column_name=\"Epilepsy\", concept_recognizer=hpo_cr, option_d=epilepsy_d, excluded_d=excluded)\n", - "column_mapper_list.append(epilepsyMapper)\n", - "epilepsyMapper.preview_column(dft)" - ] - }, - { - "cell_type": "code", - "execution_count": 26, - "id": "e6fe3413-6466-4d82-b894-be73f427369b", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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mappingcount
0Neurodevelopmental delay (HP:0012758) (excluded)6
1Neurodevelopmental delay (HP:0012758) (observed)8
2Seizure (HP:0001250) (observed)1
3Motor delay (HP:0001270) (observed)1
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" - ], - "text/plain": [ - " mapping count\n", - "0 Neurodevelopmental delay (HP:0012758) (excluded) 6\n", - "1 Neurodevelopmental delay (HP:0012758) (observed) 8\n", - "2 Seizure (HP:0001250) (observed) 1\n", - "3 Motor delay (HP:0001270) (observed) 1" - ] - }, - "execution_count": 26, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "developmental_delay_d = {\n", - " 'yes': 'Neurodevelopmental delay',\n", - " 'slight motor': 'Motor delay'}\n", - "excluded = {'no': 'Neurodevelopmental delay',}\n", - "developmental_delayMapper = OptionColumnMapper(column_name=\"Developmental delay\", concept_recognizer=hpo_cr, option_d=developmental_delay_d, excluded_d=excluded)\n", - "column_mapper_list.append(developmental_delayMapper)\n", - "developmental_delayMapper.preview_column(dft)" - ] - }, - { - "cell_type": "code", - "execution_count": 27, - "id": "fe55a058-8f2a-4bc9-8a6f-efd457d4a41f", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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mappingcount
0Developmental regression (HP:0002376) (excluded)15
1Developmental regression (HP:0002376) (observed)1
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" - ], - "text/plain": [ - " mapping count\n", - "0 Developmental regression (HP:0002376) (excluded) 15\n", - "1 Developmental regression (HP:0002376) (observed) 1" - ] - }, - "execution_count": 27, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "regression_d = {'yes after onset epilepsy': 'Developmental regression'}\n", - "excluded = {'no': 'Developmental regression',}\n", - "regressionMapper = OptionColumnMapper(column_name=\"Regression\", concept_recognizer=hpo_cr, option_d=regression_d, excluded_d=excluded)\n", - "column_mapper_list.append(regressionMapper)\n", - "regressionMapper.preview_column(dft)" - ] - }, - { - "cell_type": "code", - "execution_count": 28, - "id": "e2fca12f-66e8-4e3d-8dde-e9a1cc0aa340", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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mappingcount
0Abnormality of coordination (HP:0011443) (excluded)15
1Abnormality of coordination (HP:0011443) (observed)1
2Lower limb spasticity (HP:0002061) (observed)1
3Laryngeal dystonia (HP:0012049) (observed)1
4Mild global developmental delay (HP:0011342) (observed)1
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" - ], - "text/plain": [ - " mapping count\n", - "0 Abnormality of coordination (HP:0011443) (excluded) 15\n", - "1 Abnormality of coordination (HP:0011443) (observed) 1\n", - "2 Lower limb spasticity (HP:0002061) (observed) 1\n", - "3 Laryngeal dystonia (HP:0012049) (observed) 1\n", - "4 Mild global developmental delay (HP:0011342) (observed) 1" - ] - }, - "execution_count": 28, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "other_neuro_d = {\n", - " 'possible ataxia': 'Abnormality of coordination',\n", - " 'leg spasticity, spastic dystonia, mild learning difficulties': ['Lower limb spasticity', 'Laryngeal dystonia', 'Mild global developmental delay'], }\n", - "excluded = {'no': 'Abnormality of coordination',}\n", - "other_neuroMapper = OptionColumnMapper(column_name=\"Other neuro\", concept_recognizer=hpo_cr, option_d=other_neuro_d, excluded_d=excluded)\n", - "column_mapper_list.append(other_neuroMapper)\n", - "other_neuroMapper.preview_column(dft)" - ] - }, - { - "cell_type": "code", - "execution_count": 29, - "id": "77b2e513-fca3-41c3-9129-73e43cfd056a", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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mappingcount
0Abnormality of limbs (HP:0040064) (excluded)12
1Abnormality of limbs (HP:0040064) (observed)6
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" - ], - "text/plain": [ - " mapping count\n", - "0 Abnormality of limbs (HP:0040064) (excluded) 12\n", - "1 Abnormality of limbs (HP:0040064) (observed) 6" - ] - }, - "execution_count": 29, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "limb_defects_d = {'yes': 'Abnormality of limbs'}\n", - "excluded = {'no': 'Abnormality of limbs',}\n", - "limb_defectsMapper = OptionColumnMapper(column_name=\"Limb defects\", concept_recognizer=hpo_cr, option_d=limb_defects_d, excluded_d=excluded)\n", - "column_mapper_list.append(limb_defectsMapper)\n", - "limb_defectsMapper.preview_column(dft)" - ] - }, - { - "cell_type": "code", - "execution_count": 30, - "id": "6b24f6b2-025a-4dab-9381-a04569144826", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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mappingcount
0Patent foramen ovale (HP:0001655) (excluded)10
1Atrial septal defect (HP:0001631) (excluded)10
2Patent foramen ovale (HP:0001655) (observed)4
3Atrial septal defect (HP:0001631) (observed)3
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" - ], - "text/plain": [ - " mapping count\n", - "0 Patent foramen ovale (HP:0001655) (excluded) 10\n", - "1 Atrial septal defect (HP:0001631) (excluded) 10\n", - "2 Patent foramen ovale (HP:0001655) (observed) 4\n", - "3 Atrial septal defect (HP:0001631) (observed) 3" - ] - }, - "execution_count": 30, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "pfo_asd_d = {\n", - " 'yes': ['Patent foramen ovale', 'Atrial septal defect'],\n", - " 'PFO': 'Patent foramen ovale'}\n", - "excluded = {'no': ['Patent foramen ovale', 'Atrial septal defect'],}\n", - "pfo_asdMapper = OptionColumnMapper(column_name=\"PFO/ASD\", concept_recognizer=hpo_cr, option_d=pfo_asd_d, excluded_d=excluded)\n", - "column_mapper_list.append(pfo_asdMapper)\n", - "pfo_asdMapper.preview_column(dft)" - ] - }, - { - "cell_type": "code", - "execution_count": 31, - "id": "8a743749-de88-4f47-8f58-2167b34afef8", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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mappingcount
0Ventricular septal defect (HP:0001629) (excluded)11
1Ventricular septal defect (HP:0001629) (observed)3
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" - ], - "text/plain": [ - " mapping count\n", - "0 Ventricular septal defect (HP:0001629) (excluded) 11\n", - "1 Ventricular septal defect (HP:0001629) (observed) 3" - ] - }, - "execution_count": 31, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "vsd_d = {'yes': 'Ventricular septal defect'}\n", - "excluded = {'no': 'Ventricular septal defect',}\n", - "vsdMapper = OptionColumnMapper(column_name=\"VSD\", concept_recognizer=hpo_cr, option_d=vsd_d, excluded_d=excluded)\n", - "column_mapper_list.append(vsdMapper)\n", - "vsdMapper.preview_column(dft)" - ] - }, - { - "cell_type": "code", - "execution_count": 32, - "id": "cde28eec-772a-498b-807c-2c73e2a69f6a", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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mappingcount
0Abnormal heart morphology (HP:0001627) (excluded)10
1Biventricular hypertrophy (HP:0200128) (observed)1
2Anomalous origin of right coronary artery from the pulmonary artery (HP:0011639) (observed)1
3Pulmonary artery stenosis (HP:0004415) (observed)1
4Bicuspid aortic valve (HP:0001647) (observed)1
5Aortic aneurysm (HP:0004942) (observed)1
6Pulmonary artery aneurysm (HP:0004937) (observed)1
7Partial atrioventricular canal defect (HP:0011577) (observed)1
8Cleft anterior mitral valve leaflet (HP:0011569) (observed)1
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" - ], - "text/plain": [ - " mapping \\\n", - "0 Abnormal heart morphology (HP:0001627) (excluded) \n", - "1 Biventricular hypertrophy (HP:0200128) (observed) \n", - "2 Anomalous origin of right coronary artery from the pulmonary artery (HP:0011639) (observed) \n", - "3 Pulmonary artery stenosis (HP:0004415) (observed) \n", - "4 Bicuspid aortic valve (HP:0001647) (observed) \n", - "5 Aortic aneurysm (HP:0004942) (observed) \n", - "6 Pulmonary artery aneurysm (HP:0004937) (observed) \n", - "7 Partial atrioventricular canal defect (HP:0011577) (observed) \n", - "8 Cleft anterior mitral valve leaflet (HP:0011569) (observed) \n", - "\n", - " count \n", - "0 10 \n", - "1 1 \n", - "2 1 \n", - "3 1 \n", - "4 1 \n", - "5 1 \n", - "6 1 \n", - "7 1 \n", - "8 1 " - ] - }, - "execution_count": 32, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "other_structural_heart_d = {\n", - " 'Biventricular hypertrophy': 'Biventricular hypertrophy',\n", - " 'anomalous origin of right coronary artery': 'Anomalous origin of right coronary artery from the pulmonary artery',\n", - " 'pulmonary artery stenosis': 'Pulmonary artery stenosis',\n", - " 'yes (see text)': ['Bicuspid aortic valve', 'Aortic aneurysm', 'Pulmonary artery aneurysm', 'Partial atrioventricular canal defect', 'Cleft anterior mitral valve leaflet'] }\n", - "excluded = {'no': 'Abnormal heart morphology',}\n", - "other_structural_heartMapper = OptionColumnMapper(column_name=\"Other structural heart\", concept_recognizer=hpo_cr, option_d=other_structural_heart_d, excluded_d=excluded)\n", - "column_mapper_list.append(other_structural_heartMapper)\n", - "other_structural_heartMapper.preview_column(dft)" - ] - }, - { - "cell_type": "code", - "execution_count": 33, - "id": "c9474eff-a8bd-4050-bd23-0dfbaa730e2b", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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mappingcount
0Intrauterine growth retardation (HP:0001511) (excluded)11
1Intrauterine growth retardation (HP:0001511) (observed)3
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" - ], - "text/plain": [ - " mapping count\n", - "0 Intrauterine growth retardation (HP:0001511) (excluded) 11\n", - "1 Intrauterine growth retardation (HP:0001511) (observed) 3" - ] - }, - "execution_count": 33, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "iugr_d = { 'yes': 'Intrauterine growth retardation'}\n", - "excluded = {'no': 'Intrauterine growth retardation',}\n", - "iugrMapper = OptionColumnMapper(column_name=\"IUGR\", concept_recognizer=hpo_cr, option_d=iugr_d, excluded_d=excluded)\n", - "column_mapper_list.append(iugrMapper)\n", - "iugrMapper.preview_column(dft)" - ] - }, - { - "cell_type": "code", - "execution_count": 34, - "id": "2f30afe4-c4ac-46a4-8768-1a46af647153", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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mappingcount
0Nevus (HP:0003764) (observed)1
1Clinodactyly of the 5th finger (HP:0004209) (observed)1
2Single transverse palmar crease (HP:0000954) (observed)1
3Hypoplastic toenails (HP:0001800) (observed)1
4Intellectual disability (HP:0001249) (excluded)1
5Bilateral cryptorchidism (HP:0008689) (observed)1
6Aspiration (HP:0002835) (observed)1
7Dysphagia (HP:0002015) (observed)1
8Hydronephrosis (HP:0000126) (observed)1
9Recurrent otitis media (HP:0000403) (observed)1
10Diaphragmatic eventration (HP:0009110) (observed)1
11Hearing impairment (HP:0000365) (observed)2
12Inguinal hernia (HP:0000023) (observed)1
13Cryptorchidism (HP:0000028) (observed)1
14Failure to thrive (HP:0001508) (observed)1
15Gastrostomy tube feeding in infancy (HP:0011471) (observed)2
16Scoliosis (HP:0002650) (observed)1
17Pterygium (HP:0001059) (observed)1
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" - ], - "text/plain": [ - " mapping count\n", - "0 Nevus (HP:0003764) (observed) 1\n", - "1 Clinodactyly of the 5th finger (HP:0004209) (observed) 1\n", - "2 Single transverse palmar crease (HP:0000954) (observed) 1\n", - "3 Hypoplastic toenails (HP:0001800) (observed) 1\n", - "4 Intellectual disability (HP:0001249) (excluded) 1\n", - "5 Bilateral cryptorchidism (HP:0008689) (observed) 1\n", - "6 Aspiration (HP:0002835) (observed) 1\n", - "7 Dysphagia (HP:0002015) (observed) 1\n", - "8 Hydronephrosis (HP:0000126) (observed) 1\n", - "9 Recurrent otitis media (HP:0000403) (observed) 1\n", - "10 Diaphragmatic eventration (HP:0009110) (observed) 1\n", - "11 Hearing impairment (HP:0000365) (observed) 2\n", - "12 Inguinal hernia (HP:0000023) (observed) 1\n", - "13 Cryptorchidism (HP:0000028) (observed) 1\n", - "14 Failure to thrive (HP:0001508) (observed) 1\n", - "15 Gastrostomy tube feeding in infancy (HP:0011471) (observed) 2\n", - "16 Scoliosis (HP:0002650) (observed) 1\n", - "17 Pterygium (HP:0001059) (observed) 1" - ] - }, - "execution_count": 34, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "any_other_features_d = { #'nan': 'PLACEHOLDER',\n", - " 'Large scalp congenital naevus. Persistently raised lactates. Muscle and liver biopsies consistent with combined respiratory chain enzyme defect affecting primarily complexes I and IV in muscle and borderline IV in the liver.': ['Nevus', 'Increased circulating lactate concentration', 'Muscle abnormality related to mitochondrial dysfunction'],\n", - " 'fifth finger clinodactyly, single palmar crease, mild toenail hypoplasia': ['Clinodactyly of the 5th finger', 'Single transverse palmar crease', 'Hypoplastic toenails'],\n", - " 'bilateral cryptorchidism,dysphagia and aspiration requiring GJ dependence, OSA, right hydronephrosis': ['Bilateral cryptorchidism', 'Dysphagia', 'Aspiration', 'Gastrojejunal tube feeding in infancy', 'Obstructive sleep apnea', 'Hydronephrosis'], \n", - " 'recurrent otitis media': 'Recurrent otitis media',\n", - " 'L diaphragmatic eventration. L partial hearing loss': ['Diaphragmatic eventration', 'Hearing impairment'],\n", - " 'R inguinal hernia': 'Inguinal hernia',\n", - " 'L cryptorchidism': 'Cryptorchidism',\n", - " 'FTT requiring G tube placemenet': ['Failure to thrive', 'Gastrostomy tube feeding in infancy'],\n", - " 'G-tube for feeding.': 'Gastrostomy tube feeding in infancy',\n", - " 'G-tube': 'Gastrostomy tube feeding in infancy',\n", - " 'Scoliosis': 'Scoliosis',\n", - " 'Eye skin growth': 'Pterygium', \n", - "'hearing loss (b/l)': 'Hearing impairment'}\n", - "excluded = {'no intellectual disability': 'Intellectual disability'}\n", - "any_other_featuresMapper = OptionColumnMapper(column_name=\"Any other features\", concept_recognizer=hpo_cr, option_d=any_other_features_d, excluded_d=excluded)\n", - "column_mapper_list.append(any_other_featuresMapper)\n", - "any_other_featuresMapper.preview_column(dft)" - ] - }, - { - "cell_type": "code", - "execution_count": 35, - "id": "58ebe63b-f700-4ffc-ae4f-179100012bde", - "metadata": {}, - "outputs": [], - "source": [ - "def correct_hgvs(hgvs):\n", - " if hgvs == \"c.3649delC\":\n", - " return \"c.3649del\"\n", - " elif hgvs == \"c.3988_3990delGAG\":\n", - " return \"c.3988_3990del\"\n", - " else:\n", - " return hgvs\n", - "\n", - "dft[\"allele_1\"] = dft['NM_015425.6'].apply(lambda x: correct_hgvs(x))" - ] - }, - { - "cell_type": "code", - "execution_count": 36, - "id": "a0474e49-b597-4b60-b541-d559ee6e9a6f", - "metadata": {}, - "outputs": [], - "source": [ - "POLR1C_transcript = \"NM_015425.6\"\n", - "vman = VariantManager(df=dft, \n", - " individual_column_name=\"person_id\", \n", - " gene_symbol=\"POLR1C\",\n", - " allele_1_column_name=\"allele_1\", \n", - " transcript=POLR1C_transcript)" - ] - }, - { - "cell_type": "code", - "execution_count": 37, - "id": "b3e5aa96-2a05-4d93-8463-80a47017e7b5", - "metadata": {}, - "outputs": [], - "source": [ - "sexMapper = SexColumnMapper(column_name='Sex',male_symbol=\"male\", female_symbol=\"female\")\n", - "#sexMapper.preview_column(dft)\n", - "onsetMapper = AgeColumnMapper.hpo_onset(column_name='Onset')\n", - "#onsetMapper.preview_column(dft)\n", - "encounterMapper = AgeColumnMapper.iso8601(column_name='Age (at most recent assessment)')\n", - "#encounterMapper.preview_column(dft)" - ] - }, - { - "cell_type": "code", - "execution_count": 38, - "id": "6b25d772-879b-4ffe-bab8-7cfd76d488cf", - "metadata": {}, - "outputs": [], - "source": [ - "AFDCIN = Disease(disease_id=\"OMIM:616462\", disease_label=\"Acrofacial dysostosis, Cincinnati type\")\n", - "varMapper = VariantColumnMapper(variant_d=vman.get_variant_d(),\n", - " variant_column_name=\"allele_1\", \n", - " default_genotype=\"heterozygous\")" - ] - }, - { - "cell_type": "code", - "execution_count": 39, - "id": "016e89bb-b5fc-4f22-a412-c432f6fcb7bf", - "metadata": {}, - "outputs": [], - "source": [ - "encoder = CohortEncoder(df=dft, \n", - " hpo_cr=hpo_cr, \n", - " column_mapper_list=column_mapper_list, \n", - " individual_column_name=\"person_id\", \n", - " age_of_onset_mapper=onsetMapper, \n", - " age_at_last_encounter_mapper=encounterMapper,\n", - " sexmapper=sexMapper,\n", - " variant_mapper=varMapper,\n", - " metadata=metadata)\n", - "encoder.set_disease(AFDCIN)" - ] - }, - { - "cell_type": "code", - "execution_count": 40, - "id": "175fa419-1eed-4cae-b94c-0749344b6893", - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Could not parse the following as ISO8601 ages: na (n=1)\n", - "Could not parse the following as ISO8601 ages: adult (n=1)\n" - ] - } - ], - "source": [ - "individuals = encoder.get_individuals()" - ] - }, - { - "cell_type": "code", - "execution_count": 41, - "id": "e2075191-5e6b-4bc7-9100-52bf8f73d497", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "

Cohort validation

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Errors found with 18 of 18 phenopackets.

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Error counts
LevelError categoryCount
ERRORCONFLICT2
WARNINGREDUNDANT65
INFORMATIONNOT_MEASURED43
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A total of 310 issues were fixed and no individual was removed from the cohort.

" - ], - "text/plain": [ - "" - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "cvalidator = CohortValidator(cohort=individuals, ontology=hpo_ontology, min_hpo=1, allelic_requirement=AllelicRequirement.MONO_ALLELIC)\n", - "qc = QcVisualizer(cohort_validator=cvalidator)\n", - "display(HTML(qc.to_summary_html()))" - ] - }, - { - "cell_type": "code", - "execution_count": 42, - "id": "7309bb65-6abe-4237-bd83-701fb4bc5e9b", - "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", - "
18 phenopackets - PMID:37075751 (n=18)
IndividualDiseaseGenotypePhenotypic features
Individual 1 (MALE; P3M)Acrofacial dysostosis, Cincinnati type (OMIM:616462)NM_203290.4:c.176A>T (heterozygous)Cleft palate (HP:0000175); Metopic synostosis (HP:0011330); Cleft lip (HP:0410030); excluded: Abnormality of limbs (HP:0040064); excluded: Patent foramen ovale (HP:0001655); excluded: Microtia (HP:0008551); excluded: Low-set ears (HP:0000369); excluded: Hypotonia (HP:0001252); excluded: Hypertelorism (HP:0000316); excluded: Ptosis (HP:0000508); excluded: Ventricular septal defect (HP:0001629); excluded: Brain imaging abnormality (HP:0410263); excluded: Micrognathia (HP:0000347); excluded: Intrauterine growth retardation (HP:0001511); excluded: Joint contracture (HP:0034392); excluded: Global developmental delay (HP:0001263); excluded: Developmental regression (HP:0002376); excluded: Facial asymmetry (HP:0000324); excluded: Abnormality of coordination (HP:0011443); excluded: Infantile spasms (HP:0012469)
Individual 2 (MALE; P5Y)Acrofacial dysostosis, Cincinnati type (OMIM:616462)NM_203290.4:c.176A>T (heterozygous)Cleft palate (HP:0000175); Metopic synostosis (HP:0011330); Cleft lip (HP:0410030); excluded: Abnormality of limbs (HP:0040064); excluded: Patent foramen ovale (HP:0001655); excluded: Microtia (HP:0008551); excluded: Low-set ears (HP:0000369); excluded: Hypotonia (HP:0001252); excluded: Hypertelorism (HP:0000316); excluded: Ptosis (HP:0000508); excluded: Ventricular septal defect (HP:0001629); excluded: Brain imaging abnormality (HP:0410263); excluded: Micrognathia (HP:0000347); excluded: Intrauterine growth retardation (HP:0001511); excluded: Joint contracture (HP:0034392); excluded: Global developmental delay (HP:0001263); excluded: Developmental regression (HP:0002376); excluded: Facial asymmetry (HP:0000324); excluded: Abnormality of coordination (HP:0011443); excluded: Infantile spasms (HP:0012469)
Individual 3 (FEMALE; P1M26D)Acrofacial dysostosis, Cincinnati type (OMIM:616462)NM_015425.6:c.190del (heterozygous)Global developmental delay (HP:0001263); Hearing impairment (HP:0000365); Biventricular hypertrophy (HP:0200128); Nevus (HP:0003764); Microcephaly (HP:0000252); Hypotonia (HP:0001252); excluded: Abnormality of limbs (HP:0040064); excluded: Patent foramen ovale (HP:0001655); excluded: Microtia (HP:0008551); excluded: Low-set ears (HP:0000369); excluded: Macrocephaly (HP:0000256); excluded: Craniosynostosis (HP:0001363); excluded: Cleft lip (HP:0410030); excluded: Hypertelorism (HP:0000316); excluded: Ptosis (HP:0000508); excluded: Ventricular septal defect (HP:0001629); excluded: Micrognathia (HP:0000347); excluded: Intrauterine growth retardation (HP:0001511); excluded: Cleft palate (HP:0000175); excluded: Joint contracture (HP:0034392); excluded: Metopic synostosis (HP:0011330); excluded: Developmental regression (HP:0002376); excluded: Ventriculomegaly (HP:0002119); excluded: Facial asymmetry (HP:0000324); excluded: Abnormality of coordination (HP:0011443); excluded: Infantile spasms (HP:0012469)
Individual 4 (MALE; P11M)Acrofacial dysostosis, Cincinnati type (OMIM:616462)NM_015425.6:c.1178G>A (heterozygous)Single transverse palmar crease (HP:0000954); Low-set ears (HP:0000369); Long palpebral fissure (HP:0000637); Anomalous origin of right coronary artery from the pulmonary artery (HP:0011639); Vocal cord paralysis (HP:0001605); Hypoplastic toenails (HP:0001800); Clinodactyly of the 5th finger (HP:0004209); Short nose (HP:0003196); Hypotonia (HP:0001252); excluded: Patent foramen ovale (HP:0001655); excluded: Microtia (HP:0008551); excluded: Microcephaly (HP:0000252); excluded: Macrocephaly (HP:0000256); excluded: Craniosynostosis (HP:0001363); excluded: Cleft lip (HP:0410030); excluded: Hypertelorism (HP:0000316); excluded: Ptosis (HP:0000508); excluded: Ventricular septal defect (HP:0001629); excluded: Brain imaging abnormality (HP:0410263); excluded: Micrognathia (HP:0000347); excluded: Intrauterine growth retardation (HP:0001511); excluded: Cleft palate (HP:0000175); excluded: Joint contracture (HP:0034392); excluded: Metopic synostosis (HP:0011330); excluded: Facial asymmetry (HP:0000324); excluded: Abnormality of coordination (HP:0011443); excluded: Infantile spasms (HP:0012469)
Individual 5 (FEMALE; n/a)Acrofacial dysostosis, Cincinnati type (OMIM:616462)NM_015425.6:c.1178G>A (heterozygous)Ptosis (HP:0000508); Ventricular septal defect (HP:0001629); Vocal cord paralysis (HP:0001605); Hypotonia (HP:0001252); excluded: Craniosynostosis (HP:0001363); excluded: Cleft lip (HP:0410030); excluded: Micrognathia (HP:0000347); excluded: Hypertelorism (HP:0000316); excluded: Abnormality of limbs (HP:0040064); excluded: Metopic synostosis (HP:0011330); excluded: Joint contracture (HP:0034392); excluded: Patent foramen ovale (HP:0001655); excluded: Facial asymmetry (HP:0000324); excluded: Microtia (HP:0008551); excluded: Low-set ears (HP:0000369); excluded: Brain imaging abnormality (HP:0410263); excluded: Cleft palate (HP:0000175); excluded: Infantile spasms (HP:0012469)
Individual 6 (FEMALE; P10Y4M)Acrofacial dysostosis, Cincinnati type (OMIM:616462)NM_015425.6:c.1442G>A (heterozygous)Hypodontia (HP:0000668); Hydrocephalus (HP:0000238); Hypertelorism (HP:0000316); Cleft palate (HP:0000175); Low-set ears (HP:0000369); Facial asymmetry (HP:0000324); Ventriculomegaly (HP:0002119); Bilateral choanal atresia (HP:0004502); Micrognathia (HP:0000347); Syringomyelia (HP:0003396); Intrauterine growth retardation (HP:0001511); excluded: Abnormality of limbs (HP:0040064); excluded: Patent foramen ovale (HP:0001655); excluded: Microtia (HP:0008551); excluded: Microcephaly (HP:0000252); excluded: Macrocephaly (HP:0000256); excluded: Craniosynostosis (HP:0001363); excluded: Hypotonia (HP:0001252); excluded: Cleft lip (HP:0410030); excluded: Ptosis (HP:0000508); excluded: Ventricular septal defect (HP:0001629); excluded: Joint contracture (HP:0034392); excluded: Global developmental delay (HP:0001263); excluded: Intellectual disability (HP:0001249); excluded: Metopic synostosis (HP:0011330); excluded: Developmental regression (HP:0002376); excluded: Abnormality of coordination (HP:0011443); excluded: Infantile spasms (HP:0012469)
Individual 7 (FEMALE; P44Y)Acrofacial dysostosis, Cincinnati type (OMIM:616462)NM_015425.6:c.1442G>A (heterozygous)Cleft palate (HP:0000175); Micrognathia (HP:0000347); Low-set ears (HP:0000369); Hypertelorism (HP:0000316); excluded: Abnormality of limbs (HP:0040064); excluded: Patent foramen ovale (HP:0001655); excluded: Microtia (HP:0008551); excluded: Microcephaly (HP:0000252); excluded: Macrocephaly (HP:0000256); excluded: Craniosynostosis (HP:0001363); excluded: Hypotonia (HP:0001252); excluded: Cleft lip (HP:0410030); excluded: Ptosis (HP:0000508); excluded: Ventricular septal defect (HP:0001629); excluded: Brain imaging abnormality (HP:0410263); excluded: Joint contracture (HP:0034392); excluded: Global developmental delay (HP:0001263); excluded: Metopic synostosis (HP:0011330); excluded: Hypodontia (HP:0000668); excluded: Developmental regression (HP:0002376); excluded: Ventriculomegaly (HP:0002119); excluded: Facial asymmetry (HP:0000324); excluded: Abnormality of coordination (HP:0011443); excluded: Infantile spasms (HP:0012469)
Individual 8 (MALE; P2Y)Acrofacial dysostosis, Cincinnati type (OMIM:616462)NM_015425.6:c.1488G>T (heterozygous)Calvarial skull defect (HP:0001362); Global developmental delay (HP:0001263); Microtia (HP:0008551); Seizure (HP:0001250); Patent foramen ovale (HP:0001655); Hypertelorism (HP:0000316); Hydronephrosis (HP:0000126); Dysphagia (HP:0002015); Low-set ears (HP:0000369); Abnormality of limbs (HP:0040064); Upper eyelid coloboma (HP:0000636); Micrognathia (HP:0000347); Bilateral cryptorchidism (HP:0008689); Microcephaly (HP:0000252); Aspiration (HP:0002835); Hypotonia (HP:0001252); excluded: Craniosynostosis (HP:0001363); excluded: Cleft lip (HP:0410030); excluded: Metopic synostosis (HP:0011330); excluded: Intrauterine growth retardation (HP:0001511); excluded: Ptosis (HP:0000508); excluded: Joint contracture (HP:0034392); excluded: Ventricular septal defect (HP:0001629); excluded: Developmental regression (HP:0002376); excluded: Ventriculomegaly (HP:0002119); excluded: Facial asymmetry (HP:0000324); excluded: Macrocephaly (HP:0000256); excluded: Cleft palate (HP:0000175); excluded: Abnormality of coordination (HP:0011443); excluded: Infantile spasms (HP:0012469)
Individual 9 (MALE; P4Y)Acrofacial dysostosis, Cincinnati type (OMIM:616462)NM_015425.6:c.2583_2586del (heterozygous)Broad forehead (HP:0000337); Microtia (HP:0008551); Hypertelorism (HP:0000316); Deeply set eye (HP:0000490); Developmental regression (HP:0002376); Abnormality of coordination (HP:0011443); Dandy-Walker malformation (HP:0001305); Myoclonus (HP:0001336); Epileptic encephalopathy (HP:0200134); Atonic seizure (HP:0010819); Thick eyebrow (HP:0000574); excluded: Craniosynostosis (HP:0001363); excluded: Hypotonia (HP:0001252); excluded: Cleft lip (HP:0410030); excluded: Micrognathia (HP:0000347); excluded: Low-set ears (HP:0000369); excluded: Abnormality of limbs (HP:0040064); excluded: Metopic synostosis (HP:0011330); excluded: Intrauterine growth retardation (HP:0001511); excluded: Hypodontia (HP:0000668); excluded: Ptosis (HP:0000508); excluded: Joint contracture (HP:0034392); excluded: Facial asymmetry (HP:0000324); excluded: Microcephaly (HP:0000252); excluded: Macrocephaly (HP:0000256); excluded: Cleft palate (HP:0000175); excluded: Infantile spasms (HP:0012469)
Individual 10 (FEMALE; P7Y7M)Acrofacial dysostosis, Cincinnati type (OMIM:616462)NM_015425.6:c.3649del (heterozygous)Hypodontia (HP:0000668); Duane anomaly (HP:0009921); Ptosis (HP:0000508); Recurrent otitis media (HP:0000403); Hypertelorism (HP:0000316); Cleft palate (HP:0000175); Abnormality of limbs (HP:0040064); Micrognathia (HP:0000347); excluded: Patent foramen ovale (HP:0001655); excluded: Microtia (HP:0008551); excluded: Low-set ears (HP:0000369); excluded: Microcephaly (HP:0000252); excluded: Macrocephaly (HP:0000256); excluded: Craniosynostosis (HP:0001363); excluded: Hypotonia (HP:0001252); excluded: Cleft lip (HP:0410030); excluded: Ventricular septal defect (HP:0001629); excluded: Intrauterine growth retardation (HP:0001511); excluded: Joint contracture (HP:0034392); excluded: Global developmental delay (HP:0001263); excluded: Metopic synostosis (HP:0011330); excluded: Developmental regression (HP:0002376); excluded: Ventriculomegaly (HP:0002119); excluded: Facial asymmetry (HP:0000324); excluded: Abnormality of coordination (HP:0011443); excluded: Infantile spasms (HP:0012469)
Individual 11 (MALE; P11Y)Acrofacial dysostosis, Cincinnati type (OMIM:616462)NM_015425.6:c.3721G>A (heterozygous)Motor delay (HP:0001270); Hypertelorism (HP:0000316); Laryngeal dystonia (HP:0012049); Lower limb spasticity (HP:0002061); Mild global developmental delay (HP:0011342); Hypotonia (HP:0001252); excluded: Abnormality of limbs (HP:0040064); excluded: Microtia (HP:0008551); excluded: Low-set ears (HP:0000369); excluded: Microcephaly (HP:0000252); excluded: Macrocephaly (HP:0000256); excluded: Craniosynostosis (HP:0001363); excluded: Cleft lip (HP:0410030); excluded: Ptosis (HP:0000508); excluded: Micrognathia (HP:0000347); excluded: Intrauterine growth retardation (HP:0001511); excluded: Cleft palate (HP:0000175); excluded: Joint contracture (HP:0034392); excluded: Metopic synostosis (HP:0011330); excluded: Hypodontia (HP:0000668); excluded: Developmental regression (HP:0002376); excluded: Ventriculomegaly (HP:0002119); excluded: Facial asymmetry (HP:0000324); excluded: Infantile spasms (HP:0012469)
Individual 12 (MALE; P4Y3M)Acrofacial dysostosis, Cincinnati type (OMIM:616462)NM_015425.6:c.3850C>T (heterozygous)Pulmonary artery stenosis (HP:0004415); Microtia (HP:0008551); Ptosis (HP:0000508); Ventricular septal defect (HP:0001629); Deeply set eye (HP:0000490); Abnormality of limbs (HP:0040064); Diaphragmatic eventration (HP:0009110); Facial asymmetry (HP:0000324); Mild hearing impairment (HP:0012712); Microcephaly (HP:0000252); Intrauterine growth retardation (HP:0001511); excluded: Patent foramen ovale (HP:0001655); excluded: Low-set ears (HP:0000369); excluded: Macrocephaly (HP:0000256); excluded: Craniosynostosis (HP:0001363); excluded: Hypotonia (HP:0001252); excluded: Cleft lip (HP:0410030); excluded: Hypertelorism (HP:0000316); excluded: Brain imaging abnormality (HP:0410263); excluded: Micrognathia (HP:0000347); excluded: Cleft palate (HP:0000175); excluded: Joint contracture (HP:0034392); excluded: Global developmental delay (HP:0001263); excluded: Metopic synostosis (HP:0011330); excluded: Hypodontia (HP:0000668); excluded: Developmental regression (HP:0002376); excluded: Abnormality of coordination (HP:0011443); excluded: Infantile spasms (HP:0012469)
Individual 13 (MALE; P24Y)Acrofacial dysostosis, Cincinnati type (OMIM:616462)NM_015425.6:c.3988_3990del (heterozygous)Global developmental delay (HP:0001263); Ptosis (HP:0000508); Seizure (HP:0001250); Low-set ears (HP:0000369); Brain imaging abnormality (HP:0410263); Abnormality of limbs (HP:0040064); Hypotonia (HP:0001252); excluded: Craniosynostosis (HP:0001363); excluded: Cleft lip (HP:0410030); excluded: Micrognathia (HP:0000347); excluded: Hypertelorism (HP:0000316); excluded: Metopic synostosis (HP:0011330); excluded: Hypodontia (HP:0000668); excluded: Developmental regression (HP:0002376); excluded: Ventriculomegaly (HP:0002119); excluded: Facial asymmetry (HP:0000324); excluded: Microtia (HP:0008551); excluded: Cleft palate (HP:0000175); excluded: Abnormality of coordination (HP:0011443); excluded: Infantile spasms (HP:0012469)
Individual 14 (MALE; P6M)Acrofacial dysostosis, Cincinnati type (OMIM:616462)NM_015425.6:c.3988_3990del (heterozygous)Global developmental delay (HP:0001263); Upslanted palpebral fissure (HP:0000582); Seizure (HP:0001250); Failure to thrive (HP:0001508); Hypertelorism (HP:0000316); Low-set ears (HP:0000369); Depressed nasal bridge (HP:0005280); Brain imaging abnormality (HP:0410263); Cavum septum pellucidum (HP:0002389); Anteverted nares (HP:0000463); Inguinal hernia (HP:0000023); Micrognathia (HP:0000347); Cryptorchidism (HP:0000028); Metopic synostosis (HP:0011330); Epicanthus (HP:0000286); Hypotonia (HP:0001252); excluded: Cleft lip (HP:0410030); excluded: Abnormality of limbs (HP:0040064); excluded: Intrauterine growth retardation (HP:0001511); excluded: Ptosis (HP:0000508); excluded: Joint contracture (HP:0034392); excluded: Ventricular septal defect (HP:0001629); excluded: Developmental regression (HP:0002376); excluded: Patent foramen ovale (HP:0001655); excluded: Ventriculomegaly (HP:0002119); excluded: Facial asymmetry (HP:0000324); excluded: Microtia (HP:0008551); excluded: Microcephaly (HP:0000252); excluded: Macrocephaly (HP:0000256); excluded: Cleft palate (HP:0000175); excluded: Abnormality of coordination (HP:0011443); excluded: Infantile spasms (HP:0012469)
Individual 15 (MALE; P6Y)Acrofacial dysostosis, Cincinnati type (OMIM:616462)NM_015425.6:c.4685G>T (heterozygous)Global developmental delay (HP:0001263); Patent foramen ovale (HP:0001655); Infantile spasms (HP:0012469); Hypertelorism (HP:0000316); Median pseudocleft lip (HP:0034185); Abnormality of limbs (HP:0040064); Brain imaging abnormality (HP:0410263); Microcephaly (HP:0000252); Joint contracture (HP:0034392); Hypotonia (HP:0001252); excluded: Craniosynostosis (HP:0001363); excluded: Micrognathia (HP:0000347); excluded: Metopic synostosis (HP:0011330); excluded: Intrauterine growth retardation (HP:0001511); excluded: Ptosis (HP:0000508); excluded: Ventricular septal defect (HP:0001629); excluded: Developmental regression (HP:0002376); excluded: Ventriculomegaly (HP:0002119); excluded: Facial asymmetry (HP:0000324); excluded: Microtia (HP:0008551); excluded: Low-set ears (HP:0000369); excluded: Macrocephaly (HP:0000256); excluded: Cleft palate (HP:0000175); excluded: Abnormality of coordination (HP:0011443)
Individual 16 (MALE; P3Y)Acrofacial dysostosis, Cincinnati type (OMIM:616462)NM_015425.6:c.4685G>T (heterozygous)Global developmental delay (HP:0001263); Seizure (HP:0001250); Hypertelorism (HP:0000316); Brain imaging abnormality (HP:0410263); Microcephaly (HP:0000252); Gastrostomy tube feeding in infancy (HP:0011471); Hypotonia (HP:0001252); excluded: Craniosynostosis (HP:0001363); excluded: Cleft lip (HP:0410030); excluded: Micrognathia (HP:0000347); excluded: Abnormality of limbs (HP:0040064); excluded: Metopic synostosis (HP:0011330); excluded: Intrauterine growth retardation (HP:0001511); excluded: Ptosis (HP:0000508); excluded: Joint contracture (HP:0034392); excluded: Developmental regression (HP:0002376); excluded: Ventriculomegaly (HP:0002119); excluded: Facial asymmetry (HP:0000324); excluded: Microtia (HP:0008551); excluded: Low-set ears (HP:0000369); excluded: Macrocephaly (HP:0000256); excluded: Cleft palate (HP:0000175); excluded: Abnormality of coordination (HP:0011443); excluded: Infantile spasms (HP:0012469)
Individual 17 (FEMALE; P7Y)Acrofacial dysostosis, Cincinnati type (OMIM:616462)NM_015425.6:c.4891G>A (heterozygous)High palate (HP:0000218); Global developmental delay (HP:0001263); Microtia (HP:0008551); Seizure (HP:0001250); Aqueductal stenosis (HP:0002410); Patent foramen ovale (HP:0001655); Pterygium (HP:0001059); Hearing impairment (HP:0000365); Brain imaging abnormality (HP:0410263); Facial asymmetry (HP:0000324); Micrognathia (HP:0000347); Tracheobronchomalacia (HP:0002786); Gastrostomy tube feeding in infancy (HP:0011471); Scoliosis (HP:0002650); Intrauterine growth retardation (HP:0001511); excluded: Craniosynostosis (HP:0001363); excluded: Cleft lip (HP:0410030); excluded: Abnormality of limbs (HP:0040064); excluded: Metopic synostosis (HP:0011330); excluded: Ptosis (HP:0000508); excluded: Ventricular septal defect (HP:0001629); excluded: Developmental regression (HP:0002376); excluded: Microcephaly (HP:0000252); excluded: Macrocephaly (HP:0000256); excluded: Abnormality of coordination (HP:0011443); excluded: Infantile spasms (HP:0012469)
Individual 18 (FEMALE; P11Y)Acrofacial dysostosis, Cincinnati type (OMIM:616462)NM_015425.6:c.4913C>T (heterozygous)Global developmental delay (HP:0001263); Ptosis (HP:0000508); Patent foramen ovale (HP:0001655); Ventricular septal defect (HP:0001629); Bicuspid aortic valve (HP:0001647); Cleft anterior mitral valve leaflet (HP:0011569); Abnormality of limbs (HP:0040064); Laryngomalacia (HP:0001601); Pulmonary artery aneurysm (HP:0004937); Micrognathia (HP:0000347); Aortic aneurysm (HP:0004942); Joint contracture (HP:0034392); Partial atrioventricular canal defect (HP:0011577); Hypotonia (HP:0001252); excluded: Craniosynostosis (HP:0001363); excluded: Cleft lip (HP:0410030); excluded: Metopic synostosis (HP:0011330); excluded: Developmental regression (HP:0002376); excluded: Facial asymmetry (HP:0000324); excluded: Microtia (HP:0008551); excluded: Low-set ears (HP:0000369); excluded: Brain imaging abnormality (HP:0410263); excluded: Cleft palate (HP:0000175); excluded: Abnormality of coordination (HP:0011443); excluded: Infantile spasms (HP:0012469)
" - ], - "text/plain": [ - "" - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "individuals = cvalidator.get_error_free_individual_list()\n", - "table = PhenopacketTable(individual_list=individuals, metadata=metadata)\n", - "display(HTML(table.to_html()))" - ] - }, - { - "cell_type": "code", - "execution_count": 43, - "id": "db4424ba-a717-4363-bebd-1cefec7dfab2", - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "We output 18 GA4GH phenopackets to the directory phenopackets\n" - ] - } - ], - "source": [ - "Individual.output_individuals_as_phenopackets(individual_list=individuals,\n", - " metadata=metadata)" - ] - }, - { - "cell_type": "code", - "execution_count": 44, - "id": "b6ddb633-c59d-46d3-a897-83077b29c440", - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[pyphetools] Ingested 18 GA4GH phenopackets.\n" - ] - } - ], - "source": [ - "ingestor = PhenopacketIngestor(indir=\"phenopackets\")\n", - "ppkt_d = ingestor.get_phenopacket_dictionary()\n", - "ppkt_list = list(ppkt_d.values())" - ] - }, - { - "cell_type": "code", - "execution_count": 45, - "id": "c43871aa-6bcb-426a-b60e-1caf9fc3edc5", - "metadata": {}, - "outputs": [], - "source": [ - "builder = HpoaTableBuilder(phenopacket_list=ppkt_list)" - ] - }, - { - "cell_type": "code", - "execution_count": 46, - "id": "fad8be12-e00a-409a-b8cf-2bfee602e70f", - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "We found a total of 83 unique HPO terms\n", - "Extracted disease: Acrofacial dysostosis, Cincinnati type (OMIM:616462)\n", - "Wrote HPOA disease file to OMIM-616462.tab\n" - ] - } - ], - "source": [ - "PMID = \"PMID:37075751\" # \n", - "creator = builder.autosomal_dominant(PMID).build()\n", - "df = creator.get_dataframe()\n", - "creator.write_data_frame()" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "4f6ccbac-52ac-490e-a128-3ebeab3759df", - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "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": "3.8.10" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -} diff --git a/notebooks/POLR1A/input/POLR1A_AFDCIN_individuals.xlsx b/notebooks/POLR1A/input/POLR1A_AFDCIN_individuals.xlsx new file mode 100644 index 000000000..2647e9fc4 Binary files /dev/null and b/notebooks/POLR1A/input/POLR1A_AFDCIN_individuals.xlsx differ diff --git a/notebooks/POLR1A/input/POLR1A_Smallwood_2023.xlsx b/notebooks/POLR1A/input/POLR1A_Smallwood_2023.xlsx deleted file mode 100644 index 50df43fa1..000000000 Binary files a/notebooks/POLR1A/input/POLR1A_Smallwood_2023.xlsx and /dev/null differ diff --git a/notebooks/POLR1A/phenopackets/PMID_28051070_Brother1203.json b/notebooks/POLR1A/phenopackets/PMID_28051070_Brother1203.json index 9702a59cd..5639aedce 100644 --- a/notebooks/POLR1A/phenopackets/PMID_28051070_Brother1203.json +++ b/notebooks/POLR1A/phenopackets/PMID_28051070_Brother1203.json @@ -7,6 +7,9 @@ "iso8601duration": "P11Y" } }, + "vitalStatus": { + "status": "ALIVE" + }, "sex": "MALE" }, "phenotypicFeatures": [ @@ -299,7 +302,7 @@ } ], "metaData": { - "created": "2024-05-08T17:55:51.389721155Z", + "created": "2024-11-30T09:36:52.845809936Z", "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { @@ -338,7 +341,7 @@ "id": "hp", "name": "human phenotype ontology", "url": "http://purl.obolibrary.org/obo/hp.owl", - "version": "2024-04-26", + "version": "2024-08-13", "namespacePrefix": "HP", "iriPrefix": "http://purl.obolibrary.org/obo/HP_" } diff --git a/notebooks/POLR1A/phenopackets/PMID_28051070_Brother2204.json b/notebooks/POLR1A/phenopackets/PMID_28051070_Brother2204.json index 39e6ddc06..59c201c91 100644 --- a/notebooks/POLR1A/phenopackets/PMID_28051070_Brother2204.json +++ b/notebooks/POLR1A/phenopackets/PMID_28051070_Brother2204.json @@ -7,6 +7,9 @@ "iso8601duration": "P6Y6M" } }, + "vitalStatus": { + "status": "ALIVE" + }, "sex": "MALE" }, "phenotypicFeatures": [ @@ -317,7 +320,7 @@ } ], "metaData": { - "created": "2024-05-08T17:55:51.390962839Z", + "created": "2024-11-30T09:36:52.846722126Z", "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { @@ -356,7 +359,7 @@ "id": "hp", "name": "human phenotype ontology", "url": "http://purl.obolibrary.org/obo/hp.owl", - "version": "2024-04-26", + "version": "2024-08-13", "namespacePrefix": "HP", "iriPrefix": "http://purl.obolibrary.org/obo/HP_" } diff --git a/notebooks/POLR1A/phenopackets/PMID_36917474_Patient1.json b/notebooks/POLR1A/phenopackets/PMID_36917474_Patient1.json index 101cf355e..4afdfd181 100644 --- a/notebooks/POLR1A/phenopackets/PMID_36917474_Patient1.json +++ b/notebooks/POLR1A/phenopackets/PMID_36917474_Patient1.json @@ -7,6 +7,14 @@ "iso8601duration": "P16Y6M" } }, + "vitalStatus": { + "status": "DECEASED", + "timeOfDeath": { + "age": { + "iso8601duration": "P16Y6M" + } + } + }, "sex": "MALE" }, "phenotypicFeatures": [ @@ -320,7 +328,7 @@ } ], "metaData": { - "created": "2024-05-08T17:55:51.392045021Z", + "created": "2024-11-30T09:36:52.848232030Z", "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { @@ -359,7 +367,7 @@ "id": "hp", "name": "human phenotype ontology", "url": "http://purl.obolibrary.org/obo/hp.owl", - "version": "2024-04-26", + "version": "2024-08-13", "namespacePrefix": "HP", "iriPrefix": "http://purl.obolibrary.org/obo/HP_" } diff --git a/notebooks/POLR1A/phenopackets/PMID_36917474_Patient2.json b/notebooks/POLR1A/phenopackets/PMID_36917474_Patient2.json index c4f9c3ef7..83f227c65 100644 --- a/notebooks/POLR1A/phenopackets/PMID_36917474_Patient2.json +++ b/notebooks/POLR1A/phenopackets/PMID_36917474_Patient2.json @@ -7,6 +7,9 @@ "iso8601duration": "P2Y10M" } }, + "vitalStatus": { + "status": "ALIVE" + }, "sex": "FEMALE" }, "phenotypicFeatures": [ @@ -280,7 +283,7 @@ } ], "metaData": { - "created": "2024-05-08T17:55:51.393130064Z", + "created": "2024-11-30T09:36:52.848973035Z", "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { @@ -319,7 +322,7 @@ "id": "hp", "name": "human phenotype ontology", "url": "http://purl.obolibrary.org/obo/hp.owl", - "version": "2024-04-26", + "version": "2024-08-13", "namespacePrefix": "HP", "iriPrefix": "http://purl.obolibrary.org/obo/HP_" } diff --git a/notebooks/POLR1A/phenopackets/PMID_37075751_Individual1.json b/notebooks/POLR1A/phenopackets/PMID_37075751_Individual1.json index de9a53647..bcf53cebf 100644 --- a/notebooks/POLR1A/phenopackets/PMID_37075751_Individual1.json +++ b/notebooks/POLR1A/phenopackets/PMID_37075751_Individual1.json @@ -7,6 +7,14 @@ "iso8601duration": "P3M" } }, + "vitalStatus": { + "status": "DECEASED", + "timeOfDeath": { + "age": { + "iso8601duration": "P3M" + } + } + }, "sex": "MALE" }, "phenotypicFeatures": [ @@ -16,6 +24,12 @@ "label": "Cleft palate" } }, + { + "type": { + "id": "HP:0000204", + "label": "Cleft upper lip" + } + }, { "type": { "id": "HP:0011330", @@ -24,42 +38,43 @@ }, { "type": { - "id": "HP:0410030", - "label": "Cleft lip" - } + "id": "HP:0000286", + "label": "Epicanthus" + }, + "excluded": true }, { "type": { - "id": "HP:0040064", - "label": "Abnormality of limbs" + "id": "HP:0000582", + "label": "Upslanted palpebral fissure" }, "excluded": true }, { "type": { - "id": "HP:0001655", - "label": "Patent foramen ovale" + "id": "HP:0000637", + "label": "Long palpebral fissure" }, "excluded": true }, { "type": { - "id": "HP:0008551", - "label": "Microtia" + "id": "HP:0001655", + "label": "Patent foramen ovale" }, "excluded": true }, { "type": { - "id": "HP:0000369", - "label": "Low-set ears" + "id": "HP:0001629", + "label": "Ventricular septal defect" }, "excluded": true }, { "type": { - "id": "HP:0001252", - "label": "Hypotonia" + "id": "HP:0011968", + "label": "Feeding difficulties" }, "excluded": true }, @@ -72,43 +87,50 @@ }, { "type": { - "id": "HP:0000508", - "label": "Ptosis" + "id": "HP:0000324", + "label": "Facial asymmetry" }, "excluded": true }, { "type": { - "id": "HP:0001629", - "label": "Ventricular septal defect" + "id": "HP:0000430", + "label": "Underdeveloped nasal alae" }, "excluded": true }, { "type": { - "id": "HP:0410263", - "label": "Brain imaging abnormality" + "id": "HP:0000453", + "label": "Choanal atresia" }, "excluded": true }, { "type": { - "id": "HP:0000347", - "label": "Micrognathia" + "id": "HP:0012469", + "label": "Infantile spasms" }, "excluded": true }, { "type": { - "id": "HP:0001511", - "label": "Intrauterine growth retardation" + "id": "HP:0010819", + "label": "Atonic seizure" }, "excluded": true }, { "type": { - "id": "HP:0034392", - "label": "Joint contracture" + "id": "HP:0001336", + "label": "Myoclonus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0200134", + "label": "Epileptic encephalopathy" }, "excluded": true }, @@ -128,22 +150,134 @@ }, { "type": { - "id": "HP:0000324", - "label": "Facial asymmetry" + "id": "HP:0000218", + "label": "High palate" }, "excluded": true }, { "type": { - "id": "HP:0011443", - "label": "Abnormality of coordination" + "id": "HP:0000369", + "label": "Low-set ears" }, "excluded": true }, { "type": { - "id": "HP:0012469", - "label": "Infantile spasms" + "id": "HP:0000463", + "label": "Anteverted nares" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000347", + "label": "Micrognathia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0009921", + "label": "Duane anomaly" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000490", + "label": "Deeply set eye" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002650", + "label": "Scoliosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001605", + "label": "Vocal cord paralysis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0004209", + "label": "Clinodactyly of the 5th finger" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000625", + "label": "Eyelid coloboma" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001252", + "label": "Hypotonia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0005280", + "label": "Depressed nasal bridge" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000508", + "label": "Ptosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000365", + "label": "Hearing impairment" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0008551", + "label": "Microtia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001511", + "label": "Intrauterine growth retardation" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000954", + "label": "Single transverse palmar crease" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000028", + "label": "Cryptorchidism" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000023", + "label": "Inguinal hernia" }, "excluded": true } @@ -163,27 +297,27 @@ "interpretationStatus": "CAUSATIVE", "variantInterpretation": { "variationDescriptor": { - "id": "var_wJAPvgrqsDDfSTtQcRXfFkabN", + "id": "var_GaofATkBLBliwWsfcGMnAKchx", "geneContext": { - "valueId": "HGNC:20194", - "symbol": "POLR1C" + "valueId": "HGNC:17264", + "symbol": "POLR1A" }, "expressions": [ { "syntax": "hgvs.c", - "value": "NM_203290.4:c.176A>T" + "value": "NM_015425.6:c.176A>T" }, { "syntax": "hgvs.g", - "value": "NC_000006.12:g.43519367A>T" + "value": "NC_000002.12:g.86100074T>A" } ], "vcfRecord": { "genomeAssembly": "hg38", - "chrom": "chr6", - "pos": "43519367", - "ref": "A", - "alt": "T" + "chrom": "chr2", + "pos": "86100074", + "ref": "T", + "alt": "A" }, "moleculeContext": "genomic", "allelicState": { @@ -212,8 +346,8 @@ } ], "metaData": { - "created": "2024-03-24T09:33:00.868335008Z", - "createdBy": "ORCID:0000-0001-7941-2961", + "created": "2024-11-30T09:39:18.464895009Z", + "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { "id": "geno", @@ -251,7 +385,7 @@ "id": "hp", "name": "human phenotype ontology", "url": "http://purl.obolibrary.org/obo/hp.owl", - "version": "2024-03-06", + "version": "2024-08-13", "namespacePrefix": "HP", "iriPrefix": "http://purl.obolibrary.org/obo/HP_" } diff --git a/notebooks/POLR1A/phenopackets/PMID_37075751_Individual10.json b/notebooks/POLR1A/phenopackets/PMID_37075751_Individual10.json index bbd644adb..2eac4d602 100644 --- a/notebooks/POLR1A/phenopackets/PMID_37075751_Individual10.json +++ b/notebooks/POLR1A/phenopackets/PMID_37075751_Individual10.json @@ -7,9 +7,18 @@ "iso8601duration": "P7Y7M" } }, + "vitalStatus": { + "status": "ALIVE" + }, "sex": "FEMALE" }, "phenotypicFeatures": [ + { + "type": { + "id": "HP:0000316", + "label": "Hypertelorism" + } + }, { "type": { "id": "HP:0000668", @@ -18,45 +27,48 @@ }, { "type": { - "id": "HP:0009921", - "label": "Duane anomaly" + "id": "HP:0000175", + "label": "Cleft palate" } }, { "type": { - "id": "HP:0000508", - "label": "Ptosis" + "id": "HP:0000347", + "label": "Micrognathia" } }, { "type": { - "id": "HP:0000403", - "label": "Recurrent otitis media" + "id": "HP:0009921", + "label": "Duane anomaly" } }, { "type": { - "id": "HP:0000316", - "label": "Hypertelorism" + "id": "HP:0000508", + "label": "Ptosis" } }, { "type": { - "id": "HP:0000175", - "label": "Cleft palate" - } + "id": "HP:0000286", + "label": "Epicanthus" + }, + "excluded": true }, { "type": { - "id": "HP:0040064", - "label": "Abnormality of limbs" - } + "id": "HP:0000582", + "label": "Upslanted palpebral fissure" + }, + "excluded": true }, { "type": { - "id": "HP:0000347", - "label": "Micrognathia" - } + "id": "HP:0000637", + "label": "Long palpebral fissure" + }, + "excluded": true }, { "type": { @@ -67,78 +79,155 @@ }, { "type": { - "id": "HP:0008551", - "label": "Microtia" + "id": "HP:0001629", + "label": "Ventricular septal defect" }, "excluded": true }, { "type": { - "id": "HP:0000369", - "label": "Low-set ears" + "id": "HP:0011968", + "label": "Feeding difficulties" }, "excluded": true }, { "type": { - "id": "HP:0000252", - "label": "Microcephaly" + "id": "HP:0000324", + "label": "Facial asymmetry" }, "excluded": true }, { "type": { - "id": "HP:0000256", - "label": "Macrocephaly" + "id": "HP:0000430", + "label": "Underdeveloped nasal alae" }, "excluded": true }, { "type": { - "id": "HP:0001363", - "label": "Craniosynostosis" + "id": "HP:0000453", + "label": "Choanal atresia" }, "excluded": true }, { "type": { - "id": "HP:0001252", - "label": "Hypotonia" + "id": "HP:0012469", + "label": "Infantile spasms" }, "excluded": true }, { "type": { - "id": "HP:0410030", - "label": "Cleft lip" + "id": "HP:0010819", + "label": "Atonic seizure" }, "excluded": true }, { "type": { - "id": "HP:0001629", - "label": "Ventricular septal defect" + "id": "HP:0001336", + "label": "Myoclonus" }, "excluded": true }, { "type": { - "id": "HP:0001511", - "label": "Intrauterine growth retardation" + "id": "HP:0200134", + "label": "Epileptic encephalopathy" }, "excluded": true }, { "type": { - "id": "HP:0034392", - "label": "Joint contracture" + "id": "HP:0001263", + "label": "Global developmental delay" }, "excluded": true }, { "type": { - "id": "HP:0001263", - "label": "Global developmental delay" + "id": "HP:0002376", + "label": "Developmental regression" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000218", + "label": "High palate" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000204", + "label": "Cleft upper lip" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000369", + "label": "Low-set ears" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000463", + "label": "Anteverted nares" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000490", + "label": "Deeply set eye" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002650", + "label": "Scoliosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001605", + "label": "Vocal cord paralysis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0004209", + "label": "Clinodactyly of the 5th finger" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000625", + "label": "Eyelid coloboma" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001252", + "label": "Hypotonia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0005280", + "label": "Depressed nasal bridge" }, "excluded": true }, @@ -151,8 +240,29 @@ }, { "type": { - "id": "HP:0002376", - "label": "Developmental regression" + "id": "HP:0000365", + "label": "Hearing impairment" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0008551", + "label": "Microtia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000252", + "label": "Microcephaly" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000256", + "label": "Macrocephaly" }, "excluded": true }, @@ -165,22 +275,29 @@ }, { "type": { - "id": "HP:0000324", - "label": "Facial asymmetry" + "id": "HP:0001511", + "label": "Intrauterine growth retardation" }, "excluded": true }, { "type": { - "id": "HP:0011443", - "label": "Abnormality of coordination" + "id": "HP:0000954", + "label": "Single transverse palmar crease" }, "excluded": true }, { "type": { - "id": "HP:0012469", - "label": "Infantile spasms" + "id": "HP:0000023", + "label": "Inguinal hernia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000238", + "label": "Hydrocephalus" }, "excluded": true } @@ -200,7 +317,7 @@ "interpretationStatus": "CAUSATIVE", "variantInterpretation": { "variationDescriptor": { - "id": "var_DovRbDeHDpZQmxvinJZkEMWek", + "id": "var_eGgeQjLaXqATftWInxqZwqVKc", "geneContext": { "valueId": "HGNC:17264", "symbol": "POLR1A" @@ -249,8 +366,8 @@ } ], "metaData": { - "created": "2024-03-24T09:33:00.895974874Z", - "createdBy": "ORCID:0000-0001-7941-2961", + "created": "2024-11-30T09:39:18.473582029Z", + "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { "id": "geno", @@ -288,7 +405,7 @@ "id": "hp", "name": "human phenotype ontology", "url": "http://purl.obolibrary.org/obo/hp.owl", - "version": "2024-03-06", + "version": "2024-08-13", "namespacePrefix": "HP", "iriPrefix": "http://purl.obolibrary.org/obo/HP_" } diff --git a/notebooks/POLR1A/phenopackets/PMID_37075751_Individual11.json b/notebooks/POLR1A/phenopackets/PMID_37075751_Individual11.json index 562c5d724..0724db370 100644 --- a/notebooks/POLR1A/phenopackets/PMID_37075751_Individual11.json +++ b/notebooks/POLR1A/phenopackets/PMID_37075751_Individual11.json @@ -7,112 +7,126 @@ "iso8601duration": "P11Y" } }, + "vitalStatus": { + "status": "ALIVE" + }, "sex": "MALE" }, "phenotypicFeatures": [ { "type": { - "id": "HP:0001270", - "label": "Motor delay" + "id": "HP:0000316", + "label": "Hypertelorism" } }, { "type": { - "id": "HP:0000316", - "label": "Hypertelorism" + "id": "HP:0001252", + "label": "Hypotonia" } }, { "type": { - "id": "HP:0012049", - "label": "Laryngeal dystonia" - } + "id": "HP:0000286", + "label": "Epicanthus" + }, + "excluded": true }, { "type": { - "id": "HP:0002061", - "label": "Lower limb spasticity" - } + "id": "HP:0000582", + "label": "Upslanted palpebral fissure" + }, + "excluded": true }, { "type": { - "id": "HP:0011342", - "label": "Mild global developmental delay" - } + "id": "HP:0000637", + "label": "Long palpebral fissure" + }, + "excluded": true }, { "type": { - "id": "HP:0001252", - "label": "Hypotonia" - } + "id": "HP:0011968", + "label": "Feeding difficulties" + }, + "excluded": true }, { "type": { - "id": "HP:0040064", - "label": "Abnormality of limbs" + "id": "HP:0000324", + "label": "Facial asymmetry" }, "excluded": true }, { "type": { - "id": "HP:0008551", - "label": "Microtia" + "id": "HP:0000668", + "label": "Hypodontia" }, "excluded": true }, { "type": { - "id": "HP:0000369", - "label": "Low-set ears" + "id": "HP:0000430", + "label": "Underdeveloped nasal alae" }, "excluded": true }, { "type": { - "id": "HP:0000252", - "label": "Microcephaly" + "id": "HP:0000453", + "label": "Choanal atresia" }, "excluded": true }, { "type": { - "id": "HP:0000256", - "label": "Macrocephaly" + "id": "HP:0012469", + "label": "Infantile spasms" }, "excluded": true }, { "type": { - "id": "HP:0001363", - "label": "Craniosynostosis" + "id": "HP:0010819", + "label": "Atonic seizure" }, "excluded": true }, { "type": { - "id": "HP:0410030", - "label": "Cleft lip" + "id": "HP:0001336", + "label": "Myoclonus" }, "excluded": true }, { "type": { - "id": "HP:0000508", - "label": "Ptosis" + "id": "HP:0200134", + "label": "Epileptic encephalopathy" }, "excluded": true }, { "type": { - "id": "HP:0000347", - "label": "Micrognathia" + "id": "HP:0001263", + "label": "Global developmental delay" }, "excluded": true }, { "type": { - "id": "HP:0001511", - "label": "Intrauterine growth retardation" + "id": "HP:0002376", + "label": "Developmental regression" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000218", + "label": "High palate" }, "excluded": true }, @@ -125,8 +139,78 @@ }, { "type": { - "id": "HP:0034392", - "label": "Joint contracture" + "id": "HP:0000204", + "label": "Cleft upper lip" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000369", + "label": "Low-set ears" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000463", + "label": "Anteverted nares" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000347", + "label": "Micrognathia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0009921", + "label": "Duane anomaly" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000490", + "label": "Deeply set eye" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002650", + "label": "Scoliosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001605", + "label": "Vocal cord paralysis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0004209", + "label": "Clinodactyly of the 5th finger" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000625", + "label": "Eyelid coloboma" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0005280", + "label": "Depressed nasal bridge" }, "excluded": true }, @@ -139,15 +223,36 @@ }, { "type": { - "id": "HP:0000668", - "label": "Hypodontia" + "id": "HP:0000508", + "label": "Ptosis" }, "excluded": true }, { "type": { - "id": "HP:0002376", - "label": "Developmental regression" + "id": "HP:0000365", + "label": "Hearing impairment" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0008551", + "label": "Microtia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000252", + "label": "Microcephaly" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000256", + "label": "Macrocephaly" }, "excluded": true }, @@ -160,15 +265,36 @@ }, { "type": { - "id": "HP:0000324", - "label": "Facial asymmetry" + "id": "HP:0001511", + "label": "Intrauterine growth retardation" }, "excluded": true }, { "type": { - "id": "HP:0012469", - "label": "Infantile spasms" + "id": "HP:0000954", + "label": "Single transverse palmar crease" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000028", + "label": "Cryptorchidism" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000023", + "label": "Inguinal hernia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000238", + "label": "Hydrocephalus" }, "excluded": true } @@ -188,7 +314,7 @@ "interpretationStatus": "CAUSATIVE", "variantInterpretation": { "variationDescriptor": { - "id": "var_ABqLkdXtZzXxvcplIgWRNBrSU", + "id": "var_jDycLROQdFsjXFVblTFwbcjYN", "geneContext": { "valueId": "HGNC:17264", "symbol": "POLR1A" @@ -237,8 +363,8 @@ } ], "metaData": { - "created": "2024-03-24T09:33:00.897554874Z", - "createdBy": "ORCID:0000-0001-7941-2961", + "created": "2024-11-30T09:39:18.474283933Z", + "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { "id": "geno", @@ -276,7 +402,7 @@ "id": "hp", "name": "human phenotype ontology", "url": "http://purl.obolibrary.org/obo/hp.owl", - "version": "2024-03-06", + "version": "2024-08-13", "namespacePrefix": "HP", "iriPrefix": "http://purl.obolibrary.org/obo/HP_" } diff --git a/notebooks/POLR1A/phenopackets/PMID_37075751_Individual12.json b/notebooks/POLR1A/phenopackets/PMID_37075751_Individual12.json index c69585e5c..bb90d461f 100644 --- a/notebooks/POLR1A/phenopackets/PMID_37075751_Individual12.json +++ b/notebooks/POLR1A/phenopackets/PMID_37075751_Individual12.json @@ -7,74 +7,80 @@ "iso8601duration": "P4Y3M" } }, + "vitalStatus": { + "status": "ALIVE" + }, "sex": "MALE" }, "phenotypicFeatures": [ { "type": { - "id": "HP:0004415", - "label": "Pulmonary artery stenosis" + "id": "HP:0004325", + "label": "Decreased body weight" } }, { "type": { - "id": "HP:0008551", - "label": "Microtia" + "id": "HP:0001629", + "label": "Ventricular septal defect" } }, { "type": { - "id": "HP:0000508", - "label": "Ptosis" + "id": "HP:0000324", + "label": "Facial asymmetry" } }, { "type": { - "id": "HP:0001629", - "label": "Ventricular septal defect" + "id": "HP:0000490", + "label": "Deeply set eye" } }, { "type": { - "id": "HP:0000490", - "label": "Deeply set eye" + "id": "HP:0000508", + "label": "Ptosis" } }, { "type": { - "id": "HP:0040064", - "label": "Abnormality of limbs" + "id": "HP:0008551", + "label": "Microtia" } }, { "type": { - "id": "HP:0009110", - "label": "Diaphragmatic eventration" + "id": "HP:0000252", + "label": "Microcephaly" } }, { "type": { - "id": "HP:0000324", - "label": "Facial asymmetry" + "id": "HP:0001511", + "label": "Intrauterine growth retardation" } }, { "type": { - "id": "HP:0012712", - "label": "Mild hearing impairment" - } + "id": "HP:0000286", + "label": "Epicanthus" + }, + "excluded": true }, { "type": { - "id": "HP:0000252", - "label": "Microcephaly" - } + "id": "HP:0000582", + "label": "Upslanted palpebral fissure" + }, + "excluded": true }, { "type": { - "id": "HP:0001511", - "label": "Intrauterine growth retardation" - } + "id": "HP:0000637", + "label": "Long palpebral fissure" + }, + "excluded": true }, { "type": { @@ -85,57 +91,85 @@ }, { "type": { - "id": "HP:0000369", - "label": "Low-set ears" + "id": "HP:0011968", + "label": "Feeding difficulties" }, "excluded": true }, { "type": { - "id": "HP:0000256", - "label": "Macrocephaly" + "id": "HP:0000316", + "label": "Hypertelorism" }, "excluded": true }, { "type": { - "id": "HP:0001363", - "label": "Craniosynostosis" + "id": "HP:0000668", + "label": "Hypodontia" }, "excluded": true }, { "type": { - "id": "HP:0001252", - "label": "Hypotonia" + "id": "HP:0000430", + "label": "Underdeveloped nasal alae" }, "excluded": true }, { "type": { - "id": "HP:0410030", - "label": "Cleft lip" + "id": "HP:0000453", + "label": "Choanal atresia" }, "excluded": true }, { "type": { - "id": "HP:0000316", - "label": "Hypertelorism" + "id": "HP:0012469", + "label": "Infantile spasms" }, "excluded": true }, { "type": { - "id": "HP:0410263", - "label": "Brain imaging abnormality" + "id": "HP:0010819", + "label": "Atonic seizure" }, "excluded": true }, { "type": { - "id": "HP:0000347", - "label": "Micrognathia" + "id": "HP:0001336", + "label": "Myoclonus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0200134", + "label": "Epileptic encephalopathy" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001263", + "label": "Global developmental delay" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002376", + "label": "Developmental regression" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000218", + "label": "High palate" }, "excluded": true }, @@ -148,15 +182,85 @@ }, { "type": { - "id": "HP:0034392", - "label": "Joint contracture" + "id": "HP:0000204", + "label": "Cleft upper lip" }, "excluded": true }, { "type": { - "id": "HP:0001263", - "label": "Global developmental delay" + "id": "HP:0000369", + "label": "Low-set ears" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000463", + "label": "Anteverted nares" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000347", + "label": "Micrognathia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0009921", + "label": "Duane anomaly" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002650", + "label": "Scoliosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001605", + "label": "Vocal cord paralysis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0004209", + "label": "Clinodactyly of the 5th finger" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0004322", + "label": "Short stature" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000625", + "label": "Eyelid coloboma" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001252", + "label": "Hypotonia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0005280", + "label": "Depressed nasal bridge" }, "excluded": true }, @@ -169,29 +273,36 @@ }, { "type": { - "id": "HP:0000668", - "label": "Hypodontia" + "id": "HP:0000365", + "label": "Hearing impairment" }, "excluded": true }, { "type": { - "id": "HP:0002376", - "label": "Developmental regression" + "id": "HP:0000256", + "label": "Macrocephaly" }, "excluded": true }, { "type": { - "id": "HP:0011443", - "label": "Abnormality of coordination" + "id": "HP:0000954", + "label": "Single transverse palmar crease" }, "excluded": true }, { "type": { - "id": "HP:0012469", - "label": "Infantile spasms" + "id": "HP:0000028", + "label": "Cryptorchidism" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000023", + "label": "Inguinal hernia" }, "excluded": true } @@ -211,7 +322,7 @@ "interpretationStatus": "CAUSATIVE", "variantInterpretation": { "variationDescriptor": { - "id": "var_DxIkEHrQOJwptnoAgtXHpTZqi", + "id": "var_ZyMwUtbeCFMuWelmKBZJvCPpd", "geneContext": { "valueId": "HGNC:17264", "symbol": "POLR1A" @@ -260,8 +371,8 @@ } ], "metaData": { - "created": "2024-03-24T09:33:00.899141788Z", - "createdBy": "ORCID:0000-0001-7941-2961", + "created": "2024-11-30T09:39:18.474966049Z", + "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { "id": "geno", @@ -299,7 +410,7 @@ "id": "hp", "name": "human phenotype ontology", "url": "http://purl.obolibrary.org/obo/hp.owl", - "version": "2024-03-06", + "version": "2024-08-13", "namespacePrefix": "HP", "iriPrefix": "http://purl.obolibrary.org/obo/HP_" } diff --git a/notebooks/POLR1A/phenopackets/PMID_37075751_Individual13.json b/notebooks/POLR1A/phenopackets/PMID_37075751_Individual13.json index 1826d810b..53f99bce0 100644 --- a/notebooks/POLR1A/phenopackets/PMID_37075751_Individual13.json +++ b/notebooks/POLR1A/phenopackets/PMID_37075751_Individual13.json @@ -7,25 +7,22 @@ "iso8601duration": "P24Y" } }, + "vitalStatus": { + "status": "ALIVE" + }, "sex": "MALE" }, "phenotypicFeatures": [ { "type": { - "id": "HP:0001263", - "label": "Global developmental delay" - } - }, - { - "type": { - "id": "HP:0000508", - "label": "Ptosis" + "id": "HP:0001250", + "label": "Seizure" } }, { "type": { - "id": "HP:0001250", - "label": "Seizure" + "id": "HP:0001263", + "label": "Global developmental delay" } }, { @@ -36,40 +33,41 @@ }, { "type": { - "id": "HP:0410263", - "label": "Brain imaging abnormality" + "id": "HP:0001252", + "label": "Hypotonia" } }, { "type": { - "id": "HP:0040064", - "label": "Abnormality of limbs" + "id": "HP:0000508", + "label": "Ptosis" } }, { "type": { - "id": "HP:0001252", - "label": "Hypotonia" - } + "id": "HP:0000286", + "label": "Epicanthus" + }, + "excluded": true }, { "type": { - "id": "HP:0001363", - "label": "Craniosynostosis" + "id": "HP:0000582", + "label": "Upslanted palpebral fissure" }, "excluded": true }, { "type": { - "id": "HP:0410030", - "label": "Cleft lip" + "id": "HP:0000637", + "label": "Long palpebral fissure" }, "excluded": true }, { "type": { - "id": "HP:0000347", - "label": "Micrognathia" + "id": "HP:0011968", + "label": "Feeding difficulties" }, "excluded": true }, @@ -82,8 +80,8 @@ }, { "type": { - "id": "HP:0011330", - "label": "Metopic synostosis" + "id": "HP:0000324", + "label": "Facial asymmetry" }, "excluded": true }, @@ -94,6 +92,48 @@ }, "excluded": true }, + { + "type": { + "id": "HP:0000430", + "label": "Underdeveloped nasal alae" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000453", + "label": "Choanal atresia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0012469", + "label": "Infantile spasms" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0010819", + "label": "Atonic seizure" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001336", + "label": "Myoclonus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0200134", + "label": "Epileptic encephalopathy" + }, + "excluded": true + }, { "type": { "id": "HP:0002376", @@ -103,15 +143,99 @@ }, { "type": { - "id": "HP:0002119", - "label": "Ventriculomegaly" + "id": "HP:0000218", + "label": "High palate" }, "excluded": true }, { "type": { - "id": "HP:0000324", - "label": "Facial asymmetry" + "id": "HP:0000175", + "label": "Cleft palate" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000204", + "label": "Cleft upper lip" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000463", + "label": "Anteverted nares" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000347", + "label": "Micrognathia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0009921", + "label": "Duane anomaly" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000490", + "label": "Deeply set eye" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002650", + "label": "Scoliosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001605", + "label": "Vocal cord paralysis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0004209", + "label": "Clinodactyly of the 5th finger" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000625", + "label": "Eyelid coloboma" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0005280", + "label": "Depressed nasal bridge" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011330", + "label": "Metopic synostosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000365", + "label": "Hearing impairment" }, "excluded": true }, @@ -124,22 +248,36 @@ }, { "type": { - "id": "HP:0000175", - "label": "Cleft palate" + "id": "HP:0002119", + "label": "Ventriculomegaly" }, "excluded": true }, { "type": { - "id": "HP:0011443", - "label": "Abnormality of coordination" + "id": "HP:0000954", + "label": "Single transverse palmar crease" }, "excluded": true }, { "type": { - "id": "HP:0012469", - "label": "Infantile spasms" + "id": "HP:0000028", + "label": "Cryptorchidism" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000023", + "label": "Inguinal hernia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000238", + "label": "Hydrocephalus" }, "excluded": true } @@ -159,7 +297,7 @@ "interpretationStatus": "CAUSATIVE", "variantInterpretation": { "variationDescriptor": { - "id": "var_drHbkvFslxHRGKUmbIeBTGasO", + "id": "var_NRnNcOFBpYSOWLdhYOGhLirZG", "geneContext": { "valueId": "HGNC:17264", "symbol": "POLR1A" @@ -208,8 +346,8 @@ } ], "metaData": { - "created": "2024-03-24T09:33:00.901484966Z", - "createdBy": "ORCID:0000-0001-7941-2961", + "created": "2024-11-30T09:39:18.475667953Z", + "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { "id": "geno", @@ -247,7 +385,7 @@ "id": "hp", "name": "human phenotype ontology", "url": "http://purl.obolibrary.org/obo/hp.owl", - "version": "2024-03-06", + "version": "2024-08-13", "namespacePrefix": "HP", "iriPrefix": "http://purl.obolibrary.org/obo/HP_" } diff --git a/notebooks/POLR1A/phenopackets/PMID_37075751_Individual14.json b/notebooks/POLR1A/phenopackets/PMID_37075751_Individual14.json index f1a2608d5..bdd5c8047 100644 --- a/notebooks/POLR1A/phenopackets/PMID_37075751_Individual14.json +++ b/notebooks/POLR1A/phenopackets/PMID_37075751_Individual14.json @@ -7,13 +7,16 @@ "iso8601duration": "P6M" } }, + "vitalStatus": { + "status": "ALIVE" + }, "sex": "MALE" }, "phenotypicFeatures": [ { "type": { - "id": "HP:0001263", - "label": "Global developmental delay" + "id": "HP:0000286", + "label": "Epicanthus" } }, { @@ -24,20 +27,26 @@ }, { "type": { - "id": "HP:0001250", - "label": "Seizure" + "id": "HP:0000316", + "label": "Hypertelorism" } }, { "type": { - "id": "HP:0001508", - "label": "Failure to thrive" + "id": "HP:0000430", + "label": "Underdeveloped nasal alae" } }, { "type": { - "id": "HP:0000316", - "label": "Hypertelorism" + "id": "HP:0001250", + "label": "Seizure" + } + }, + { + "type": { + "id": "HP:0001263", + "label": "Global developmental delay" } }, { @@ -48,38 +57,38 @@ }, { "type": { - "id": "HP:0005280", - "label": "Depressed nasal bridge" + "id": "HP:0000463", + "label": "Anteverted nares" } }, { "type": { - "id": "HP:0410263", - "label": "Brain imaging abnormality" + "id": "HP:0000347", + "label": "Micrognathia" } }, { "type": { - "id": "HP:0002389", - "label": "Cavum septum pellucidum" + "id": "HP:0004322", + "label": "Short stature" } }, { "type": { - "id": "HP:0000463", - "label": "Anteverted nares" + "id": "HP:0001252", + "label": "Hypotonia" } }, { "type": { - "id": "HP:0000023", - "label": "Inguinal hernia" + "id": "HP:0005280", + "label": "Depressed nasal bridge" } }, { "type": { - "id": "HP:0000347", - "label": "Micrognathia" + "id": "HP:0011330", + "label": "Metopic synostosis" } }, { @@ -90,61 +99,77 @@ }, { "type": { - "id": "HP:0011330", - "label": "Metopic synostosis" + "id": "HP:0000023", + "label": "Inguinal hernia" } }, { "type": { - "id": "HP:0000286", - "label": "Epicanthus" - } + "id": "HP:0000637", + "label": "Long palpebral fissure" + }, + "excluded": true }, { "type": { - "id": "HP:0001252", - "label": "Hypotonia" - } + "id": "HP:0001655", + "label": "Patent foramen ovale" + }, + "excluded": true }, { "type": { - "id": "HP:0410030", - "label": "Cleft lip" + "id": "HP:0001629", + "label": "Ventricular septal defect" }, "excluded": true }, { "type": { - "id": "HP:0040064", - "label": "Abnormality of limbs" + "id": "HP:0011968", + "label": "Feeding difficulties" }, "excluded": true }, { "type": { - "id": "HP:0001511", - "label": "Intrauterine growth retardation" + "id": "HP:0000324", + "label": "Facial asymmetry" }, "excluded": true }, { "type": { - "id": "HP:0000508", - "label": "Ptosis" + "id": "HP:0000453", + "label": "Choanal atresia" }, "excluded": true }, { "type": { - "id": "HP:0034392", - "label": "Joint contracture" + "id": "HP:0012469", + "label": "Infantile spasms" }, "excluded": true }, { "type": { - "id": "HP:0001629", - "label": "Ventricular septal defect" + "id": "HP:0010819", + "label": "Atonic seizure" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001336", + "label": "Myoclonus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0200134", + "label": "Epileptic encephalopathy" }, "excluded": true }, @@ -157,22 +182,78 @@ }, { "type": { - "id": "HP:0001655", - "label": "Patent foramen ovale" + "id": "HP:0000218", + "label": "High palate" }, "excluded": true }, { "type": { - "id": "HP:0002119", - "label": "Ventriculomegaly" + "id": "HP:0000175", + "label": "Cleft palate" }, "excluded": true }, { "type": { - "id": "HP:0000324", - "label": "Facial asymmetry" + "id": "HP:0000204", + "label": "Cleft upper lip" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0009921", + "label": "Duane anomaly" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000490", + "label": "Deeply set eye" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002650", + "label": "Scoliosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001605", + "label": "Vocal cord paralysis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0004209", + "label": "Clinodactyly of the 5th finger" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000625", + "label": "Eyelid coloboma" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000508", + "label": "Ptosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000365", + "label": "Hearing impairment" }, "excluded": true }, @@ -199,22 +280,29 @@ }, { "type": { - "id": "HP:0000175", - "label": "Cleft palate" + "id": "HP:0002119", + "label": "Ventriculomegaly" }, "excluded": true }, { "type": { - "id": "HP:0011443", - "label": "Abnormality of coordination" + "id": "HP:0001511", + "label": "Intrauterine growth retardation" }, "excluded": true }, { "type": { - "id": "HP:0012469", - "label": "Infantile spasms" + "id": "HP:0000954", + "label": "Single transverse palmar crease" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000238", + "label": "Hydrocephalus" }, "excluded": true } @@ -234,7 +322,7 @@ "interpretationStatus": "CAUSATIVE", "variantInterpretation": { "variationDescriptor": { - "id": "var_drHbkvFslxHRGKUmbIeBTGasO", + "id": "var_NRnNcOFBpYSOWLdhYOGhLirZG", "geneContext": { "valueId": "HGNC:17264", "symbol": "POLR1A" @@ -283,8 +371,8 @@ } ], "metaData": { - "created": "2024-03-24T09:33:00.903965950Z", - "createdBy": "ORCID:0000-0001-7941-2961", + "created": "2024-11-30T09:39:18.476309061Z", + "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { "id": "geno", @@ -322,7 +410,7 @@ "id": "hp", "name": "human phenotype ontology", "url": "http://purl.obolibrary.org/obo/hp.owl", - "version": "2024-03-06", + "version": "2024-08-13", "namespacePrefix": "HP", "iriPrefix": "http://purl.obolibrary.org/obo/HP_" } diff --git a/notebooks/POLR1A/phenopackets/PMID_37075751_Individual15.json b/notebooks/POLR1A/phenopackets/PMID_37075751_Individual15.json index 0f2c5105c..9422d855a 100644 --- a/notebooks/POLR1A/phenopackets/PMID_37075751_Individual15.json +++ b/notebooks/POLR1A/phenopackets/PMID_37075751_Individual15.json @@ -7,19 +7,22 @@ "iso8601duration": "P6Y" } }, + "vitalStatus": { + "status": "ALIVE" + }, "sex": "MALE" }, "phenotypicFeatures": [ { "type": { - "id": "HP:0001263", - "label": "Global developmental delay" + "id": "HP:0001655", + "label": "Patent foramen ovale" } }, { "type": { - "id": "HP:0001655", - "label": "Patent foramen ovale" + "id": "HP:0000316", + "label": "Hypertelorism" } }, { @@ -30,85 +33,96 @@ }, { "type": { - "id": "HP:0000316", - "label": "Hypertelorism" + "id": "HP:0001263", + "label": "Global developmental delay" } }, { "type": { - "id": "HP:0034185", - "label": "Median pseudocleft lip" + "id": "HP:0001252", + "label": "Hypotonia" } }, { "type": { - "id": "HP:0040064", - "label": "Abnormality of limbs" + "id": "HP:0000252", + "label": "Microcephaly" } }, { "type": { - "id": "HP:0410263", - "label": "Brain imaging abnormality" - } + "id": "HP:0000286", + "label": "Epicanthus" + }, + "excluded": true }, { "type": { - "id": "HP:0000252", - "label": "Microcephaly" - } + "id": "HP:0000582", + "label": "Upslanted palpebral fissure" + }, + "excluded": true }, { "type": { - "id": "HP:0034392", - "label": "Joint contracture" - } + "id": "HP:0000637", + "label": "Long palpebral fissure" + }, + "excluded": true }, { "type": { - "id": "HP:0001252", - "label": "Hypotonia" - } + "id": "HP:0001629", + "label": "Ventricular septal defect" + }, + "excluded": true }, { "type": { - "id": "HP:0001363", - "label": "Craniosynostosis" + "id": "HP:0011968", + "label": "Feeding difficulties" }, "excluded": true }, { "type": { - "id": "HP:0000347", - "label": "Micrognathia" + "id": "HP:0000324", + "label": "Facial asymmetry" }, "excluded": true }, { "type": { - "id": "HP:0011330", - "label": "Metopic synostosis" + "id": "HP:0000430", + "label": "Underdeveloped nasal alae" }, "excluded": true }, { "type": { - "id": "HP:0001511", - "label": "Intrauterine growth retardation" + "id": "HP:0000453", + "label": "Choanal atresia" }, "excluded": true }, { "type": { - "id": "HP:0000508", - "label": "Ptosis" + "id": "HP:0010819", + "label": "Atonic seizure" }, "excluded": true }, { "type": { - "id": "HP:0001629", - "label": "Ventricular septal defect" + "id": "HP:0001336", + "label": "Myoclonus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0200134", + "label": "Epileptic encephalopathy" }, "excluded": true }, @@ -121,22 +135,22 @@ }, { "type": { - "id": "HP:0002119", - "label": "Ventriculomegaly" + "id": "HP:0000218", + "label": "High palate" }, "excluded": true }, { "type": { - "id": "HP:0000324", - "label": "Facial asymmetry" + "id": "HP:0000175", + "label": "Cleft palate" }, "excluded": true }, { "type": { - "id": "HP:0008551", - "label": "Microtia" + "id": "HP:0000204", + "label": "Cleft upper lip" }, "excluded": true }, @@ -147,6 +161,104 @@ }, "excluded": true }, + { + "type": { + "id": "HP:0000463", + "label": "Anteverted nares" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000347", + "label": "Micrognathia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0009921", + "label": "Duane anomaly" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000490", + "label": "Deeply set eye" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002650", + "label": "Scoliosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001605", + "label": "Vocal cord paralysis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0004209", + "label": "Clinodactyly of the 5th finger" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0004322", + "label": "Short stature" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000625", + "label": "Eyelid coloboma" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0005280", + "label": "Depressed nasal bridge" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011330", + "label": "Metopic synostosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000508", + "label": "Ptosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000365", + "label": "Hearing impairment" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0008551", + "label": "Microtia" + }, + "excluded": true + }, { "type": { "id": "HP:0000256", @@ -156,15 +268,43 @@ }, { "type": { - "id": "HP:0000175", - "label": "Cleft palate" + "id": "HP:0002119", + "label": "Ventriculomegaly" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001511", + "label": "Intrauterine growth retardation" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000954", + "label": "Single transverse palmar crease" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000028", + "label": "Cryptorchidism" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000023", + "label": "Inguinal hernia" }, "excluded": true }, { "type": { - "id": "HP:0011443", - "label": "Abnormality of coordination" + "id": "HP:0000238", + "label": "Hydrocephalus" }, "excluded": true } @@ -184,7 +324,7 @@ "interpretationStatus": "CAUSATIVE", "variantInterpretation": { "variationDescriptor": { - "id": "var_jSTXZzveaGIDlrQGDsifuQLmq", + "id": "var_KlgdyEMsQVqMXluGArwguefjW", "geneContext": { "valueId": "HGNC:17264", "symbol": "POLR1A" @@ -233,8 +373,8 @@ } ], "metaData": { - "created": "2024-03-24T09:33:00.905636072Z", - "createdBy": "ORCID:0000-0001-7941-2961", + "created": "2024-11-30T09:39:18.477052927Z", + "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { "id": "geno", @@ -272,7 +412,7 @@ "id": "hp", "name": "human phenotype ontology", "url": "http://purl.obolibrary.org/obo/hp.owl", - "version": "2024-03-06", + "version": "2024-08-13", "namespacePrefix": "HP", "iriPrefix": "http://purl.obolibrary.org/obo/HP_" } diff --git a/notebooks/POLR1A/phenopackets/PMID_37075751_Individual16.json b/notebooks/POLR1A/phenopackets/PMID_37075751_Individual16.json index 2c6376af5..696230506 100644 --- a/notebooks/POLR1A/phenopackets/PMID_37075751_Individual16.json +++ b/notebooks/POLR1A/phenopackets/PMID_37075751_Individual16.json @@ -7,13 +7,22 @@ "iso8601duration": "P3Y" } }, + "vitalStatus": { + "status": "ALIVE" + }, "sex": "MALE" }, "phenotypicFeatures": [ { "type": { - "id": "HP:0001263", - "label": "Global developmental delay" + "id": "HP:0011968", + "label": "Feeding difficulties" + } + }, + { + "type": { + "id": "HP:0000316", + "label": "Hypertelorism" } }, { @@ -24,14 +33,20 @@ }, { "type": { - "id": "HP:0000316", - "label": "Hypertelorism" + "id": "HP:0001263", + "label": "Global developmental delay" } }, { "type": { - "id": "HP:0410263", - "label": "Brain imaging abnormality" + "id": "HP:0004322", + "label": "Short stature" + } + }, + { + "type": { + "id": "HP:0001252", + "label": "Hypotonia" } }, { @@ -42,69 +57,71 @@ }, { "type": { - "id": "HP:0011471", - "label": "Gastrostomy tube feeding in infancy" - } + "id": "HP:0000286", + "label": "Epicanthus" + }, + "excluded": true }, { "type": { - "id": "HP:0001252", - "label": "Hypotonia" - } + "id": "HP:0000582", + "label": "Upslanted palpebral fissure" + }, + "excluded": true }, { "type": { - "id": "HP:0001363", - "label": "Craniosynostosis" + "id": "HP:0000637", + "label": "Long palpebral fissure" }, "excluded": true }, { "type": { - "id": "HP:0410030", - "label": "Cleft lip" + "id": "HP:0000324", + "label": "Facial asymmetry" }, "excluded": true }, { "type": { - "id": "HP:0000347", - "label": "Micrognathia" + "id": "HP:0000430", + "label": "Underdeveloped nasal alae" }, "excluded": true }, { "type": { - "id": "HP:0040064", - "label": "Abnormality of limbs" + "id": "HP:0000453", + "label": "Choanal atresia" }, "excluded": true }, { "type": { - "id": "HP:0011330", - "label": "Metopic synostosis" + "id": "HP:0012469", + "label": "Infantile spasms" }, "excluded": true }, { "type": { - "id": "HP:0001511", - "label": "Intrauterine growth retardation" + "id": "HP:0010819", + "label": "Atonic seizure" }, "excluded": true }, { "type": { - "id": "HP:0000508", - "label": "Ptosis" + "id": "HP:0001336", + "label": "Myoclonus" }, "excluded": true }, { "type": { - "id": "HP:0034392", - "label": "Joint contracture" + "id": "HP:0200134", + "label": "Epileptic encephalopathy" }, "excluded": true }, @@ -117,22 +134,22 @@ }, { "type": { - "id": "HP:0002119", - "label": "Ventriculomegaly" + "id": "HP:0000218", + "label": "High palate" }, "excluded": true }, { "type": { - "id": "HP:0000324", - "label": "Facial asymmetry" + "id": "HP:0000175", + "label": "Cleft palate" }, "excluded": true }, { "type": { - "id": "HP:0008551", - "label": "Microtia" + "id": "HP:0000204", + "label": "Cleft upper lip" }, "excluded": true }, @@ -143,6 +160,97 @@ }, "excluded": true }, + { + "type": { + "id": "HP:0000463", + "label": "Anteverted nares" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000347", + "label": "Micrognathia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0009921", + "label": "Duane anomaly" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000490", + "label": "Deeply set eye" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002650", + "label": "Scoliosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001605", + "label": "Vocal cord paralysis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0004209", + "label": "Clinodactyly of the 5th finger" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000625", + "label": "Eyelid coloboma" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0005280", + "label": "Depressed nasal bridge" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011330", + "label": "Metopic synostosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000508", + "label": "Ptosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000365", + "label": "Hearing impairment" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0008551", + "label": "Microtia" + }, + "excluded": true + }, { "type": { "id": "HP:0000256", @@ -152,22 +260,43 @@ }, { "type": { - "id": "HP:0000175", - "label": "Cleft palate" + "id": "HP:0002119", + "label": "Ventriculomegaly" }, "excluded": true }, { "type": { - "id": "HP:0011443", - "label": "Abnormality of coordination" + "id": "HP:0001511", + "label": "Intrauterine growth retardation" }, "excluded": true }, { "type": { - "id": "HP:0012469", - "label": "Infantile spasms" + "id": "HP:0000954", + "label": "Single transverse palmar crease" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000028", + "label": "Cryptorchidism" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000023", + "label": "Inguinal hernia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000238", + "label": "Hydrocephalus" }, "excluded": true } @@ -187,7 +316,7 @@ "interpretationStatus": "CAUSATIVE", "variantInterpretation": { "variationDescriptor": { - "id": "var_jSTXZzveaGIDlrQGDsifuQLmq", + "id": "var_KlgdyEMsQVqMXluGArwguefjW", "geneContext": { "valueId": "HGNC:17264", "symbol": "POLR1A" @@ -236,8 +365,8 @@ } ], "metaData": { - "created": "2024-03-24T09:33:00.912399053Z", - "createdBy": "ORCID:0000-0001-7941-2961", + "created": "2024-11-30T09:39:18.477770090Z", + "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { "id": "geno", @@ -275,7 +404,7 @@ "id": "hp", "name": "human phenotype ontology", "url": "http://purl.obolibrary.org/obo/hp.owl", - "version": "2024-03-06", + "version": "2024-08-13", "namespacePrefix": "HP", "iriPrefix": "http://purl.obolibrary.org/obo/HP_" } diff --git a/notebooks/POLR1A/phenopackets/PMID_37075751_Individual17.json b/notebooks/POLR1A/phenopackets/PMID_37075751_Individual17.json index b98896027..9e2cb182c 100644 --- a/notebooks/POLR1A/phenopackets/PMID_37075751_Individual17.json +++ b/notebooks/POLR1A/phenopackets/PMID_37075751_Individual17.json @@ -7,25 +7,28 @@ "iso8601duration": "P7Y" } }, + "vitalStatus": { + "status": "ALIVE" + }, "sex": "FEMALE" }, "phenotypicFeatures": [ { "type": { - "id": "HP:0000218", - "label": "High palate" + "id": "HP:0001655", + "label": "Patent foramen ovale" } }, { "type": { - "id": "HP:0001263", - "label": "Global developmental delay" + "id": "HP:0011968", + "label": "Feeding difficulties" } }, { "type": { - "id": "HP:0008551", - "label": "Microtia" + "id": "HP:0000324", + "label": "Facial asymmetry" } }, { @@ -36,20 +39,26 @@ }, { "type": { - "id": "HP:0002410", - "label": "Aqueductal stenosis" + "id": "HP:0001263", + "label": "Global developmental delay" } }, { "type": { - "id": "HP:0001655", - "label": "Patent foramen ovale" + "id": "HP:0000218", + "label": "High palate" } }, { "type": { - "id": "HP:0001059", - "label": "Pterygium" + "id": "HP:0000347", + "label": "Micrognathia" + } + }, + { + "type": { + "id": "HP:0002650", + "label": "Scoliosis" } }, { @@ -60,85 +69,89 @@ }, { "type": { - "id": "HP:0410263", - "label": "Brain imaging abnormality" + "id": "HP:0008551", + "label": "Microtia" } }, { "type": { - "id": "HP:0000324", - "label": "Facial asymmetry" + "id": "HP:0002119", + "label": "Ventriculomegaly" } }, { "type": { - "id": "HP:0000347", - "label": "Micrognathia" + "id": "HP:0001511", + "label": "Intrauterine growth retardation" } }, { "type": { - "id": "HP:0002786", - "label": "Tracheobronchomalacia" - } + "id": "HP:0000286", + "label": "Epicanthus" + }, + "excluded": true }, { "type": { - "id": "HP:0011471", - "label": "Gastrostomy tube feeding in infancy" - } + "id": "HP:0000582", + "label": "Upslanted palpebral fissure" + }, + "excluded": true }, { "type": { - "id": "HP:0002650", - "label": "Scoliosis" - } + "id": "HP:0000637", + "label": "Long palpebral fissure" + }, + "excluded": true }, { "type": { - "id": "HP:0001511", - "label": "Intrauterine growth retardation" - } + "id": "HP:0001629", + "label": "Ventricular septal defect" + }, + "excluded": true }, { "type": { - "id": "HP:0001363", - "label": "Craniosynostosis" + "id": "HP:0000430", + "label": "Underdeveloped nasal alae" }, "excluded": true }, { "type": { - "id": "HP:0410030", - "label": "Cleft lip" + "id": "HP:0000453", + "label": "Choanal atresia" }, "excluded": true }, { "type": { - "id": "HP:0040064", - "label": "Abnormality of limbs" + "id": "HP:0012469", + "label": "Infantile spasms" }, "excluded": true }, { "type": { - "id": "HP:0011330", - "label": "Metopic synostosis" + "id": "HP:0010819", + "label": "Atonic seizure" }, "excluded": true }, { "type": { - "id": "HP:0000508", - "label": "Ptosis" + "id": "HP:0001336", + "label": "Myoclonus" }, "excluded": true }, { "type": { - "id": "HP:0001629", - "label": "Ventricular septal defect" + "id": "HP:0200134", + "label": "Epileptic encephalopathy" }, "excluded": true }, @@ -149,6 +162,90 @@ }, "excluded": true }, + { + "type": { + "id": "HP:0000175", + "label": "Cleft palate" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000204", + "label": "Cleft upper lip" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000463", + "label": "Anteverted nares" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0009921", + "label": "Duane anomaly" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000490", + "label": "Deeply set eye" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001605", + "label": "Vocal cord paralysis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0004209", + "label": "Clinodactyly of the 5th finger" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0004322", + "label": "Short stature" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000625", + "label": "Eyelid coloboma" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0005280", + "label": "Depressed nasal bridge" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011330", + "label": "Metopic synostosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000508", + "label": "Ptosis" + }, + "excluded": true + }, { "type": { "id": "HP:0000252", @@ -165,15 +262,22 @@ }, { "type": { - "id": "HP:0011443", - "label": "Abnormality of coordination" + "id": "HP:0000954", + "label": "Single transverse palmar crease" }, "excluded": true }, { "type": { - "id": "HP:0012469", - "label": "Infantile spasms" + "id": "HP:0000023", + "label": "Inguinal hernia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000238", + "label": "Hydrocephalus" }, "excluded": true } @@ -193,7 +297,7 @@ "interpretationStatus": "CAUSATIVE", "variantInterpretation": { "variationDescriptor": { - "id": "var_yDvxkRMNPRPJsJUcdacqxFXZE", + "id": "var_vvpdlaBhTRZQgopJVehsFoVOG", "geneContext": { "valueId": "HGNC:17264", "symbol": "POLR1A" @@ -242,8 +346,8 @@ } ], "metaData": { - "created": "2024-03-24T09:33:00.914308071Z", - "createdBy": "ORCID:0000-0001-7941-2961", + "created": "2024-11-30T09:39:18.478501796Z", + "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { "id": "geno", @@ -281,7 +385,7 @@ "id": "hp", "name": "human phenotype ontology", "url": "http://purl.obolibrary.org/obo/hp.owl", - "version": "2024-03-06", + "version": "2024-08-13", "namespacePrefix": "HP", "iriPrefix": "http://purl.obolibrary.org/obo/HP_" } diff --git a/notebooks/POLR1A/phenopackets/PMID_37075751_Individual18.json b/notebooks/POLR1A/phenopackets/PMID_37075751_Individual18.json index eeb5a6310..9f7140b5d 100644 --- a/notebooks/POLR1A/phenopackets/PMID_37075751_Individual18.json +++ b/notebooks/POLR1A/phenopackets/PMID_37075751_Individual18.json @@ -7,111 +7,128 @@ "iso8601duration": "P11Y" } }, + "vitalStatus": { + "status": "ALIVE" + }, "sex": "FEMALE" }, "phenotypicFeatures": [ { "type": { - "id": "HP:0001263", - "label": "Global developmental delay" + "id": "HP:0001655", + "label": "Patent foramen ovale" } }, { "type": { - "id": "HP:0000508", - "label": "Ptosis" + "id": "HP:0001629", + "label": "Ventricular septal defect" } }, { "type": { - "id": "HP:0001655", - "label": "Patent foramen ovale" + "id": "HP:0001263", + "label": "Global developmental delay" } }, { "type": { - "id": "HP:0001629", - "label": "Ventricular septal defect" + "id": "HP:0000347", + "label": "Micrognathia" } }, { "type": { - "id": "HP:0001647", - "label": "Bicuspid aortic valve" + "id": "HP:0004322", + "label": "Short stature" } }, { "type": { - "id": "HP:0011569", - "label": "Cleft anterior mitral valve leaflet" + "id": "HP:0001252", + "label": "Hypotonia" } }, { "type": { - "id": "HP:0040064", - "label": "Abnormality of limbs" + "id": "HP:0000508", + "label": "Ptosis" } }, { "type": { - "id": "HP:0001601", - "label": "Laryngomalacia" - } + "id": "HP:0000286", + "label": "Epicanthus" + }, + "excluded": true }, { "type": { - "id": "HP:0004937", - "label": "Pulmonary artery aneurysm" - } + "id": "HP:0000582", + "label": "Upslanted palpebral fissure" + }, + "excluded": true }, { "type": { - "id": "HP:0000347", - "label": "Micrognathia" - } + "id": "HP:0000637", + "label": "Long palpebral fissure" + }, + "excluded": true }, { "type": { - "id": "HP:0004942", - "label": "Aortic aneurysm" - } + "id": "HP:0011968", + "label": "Feeding difficulties" + }, + "excluded": true }, { "type": { - "id": "HP:0034392", - "label": "Joint contracture" - } + "id": "HP:0000324", + "label": "Facial asymmetry" + }, + "excluded": true }, { "type": { - "id": "HP:0011577", - "label": "Partial atrioventricular canal defect" - } + "id": "HP:0000430", + "label": "Underdeveloped nasal alae" + }, + "excluded": true }, { "type": { - "id": "HP:0001252", - "label": "Hypotonia" - } + "id": "HP:0000453", + "label": "Choanal atresia" + }, + "excluded": true }, { "type": { - "id": "HP:0001363", - "label": "Craniosynostosis" + "id": "HP:0012469", + "label": "Infantile spasms" }, "excluded": true }, { "type": { - "id": "HP:0410030", - "label": "Cleft lip" + "id": "HP:0010819", + "label": "Atonic seizure" }, "excluded": true }, { "type": { - "id": "HP:0011330", - "label": "Metopic synostosis" + "id": "HP:0001336", + "label": "Myoclonus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0200134", + "label": "Epileptic encephalopathy" }, "excluded": true }, @@ -124,15 +141,22 @@ }, { "type": { - "id": "HP:0000324", - "label": "Facial asymmetry" + "id": "HP:0000218", + "label": "High palate" }, "excluded": true }, { "type": { - "id": "HP:0008551", - "label": "Microtia" + "id": "HP:0000175", + "label": "Cleft palate" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000204", + "label": "Cleft upper lip" }, "excluded": true }, @@ -145,29 +169,92 @@ }, { "type": { - "id": "HP:0410263", - "label": "Brain imaging abnormality" + "id": "HP:0000463", + "label": "Anteverted nares" }, "excluded": true }, { "type": { - "id": "HP:0000175", - "label": "Cleft palate" + "id": "HP:0009921", + "label": "Duane anomaly" }, "excluded": true }, { "type": { - "id": "HP:0011443", - "label": "Abnormality of coordination" + "id": "HP:0000490", + "label": "Deeply set eye" }, "excluded": true }, { "type": { - "id": "HP:0012469", - "label": "Infantile spasms" + "id": "HP:0002650", + "label": "Scoliosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001605", + "label": "Vocal cord paralysis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0004209", + "label": "Clinodactyly of the 5th finger" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000625", + "label": "Eyelid coloboma" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0005280", + "label": "Depressed nasal bridge" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011330", + "label": "Metopic synostosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000365", + "label": "Hearing impairment" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0008551", + "label": "Microtia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000954", + "label": "Single transverse palmar crease" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000023", + "label": "Inguinal hernia" }, "excluded": true } @@ -187,7 +274,7 @@ "interpretationStatus": "CAUSATIVE", "variantInterpretation": { "variationDescriptor": { - "id": "var_wYGsPGrdztXjAslWdipZPaBXu", + "id": "var_GWKnvQcIqrJkffhfMTTwthiNX", "geneContext": { "valueId": "HGNC:17264", "symbol": "POLR1A" @@ -236,8 +323,8 @@ } ], "metaData": { - "created": "2024-03-24T09:33:00.916481971Z", - "createdBy": "ORCID:0000-0001-7941-2961", + "created": "2024-11-30T09:39:18.479452848Z", + "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { "id": "geno", @@ -275,7 +362,7 @@ "id": "hp", "name": "human phenotype ontology", "url": "http://purl.obolibrary.org/obo/hp.owl", - "version": "2024-03-06", + "version": "2024-08-13", "namespacePrefix": "HP", "iriPrefix": "http://purl.obolibrary.org/obo/HP_" } diff --git a/notebooks/POLR1A/phenopackets/PMID_37075751_Individual2.json b/notebooks/POLR1A/phenopackets/PMID_37075751_Individual2.json index bfb1dec6d..d7cac2f48 100644 --- a/notebooks/POLR1A/phenopackets/PMID_37075751_Individual2.json +++ b/notebooks/POLR1A/phenopackets/PMID_37075751_Individual2.json @@ -7,6 +7,9 @@ "iso8601duration": "P5Y" } }, + "vitalStatus": { + "status": "ALIVE" + }, "sex": "MALE" }, "phenotypicFeatures": [ @@ -16,6 +19,12 @@ "label": "Cleft palate" } }, + { + "type": { + "id": "HP:0000204", + "label": "Cleft upper lip" + } + }, { "type": { "id": "HP:0011330", @@ -24,42 +33,43 @@ }, { "type": { - "id": "HP:0410030", - "label": "Cleft lip" - } + "id": "HP:0000286", + "label": "Epicanthus" + }, + "excluded": true }, { "type": { - "id": "HP:0040064", - "label": "Abnormality of limbs" + "id": "HP:0000582", + "label": "Upslanted palpebral fissure" }, "excluded": true }, { "type": { - "id": "HP:0001655", - "label": "Patent foramen ovale" + "id": "HP:0000637", + "label": "Long palpebral fissure" }, "excluded": true }, { "type": { - "id": "HP:0008551", - "label": "Microtia" + "id": "HP:0001655", + "label": "Patent foramen ovale" }, "excluded": true }, { "type": { - "id": "HP:0000369", - "label": "Low-set ears" + "id": "HP:0001629", + "label": "Ventricular septal defect" }, "excluded": true }, { "type": { - "id": "HP:0001252", - "label": "Hypotonia" + "id": "HP:0011968", + "label": "Feeding difficulties" }, "excluded": true }, @@ -72,43 +82,50 @@ }, { "type": { - "id": "HP:0000508", - "label": "Ptosis" + "id": "HP:0000324", + "label": "Facial asymmetry" }, "excluded": true }, { "type": { - "id": "HP:0001629", - "label": "Ventricular septal defect" + "id": "HP:0000430", + "label": "Underdeveloped nasal alae" }, "excluded": true }, { "type": { - "id": "HP:0410263", - "label": "Brain imaging abnormality" + "id": "HP:0000453", + "label": "Choanal atresia" }, "excluded": true }, { "type": { - "id": "HP:0000347", - "label": "Micrognathia" + "id": "HP:0012469", + "label": "Infantile spasms" }, "excluded": true }, { "type": { - "id": "HP:0001511", - "label": "Intrauterine growth retardation" + "id": "HP:0010819", + "label": "Atonic seizure" }, "excluded": true }, { "type": { - "id": "HP:0034392", - "label": "Joint contracture" + "id": "HP:0001336", + "label": "Myoclonus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0200134", + "label": "Epileptic encephalopathy" }, "excluded": true }, @@ -128,22 +145,134 @@ }, { "type": { - "id": "HP:0000324", - "label": "Facial asymmetry" + "id": "HP:0000218", + "label": "High palate" }, "excluded": true }, { "type": { - "id": "HP:0011443", - "label": "Abnormality of coordination" + "id": "HP:0000369", + "label": "Low-set ears" }, "excluded": true }, { "type": { - "id": "HP:0012469", - "label": "Infantile spasms" + "id": "HP:0000463", + "label": "Anteverted nares" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000347", + "label": "Micrognathia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0009921", + "label": "Duane anomaly" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000490", + "label": "Deeply set eye" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002650", + "label": "Scoliosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001605", + "label": "Vocal cord paralysis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0004209", + "label": "Clinodactyly of the 5th finger" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000625", + "label": "Eyelid coloboma" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001252", + "label": "Hypotonia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0005280", + "label": "Depressed nasal bridge" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000508", + "label": "Ptosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000365", + "label": "Hearing impairment" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0008551", + "label": "Microtia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001511", + "label": "Intrauterine growth retardation" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000954", + "label": "Single transverse palmar crease" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000028", + "label": "Cryptorchidism" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000023", + "label": "Inguinal hernia" }, "excluded": true } @@ -163,27 +292,27 @@ "interpretationStatus": "CAUSATIVE", "variantInterpretation": { "variationDescriptor": { - "id": "var_wJAPvgrqsDDfSTtQcRXfFkabN", + "id": "var_GaofATkBLBliwWsfcGMnAKchx", "geneContext": { - "valueId": "HGNC:20194", - "symbol": "POLR1C" + "valueId": "HGNC:17264", + "symbol": "POLR1A" }, "expressions": [ { "syntax": "hgvs.c", - "value": "NM_203290.4:c.176A>T" + "value": "NM_015425.6:c.176A>T" }, { "syntax": "hgvs.g", - "value": "NC_000006.12:g.43519367A>T" + "value": "NC_000002.12:g.86100074T>A" } ], "vcfRecord": { "genomeAssembly": "hg38", - "chrom": "chr6", - "pos": "43519367", - "ref": "A", - "alt": "T" + "chrom": "chr2", + "pos": "86100074", + "ref": "T", + "alt": "A" }, "moleculeContext": "genomic", "allelicState": { @@ -212,8 +341,8 @@ } ], "metaData": { - "created": "2024-03-24T09:33:00.870954990Z", - "createdBy": "ORCID:0000-0001-7941-2961", + "created": "2024-11-30T09:39:18.467180967Z", + "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { "id": "geno", @@ -251,7 +380,7 @@ "id": "hp", "name": "human phenotype ontology", "url": "http://purl.obolibrary.org/obo/hp.owl", - "version": "2024-03-06", + "version": "2024-08-13", "namespacePrefix": "HP", "iriPrefix": "http://purl.obolibrary.org/obo/HP_" } diff --git a/notebooks/POLR1A/phenopackets/PMID_37075751_Individual3.json b/notebooks/POLR1A/phenopackets/PMID_37075751_Individual3.json index eda18c151..76bd95bba 100644 --- a/notebooks/POLR1A/phenopackets/PMID_37075751_Individual3.json +++ b/notebooks/POLR1A/phenopackets/PMID_37075751_Individual3.json @@ -4,34 +4,42 @@ "id": "Individual 3", "timeAtLastEncounter": { "age": { - "iso8601duration": "P1M26D" + "iso8601duration": "P8W" + } + }, + "vitalStatus": { + "status": "DECEASED", + "timeOfDeath": { + "age": { + "iso8601duration": "P8W" + } } }, "sex": "FEMALE" }, "phenotypicFeatures": [ - { - "type": { - "id": "HP:0001263", - "label": "Global developmental delay" - } - }, { "type": { "id": "HP:0000365", "label": "Hearing impairment" + }, + "onset": { + "ontologyClass": { + "id": "HP:0003577", + "label": "Congenital onset" + } } }, { "type": { - "id": "HP:0200128", - "label": "Biventricular hypertrophy" + "id": "HP:0001263", + "label": "Global developmental delay" } }, { "type": { - "id": "HP:0003764", - "label": "Nevus" + "id": "HP:0001252", + "label": "Hypotonia" } }, { @@ -42,14 +50,22 @@ }, { "type": { - "id": "HP:0001252", - "label": "Hypotonia" - } + "id": "HP:0000286", + "label": "Epicanthus" + }, + "excluded": true }, { "type": { - "id": "HP:0040064", - "label": "Abnormality of limbs" + "id": "HP:0000582", + "label": "Upslanted palpebral fissure" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000637", + "label": "Long palpebral fissure" }, "excluded": true }, @@ -62,71 +78,85 @@ }, { "type": { - "id": "HP:0008551", - "label": "Microtia" + "id": "HP:0001629", + "label": "Ventricular septal defect" }, "excluded": true }, { "type": { - "id": "HP:0000369", - "label": "Low-set ears" + "id": "HP:0011968", + "label": "Feeding difficulties" }, "excluded": true }, { "type": { - "id": "HP:0000256", - "label": "Macrocephaly" + "id": "HP:0000316", + "label": "Hypertelorism" }, "excluded": true }, { "type": { - "id": "HP:0001363", - "label": "Craniosynostosis" + "id": "HP:0000324", + "label": "Facial asymmetry" }, "excluded": true }, { "type": { - "id": "HP:0410030", - "label": "Cleft lip" + "id": "HP:0000430", + "label": "Underdeveloped nasal alae" }, "excluded": true }, { "type": { - "id": "HP:0000316", - "label": "Hypertelorism" + "id": "HP:0000453", + "label": "Choanal atresia" }, "excluded": true }, { "type": { - "id": "HP:0000508", - "label": "Ptosis" + "id": "HP:0012469", + "label": "Infantile spasms" }, "excluded": true }, { "type": { - "id": "HP:0001629", - "label": "Ventricular septal defect" + "id": "HP:0010819", + "label": "Atonic seizure" }, "excluded": true }, { "type": { - "id": "HP:0000347", - "label": "Micrognathia" + "id": "HP:0001336", + "label": "Myoclonus" }, "excluded": true }, { "type": { - "id": "HP:0001511", - "label": "Intrauterine growth retardation" + "id": "HP:0200134", + "label": "Epileptic encephalopathy" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002376", + "label": "Developmental regression" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000218", + "label": "High palate" }, "excluded": true }, @@ -139,8 +169,78 @@ }, { "type": { - "id": "HP:0034392", - "label": "Joint contracture" + "id": "HP:0000204", + "label": "Cleft upper lip" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000369", + "label": "Low-set ears" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000463", + "label": "Anteverted nares" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000347", + "label": "Micrognathia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0009921", + "label": "Duane anomaly" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000490", + "label": "Deeply set eye" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002650", + "label": "Scoliosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001605", + "label": "Vocal cord paralysis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0004209", + "label": "Clinodactyly of the 5th finger" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000625", + "label": "Eyelid coloboma" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0005280", + "label": "Depressed nasal bridge" }, "excluded": true }, @@ -153,8 +253,22 @@ }, { "type": { - "id": "HP:0002376", - "label": "Developmental regression" + "id": "HP:0000508", + "label": "Ptosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0008551", + "label": "Microtia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000256", + "label": "Macrocephaly" }, "excluded": true }, @@ -167,22 +281,29 @@ }, { "type": { - "id": "HP:0000324", - "label": "Facial asymmetry" + "id": "HP:0001511", + "label": "Intrauterine growth retardation" }, "excluded": true }, { "type": { - "id": "HP:0011443", - "label": "Abnormality of coordination" + "id": "HP:0000954", + "label": "Single transverse palmar crease" }, "excluded": true }, { "type": { - "id": "HP:0012469", - "label": "Infantile spasms" + "id": "HP:0000023", + "label": "Inguinal hernia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000238", + "label": "Hydrocephalus" }, "excluded": true } @@ -202,7 +323,7 @@ "interpretationStatus": "CAUSATIVE", "variantInterpretation": { "variationDescriptor": { - "id": "var_YqiHvswQLeEZoDqjbMsYDGDuf", + "id": "var_hMEfkvVMpQvuUeeizDWPWuSjZ", "geneContext": { "valueId": "HGNC:17264", "symbol": "POLR1A" @@ -251,8 +372,8 @@ } ], "metaData": { - "created": "2024-03-24T09:33:00.872559070Z", - "createdBy": "ORCID:0000-0001-7941-2961", + "created": "2024-11-30T09:39:18.467973947Z", + "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { "id": "geno", @@ -290,7 +411,7 @@ "id": "hp", "name": "human phenotype ontology", "url": "http://purl.obolibrary.org/obo/hp.owl", - "version": "2024-03-06", + "version": "2024-08-13", "namespacePrefix": "HP", "iriPrefix": "http://purl.obolibrary.org/obo/HP_" } diff --git a/notebooks/POLR1A/phenopackets/PMID_37075751_Individual4.json b/notebooks/POLR1A/phenopackets/PMID_37075751_Individual4.json index 16df787ea..f865ef7d2 100644 --- a/notebooks/POLR1A/phenopackets/PMID_37075751_Individual4.json +++ b/notebooks/POLR1A/phenopackets/PMID_37075751_Individual4.json @@ -7,13 +7,16 @@ "iso8601duration": "P11M" } }, + "vitalStatus": { + "status": "ALIVE" + }, "sex": "MALE" }, "phenotypicFeatures": [ { "type": { - "id": "HP:0000954", - "label": "Single transverse palmar crease" + "id": "HP:0000637", + "label": "Long palpebral fissure" } }, { @@ -24,45 +27,53 @@ }, { "type": { - "id": "HP:0000637", - "label": "Long palpebral fissure" + "id": "HP:0000463", + "label": "Anteverted nares" } }, { "type": { - "id": "HP:0011639", - "label": "Anomalous origin of right coronary artery from the pulmonary artery" + "id": "HP:0001605", + "label": "Vocal cord paralysis" } }, { "type": { - "id": "HP:0001605", - "label": "Vocal cord paralysis" + "id": "HP:0004209", + "label": "Clinodactyly of the 5th finger" } }, { "type": { - "id": "HP:0001800", - "label": "Hypoplastic toenails" + "id": "HP:0004322", + "label": "Short stature" } }, { "type": { - "id": "HP:0004209", - "label": "Clinodactyly of the 5th finger" + "id": "HP:0001252", + "label": "Hypotonia" } }, { "type": { - "id": "HP:0003196", - "label": "Short nose" + "id": "HP:0000954", + "label": "Single transverse palmar crease" } }, { "type": { - "id": "HP:0001252", - "label": "Hypotonia" - } + "id": "HP:0000286", + "label": "Epicanthus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000582", + "label": "Upslanted palpebral fissure" + }, + "excluded": true }, { "type": { @@ -73,78 +84,78 @@ }, { "type": { - "id": "HP:0008551", - "label": "Microtia" + "id": "HP:0001629", + "label": "Ventricular septal defect" }, "excluded": true }, { "type": { - "id": "HP:0000252", - "label": "Microcephaly" + "id": "HP:0011968", + "label": "Feeding difficulties" }, "excluded": true }, { "type": { - "id": "HP:0000256", - "label": "Macrocephaly" + "id": "HP:0000316", + "label": "Hypertelorism" }, "excluded": true }, { "type": { - "id": "HP:0001363", - "label": "Craniosynostosis" + "id": "HP:0000324", + "label": "Facial asymmetry" }, "excluded": true }, { "type": { - "id": "HP:0410030", - "label": "Cleft lip" + "id": "HP:0000430", + "label": "Underdeveloped nasal alae" }, "excluded": true }, { "type": { - "id": "HP:0000316", - "label": "Hypertelorism" + "id": "HP:0000453", + "label": "Choanal atresia" }, "excluded": true }, { "type": { - "id": "HP:0000508", - "label": "Ptosis" + "id": "HP:0012469", + "label": "Infantile spasms" }, "excluded": true }, { "type": { - "id": "HP:0001629", - "label": "Ventricular septal defect" + "id": "HP:0010819", + "label": "Atonic seizure" }, "excluded": true }, { "type": { - "id": "HP:0410263", - "label": "Brain imaging abnormality" + "id": "HP:0001336", + "label": "Myoclonus" }, "excluded": true }, { "type": { - "id": "HP:0000347", - "label": "Micrognathia" + "id": "HP:0200134", + "label": "Epileptic encephalopathy" }, "excluded": true }, { "type": { - "id": "HP:0001511", - "label": "Intrauterine growth retardation" + "id": "HP:0000218", + "label": "High palate" }, "excluded": true }, @@ -157,8 +168,50 @@ }, { "type": { - "id": "HP:0034392", - "label": "Joint contracture" + "id": "HP:0000204", + "label": "Cleft upper lip" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000347", + "label": "Micrognathia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0009921", + "label": "Duane anomaly" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000490", + "label": "Deeply set eye" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002650", + "label": "Scoliosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000625", + "label": "Eyelid coloboma" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0005280", + "label": "Depressed nasal bridge" }, "excluded": true }, @@ -171,22 +224,57 @@ }, { "type": { - "id": "HP:0000324", - "label": "Facial asymmetry" + "id": "HP:0000508", + "label": "Ptosis" }, "excluded": true }, { "type": { - "id": "HP:0011443", - "label": "Abnormality of coordination" + "id": "HP:0000365", + "label": "Hearing impairment" }, "excluded": true }, { "type": { - "id": "HP:0012469", - "label": "Infantile spasms" + "id": "HP:0008551", + "label": "Microtia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000252", + "label": "Microcephaly" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000256", + "label": "Macrocephaly" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001511", + "label": "Intrauterine growth retardation" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000028", + "label": "Cryptorchidism" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000023", + "label": "Inguinal hernia" }, "excluded": true } @@ -206,7 +294,7 @@ "interpretationStatus": "CAUSATIVE", "variantInterpretation": { "variationDescriptor": { - "id": "var_LUVepDdZPbDgRhbbDMfMHQFjL", + "id": "var_tGfyshcGYVZxFRDRCjbZryFgQ", "geneContext": { "valueId": "HGNC:17264", "symbol": "POLR1A" @@ -255,8 +343,8 @@ } ], "metaData": { - "created": "2024-03-24T09:33:00.874819040Z", - "createdBy": "ORCID:0000-0001-7941-2961", + "created": "2024-11-30T09:39:18.468759059Z", + "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { "id": "geno", @@ -294,7 +382,7 @@ "id": "hp", "name": "human phenotype ontology", "url": "http://purl.obolibrary.org/obo/hp.owl", - "version": "2024-03-06", + "version": "2024-08-13", "namespacePrefix": "HP", "iriPrefix": "http://purl.obolibrary.org/obo/HP_" } diff --git a/notebooks/POLR1A/phenopackets/PMID_37075751_Individual5.json b/notebooks/POLR1A/phenopackets/PMID_37075751_Individual5.json index 43bec66d1..b7c53b767 100644 --- a/notebooks/POLR1A/phenopackets/PMID_37075751_Individual5.json +++ b/notebooks/POLR1A/phenopackets/PMID_37075751_Individual5.json @@ -2,15 +2,12 @@ "id": "PMID_37075751_Individual_5", "subject": { "id": "Individual 5", + "vitalStatus": { + "status": "ALIVE" + }, "sex": "FEMALE" }, "phenotypicFeatures": [ - { - "type": { - "id": "HP:0000508", - "label": "Ptosis" - } - }, { "type": { "id": "HP:0001629", @@ -23,6 +20,12 @@ "label": "Vocal cord paralysis" } }, + { + "type": { + "id": "HP:0004322", + "label": "Short stature" + } + }, { "type": { "id": "HP:0001252", @@ -31,22 +34,42 @@ }, { "type": { - "id": "HP:0001363", - "label": "Craniosynostosis" + "id": "HP:0000508", + "label": "Ptosis" + } + }, + { + "type": { + "id": "HP:0000286", + "label": "Epicanthus" }, "excluded": true }, { "type": { - "id": "HP:0410030", - "label": "Cleft lip" + "id": "HP:0000582", + "label": "Upslanted palpebral fissure" }, "excluded": true }, { "type": { - "id": "HP:0000347", - "label": "Micrognathia" + "id": "HP:0000637", + "label": "Long palpebral fissure" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001655", + "label": "Patent foramen ovale" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011968", + "label": "Feeding difficulties" }, "excluded": true }, @@ -59,57 +82,57 @@ }, { "type": { - "id": "HP:0040064", - "label": "Abnormality of limbs" + "id": "HP:0000324", + "label": "Facial asymmetry" }, "excluded": true }, { "type": { - "id": "HP:0011330", - "label": "Metopic synostosis" + "id": "HP:0000430", + "label": "Underdeveloped nasal alae" }, "excluded": true }, { "type": { - "id": "HP:0034392", - "label": "Joint contracture" + "id": "HP:0000453", + "label": "Choanal atresia" }, "excluded": true }, { "type": { - "id": "HP:0001655", - "label": "Patent foramen ovale" + "id": "HP:0012469", + "label": "Infantile spasms" }, "excluded": true }, { "type": { - "id": "HP:0000324", - "label": "Facial asymmetry" + "id": "HP:0010819", + "label": "Atonic seizure" }, "excluded": true }, { "type": { - "id": "HP:0008551", - "label": "Microtia" + "id": "HP:0001336", + "label": "Myoclonus" }, "excluded": true }, { "type": { - "id": "HP:0000369", - "label": "Low-set ears" + "id": "HP:0200134", + "label": "Epileptic encephalopathy" }, "excluded": true }, { "type": { - "id": "HP:0410263", - "label": "Brain imaging abnormality" + "id": "HP:0000218", + "label": "High palate" }, "excluded": true }, @@ -122,8 +145,106 @@ }, { "type": { - "id": "HP:0012469", - "label": "Infantile spasms" + "id": "HP:0000204", + "label": "Cleft upper lip" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000369", + "label": "Low-set ears" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000463", + "label": "Anteverted nares" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000347", + "label": "Micrognathia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0009921", + "label": "Duane anomaly" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000490", + "label": "Deeply set eye" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002650", + "label": "Scoliosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0004209", + "label": "Clinodactyly of the 5th finger" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000625", + "label": "Eyelid coloboma" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0005280", + "label": "Depressed nasal bridge" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011330", + "label": "Metopic synostosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000365", + "label": "Hearing impairment" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0008551", + "label": "Microtia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000954", + "label": "Single transverse palmar crease" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000023", + "label": "Inguinal hernia" }, "excluded": true } @@ -143,7 +264,7 @@ "interpretationStatus": "CAUSATIVE", "variantInterpretation": { "variationDescriptor": { - "id": "var_LUVepDdZPbDgRhbbDMfMHQFjL", + "id": "var_tGfyshcGYVZxFRDRCjbZryFgQ", "geneContext": { "valueId": "HGNC:17264", "symbol": "POLR1A" @@ -186,8 +307,8 @@ } ], "metaData": { - "created": "2024-03-24T09:33:00.886000156Z", - "createdBy": "ORCID:0000-0001-7941-2961", + "created": "2024-11-30T09:39:18.469804048Z", + "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { "id": "geno", @@ -225,7 +346,7 @@ "id": "hp", "name": "human phenotype ontology", "url": "http://purl.obolibrary.org/obo/hp.owl", - "version": "2024-03-06", + "version": "2024-08-13", "namespacePrefix": "HP", "iriPrefix": "http://purl.obolibrary.org/obo/HP_" } diff --git a/notebooks/POLR1A/phenopackets/PMID_37075751_Individual6.json b/notebooks/POLR1A/phenopackets/PMID_37075751_Individual6.json index b4fcf0ab7..a623fe0fc 100644 --- a/notebooks/POLR1A/phenopackets/PMID_37075751_Individual6.json +++ b/notebooks/POLR1A/phenopackets/PMID_37075751_Individual6.json @@ -7,25 +7,34 @@ "iso8601duration": "P10Y4M" } }, + "vitalStatus": { + "status": "ALIVE" + }, "sex": "FEMALE" }, "phenotypicFeatures": [ { "type": { - "id": "HP:0000668", - "label": "Hypodontia" + "id": "HP:0000316", + "label": "Hypertelorism" } }, { "type": { - "id": "HP:0000238", - "label": "Hydrocephalus" + "id": "HP:0000324", + "label": "Facial asymmetry" } }, { "type": { - "id": "HP:0000316", - "label": "Hypertelorism" + "id": "HP:0000668", + "label": "Hypodontia" + } + }, + { + "type": { + "id": "HP:0000453", + "label": "Choanal atresia" } }, { @@ -42,8 +51,8 @@ }, { "type": { - "id": "HP:0000324", - "label": "Facial asymmetry" + "id": "HP:0000347", + "label": "Micrognathia" } }, { @@ -54,32 +63,34 @@ }, { "type": { - "id": "HP:0004502", - "label": "Bilateral choanal atresia" + "id": "HP:0001511", + "label": "Intrauterine growth retardation" } }, { "type": { - "id": "HP:0000347", - "label": "Micrognathia" + "id": "HP:0000238", + "label": "Hydrocephalus" } }, { "type": { - "id": "HP:0003396", - "label": "Syringomyelia" - } + "id": "HP:0000286", + "label": "Epicanthus" + }, + "excluded": true }, { "type": { - "id": "HP:0001511", - "label": "Intrauterine growth retardation" - } + "id": "HP:0000582", + "label": "Upslanted palpebral fissure" + }, + "excluded": true }, { "type": { - "id": "HP:0040064", - "label": "Abnormality of limbs" + "id": "HP:0000637", + "label": "Long palpebral fissure" }, "excluded": true }, @@ -92,78 +103,148 @@ }, { "type": { - "id": "HP:0008551", - "label": "Microtia" + "id": "HP:0001629", + "label": "Ventricular septal defect" }, "excluded": true }, { "type": { - "id": "HP:0000252", - "label": "Microcephaly" + "id": "HP:0011968", + "label": "Feeding difficulties" }, "excluded": true }, { "type": { - "id": "HP:0000256", - "label": "Macrocephaly" + "id": "HP:0000430", + "label": "Underdeveloped nasal alae" }, "excluded": true }, { "type": { - "id": "HP:0001363", - "label": "Craniosynostosis" + "id": "HP:0012469", + "label": "Infantile spasms" }, "excluded": true }, { "type": { - "id": "HP:0001252", - "label": "Hypotonia" + "id": "HP:0010819", + "label": "Atonic seizure" }, "excluded": true }, { "type": { - "id": "HP:0410030", - "label": "Cleft lip" + "id": "HP:0001336", + "label": "Myoclonus" }, "excluded": true }, { "type": { - "id": "HP:0000508", - "label": "Ptosis" + "id": "HP:0200134", + "label": "Epileptic encephalopathy" }, "excluded": true }, { "type": { - "id": "HP:0001629", - "label": "Ventricular septal defect" + "id": "HP:0001263", + "label": "Global developmental delay" }, "excluded": true }, { "type": { - "id": "HP:0034392", - "label": "Joint contracture" + "id": "HP:0002376", + "label": "Developmental regression" }, "excluded": true }, { "type": { - "id": "HP:0001263", - "label": "Global developmental delay" + "id": "HP:0000218", + "label": "High palate" }, "excluded": true }, { "type": { - "id": "HP:0001249", - "label": "Intellectual disability" + "id": "HP:0000204", + "label": "Cleft upper lip" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000463", + "label": "Anteverted nares" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0009921", + "label": "Duane anomaly" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000490", + "label": "Deeply set eye" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002650", + "label": "Scoliosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001605", + "label": "Vocal cord paralysis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0004209", + "label": "Clinodactyly of the 5th finger" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0004322", + "label": "Short stature" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000625", + "label": "Eyelid coloboma" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001252", + "label": "Hypotonia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0005280", + "label": "Depressed nasal bridge" }, "excluded": true }, @@ -176,22 +257,50 @@ }, { "type": { - "id": "HP:0002376", - "label": "Developmental regression" + "id": "HP:0000508", + "label": "Ptosis" }, "excluded": true }, { "type": { - "id": "HP:0011443", - "label": "Abnormality of coordination" + "id": "HP:0000365", + "label": "Hearing impairment" }, "excluded": true }, { "type": { - "id": "HP:0012469", - "label": "Infantile spasms" + "id": "HP:0008551", + "label": "Microtia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000252", + "label": "Microcephaly" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000256", + "label": "Macrocephaly" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000954", + "label": "Single transverse palmar crease" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000023", + "label": "Inguinal hernia" }, "excluded": true } @@ -211,7 +320,7 @@ "interpretationStatus": "CAUSATIVE", "variantInterpretation": { "variationDescriptor": { - "id": "var_ZBBxQUiAjGGjlYdsisHpdwxuh", + "id": "var_DvSEsdeGVnhrxFpLMUSUfgnDt", "geneContext": { "valueId": "HGNC:17264", "symbol": "POLR1A" @@ -260,8 +369,8 @@ } ], "metaData": { - "created": "2024-03-24T09:33:00.888334035Z", - "createdBy": "ORCID:0000-0001-7941-2961", + "created": "2024-11-30T09:39:18.470554113Z", + "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { "id": "geno", @@ -299,7 +408,7 @@ "id": "hp", "name": "human phenotype ontology", "url": "http://purl.obolibrary.org/obo/hp.owl", - "version": "2024-03-06", + "version": "2024-08-13", "namespacePrefix": "HP", "iriPrefix": "http://purl.obolibrary.org/obo/HP_" } diff --git a/notebooks/POLR1A/phenopackets/PMID_37075751_Individual7.json b/notebooks/POLR1A/phenopackets/PMID_37075751_Individual7.json index fead24075..99d0f9e88 100644 --- a/notebooks/POLR1A/phenopackets/PMID_37075751_Individual7.json +++ b/notebooks/POLR1A/phenopackets/PMID_37075751_Individual7.json @@ -7,19 +7,22 @@ "iso8601duration": "P44Y" } }, + "vitalStatus": { + "status": "ALIVE" + }, "sex": "FEMALE" }, "phenotypicFeatures": [ { "type": { - "id": "HP:0000175", - "label": "Cleft palate" + "id": "HP:0000316", + "label": "Hypertelorism" } }, { "type": { - "id": "HP:0000347", - "label": "Micrognathia" + "id": "HP:0000175", + "label": "Cleft palate" } }, { @@ -30,14 +33,28 @@ }, { "type": { - "id": "HP:0000316", - "label": "Hypertelorism" + "id": "HP:0000347", + "label": "Micrognathia" } }, { "type": { - "id": "HP:0040064", - "label": "Abnormality of limbs" + "id": "HP:0000286", + "label": "Epicanthus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000582", + "label": "Upslanted palpebral fissure" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000637", + "label": "Long palpebral fissure" }, "excluded": true }, @@ -50,71 +67,71 @@ }, { "type": { - "id": "HP:0008551", - "label": "Microtia" + "id": "HP:0001629", + "label": "Ventricular septal defect" }, "excluded": true }, { "type": { - "id": "HP:0000252", - "label": "Microcephaly" + "id": "HP:0011968", + "label": "Feeding difficulties" }, "excluded": true }, { "type": { - "id": "HP:0000256", - "label": "Macrocephaly" + "id": "HP:0000324", + "label": "Facial asymmetry" }, "excluded": true }, { "type": { - "id": "HP:0001363", - "label": "Craniosynostosis" + "id": "HP:0000668", + "label": "Hypodontia" }, "excluded": true }, { "type": { - "id": "HP:0001252", - "label": "Hypotonia" + "id": "HP:0000430", + "label": "Underdeveloped nasal alae" }, "excluded": true }, { "type": { - "id": "HP:0410030", - "label": "Cleft lip" + "id": "HP:0000453", + "label": "Choanal atresia" }, "excluded": true }, { "type": { - "id": "HP:0000508", - "label": "Ptosis" + "id": "HP:0012469", + "label": "Infantile spasms" }, "excluded": true }, { "type": { - "id": "HP:0001629", - "label": "Ventricular septal defect" + "id": "HP:0010819", + "label": "Atonic seizure" }, "excluded": true }, { "type": { - "id": "HP:0410263", - "label": "Brain imaging abnormality" + "id": "HP:0001336", + "label": "Myoclonus" }, "excluded": true }, { "type": { - "id": "HP:0034392", - "label": "Joint contracture" + "id": "HP:0200134", + "label": "Epileptic encephalopathy" }, "excluded": true }, @@ -125,6 +142,90 @@ }, "excluded": true }, + { + "type": { + "id": "HP:0002376", + "label": "Developmental regression" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000218", + "label": "High palate" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000204", + "label": "Cleft upper lip" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000463", + "label": "Anteverted nares" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0009921", + "label": "Duane anomaly" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000490", + "label": "Deeply set eye" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002650", + "label": "Scoliosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001605", + "label": "Vocal cord paralysis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0004209", + "label": "Clinodactyly of the 5th finger" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000625", + "label": "Eyelid coloboma" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001252", + "label": "Hypotonia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0005280", + "label": "Depressed nasal bridge" + }, + "excluded": true + }, { "type": { "id": "HP:0011330", @@ -134,15 +235,36 @@ }, { "type": { - "id": "HP:0000668", - "label": "Hypodontia" + "id": "HP:0000508", + "label": "Ptosis" }, "excluded": true }, { "type": { - "id": "HP:0002376", - "label": "Developmental regression" + "id": "HP:0000365", + "label": "Hearing impairment" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0008551", + "label": "Microtia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000252", + "label": "Microcephaly" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000256", + "label": "Macrocephaly" }, "excluded": true }, @@ -155,22 +277,22 @@ }, { "type": { - "id": "HP:0000324", - "label": "Facial asymmetry" + "id": "HP:0000954", + "label": "Single transverse palmar crease" }, "excluded": true }, { "type": { - "id": "HP:0011443", - "label": "Abnormality of coordination" + "id": "HP:0000023", + "label": "Inguinal hernia" }, "excluded": true }, { "type": { - "id": "HP:0012469", - "label": "Infantile spasms" + "id": "HP:0000238", + "label": "Hydrocephalus" }, "excluded": true } @@ -190,7 +312,7 @@ "interpretationStatus": "CAUSATIVE", "variantInterpretation": { "variationDescriptor": { - "id": "var_ZBBxQUiAjGGjlYdsisHpdwxuh", + "id": "var_DvSEsdeGVnhrxFpLMUSUfgnDt", "geneContext": { "valueId": "HGNC:17264", "symbol": "POLR1A" @@ -239,8 +361,8 @@ } ], "metaData": { - "created": "2024-03-24T09:33:00.890089988Z", - "createdBy": "ORCID:0000-0001-7941-2961", + "created": "2024-11-30T09:39:18.471320152Z", + "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { "id": "geno", @@ -278,7 +400,7 @@ "id": "hp", "name": "human phenotype ontology", "url": "http://purl.obolibrary.org/obo/hp.owl", - "version": "2024-03-06", + "version": "2024-08-13", "namespacePrefix": "HP", "iriPrefix": "http://purl.obolibrary.org/obo/HP_" } diff --git a/notebooks/POLR1A/phenopackets/PMID_37075751_Individual8.json b/notebooks/POLR1A/phenopackets/PMID_37075751_Individual8.json index a57c646df..de1bbf748 100644 --- a/notebooks/POLR1A/phenopackets/PMID_37075751_Individual8.json +++ b/notebooks/POLR1A/phenopackets/PMID_37075751_Individual8.json @@ -7,151 +7,164 @@ "iso8601duration": "P2Y" } }, + "vitalStatus": { + "status": "DECEASED", + "timeOfDeath": { + "age": { + "iso8601duration": "P2Y" + } + } + }, "sex": "MALE" }, "phenotypicFeatures": [ { "type": { - "id": "HP:0001362", - "label": "Calvarial skull defect" + "id": "HP:0001655", + "label": "Patent foramen ovale" } }, { "type": { - "id": "HP:0001263", - "label": "Global developmental delay" + "id": "HP:0000316", + "label": "Hypertelorism" } }, { "type": { - "id": "HP:0008551", - "label": "Microtia" + "id": "HP:0001250", + "label": "Seizure" } }, { "type": { - "id": "HP:0001250", - "label": "Seizure" + "id": "HP:0001263", + "label": "Global developmental delay" } }, { "type": { - "id": "HP:0001655", - "label": "Patent foramen ovale" + "id": "HP:0000369", + "label": "Low-set ears" } }, { "type": { - "id": "HP:0000316", - "label": "Hypertelorism" + "id": "HP:0000347", + "label": "Micrognathia" } }, { "type": { - "id": "HP:0000126", - "label": "Hydronephrosis" + "id": "HP:0000625", + "label": "Eyelid coloboma" } }, { "type": { - "id": "HP:0002015", - "label": "Dysphagia" + "id": "HP:0001252", + "label": "Hypotonia" } }, { "type": { - "id": "HP:0000369", - "label": "Low-set ears" + "id": "HP:0008551", + "label": "Microtia" } }, { "type": { - "id": "HP:0040064", - "label": "Abnormality of limbs" + "id": "HP:0000252", + "label": "Microcephaly" } }, { "type": { - "id": "HP:0000636", - "label": "Upper eyelid coloboma" + "id": "HP:0000028", + "label": "Cryptorchidism" } }, { "type": { - "id": "HP:0000347", - "label": "Micrognathia" - } + "id": "HP:0000286", + "label": "Epicanthus" + }, + "excluded": true }, { "type": { - "id": "HP:0008689", - "label": "Bilateral cryptorchidism" - } + "id": "HP:0000582", + "label": "Upslanted palpebral fissure" + }, + "excluded": true }, { "type": { - "id": "HP:0000252", - "label": "Microcephaly" - } + "id": "HP:0000637", + "label": "Long palpebral fissure" + }, + "excluded": true }, { "type": { - "id": "HP:0002835", - "label": "Aspiration" - } + "id": "HP:0001629", + "label": "Ventricular septal defect" + }, + "excluded": true }, { "type": { - "id": "HP:0001252", - "label": "Hypotonia" - } + "id": "HP:0011968", + "label": "Feeding difficulties" + }, + "excluded": true }, { "type": { - "id": "HP:0001363", - "label": "Craniosynostosis" + "id": "HP:0000324", + "label": "Facial asymmetry" }, "excluded": true }, { "type": { - "id": "HP:0410030", - "label": "Cleft lip" + "id": "HP:0000430", + "label": "Underdeveloped nasal alae" }, "excluded": true }, { "type": { - "id": "HP:0011330", - "label": "Metopic synostosis" + "id": "HP:0000453", + "label": "Choanal atresia" }, "excluded": true }, { "type": { - "id": "HP:0001511", - "label": "Intrauterine growth retardation" + "id": "HP:0012469", + "label": "Infantile spasms" }, "excluded": true }, { "type": { - "id": "HP:0000508", - "label": "Ptosis" + "id": "HP:0010819", + "label": "Atonic seizure" }, "excluded": true }, { "type": { - "id": "HP:0034392", - "label": "Joint contracture" + "id": "HP:0001336", + "label": "Myoclonus" }, "excluded": true }, { "type": { - "id": "HP:0001629", - "label": "Ventricular septal defect" + "id": "HP:0200134", + "label": "Epileptic encephalopathy" }, "excluded": true }, @@ -164,15 +177,99 @@ }, { "type": { - "id": "HP:0002119", - "label": "Ventriculomegaly" + "id": "HP:0000218", + "label": "High palate" }, "excluded": true }, { "type": { - "id": "HP:0000324", - "label": "Facial asymmetry" + "id": "HP:0000175", + "label": "Cleft palate" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000204", + "label": "Cleft upper lip" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000463", + "label": "Anteverted nares" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0009921", + "label": "Duane anomaly" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000490", + "label": "Deeply set eye" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002650", + "label": "Scoliosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001605", + "label": "Vocal cord paralysis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0004209", + "label": "Clinodactyly of the 5th finger" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0004322", + "label": "Short stature" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0005280", + "label": "Depressed nasal bridge" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011330", + "label": "Metopic synostosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000508", + "label": "Ptosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000365", + "label": "Hearing impairment" }, "excluded": true }, @@ -185,22 +282,36 @@ }, { "type": { - "id": "HP:0000175", - "label": "Cleft palate" + "id": "HP:0002119", + "label": "Ventriculomegaly" }, "excluded": true }, { "type": { - "id": "HP:0011443", - "label": "Abnormality of coordination" + "id": "HP:0001511", + "label": "Intrauterine growth retardation" }, "excluded": true }, { "type": { - "id": "HP:0012469", - "label": "Infantile spasms" + "id": "HP:0000954", + "label": "Single transverse palmar crease" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000023", + "label": "Inguinal hernia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000238", + "label": "Hydrocephalus" }, "excluded": true } @@ -220,7 +331,7 @@ "interpretationStatus": "CAUSATIVE", "variantInterpretation": { "variationDescriptor": { - "id": "var_iygScrwwlerUfZjpHwSJuzbMr", + "id": "var_MPrdmHWPVpfqeRylKUlSmnaTe", "geneContext": { "valueId": "HGNC:17264", "symbol": "POLR1A" @@ -269,8 +380,8 @@ } ], "metaData": { - "created": "2024-03-24T09:33:00.892151117Z", - "createdBy": "ORCID:0000-0001-7941-2961", + "created": "2024-11-30T09:39:18.472112178Z", + "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { "id": "geno", @@ -308,7 +419,7 @@ "id": "hp", "name": "human phenotype ontology", "url": "http://purl.obolibrary.org/obo/hp.owl", - "version": "2024-03-06", + "version": "2024-08-13", "namespacePrefix": "HP", "iriPrefix": "http://purl.obolibrary.org/obo/HP_" } diff --git a/notebooks/POLR1A/phenopackets/PMID_37075751_Individual9.json b/notebooks/POLR1A/phenopackets/PMID_37075751_Individual9.json index aedf88244..15f9ce239 100644 --- a/notebooks/POLR1A/phenopackets/PMID_37075751_Individual9.json +++ b/notebooks/POLR1A/phenopackets/PMID_37075751_Individual9.json @@ -7,19 +7,22 @@ "iso8601duration": "P4Y" } }, + "vitalStatus": { + "status": "ALIVE" + }, "sex": "MALE" }, "phenotypicFeatures": [ { "type": { - "id": "HP:0000337", - "label": "Broad forehead" + "id": "HP:0000286", + "label": "Epicanthus" } }, { "type": { - "id": "HP:0008551", - "label": "Microtia" + "id": "HP:0000582", + "label": "Upslanted palpebral fissure" } }, { @@ -30,8 +33,26 @@ }, { "type": { - "id": "HP:0000490", - "label": "Deeply set eye" + "id": "HP:0000430", + "label": "Underdeveloped nasal alae" + } + }, + { + "type": { + "id": "HP:0010819", + "label": "Atonic seizure" + } + }, + { + "type": { + "id": "HP:0001336", + "label": "Myoclonus" + } + }, + { + "type": { + "id": "HP:0200134", + "label": "Epileptic encephalopathy" } }, { @@ -42,65 +63,94 @@ }, { "type": { - "id": "HP:0011443", - "label": "Abnormality of coordination" + "id": "HP:0000463", + "label": "Anteverted nares" } }, { "type": { - "id": "HP:0001305", - "label": "Dandy-Walker malformation" + "id": "HP:0000490", + "label": "Deeply set eye" } }, { "type": { - "id": "HP:0001336", - "label": "Myoclonus" + "id": "HP:0004322", + "label": "Short stature" } }, { "type": { - "id": "HP:0200134", - "label": "Epileptic encephalopathy" + "id": "HP:0005280", + "label": "Depressed nasal bridge" } }, { "type": { - "id": "HP:0010819", - "label": "Atonic seizure" + "id": "HP:0008551", + "label": "Microtia" } }, { "type": { - "id": "HP:0000574", - "label": "Thick eyebrow" - } + "id": "HP:0000637", + "label": "Long palpebral fissure" + }, + "excluded": true }, { "type": { - "id": "HP:0001363", - "label": "Craniosynostosis" + "id": "HP:0000324", + "label": "Facial asymmetry" }, "excluded": true }, { "type": { - "id": "HP:0001252", - "label": "Hypotonia" + "id": "HP:0000668", + "label": "Hypodontia" }, "excluded": true }, { "type": { - "id": "HP:0410030", - "label": "Cleft lip" + "id": "HP:0000453", + "label": "Choanal atresia" }, "excluded": true }, { "type": { - "id": "HP:0000347", - "label": "Micrognathia" + "id": "HP:0012469", + "label": "Infantile spasms" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001263", + "label": "Global developmental delay" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000218", + "label": "High palate" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000175", + "label": "Cleft palate" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000204", + "label": "Cleft upper lip" }, "excluded": true }, @@ -113,50 +163,71 @@ }, { "type": { - "id": "HP:0040064", - "label": "Abnormality of limbs" + "id": "HP:0000347", + "label": "Micrognathia" }, "excluded": true }, { "type": { - "id": "HP:0011330", - "label": "Metopic synostosis" + "id": "HP:0009921", + "label": "Duane anomaly" }, "excluded": true }, { "type": { - "id": "HP:0001511", - "label": "Intrauterine growth retardation" + "id": "HP:0002650", + "label": "Scoliosis" }, "excluded": true }, { "type": { - "id": "HP:0000668", - "label": "Hypodontia" + "id": "HP:0001605", + "label": "Vocal cord paralysis" }, "excluded": true }, { "type": { - "id": "HP:0000508", - "label": "Ptosis" + "id": "HP:0004209", + "label": "Clinodactyly of the 5th finger" }, "excluded": true }, { "type": { - "id": "HP:0034392", - "label": "Joint contracture" + "id": "HP:0000625", + "label": "Eyelid coloboma" }, "excluded": true }, { "type": { - "id": "HP:0000324", - "label": "Facial asymmetry" + "id": "HP:0001252", + "label": "Hypotonia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011330", + "label": "Metopic synostosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000508", + "label": "Ptosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000365", + "label": "Hearing impairment" }, "excluded": true }, @@ -176,15 +247,43 @@ }, { "type": { - "id": "HP:0000175", - "label": "Cleft palate" + "id": "HP:0002119", + "label": "Ventriculomegaly" }, "excluded": true }, { "type": { - "id": "HP:0012469", - "label": "Infantile spasms" + "id": "HP:0001511", + "label": "Intrauterine growth retardation" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000954", + "label": "Single transverse palmar crease" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000028", + "label": "Cryptorchidism" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000023", + "label": "Inguinal hernia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000238", + "label": "Hydrocephalus" }, "excluded": true } @@ -204,7 +303,7 @@ "interpretationStatus": "CAUSATIVE", "variantInterpretation": { "variationDescriptor": { - "id": "var_FLylsbyProaBQQMXGVhqQjDpm", + "id": "var_gGmYppVGtCJDRobsZiyardnFc", "geneContext": { "valueId": "HGNC:17264", "symbol": "POLR1A" @@ -253,8 +352,8 @@ } ], "metaData": { - "created": "2024-03-24T09:33:00.894276142Z", - "createdBy": "ORCID:0000-0001-7941-2961", + "created": "2024-11-30T09:39:18.472865104Z", + "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { "id": "geno", @@ -292,7 +391,7 @@ "id": "hp", "name": "human phenotype ontology", "url": "http://purl.obolibrary.org/obo/hp.owl", - "version": "2024-03-06", + "version": "2024-08-13", "namespacePrefix": "HP", "iriPrefix": "http://purl.obolibrary.org/obo/HP_" }