diff --git a/notebooks/NFU1/NFU1_SPG93_individuals.ipynb b/notebooks/NFU1/NFU1_SPG93_individuals.ipynb new file mode 100644 index 00000000..c9f73b46 --- /dev/null +++ b/notebooks/NFU1/NFU1_SPG93_individuals.ipynb @@ -0,0 +1,289 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# NFU1\n", + "[autosomal recessive spastic paraplegia-93 (SPG93) ](https://omim.org/entry/620938) is caused by homozygous or compound heterozygous mutation in the NFU1 gene." + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Using pyphetools version 0.9.115\n" + ] + } + ], + "source": [ + "from pyphetools.creation import TemplateImporter, Moi\n", + "from pyphetools.visualization import IndividualTable, QcVisualizer\n", + "from IPython.display import display, HTML\n", + "import pyphetools\n", + "print(f\"Using pyphetools version {pyphetools.__version__}\")" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "template = \"input/NFU1_SPG93_individuals.xlsx\"\n", + "created_by = \"0000-0002-0736-9199\"" + ] + }, + { + "cell_type": "code", + "execution_count": 28, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "HPO version 2024-12-12\n", + "Created encoders for 63 fields\n", + "Importing OMIM:620938, Spastic paraplegia 93, autosomal recessive, HGNC:16287, NFU1, NM_001002755.4\n", + "We output 21 GA4GH phenopackets to the directory phenopackets\n" + ] + } + ], + "source": [ + "timporter = TemplateImporter(template=template, created_by=created_by)\n", + "individual_list, cvalidator = timporter.import_phenopackets_from_template()" + ] + }, + { + "cell_type": "code", + "execution_count": 29, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "

Cohort validation

\n", + "

Errors found with 17 of 21 phenopackets.

\n", + "\n", + "\n", + "\n", + "\n", + "
Error counts
LevelError categoryCount
WARNINGREDUNDANT21
\n", + "

A total of 21 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": 30, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "
21 phenopackets - PMID:36256512 (n=19); PMID:25758857 (n=1); PMID:32747156 (n=1)
IndividualDiseaseGenotypePhenotypic features
F1-II:1 (FEMALE; P17Y)Spastic paraplegia 93, autosomal recessive (OMIM:620938)NM_001002755.4:c.721G>C (homozygous)Developmental regression (HP:0002376): onset ; Strabismus (HP:0000486): onset ; External ophthalmoplegia (HP:0000544): onset ; Brisk reflexes (HP:0001348): onset ; Hypoplasia of the corpus callosum (HP:0002079): onset ; Enlarged cisterna magna (HP:0002280): onset ; excluded: Global developmental delay (HP:0001263): onset ; excluded: Lactic acidosis (HP:0003128): onset ; excluded: Nystagmus (HP:0000639): onset ; excluded: Optic atrophy (HP:0000648): onset ; excluded: Ptosis (HP:0000508): onset ; excluded: Knee clonus (HP:0011449): onset ; excluded: Ankle clonus (HP:0011448): onset ; excluded: Babinski sign (HP:0003487): onset ; excluded: Reduced cerebral white matter volume (HP:0034295): onset ; excluded: Peripheral demyelination (HP:0011096): onset ; excluded: Encephalopathy (HP:0001298): onset ; excluded: Talipes equinovarus (HP:0001762): onset ; excluded: Peripheral neuropathy (HP:0009830): onset
TimeElement(element=Age(iso8601duration=P9M14D)): Spastic paraplegia (HP:0001258): onset age {\n", + " iso8601duration: \"P9M14D\"\n", + "}\n", + "
F1-II:2 (FEMALE; P10Y)Spastic paraplegia 93, autosomal recessive (OMIM:620938)NM_001002755.4:c.721G>C (homozygous)Delayed ability to walk (HP:0031936): onset ; Strabismus (HP:0000486): onset ; Hypertonia (HP:0001276): onset ; Brisk reflexes (HP:0001348): onset ; Reduced cerebral white matter volume (HP:0034295): onset ; Hypoplasia of the corpus callosum (HP:0002079): onset ; Enlarged cisterna magna (HP:0002280): onset ; excluded: Global developmental delay (HP:0001263): onset ; excluded: Lactic acidosis (HP:0003128): onset ; excluded: Developmental regression (HP:0002376): onset ; excluded: Nystagmus (HP:0000639): onset ; excluded: Optic atrophy (HP:0000648): onset ; excluded: Ptosis (HP:0000508): onset ; excluded: External ophthalmoplegia (HP:0000544): onset ; excluded: Knee clonus (HP:0011449): onset ; excluded: Ankle clonus (HP:0011448): onset ; excluded: Babinski sign (HP:0003487): onset ; excluded: Peripheral demyelination (HP:0011096): onset ; excluded: Encephalopathy (HP:0001298): onset ; excluded: Talipes equinovarus (HP:0001762): onset ; excluded: Peripheral neuropathy (HP:0009830): onset
TimeElement(element=Age(iso8601duration=P6M)): Paraplegia (HP:0010550): onset age {\n", + " iso8601duration: \"P6M\"\n", + "}\n", + "
F2-II:1 (MALE; P25Y)Spastic paraplegia 93, autosomal recessive (OMIM:620938)
  • NM_001002755.4:c.298G>C (heterozygous)
  • NM_001002755.4:c.301A>G (heterozygous)
Developmental regression (HP:0002376): onset ; Hypertonia (HP:0001276): onset ; Brisk reflexes (HP:0001348): onset ; Clonus (HP:0002169): onset ; excluded: Gait ataxia (HP:0002066): onset ; excluded: Global developmental delay (HP:0001263): onset ; excluded: Lactic acidosis (HP:0003128): onset ; excluded: Babinski sign (HP:0003487): onset ; excluded: Reduced cerebral white matter volume (HP:0034295): onset ; excluded: Hypoplasia of the corpus callosum (HP:0002079): onset ; excluded: Peripheral demyelination (HP:0011096): onset ; excluded: Enlarged cisterna magna (HP:0002280): onset ; excluded: Encephalopathy (HP:0001298): onset ; excluded: Talipes equinovarus (HP:0001762): onset ; excluded: Peripheral neuropathy (HP:0009830): onset
TimeElement(element=Age(iso8601duration=P1Y)): Paraplegia (HP:0010550): onset age {\n", + " iso8601duration: \"P1Y\"\n", + "}\n", + "
F3-II:1 (FEMALE; P12Y)Spastic paraplegia 93, autosomal recessive (OMIM:620938)NM_001002755.4:c.362T>C (homozygous)Global developmental delay (HP:0001263): onset ; Delayed ability to walk (HP:0031936): onset ; Hypertonia (HP:0001276): onset ; Brisk reflexes (HP:0001348): onset ; Knee clonus (HP:0011449): onset ; excluded: Gait ataxia (HP:0002066): onset ; excluded: Lactic acidosis (HP:0003128): onset ; excluded: Developmental regression (HP:0002376): onset ; excluded: Ankle clonus (HP:0011448): onset ; excluded: Babinski sign (HP:0003487): onset ; excluded: Reduced cerebral white matter volume (HP:0034295): onset ; excluded: Hypoplasia of the corpus callosum (HP:0002079): onset ; excluded: Peripheral demyelination (HP:0011096): onset ; excluded: Enlarged cisterna magna (HP:0002280): onset ; excluded: Encephalopathy (HP:0001298): onset ; excluded: Talipes equinovarus (HP:0001762): onset ; excluded: Peripheral neuropathy (HP:0009830): onset
TimeElement(element=Age(iso8601duration=P1Y)): Paraplegia (HP:0010550): onset age {\n", + " iso8601duration: \"P1Y\"\n", + "}\n", + "
F3-II:2 (MALE; P9Y)Spastic paraplegia 93, autosomal recessive (OMIM:620938)NM_001002755.4:c.362T>C (homozygous)Global developmental delay (HP:0001263): onset ; Delayed ability to walk (HP:0031936): onset ; Hypertonia (HP:0001276): onset ; Brisk reflexes (HP:0001348): onset ; Knee clonus (HP:0011449): onset ; excluded: Gait ataxia (HP:0002066): onset ; excluded: Lactic acidosis (HP:0003128): onset ; excluded: Developmental regression (HP:0002376): onset ; excluded: Ankle clonus (HP:0011448): onset ; excluded: Babinski sign (HP:0003487): onset ; excluded: Talipes equinovarus (HP:0001762): onset ; excluded: Peripheral neuropathy (HP:0009830): onset
TimeElement(element=Age(iso8601duration=P1Y)): Paraplegia (HP:0010550): onset age {\n", + " iso8601duration: \"P1Y\"\n", + "}\n", + "
F4-II:4 (FEMALE; P2Y)Spastic paraplegia 93, autosomal recessive (OMIM:620938)NM_001002755.4:c.362T>C (homozygous)Developmental regression (HP:0002376): onset ; Delayed ability to walk (HP:0031936): onset ; Hypertonia (HP:0001276): onset ; Brisk reflexes (HP:0001348): onset ; Knee clonus (HP:0011449): onset ; Ankle clonus (HP:0011448): onset ; excluded: Gait ataxia (HP:0002066): onset ; excluded: Lactic acidosis (HP:0003128): onset ; excluded: Babinski sign (HP:0003487): onset ; excluded: Talipes equinovarus (HP:0001762): onset ; excluded: Peripheral neuropathy (HP:0009830): onset
TimeElement(element=Age(iso8601duration=P2Y9M)): Paraplegia (HP:0010550): onset age {\n", + " iso8601duration: \"P2Y9M\"\n", + "}\n", + "
F4-II:5 (FEMALE; P6Y)Spastic paraplegia 93, autosomal recessive (OMIM:620938)NM_001002755.4:c.362T>C (homozygous)Hypertonia (HP:0001276): onset ; Brisk reflexes (HP:0001348): onset ; Knee clonus (HP:0011449): onset ; Ankle clonus (HP:0011448): onset ; Reduced cerebral white matter volume (HP:0034295): onset ; Hypoplasia of the corpus callosum (HP:0002079): onset ; Enlarged cisterna magna (HP:0002280): onset ; excluded: Gait ataxia (HP:0002066): onset ; excluded: Global developmental delay (HP:0001263): onset ; excluded: Lactic acidosis (HP:0003128): onset ; excluded: Developmental regression (HP:0002376): onset ; excluded: Babinski sign (HP:0003487): onset ; excluded: Peripheral demyelination (HP:0011096): onset ; excluded: Encephalopathy (HP:0001298): onset ; excluded: Talipes equinovarus (HP:0001762): onset ; excluded: Peripheral neuropathy (HP:0009830): onset
TimeElement(element=Age(iso8601duration=P11M)): Paraplegia (HP:0010550): onset age {\n", + " iso8601duration: \"P11M\"\n", + "}\n", + "
F4-II:6 (FEMALE; P2Y6M)Spastic paraplegia 93, autosomal recessive (OMIM:620938)NM_001002755.4:c.362T>C (homozygous)Global developmental delay (HP:0001263): onset ; Developmental regression (HP:0002376): onset ; Delayed ability to walk (HP:0031936): onset ; Hypertonia (HP:0001276): onset ; Brisk reflexes (HP:0001348): onset ; Knee clonus (HP:0011449): onset ; Ankle clonus (HP:0011448): onset ; Reduced cerebral white matter volume (HP:0034295): onset ; Hypoplasia of the corpus callosum (HP:0002079): onset ; Enlarged cisterna magna (HP:0002280): onset ; excluded: Gait ataxia (HP:0002066): onset ; excluded: Lactic acidosis (HP:0003128): onset ; excluded: Babinski sign (HP:0003487): onset ; excluded: Peripheral demyelination (HP:0011096): onset ; excluded: Encephalopathy (HP:0001298): onset ; excluded: Talipes equinovarus (HP:0001762): onset ; excluded: Peripheral neuropathy (HP:0009830): onset
TimeElement(element=Age(iso8601duration=P1Y)): Paraplegia (HP:0010550): onset age {\n", + " iso8601duration: \"P1Y\"\n", + "}\n", + "
F5-II:1 (FEMALE; P6M)Spastic paraplegia 93, autosomal recessive (OMIM:620938)NM_001002755.4:c.362T>C (homozygous)Developmental regression (HP:0002376): onset ; Brisk reflexes (HP:0001348): onset ; Reduced cerebral white matter volume (HP:0034295): onset ; excluded: Gait ataxia (HP:0002066): onset ; excluded: Hypertonia (HP:0001276): onset ; excluded: Knee clonus (HP:0011449): onset ; excluded: Ankle clonus (HP:0011448): onset ; excluded: Babinski sign (HP:0003487): onset ; excluded: Hypoplasia of the corpus callosum (HP:0002079): onset ; excluded: Peripheral demyelination (HP:0011096): onset ; excluded: Enlarged cisterna magna (HP:0002280): onset ; excluded: Encephalopathy (HP:0001298): onset ; excluded: Talipes equinovarus (HP:0001762): onset ; excluded: Peripheral neuropathy (HP:0009830): onset
TimeElement(element=Age(iso8601duration=P5M)): Fever (HP:0001945): onset age {\n", + " iso8601duration: \"P5M\"\n", + "}\n", + "; Hypotonia (HP:0001252): onset age {\n", + " iso8601duration: \"P5M\"\n", + "}\n", + "; Respiratory failure (HP:0002878): onset age {\n", + " iso8601duration: \"P5M\"\n", + "}\n", + "; Acidosis (HP:0001941): onset age {\n", + " iso8601duration: \"P5M\"\n", + "}\n", + "
F5-II:2 (MALE; P4Y7M)Spastic paraplegia 93, autosomal recessive (OMIM:620938)NM_001002755.4:c.362T>C (homozygous)Developmental regression (HP:0002376): onset ; Delayed ability to walk (HP:0031936): onset ; Hypertonia (HP:0001276): onset ; Brisk reflexes (HP:0001348): onset ; Reduced cerebral white matter volume (HP:0034295): onset ; Hypoplasia of the corpus callosum (HP:0002079): onset ; Enlarged cisterna magna (HP:0002280): onset ; excluded: Gait ataxia (HP:0002066): onset ; excluded: Lactic acidosis (HP:0003128): onset ; excluded: Knee clonus (HP:0011449): onset ; excluded: Ankle clonus (HP:0011448): onset ; excluded: Babinski sign (HP:0003487): onset ; excluded: Peripheral demyelination (HP:0011096): onset ; excluded: Encephalopathy (HP:0001298): onset ; excluded: Talipes equinovarus (HP:0001762): onset ; excluded: Peripheral neuropathy (HP:0009830): onset
TimeElement(element=Age(iso8601duration=P1Y2M)): Paraplegia (HP:0010550): onset age {\n", + " iso8601duration: \"P1Y2M\"\n", + "}\n", + "
F6-II:2 (MALE; P3Y)Spastic paraplegia 93, autosomal recessive (OMIM:620938)NM_001002755.4:c.362T>C (homozygous)Lactic acidosis (HP:0003128): onset ; Developmental regression (HP:0002376): onset ; Brisk reflexes (HP:0001348): onset ; Knee clonus (HP:0011449): onset ; Ankle clonus (HP:0011448): onset ; Babinski sign (HP:0003487): onset ; Reduced cerebral white matter volume (HP:0034295): onset ; Hypoplasia of the corpus callosum (HP:0002079): onset ; Enlarged cisterna magna (HP:0002280): onset ; excluded: Gait ataxia (HP:0002066): onset ; excluded: Strabismus (HP:0000486): onset ; excluded: Nystagmus (HP:0000639): onset ; excluded: Optic atrophy (HP:0000648): onset ; excluded: Ptosis (HP:0000508): onset ; excluded: External ophthalmoplegia (HP:0000544): onset ; excluded: Peripheral demyelination (HP:0011096): onset ; excluded: Encephalopathy (HP:0001298): onset ; excluded: Talipes equinovarus (HP:0001762): onset ; excluded: Peripheral neuropathy (HP:0009830): onset
TimeElement(element=Age(iso8601duration=P1Y)): Gait disturbance (HP:0001288): onset age {\n", + " iso8601duration: \"P1Y\"\n", + "}\n", + "; Progressive spastic paraplegia (HP:0007020): onset age {\n", + " iso8601duration: \"P1Y\"\n", + "}\n", + "
F6-II:3 (MALE; P2Y3M)Spastic paraplegia 93, autosomal recessive (OMIM:620938)NM_001002755.4:c.362T>C (homozygous)Lactic acidosis (HP:0003128): onset ; Developmental regression (HP:0002376): onset ; Brisk reflexes (HP:0001348): onset ; Knee clonus (HP:0011449): onset ; Ankle clonus (HP:0011448): onset ; Babinski sign (HP:0003487): onset ; excluded: Gait ataxia (HP:0002066): onset ; excluded: Strabismus (HP:0000486): onset ; excluded: Nystagmus (HP:0000639): onset ; excluded: Optic atrophy (HP:0000648): onset ; excluded: Ptosis (HP:0000508): onset ; excluded: External ophthalmoplegia (HP:0000544): onset ; excluded: Hypoplasia of the corpus callosum (HP:0002079): onset ; excluded: Peripheral demyelination (HP:0011096): onset ; excluded: Enlarged cisterna magna (HP:0002280): onset ; excluded: Encephalopathy (HP:0001298): onset ; excluded: Talipes equinovarus (HP:0001762): onset ; excluded: Peripheral neuropathy (HP:0009830): onset
TimeElement(element=Age(iso8601duration=P10M)): Lower limb spasticity (HP:0002061): onset age {\n", + " iso8601duration: \"P10M\"\n", + "}\n", + "
F7-II:1 (MALE; P10Y)Spastic paraplegia 93, autosomal recessive (OMIM:620938)NM_001002755.4:c.295C>G (homozygous)Delayed ability to walk (HP:0031936): onset ; Hypertonia (HP:0001276): onset ; Brisk reflexes (HP:0001348): onset ; Hypoplasia of the corpus callosum (HP:0002079): onset ; Enlarged cisterna magna (HP:0002280): onset ; Talipes equinovarus (HP:0001762): onset ; excluded: Gait ataxia (HP:0002066): onset ; excluded: Lactic acidosis (HP:0003128): onset ; excluded: Developmental regression (HP:0002376): onset ; excluded: Knee clonus (HP:0011449): onset ; excluded: Ankle clonus (HP:0011448): onset ; excluded: Babinski sign (HP:0003487): onset ; excluded: Reduced cerebral white matter volume (HP:0034295): onset ; excluded: Peripheral demyelination (HP:0011096): onset ; excluded: Encephalopathy (HP:0001298): onset ; excluded: Peripheral neuropathy (HP:0009830): onset
TimeElement(element=Age(iso8601duration=P3M)): Paraplegia (HP:0010550): onset age {\n", + " iso8601duration: \"P3M\"\n", + "}\n", + "
F7-II:2 (MALE; P6Y)Spastic paraplegia 93, autosomal recessive (OMIM:620938)NM_001002755.4:c.295C>G (homozygous)Delayed ability to walk (HP:0031936): onset ; Hypertonia (HP:0001276): onset ; Brisk reflexes (HP:0001348): onset ; Talipes equinovarus (HP:0001762): onset ; excluded: Gait ataxia (HP:0002066): onset ; excluded: Lactic acidosis (HP:0003128): onset ; excluded: Developmental regression (HP:0002376): onset ; excluded: Knee clonus (HP:0011449): onset ; excluded: Ankle clonus (HP:0011448): onset ; excluded: Babinski sign (HP:0003487): onset ; excluded: Reduced cerebral white matter volume (HP:0034295): onset ; excluded: Hypoplasia of the corpus callosum (HP:0002079): onset ; excluded: Peripheral demyelination (HP:0011096): onset ; excluded: Enlarged cisterna magna (HP:0002280): onset ; excluded: Encephalopathy (HP:0001298): onset ; excluded: Peripheral neuropathy (HP:0009830): onset
TimeElement(element=Age(iso8601duration=P3M)): Paraplegia (HP:0010550): onset age {\n", + " iso8601duration: \"P3M\"\n", + "}\n", + "
F8-II:5 (MALE; P7Y7M)Spastic paraplegia 93, autosomal recessive (OMIM:620938)NM_001002755.4:c.263T>C (homozygous)Developmental regression (HP:0002376): onset ; Hypertonia (HP:0001276): onset ; Brisk reflexes (HP:0001348): onset ; excluded: Gait ataxia (HP:0002066): onset ; excluded: Lactic acidosis (HP:0003128): onset ; excluded: Strabismus (HP:0000486): onset ; excluded: Nystagmus (HP:0000639): onset ; excluded: Optic atrophy (HP:0000648): onset ; excluded: Ptosis (HP:0000508): onset ; excluded: External ophthalmoplegia (HP:0000544): onset ; excluded: Knee clonus (HP:0011449): onset ; excluded: Ankle clonus (HP:0011448): onset ; excluded: Babinski sign (HP:0003487): onset ; excluded: Talipes equinovarus (HP:0001762): onset ; excluded: Peripheral neuropathy (HP:0009830): onset
TimeElement(element=Age(iso8601duration=P1Y6M)): Frequent falls (HP:0002359): onset age {\n", + " iso8601duration: \"P1Y6M\"\n", + "}\n", + "
F8-II:6 (MALE; P6Y6M)Spastic paraplegia 93, autosomal recessive (OMIM:620938)NM_001002755.4:c.263T>C (homozygous)Developmental regression (HP:0002376): onset ; Hypertonia (HP:0001276): onset ; Brisk reflexes (HP:0001348): onset ; excluded: Gait ataxia (HP:0002066): onset ; excluded: Lactic acidosis (HP:0003128): onset ; excluded: Strabismus (HP:0000486): onset ; excluded: Nystagmus (HP:0000639): onset ; excluded: Optic atrophy (HP:0000648): onset ; excluded: Ptosis (HP:0000508): onset ; excluded: External ophthalmoplegia (HP:0000544): onset ; excluded: Knee clonus (HP:0011449): onset ; excluded: Ankle clonus (HP:0011448): onset ; excluded: Babinski sign (HP:0003487): onset ; excluded: Talipes equinovarus (HP:0001762): onset ; excluded: Peripheral neuropathy (HP:0009830): onset
TimeElement(element=Age(iso8601duration=P1Y6M)): Frequent falls (HP:0002359): onset age {\n", + " iso8601duration: \"P1Y6M\"\n", + "}\n", + "
F9-II:1 (MALE; P12Y)Spastic paraplegia 93, autosomal recessive (OMIM:620938)
  • NM_001002755.4:c.548C>G (heterozygous)
  • NM_001002755.4:c.629G>T (heterozygous)
Developmental regression (HP:0002376): onset ; Ptosis (HP:0000508): onset ; Peripheral neuropathy (HP:0009830): onset ; excluded: Gait ataxia (HP:0002066): onset ; excluded: Lactic acidosis (HP:0003128): onset ; excluded: Strabismus (HP:0000486): onset ; excluded: Nystagmus (HP:0000639): onset ; excluded: Optic atrophy (HP:0000648): onset ; excluded: External ophthalmoplegia (HP:0000544): onset ; excluded: Reduced cerebral white matter volume (HP:0034295): onset ; excluded: Hypoplasia of the corpus callosum (HP:0002079): onset ; excluded: Peripheral demyelination (HP:0011096): onset ; excluded: Enlarged cisterna magna (HP:0002280): onset ; excluded: Encephalopathy (HP:0001298): onset ; excluded: Talipes equinovarus (HP:0001762): onset
F10-II:1 (MALE; P12M)Spastic paraplegia 93, autosomal recessive (OMIM:620938)
  • NM_001002755.4:c.629G>T (heterozygous)
  • NM_001002755.4:c.398T>C (heterozygous)
Global developmental delay (HP:0001263): onset ; Developmental regression (HP:0002376): onset ; Reduced cerebral white matter volume (HP:0034295): onset ; Hypoplasia of the corpus callosum (HP:0002079): onset ; Peripheral demyelination (HP:0011096): onset ; Enlarged cisterna magna (HP:0002280): onset ; Encephalopathy (HP:0001298): onset ; excluded: Lactic acidosis (HP:0003128): onset ; excluded: Hypertonia (HP:0001276): onset ; excluded: Brisk reflexes (HP:0001348): onset ; excluded: Knee clonus (HP:0011449): onset ; excluded: Ankle clonus (HP:0011448): onset ; excluded: Babinski sign (HP:0003487): onset ; excluded: Talipes equinovarus (HP:0001762): onset ; excluded: Peripheral neuropathy (HP:0009830): onset
TimeElement(element=Age(iso8601duration=P6M)): Hypotonia (HP:0001252): onset age {\n", + " iso8601duration: \"P6M\"\n", + "}\n", + "; Generalized-onset seizure (HP:0002197): onset age {\n", + " iso8601duration: \"P6M\"\n", + "}\n", + "; Status epilepticus (HP:0002133): onset age {\n", + " iso8601duration: \"P6M\"\n", + "}\n", + "
F10-II:2 (FEMALE; P2Y)Spastic paraplegia 93, autosomal recessive (OMIM:620938)
  • NM_001002755.4:c.629G>T (heterozygous)
  • NM_001002755.4:c.398T>C (heterozygous)
Global developmental delay (HP:0001263): onset ; Developmental regression (HP:0002376): onset ; Nystagmus (HP:0000639): onset ; Optic atrophy (HP:0000648): onset ; Reduced cerebral white matter volume (HP:0034295): onset ; Hypoplasia of the corpus callosum (HP:0002079): onset ; Enlarged cisterna magna (HP:0002280): onset ; excluded: Lactic acidosis (HP:0003128): onset ; excluded: Strabismus (HP:0000486): onset ; excluded: External ophthalmoplegia (HP:0000544): onset ; excluded: Peripheral demyelination (HP:0011096): onset ; excluded: Encephalopathy (HP:0001298): onset ; excluded: Talipes equinovarus (HP:0001762): onset ; excluded: Peripheral neuropathy (HP:0009830): onset
TimeElement(element=Age(iso8601duration=P3M)): Hypotonia (HP:0001252): onset age {\n", + " iso8601duration: \"P3M\"\n", + "}\n", + "
TimeElement(element=Age(iso8601duration=P2Y)): Lower limb spasticity (HP:0002061): onset age {\n", + " iso8601duration: \"P2Y\"\n", + "}\n", + "
Clinical data (MALE; P30Y)Spastic paraplegia 93, autosomal recessive (OMIM:620938)
  • NM_001002755.4:c.146del (heterozygous)
  • NM_001002755.4:c.565G>A (heterozygous)
Global developmental delay (HP:0001263): onset ; Spastic paraplegia (HP:0001258): onset ; Brisk reflexes (HP:0001348): onset ; Peripheral neuropathy (HP:0009830): onset ; Scoliosis (HP:0002650): onset ; Hypoesthesia (HP:0033748): onset ; excluded: Lactic acidosis (HP:0003128): onset ; excluded: Knee clonus (HP:0011449): onset ; excluded: Ankle clonus (HP:0011448): onset ; excluded: Babinski sign (HP:0003487): onset ; excluded: Reduced cerebral white matter volume (HP:0034295): onset ; excluded: Hypoplasia of the corpus callosum (HP:0002079): onset ; excluded: Peripheral demyelination (HP:0011096): onset ; excluded: Enlarged cisterna magna (HP:0002280): onset ; excluded: Encephalopathy (HP:0001298): onset ; excluded: Talipes equinovarus (HP:0001762): onset
TimeElement(element=Age(iso8601duration=P1Y6M)): Developmental regression (HP:0002376): onset age {\n", + " iso8601duration: \"P1Y6M\"\n", + "}\n", + "; Spastic tetraplegia (HP:0002510): onset age {\n", + " iso8601duration: \"P1Y6M\"\n", + "}\n", + "
TimeElement(element=Age(iso8601duration=P30Y)): Corpus callosum atrophy (HP:0007371): onset age {\n", + " iso8601duration: \"P30Y\"\n", + "}\n", + "; Reduced brain N-acetyl aspartate level by MRS (HP:0012708): onset age {\n", + " iso8601duration: \"P30Y\"\n", + "}\n", + "; Elevated brain choline level by MRS (HP:0012706): onset age {\n", + " iso8601duration: \"P30Y\"\n", + "}\n", + "; Elevated brain lactate level by MRS (HP:0012707): onset age {\n", + " iso8601duration: \"P30Y\"\n", + "}\n", + "
patient (FEMALE; P3Y6M)Spastic paraplegia 93, autosomal recessive (OMIM:620938)NM_001002755.4:c.565G>A (homozygous)Global developmental delay (HP:0001263): onset ; Developmental regression (HP:0002376): onset ; excluded: Gait ataxia (HP:0002066): onset ; excluded: Lactic acidosis (HP:0003128): onset ; excluded: Reduced cerebral white matter volume (HP:0034295): onset ; excluded: Hypoplasia of the corpus callosum (HP:0002079): onset ; excluded: Peripheral demyelination (HP:0011096): onset ; excluded: Enlarged cisterna magna (HP:0002280): onset ; excluded: Encephalopathy (HP:0001298): onset ; excluded: Talipes equinovarus (HP:0001762): onset ; excluded: Peripheral neuropathy (HP:0009830): onset
TimeElement(element=Age(iso8601duration=P1Y11M)): Loss of ambulation (HP:0002505): onset age {\n", + " iso8601duration: \"P1Y11M\"\n", + "}\n", + "
" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "table = IndividualTable(cvalidator.get_error_free_individual_list())\n", + "display(HTML(table.to_html()))" + ] + }, + { + "cell_type": "code", + "execution_count": 31, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[pyphetools] Ingested 21 GA4GH phenopackets.\n", + "[INFO] Extracted 21 from 21 phenopackets with OMIM:620938\n", + "\n", + "\tSpastic paraplegia 93, autosomal recessive (OMIM:620938): n=21\n", + "We found a total of 43 unique HPO terms\n", + "Extracted disease: Spastic paraplegia 93, autosomal recessive (OMIM:620938)\n", + "Wrote HPOA disease file to OMIM-620938.tab\n" + ] + } + ], + "source": [ + "pmid = \"PMID:36256512\"\n", + "df = timporter.create_hpoa_from_phenopackets(pmid=pmid, mode_of_inheritance=Moi.AR, target=\"OMIM:620938\")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "ps24venv", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.12.8" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/notebooks/NFU1/input/NFU1_SPG93_individuals.xlsx b/notebooks/NFU1/input/NFU1_SPG93_individuals.xlsx new file mode 100644 index 00000000..a2c6969c Binary files /dev/null and b/notebooks/NFU1/input/NFU1_SPG93_individuals.xlsx differ diff --git a/notebooks/NFU1/phenopackets/PMID_25758857_Clinicaldata.json b/notebooks/NFU1/phenopackets/PMID_25758857_Clinicaldata.json new file mode 100644 index 00000000..6a4e14bf --- /dev/null +++ b/notebooks/NFU1/phenopackets/PMID_25758857_Clinicaldata.json @@ -0,0 +1,340 @@ +{ + "id": "PMID_25758857_Clinical_data", + "subject": { + "id": "Clinical data", + "timeAtLastEncounter": { + "age": { + "iso8601duration": "P30Y" + } + }, + "vitalStatus": { + "status": "ALIVE" + }, + "sex": "MALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0002376", + "label": "Developmental regression" + }, + "onset": { + "age": { + "iso8601duration": "P1Y6M" + } + } + }, + { + "type": { + "id": "HP:0002510", + "label": "Spastic tetraplegia" + }, + "onset": { + "age": { + "iso8601duration": "P1Y6M" + } + } + }, + { + "type": { + "id": "HP:0007371", + "label": "Corpus callosum atrophy" + }, + "onset": { + "age": { + "iso8601duration": "P30Y" + } + } + }, + { + "type": { + "id": "HP:0012708", + "label": "Reduced brain N-acetyl aspartate level by MRS" + }, + "onset": { + "age": { + "iso8601duration": "P30Y" + } + } + }, + { + "type": { + "id": "HP:0012706", + "label": "Elevated brain choline level by MRS" + }, + "onset": { + "age": { + "iso8601duration": "P30Y" + } + } + }, + { + "type": { + "id": "HP:0012707", + "label": "Elevated brain lactate level by MRS" + }, + "onset": { + "age": { + "iso8601duration": "P30Y" + } + } + }, + { + "type": { + "id": "HP:0001263", + "label": "Global developmental delay" + } + }, + { + "type": { + "id": "HP:0001258", + "label": "Spastic paraplegia" + } + }, + { + "type": { + "id": "HP:0001348", + "label": "Brisk reflexes" + } + }, + { + "type": { + "id": "HP:0009830", + "label": "Peripheral neuropathy" + } + }, + { + "type": { + "id": "HP:0002650", + "label": "Scoliosis" + } + }, + { + "type": { + "id": "HP:0033748", + "label": "Hypoesthesia" + } + }, + { + "type": { + "id": "HP:0003128", + "label": "Lactic acidosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011449", + "label": "Knee clonus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011448", + "label": "Ankle clonus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0003487", + "label": "Babinski sign" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0034295", + "label": "Reduced cerebral white matter volume" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002079", + "label": "Hypoplasia of the corpus callosum" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011096", + "label": "Peripheral demyelination" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002280", + "label": "Enlarged cisterna magna" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001298", + "label": "Encephalopathy" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001762", + "label": "Talipes equinovarus" + }, + "excluded": true + } + ], + "interpretations": [ + { + "id": "Clinical data", + "progressStatus": "SOLVED", + "diagnosis": { + "disease": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "genomicInterpretations": [ + { + "subjectOrBiosampleId": "Clinical data", + "interpretationStatus": "CAUSATIVE", + "variantInterpretation": { + "variationDescriptor": { + "id": "var_cYmLabuPpRVpvlDrtvAMveVDg", + "geneContext": { + "valueId": "HGNC:16287", + "symbol": "NFU1" + }, + "expressions": [ + { + "syntax": "hgvs.c", + "value": "NM_001002755.4:c.146del" + }, + { + "syntax": "hgvs.g", + "value": "NC_000002.12:g.69431923del" + } + ], + "vcfRecord": { + "genomeAssembly": "hg38", + "chrom": "chr2", + "pos": "69431921", + "ref": "AG", + "alt": "A" + }, + "moleculeContext": "genomic", + "allelicState": { + "id": "GENO:0000135", + "label": "heterozygous" + } + } + } + }, + { + "subjectOrBiosampleId": "Clinical data", + "interpretationStatus": "CAUSATIVE", + "variantInterpretation": { + "variationDescriptor": { + "id": "var_pERkyPThsHVjQJcPrnvKMXUeV", + "geneContext": { + "valueId": "HGNC:16287", + "symbol": "NFU1" + }, + "expressions": [ + { + "syntax": "hgvs.c", + "value": "NM_001002755.4:c.565G>A" + }, + { + "syntax": "hgvs.g", + "value": "NC_000002.12:g.69400519C>T" + } + ], + "vcfRecord": { + "genomeAssembly": "hg38", + "chrom": "chr2", + "pos": "69400519", + "ref": "C", + "alt": "T" + }, + "moleculeContext": "genomic", + "allelicState": { + "id": "GENO:0000135", + "label": "heterozygous" + } + } + } + } + ] + } + } + ], + "diseases": [ + { + "term": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "onset": { + "age": { + "iso8601duration": "P1Y6M" + } + } + } + ], + "metaData": { + "created": "2025-01-08T13:24:32.127840995Z", + "createdBy": "ORCID:0000-0002-0736-9199", + "resources": [ + { + "id": "geno", + "name": "Genotype Ontology", + "url": "http://purl.obolibrary.org/obo/geno.owl", + "version": "2022-03-05", + "namespacePrefix": "GENO", + "iriPrefix": "http://purl.obolibrary.org/obo/GENO_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "06/01/23", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "omim", + "name": "An Online Catalog of Human Genes and Genetic Disorders", + "url": "https://www.omim.org", + "version": "January 4, 2023", + "namespacePrefix": "OMIM", + "iriPrefix": "https://www.omim.org/entry/" + }, + { + "id": "so", + "name": "Sequence types and features ontology", + "url": "http://purl.obolibrary.org/obo/so.obo", + "version": "2021-11-22", + "namespacePrefix": "SO", + "iriPrefix": "http://purl.obolibrary.org/obo/SO_" + }, + { + "id": "hp", + "name": "human phenotype ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2024-12-12", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + } + ], + "phenopacketSchemaVersion": "2.0", + "externalReferences": [ + { + "id": "PMID:25758857", + "reference": "https://pubmed.ncbi.nlm.nih.gov/25758857", + "description": "New spastic paraplegia phenotype associated to mutation of NFU1" + } + ] + } +} \ No newline at end of file diff --git a/notebooks/NFU1/phenopackets/PMID_32747156_patient.json b/notebooks/NFU1/phenopackets/PMID_32747156_patient.json new file mode 100644 index 00000000..774a0c7a --- /dev/null +++ b/notebooks/NFU1/phenopackets/PMID_32747156_patient.json @@ -0,0 +1,219 @@ +{ + "id": "PMID_32747156_patient", + "subject": { + "id": "patient", + "timeAtLastEncounter": { + "age": { + "iso8601duration": "P3Y6M" + } + }, + "vitalStatus": { + "status": "ALIVE" + }, + "sex": "FEMALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0002505", + "label": "Loss of ambulation" + }, + "onset": { + "age": { + "iso8601duration": "P1Y11M" + } + } + }, + { + "type": { + "id": "HP:0001263", + "label": "Global developmental delay" + } + }, + { + "type": { + "id": "HP:0002376", + "label": "Developmental regression" + } + }, + { + "type": { + "id": "HP:0002066", + "label": "Gait ataxia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0003128", + "label": "Lactic acidosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0034295", + "label": "Reduced cerebral white matter volume" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002079", + "label": "Hypoplasia of the corpus callosum" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011096", + "label": "Peripheral demyelination" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002280", + "label": "Enlarged cisterna magna" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001298", + "label": "Encephalopathy" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001762", + "label": "Talipes equinovarus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0009830", + "label": "Peripheral neuropathy" + }, + "excluded": true + } + ], + "interpretations": [ + { + "id": "patient", + "progressStatus": "SOLVED", + "diagnosis": { + "disease": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "genomicInterpretations": [ + { + "subjectOrBiosampleId": "patient", + "interpretationStatus": "CAUSATIVE", + "variantInterpretation": { + "variationDescriptor": { + "id": "var_pERkyPThsHVjQJcPrnvKMXUeV", + "geneContext": { + "valueId": "HGNC:16287", + "symbol": "NFU1" + }, + "expressions": [ + { + "syntax": "hgvs.c", + "value": "NM_001002755.4:c.565G>A" + }, + { + "syntax": "hgvs.g", + "value": "NC_000002.12:g.69400519C>T" + } + ], + "vcfRecord": { + "genomeAssembly": "hg38", + "chrom": "chr2", + "pos": "69400519", + "ref": "C", + "alt": "T" + }, + "moleculeContext": "genomic", + "allelicState": { + "id": "GENO:0000136", + "label": "homozygous" + } + } + } + } + ] + } + } + ], + "diseases": [ + { + "term": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "onset": { + "age": { + "iso8601duration": "P1Y11M" + } + } + } + ], + "metaData": { + "created": "2025-01-08T13:24:32.128517866Z", + "createdBy": "ORCID:0000-0002-0736-9199", + "resources": [ + { + "id": "geno", + "name": "Genotype Ontology", + "url": "http://purl.obolibrary.org/obo/geno.owl", + "version": "2022-03-05", + "namespacePrefix": "GENO", + "iriPrefix": "http://purl.obolibrary.org/obo/GENO_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "06/01/23", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "omim", + "name": "An Online Catalog of Human Genes and Genetic Disorders", + "url": "https://www.omim.org", + "version": "January 4, 2023", + "namespacePrefix": "OMIM", + "iriPrefix": "https://www.omim.org/entry/" + }, + { + "id": "so", + "name": "Sequence types and features ontology", + "url": "http://purl.obolibrary.org/obo/so.obo", + "version": "2021-11-22", + "namespacePrefix": "SO", + "iriPrefix": "http://purl.obolibrary.org/obo/SO_" + }, + { + "id": "hp", + "name": "human phenotype ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2024-12-12", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + } + ], + "phenopacketSchemaVersion": "2.0", + "externalReferences": [ + { + "id": "PMID:32747156", + "reference": "https://pubmed.ncbi.nlm.nih.gov/32747156", + "description": "A genetic mimic of cerebral palsy: Homozygous NFU1 mutation with marked intrafamilial phenotypic variation" + } + ] + } +} \ No newline at end of file diff --git a/notebooks/NFU1/phenopackets/PMID_36256512_F1-II1.json b/notebooks/NFU1/phenopackets/PMID_36256512_F1-II1.json new file mode 100644 index 00000000..650b8d95 --- /dev/null +++ b/notebooks/NFU1/phenopackets/PMID_36256512_F1-II1.json @@ -0,0 +1,271 @@ +{ + "id": "PMID_36256512_F1_II_1", + "subject": { + "id": "F1-II:1 ", + "timeAtLastEncounter": { + "age": { + "iso8601duration": "P17Y" + } + }, + "vitalStatus": { + "status": "ALIVE" + }, + "sex": "FEMALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0001258", + "label": "Spastic paraplegia" + }, + "onset": { + "age": { + "iso8601duration": "P9M14D" + } + } + }, + { + "type": { + "id": "HP:0002376", + "label": "Developmental regression" + } + }, + { + "type": { + "id": "HP:0000486", + "label": "Strabismus" + } + }, + { + "type": { + "id": "HP:0000544", + "label": "External ophthalmoplegia" + } + }, + { + "type": { + "id": "HP:0001348", + "label": "Brisk reflexes" + } + }, + { + "type": { + "id": "HP:0002079", + "label": "Hypoplasia of the corpus callosum" + } + }, + { + "type": { + "id": "HP:0002280", + "label": "Enlarged cisterna magna" + } + }, + { + "type": { + "id": "HP:0001263", + "label": "Global developmental delay" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0003128", + "label": "Lactic acidosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000639", + "label": "Nystagmus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000648", + "label": "Optic atrophy" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000508", + "label": "Ptosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011449", + "label": "Knee clonus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011448", + "label": "Ankle clonus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0003487", + "label": "Babinski sign" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0034295", + "label": "Reduced cerebral white matter volume" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011096", + "label": "Peripheral demyelination" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001298", + "label": "Encephalopathy" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001762", + "label": "Talipes equinovarus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0009830", + "label": "Peripheral neuropathy" + }, + "excluded": true + } + ], + "interpretations": [ + { + "id": "F1-II:1 ", + "progressStatus": "SOLVED", + "diagnosis": { + "disease": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "genomicInterpretations": [ + { + "subjectOrBiosampleId": "F1-II:1 ", + "interpretationStatus": "CAUSATIVE", + "variantInterpretation": { + "variationDescriptor": { + "id": "var_ZQQeYMIdlhfXinIaWwWwWOJan", + "geneContext": { + "valueId": "HGNC:16287", + "symbol": "NFU1" + }, + "expressions": [ + { + "syntax": "hgvs.c", + "value": "NM_001002755.4:c.721G>C" + }, + { + "syntax": "hgvs.g", + "value": "NC_000002.12:g.69396290C>G" + } + ], + "vcfRecord": { + "genomeAssembly": "hg38", + "chrom": "chr2", + "pos": "69396290", + "ref": "C", + "alt": "G" + }, + "moleculeContext": "genomic", + "allelicState": { + "id": "GENO:0000136", + "label": "homozygous" + } + } + } + } + ] + } + } + ], + "diseases": [ + { + "term": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "onset": { + "age": { + "iso8601duration": "P9M14D" + } + } + } + ], + "metaData": { + "created": "2025-01-08T13:24:32.117317914Z", + "createdBy": "ORCID:0000-0002-0736-9199", + "resources": [ + { + "id": "geno", + "name": "Genotype Ontology", + "url": "http://purl.obolibrary.org/obo/geno.owl", + "version": "2022-03-05", + "namespacePrefix": "GENO", + "iriPrefix": "http://purl.obolibrary.org/obo/GENO_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "06/01/23", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "omim", + "name": "An Online Catalog of Human Genes and Genetic Disorders", + "url": "https://www.omim.org", + "version": "January 4, 2023", + "namespacePrefix": "OMIM", + "iriPrefix": "https://www.omim.org/entry/" + }, + { + "id": "so", + "name": "Sequence types and features ontology", + "url": "http://purl.obolibrary.org/obo/so.obo", + "version": "2021-11-22", + "namespacePrefix": "SO", + "iriPrefix": "http://purl.obolibrary.org/obo/SO_" + }, + { + "id": "hp", + "name": "human phenotype ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2024-12-12", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + } + ], + "phenopacketSchemaVersion": "2.0", + "externalReferences": [ + { + "id": "PMID:36256512", + "reference": "https://pubmed.ncbi.nlm.nih.gov/36256512", + "description": "Phenotypic continuum of NFU1-related disorders" + } + ] + } +} \ No newline at end of file diff --git a/notebooks/NFU1/phenopackets/PMID_36256512_F1-II2.json b/notebooks/NFU1/phenopackets/PMID_36256512_F1-II2.json new file mode 100644 index 00000000..ed0e737e --- /dev/null +++ b/notebooks/NFU1/phenopackets/PMID_36256512_F1-II2.json @@ -0,0 +1,284 @@ +{ + "id": "PMID_36256512_F1_II_2", + "subject": { + "id": "F1-II:2 ", + "timeAtLastEncounter": { + "age": { + "iso8601duration": "P10Y" + } + }, + "vitalStatus": { + "status": "ALIVE" + }, + "sex": "FEMALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0010550", + "label": "Paraplegia" + }, + "onset": { + "age": { + "iso8601duration": "P6M" + } + } + }, + { + "type": { + "id": "HP:0031936", + "label": "Delayed ability to walk" + } + }, + { + "type": { + "id": "HP:0000486", + "label": "Strabismus" + } + }, + { + "type": { + "id": "HP:0001276", + "label": "Hypertonia" + } + }, + { + "type": { + "id": "HP:0001348", + "label": "Brisk reflexes" + } + }, + { + "type": { + "id": "HP:0034295", + "label": "Reduced cerebral white matter volume" + } + }, + { + "type": { + "id": "HP:0002079", + "label": "Hypoplasia of the corpus callosum" + } + }, + { + "type": { + "id": "HP:0002280", + "label": "Enlarged cisterna magna" + } + }, + { + "type": { + "id": "HP:0001263", + "label": "Global developmental delay" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0003128", + "label": "Lactic acidosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002376", + "label": "Developmental regression" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000639", + "label": "Nystagmus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000648", + "label": "Optic atrophy" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000508", + "label": "Ptosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000544", + "label": "External ophthalmoplegia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011449", + "label": "Knee clonus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011448", + "label": "Ankle clonus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0003487", + "label": "Babinski sign" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011096", + "label": "Peripheral demyelination" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001298", + "label": "Encephalopathy" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001762", + "label": "Talipes equinovarus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0009830", + "label": "Peripheral neuropathy" + }, + "excluded": true + } + ], + "interpretations": [ + { + "id": "F1-II:2 ", + "progressStatus": "SOLVED", + "diagnosis": { + "disease": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "genomicInterpretations": [ + { + "subjectOrBiosampleId": "F1-II:2 ", + "interpretationStatus": "CAUSATIVE", + "variantInterpretation": { + "variationDescriptor": { + "id": "var_ZQQeYMIdlhfXinIaWwWwWOJan", + "geneContext": { + "valueId": "HGNC:16287", + "symbol": "NFU1" + }, + "expressions": [ + { + "syntax": "hgvs.c", + "value": "NM_001002755.4:c.721G>C" + }, + { + "syntax": "hgvs.g", + "value": "NC_000002.12:g.69396290C>G" + } + ], + "vcfRecord": { + "genomeAssembly": "hg38", + "chrom": "chr2", + "pos": "69396290", + "ref": "C", + "alt": "G" + }, + "moleculeContext": "genomic", + "allelicState": { + "id": "GENO:0000136", + "label": "homozygous" + } + } + } + } + ] + } + } + ], + "diseases": [ + { + "term": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "onset": { + "age": { + "iso8601duration": "P6M" + } + } + } + ], + "metaData": { + "created": "2025-01-08T13:24:32.118144035Z", + "createdBy": "ORCID:0000-0002-0736-9199", + "resources": [ + { + "id": "geno", + "name": "Genotype Ontology", + "url": "http://purl.obolibrary.org/obo/geno.owl", + "version": "2022-03-05", + "namespacePrefix": "GENO", + "iriPrefix": "http://purl.obolibrary.org/obo/GENO_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "06/01/23", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "omim", + "name": "An Online Catalog of Human Genes and Genetic Disorders", + "url": "https://www.omim.org", + "version": "January 4, 2023", + "namespacePrefix": "OMIM", + "iriPrefix": "https://www.omim.org/entry/" + }, + { + "id": "so", + "name": "Sequence types and features ontology", + "url": "http://purl.obolibrary.org/obo/so.obo", + "version": "2021-11-22", + "namespacePrefix": "SO", + "iriPrefix": "http://purl.obolibrary.org/obo/SO_" + }, + { + "id": "hp", + "name": "human phenotype ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2024-12-12", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + } + ], + "phenopacketSchemaVersion": "2.0", + "externalReferences": [ + { + "id": "PMID:36256512", + "reference": "https://pubmed.ncbi.nlm.nih.gov/36256512", + "description": "Phenotypic continuum of NFU1-related disorders" + } + ] + } +} \ No newline at end of file diff --git a/notebooks/NFU1/phenopackets/PMID_36256512_F10-II1.json b/notebooks/NFU1/phenopackets/PMID_36256512_F10-II1.json new file mode 100644 index 00000000..43ba027c --- /dev/null +++ b/notebooks/NFU1/phenopackets/PMID_36256512_F10-II1.json @@ -0,0 +1,304 @@ +{ + "id": "PMID_36256512_F10_II_1", + "subject": { + "id": "F10-II:1 ", + "timeAtLastEncounter": { + "age": { + "iso8601duration": "P12M" + } + }, + "vitalStatus": { + "status": "DECEASED", + "timeOfDeath": { + "age": { + "iso8601duration": "P12M" + } + } + }, + "sex": "MALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0001252", + "label": "Hypotonia" + }, + "onset": { + "age": { + "iso8601duration": "P6M" + } + } + }, + { + "type": { + "id": "HP:0002197", + "label": "Generalized-onset seizure" + }, + "onset": { + "age": { + "iso8601duration": "P6M" + } + } + }, + { + "type": { + "id": "HP:0002133", + "label": "Status epilepticus" + }, + "onset": { + "age": { + "iso8601duration": "P6M" + } + } + }, + { + "type": { + "id": "HP:0001263", + "label": "Global developmental delay" + } + }, + { + "type": { + "id": "HP:0002376", + "label": "Developmental regression" + } + }, + { + "type": { + "id": "HP:0034295", + "label": "Reduced cerebral white matter volume" + } + }, + { + "type": { + "id": "HP:0002079", + "label": "Hypoplasia of the corpus callosum" + } + }, + { + "type": { + "id": "HP:0011096", + "label": "Peripheral demyelination" + } + }, + { + "type": { + "id": "HP:0002280", + "label": "Enlarged cisterna magna" + } + }, + { + "type": { + "id": "HP:0001298", + "label": "Encephalopathy" + } + }, + { + "type": { + "id": "HP:0003128", + "label": "Lactic acidosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001276", + "label": "Hypertonia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001348", + "label": "Brisk reflexes" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011449", + "label": "Knee clonus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011448", + "label": "Ankle clonus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0003487", + "label": "Babinski sign" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001762", + "label": "Talipes equinovarus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0009830", + "label": "Peripheral neuropathy" + }, + "excluded": true + } + ], + "interpretations": [ + { + "id": "F10-II:1 ", + "progressStatus": "SOLVED", + "diagnosis": { + "disease": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "genomicInterpretations": [ + { + "subjectOrBiosampleId": "F10-II:1 ", + "interpretationStatus": "CAUSATIVE", + "variantInterpretation": { + "variationDescriptor": { + "id": "var_umwWlfSAhhWeqdQHJoPUspywm", + "geneContext": { + "valueId": "HGNC:16287", + "symbol": "NFU1" + }, + "expressions": [ + { + "syntax": "hgvs.c", + "value": "NM_001002755.4:c.629G>T" + }, + { + "syntax": "hgvs.g", + "value": "NC_000002.12:g.69400455C>A" + } + ], + "vcfRecord": { + "genomeAssembly": "hg38", + "chrom": "chr2", + "pos": "69400455", + "ref": "C", + "alt": "A" + }, + "moleculeContext": "genomic", + "allelicState": { + "id": "GENO:0000135", + "label": "heterozygous" + } + } + } + }, + { + "subjectOrBiosampleId": "F10-II:1 ", + "interpretationStatus": "CAUSATIVE", + "variantInterpretation": { + "variationDescriptor": { + "id": "var_tXaIVbYnVXbNfTUakBUsTaMQk", + "geneContext": { + "valueId": "HGNC:16287", + "symbol": "NFU1" + }, + "expressions": [ + { + "syntax": "hgvs.c", + "value": "NM_001002755.4:c.398T>C" + }, + { + "syntax": "hgvs.g", + "value": "NC_000002.12:g.69415271A>G" + } + ], + "vcfRecord": { + "genomeAssembly": "hg38", + "chrom": "chr2", + "pos": "69415271", + "ref": "A", + "alt": "G" + }, + "moleculeContext": "genomic", + "allelicState": { + "id": "GENO:0000135", + "label": "heterozygous" + } + } + } + } + ] + } + } + ], + "diseases": [ + { + "term": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "onset": { + "age": { + "iso8601duration": "P6M" + } + } + } + ], + "metaData": { + "created": "2025-01-08T13:24:32.126676082Z", + "createdBy": "ORCID:0000-0002-0736-9199", + "resources": [ + { + "id": "geno", + "name": "Genotype Ontology", + "url": "http://purl.obolibrary.org/obo/geno.owl", + "version": "2022-03-05", + "namespacePrefix": "GENO", + "iriPrefix": "http://purl.obolibrary.org/obo/GENO_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "06/01/23", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "omim", + "name": "An Online Catalog of Human Genes and Genetic Disorders", + "url": "https://www.omim.org", + "version": "January 4, 2023", + "namespacePrefix": "OMIM", + "iriPrefix": "https://www.omim.org/entry/" + }, + { + "id": "so", + "name": "Sequence types and features ontology", + "url": "http://purl.obolibrary.org/obo/so.obo", + "version": "2021-11-22", + "namespacePrefix": "SO", + "iriPrefix": "http://purl.obolibrary.org/obo/SO_" + }, + { + "id": "hp", + "name": "human phenotype ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2024-12-12", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + } + ], + "phenopacketSchemaVersion": "2.0", + "externalReferences": [ + { + "id": "PMID:36256512", + "reference": "https://pubmed.ncbi.nlm.nih.gov/36256512", + "description": "Phenotypic continuum of NFU1-related disorders" + } + ] + } +} \ No newline at end of file diff --git a/notebooks/NFU1/phenopackets/PMID_36256512_F10-II2.json b/notebooks/NFU1/phenopackets/PMID_36256512_F10-II2.json new file mode 100644 index 00000000..8c590e64 --- /dev/null +++ b/notebooks/NFU1/phenopackets/PMID_36256512_F10-II2.json @@ -0,0 +1,286 @@ +{ + "id": "PMID_36256512_F10_II_2", + "subject": { + "id": "F10-II:2", + "timeAtLastEncounter": { + "age": { + "iso8601duration": "P2Y" + } + }, + "vitalStatus": { + "status": "DECEASED", + "timeOfDeath": { + "age": { + "iso8601duration": "P2Y" + } + } + }, + "sex": "FEMALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0001252", + "label": "Hypotonia" + }, + "onset": { + "age": { + "iso8601duration": "P3M" + } + } + }, + { + "type": { + "id": "HP:0002061", + "label": "Lower limb spasticity" + }, + "onset": { + "age": { + "iso8601duration": "P2Y" + } + } + }, + { + "type": { + "id": "HP:0001263", + "label": "Global developmental delay" + } + }, + { + "type": { + "id": "HP:0002376", + "label": "Developmental regression" + } + }, + { + "type": { + "id": "HP:0000639", + "label": "Nystagmus" + } + }, + { + "type": { + "id": "HP:0000648", + "label": "Optic atrophy" + } + }, + { + "type": { + "id": "HP:0034295", + "label": "Reduced cerebral white matter volume" + } + }, + { + "type": { + "id": "HP:0002079", + "label": "Hypoplasia of the corpus callosum" + } + }, + { + "type": { + "id": "HP:0002280", + "label": "Enlarged cisterna magna" + } + }, + { + "type": { + "id": "HP:0003128", + "label": "Lactic acidosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000486", + "label": "Strabismus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000544", + "label": "External ophthalmoplegia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011096", + "label": "Peripheral demyelination" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001298", + "label": "Encephalopathy" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001762", + "label": "Talipes equinovarus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0009830", + "label": "Peripheral neuropathy" + }, + "excluded": true + } + ], + "interpretations": [ + { + "id": "F10-II:2", + "progressStatus": "SOLVED", + "diagnosis": { + "disease": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "genomicInterpretations": [ + { + "subjectOrBiosampleId": "F10-II:2", + "interpretationStatus": "CAUSATIVE", + "variantInterpretation": { + "variationDescriptor": { + "id": "var_umwWlfSAhhWeqdQHJoPUspywm", + "geneContext": { + "valueId": "HGNC:16287", + "symbol": "NFU1" + }, + "expressions": [ + { + "syntax": "hgvs.c", + "value": "NM_001002755.4:c.629G>T" + }, + { + "syntax": "hgvs.g", + "value": "NC_000002.12:g.69400455C>A" + } + ], + "vcfRecord": { + "genomeAssembly": "hg38", + "chrom": "chr2", + "pos": "69400455", + "ref": "C", + "alt": "A" + }, + "moleculeContext": "genomic", + "allelicState": { + "id": "GENO:0000135", + "label": "heterozygous" + } + } + } + }, + { + "subjectOrBiosampleId": "F10-II:2", + "interpretationStatus": "CAUSATIVE", + "variantInterpretation": { + "variationDescriptor": { + "id": "var_tXaIVbYnVXbNfTUakBUsTaMQk", + "geneContext": { + "valueId": "HGNC:16287", + "symbol": "NFU1" + }, + "expressions": [ + { + "syntax": "hgvs.c", + "value": "NM_001002755.4:c.398T>C" + }, + { + "syntax": "hgvs.g", + "value": "NC_000002.12:g.69415271A>G" + } + ], + "vcfRecord": { + "genomeAssembly": "hg38", + "chrom": "chr2", + "pos": "69415271", + "ref": "A", + "alt": "G" + }, + "moleculeContext": "genomic", + "allelicState": { + "id": "GENO:0000135", + "label": "heterozygous" + } + } + } + } + ] + } + } + ], + "diseases": [ + { + "term": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "onset": { + "age": { + "iso8601duration": "P3M" + } + } + } + ], + "metaData": { + "created": "2025-01-08T13:24:32.127288103Z", + "createdBy": "ORCID:0000-0002-0736-9199", + "resources": [ + { + "id": "geno", + "name": "Genotype Ontology", + "url": "http://purl.obolibrary.org/obo/geno.owl", + "version": "2022-03-05", + "namespacePrefix": "GENO", + "iriPrefix": "http://purl.obolibrary.org/obo/GENO_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "06/01/23", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "omim", + "name": "An Online Catalog of Human Genes and Genetic Disorders", + "url": "https://www.omim.org", + "version": "January 4, 2023", + "namespacePrefix": "OMIM", + "iriPrefix": "https://www.omim.org/entry/" + }, + { + "id": "so", + "name": "Sequence types and features ontology", + "url": "http://purl.obolibrary.org/obo/so.obo", + "version": "2021-11-22", + "namespacePrefix": "SO", + "iriPrefix": "http://purl.obolibrary.org/obo/SO_" + }, + { + "id": "hp", + "name": "human phenotype ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2024-12-12", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + } + ], + "phenopacketSchemaVersion": "2.0", + "externalReferences": [ + { + "id": "PMID:36256512", + "reference": "https://pubmed.ncbi.nlm.nih.gov/36256512", + "description": "Phenotypic continuum of NFU1-related disorders" + } + ] + } +} \ No newline at end of file diff --git a/notebooks/NFU1/phenopackets/PMID_36256512_F2-II1.json b/notebooks/NFU1/phenopackets/PMID_36256512_F2-II1.json new file mode 100644 index 00000000..7209cd12 --- /dev/null +++ b/notebooks/NFU1/phenopackets/PMID_36256512_F2-II1.json @@ -0,0 +1,280 @@ +{ + "id": "PMID_36256512_F2_II_1", + "subject": { + "id": "F2-II:1", + "timeAtLastEncounter": { + "age": { + "iso8601duration": "P25Y" + } + }, + "vitalStatus": { + "status": "ALIVE" + }, + "sex": "MALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0010550", + "label": "Paraplegia" + }, + "onset": { + "age": { + "iso8601duration": "P1Y" + } + } + }, + { + "type": { + "id": "HP:0002376", + "label": "Developmental regression" + } + }, + { + "type": { + "id": "HP:0001276", + "label": "Hypertonia" + } + }, + { + "type": { + "id": "HP:0001348", + "label": "Brisk reflexes" + } + }, + { + "type": { + "id": "HP:0002169", + "label": "Clonus" + } + }, + { + "type": { + "id": "HP:0002066", + "label": "Gait ataxia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001263", + "label": "Global developmental delay" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0003128", + "label": "Lactic acidosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0003487", + "label": "Babinski sign" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0034295", + "label": "Reduced cerebral white matter volume" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002079", + "label": "Hypoplasia of the corpus callosum" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011096", + "label": "Peripheral demyelination" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002280", + "label": "Enlarged cisterna magna" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001298", + "label": "Encephalopathy" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001762", + "label": "Talipes equinovarus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0009830", + "label": "Peripheral neuropathy" + }, + "excluded": true + } + ], + "interpretations": [ + { + "id": "F2-II:1", + "progressStatus": "SOLVED", + "diagnosis": { + "disease": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "genomicInterpretations": [ + { + "subjectOrBiosampleId": "F2-II:1", + "interpretationStatus": "CAUSATIVE", + "variantInterpretation": { + "variationDescriptor": { + "id": "var_FclYOplixmmKaOKQlDXSiBKac", + "geneContext": { + "valueId": "HGNC:16287", + "symbol": "NFU1" + }, + "expressions": [ + { + "syntax": "hgvs.c", + "value": "NM_001002755.4:c.298G>C" + }, + { + "syntax": "hgvs.g", + "value": "NC_000002.12:g.69423586C>G" + } + ], + "vcfRecord": { + "genomeAssembly": "hg38", + "chrom": "chr2", + "pos": "69423586", + "ref": "C", + "alt": "G" + }, + "moleculeContext": "genomic", + "allelicState": { + "id": "GENO:0000135", + "label": "heterozygous" + } + } + } + }, + { + "subjectOrBiosampleId": "F2-II:1", + "interpretationStatus": "CAUSATIVE", + "variantInterpretation": { + "variationDescriptor": { + "id": "var_fGGLfkrnEvppGknggyHijEPFh", + "geneContext": { + "valueId": "HGNC:16287", + "symbol": "NFU1" + }, + "expressions": [ + { + "syntax": "hgvs.c", + "value": "NM_001002755.4:c.301A>G" + }, + { + "syntax": "hgvs.g", + "value": "NC_000002.12:g.69423583T>C" + } + ], + "vcfRecord": { + "genomeAssembly": "hg38", + "chrom": "chr2", + "pos": "69423583", + "ref": "T", + "alt": "C" + }, + "moleculeContext": "genomic", + "allelicState": { + "id": "GENO:0000135", + "label": "heterozygous" + } + } + } + } + ] + } + } + ], + "diseases": [ + { + "term": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "onset": { + "age": { + "iso8601duration": "P1Y" + } + } + } + ], + "metaData": { + "created": "2025-01-08T13:24:32.118804931Z", + "createdBy": "ORCID:0000-0002-0736-9199", + "resources": [ + { + "id": "geno", + "name": "Genotype Ontology", + "url": "http://purl.obolibrary.org/obo/geno.owl", + "version": "2022-03-05", + "namespacePrefix": "GENO", + "iriPrefix": "http://purl.obolibrary.org/obo/GENO_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "06/01/23", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "omim", + "name": "An Online Catalog of Human Genes and Genetic Disorders", + "url": "https://www.omim.org", + "version": "January 4, 2023", + "namespacePrefix": "OMIM", + "iriPrefix": "https://www.omim.org/entry/" + }, + { + "id": "so", + "name": "Sequence types and features ontology", + "url": "http://purl.obolibrary.org/obo/so.obo", + "version": "2021-11-22", + "namespacePrefix": "SO", + "iriPrefix": "http://purl.obolibrary.org/obo/SO_" + }, + { + "id": "hp", + "name": "human phenotype ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2024-12-12", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + } + ], + "phenopacketSchemaVersion": "2.0", + "externalReferences": [ + { + "id": "PMID:36256512", + "reference": "https://pubmed.ncbi.nlm.nih.gov/36256512", + "description": "Phenotypic continuum of NFU1-related disorders" + } + ] + } +} \ No newline at end of file diff --git a/notebooks/NFU1/phenopackets/PMID_36256512_F3-II1.json b/notebooks/NFU1/phenopackets/PMID_36256512_F3-II1.json new file mode 100644 index 00000000..eebc6132 --- /dev/null +++ b/notebooks/NFU1/phenopackets/PMID_36256512_F3-II1.json @@ -0,0 +1,258 @@ +{ + "id": "PMID_36256512_F3_II_1", + "subject": { + "id": "F3-II:1 ", + "timeAtLastEncounter": { + "age": { + "iso8601duration": "P12Y" + } + }, + "vitalStatus": { + "status": "ALIVE" + }, + "sex": "FEMALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0010550", + "label": "Paraplegia" + }, + "onset": { + "age": { + "iso8601duration": "P1Y" + } + } + }, + { + "type": { + "id": "HP:0001263", + "label": "Global developmental delay" + } + }, + { + "type": { + "id": "HP:0031936", + "label": "Delayed ability to walk" + } + }, + { + "type": { + "id": "HP:0001276", + "label": "Hypertonia" + } + }, + { + "type": { + "id": "HP:0001348", + "label": "Brisk reflexes" + } + }, + { + "type": { + "id": "HP:0011449", + "label": "Knee clonus" + } + }, + { + "type": { + "id": "HP:0002066", + "label": "Gait ataxia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0003128", + "label": "Lactic acidosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002376", + "label": "Developmental regression" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011448", + "label": "Ankle clonus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0003487", + "label": "Babinski sign" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0034295", + "label": "Reduced cerebral white matter volume" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002079", + "label": "Hypoplasia of the corpus callosum" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011096", + "label": "Peripheral demyelination" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002280", + "label": "Enlarged cisterna magna" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001298", + "label": "Encephalopathy" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001762", + "label": "Talipes equinovarus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0009830", + "label": "Peripheral neuropathy" + }, + "excluded": true + } + ], + "interpretations": [ + { + "id": "F3-II:1 ", + "progressStatus": "SOLVED", + "diagnosis": { + "disease": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "genomicInterpretations": [ + { + "subjectOrBiosampleId": "F3-II:1 ", + "interpretationStatus": "CAUSATIVE", + "variantInterpretation": { + "variationDescriptor": { + "id": "var_VOLSOfckDsHOqwSjqDnpkrjMW", + "geneContext": { + "valueId": "HGNC:16287", + "symbol": "NFU1" + }, + "expressions": [ + { + "syntax": "hgvs.c", + "value": "NM_001002755.4:c.362T>C" + }, + { + "syntax": "hgvs.g", + "value": "NC_000002.12:g.69419545A>G" + } + ], + "vcfRecord": { + "genomeAssembly": "hg38", + "chrom": "chr2", + "pos": "69419545", + "ref": "A", + "alt": "G" + }, + "moleculeContext": "genomic", + "allelicState": { + "id": "GENO:0000136", + "label": "homozygous" + } + } + } + } + ] + } + } + ], + "diseases": [ + { + "term": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "onset": { + "age": { + "iso8601duration": "P1Y" + } + } + } + ], + "metaData": { + "created": "2025-01-08T13:24:32.119359016Z", + "createdBy": "ORCID:0000-0002-0736-9199", + "resources": [ + { + "id": "geno", + "name": "Genotype Ontology", + "url": "http://purl.obolibrary.org/obo/geno.owl", + "version": "2022-03-05", + "namespacePrefix": "GENO", + "iriPrefix": "http://purl.obolibrary.org/obo/GENO_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "06/01/23", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "omim", + "name": "An Online Catalog of Human Genes and Genetic Disorders", + "url": "https://www.omim.org", + "version": "January 4, 2023", + "namespacePrefix": "OMIM", + "iriPrefix": "https://www.omim.org/entry/" + }, + { + "id": "so", + "name": "Sequence types and features ontology", + "url": "http://purl.obolibrary.org/obo/so.obo", + "version": "2021-11-22", + "namespacePrefix": "SO", + "iriPrefix": "http://purl.obolibrary.org/obo/SO_" + }, + { + "id": "hp", + "name": "human phenotype ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2024-12-12", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + } + ], + "phenopacketSchemaVersion": "2.0", + "externalReferences": [ + { + "id": "PMID:36256512", + "reference": "https://pubmed.ncbi.nlm.nih.gov/36256512", + "description": "Phenotypic continuum of NFU1-related disorders" + } + ] + } +} \ No newline at end of file diff --git a/notebooks/NFU1/phenopackets/PMID_36256512_F3-II2.json b/notebooks/NFU1/phenopackets/PMID_36256512_F3-II2.json new file mode 100644 index 00000000..dfee2ecd --- /dev/null +++ b/notebooks/NFU1/phenopackets/PMID_36256512_F3-II2.json @@ -0,0 +1,223 @@ +{ + "id": "PMID_36256512_F3_II_2", + "subject": { + "id": "F3-II:2 ", + "timeAtLastEncounter": { + "age": { + "iso8601duration": "P9Y" + } + }, + "vitalStatus": { + "status": "ALIVE" + }, + "sex": "MALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0010550", + "label": "Paraplegia" + }, + "onset": { + "age": { + "iso8601duration": "P1Y" + } + } + }, + { + "type": { + "id": "HP:0001263", + "label": "Global developmental delay" + } + }, + { + "type": { + "id": "HP:0031936", + "label": "Delayed ability to walk" + } + }, + { + "type": { + "id": "HP:0001276", + "label": "Hypertonia" + } + }, + { + "type": { + "id": "HP:0001348", + "label": "Brisk reflexes" + } + }, + { + "type": { + "id": "HP:0011449", + "label": "Knee clonus" + } + }, + { + "type": { + "id": "HP:0002066", + "label": "Gait ataxia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0003128", + "label": "Lactic acidosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002376", + "label": "Developmental regression" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011448", + "label": "Ankle clonus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0003487", + "label": "Babinski sign" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001762", + "label": "Talipes equinovarus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0009830", + "label": "Peripheral neuropathy" + }, + "excluded": true + } + ], + "interpretations": [ + { + "id": "F3-II:2 ", + "progressStatus": "SOLVED", + "diagnosis": { + "disease": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "genomicInterpretations": [ + { + "subjectOrBiosampleId": "F3-II:2 ", + "interpretationStatus": "CAUSATIVE", + "variantInterpretation": { + "variationDescriptor": { + "id": "var_VOLSOfckDsHOqwSjqDnpkrjMW", + "geneContext": { + "valueId": "HGNC:16287", + "symbol": "NFU1" + }, + "expressions": [ + { + "syntax": "hgvs.c", + "value": "NM_001002755.4:c.362T>C" + }, + { + "syntax": "hgvs.g", + "value": "NC_000002.12:g.69419545A>G" + } + ], + "vcfRecord": { + "genomeAssembly": "hg38", + "chrom": "chr2", + "pos": "69419545", + "ref": "A", + "alt": "G" + }, + "moleculeContext": "genomic", + "allelicState": { + "id": "GENO:0000136", + "label": "homozygous" + } + } + } + } + ] + } + } + ], + "diseases": [ + { + "term": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "onset": { + "age": { + "iso8601duration": "P1Y" + } + } + } + ], + "metaData": { + "created": "2025-01-08T13:24:32.119869947Z", + "createdBy": "ORCID:0000-0002-0736-9199", + "resources": [ + { + "id": "geno", + "name": "Genotype Ontology", + "url": "http://purl.obolibrary.org/obo/geno.owl", + "version": "2022-03-05", + "namespacePrefix": "GENO", + "iriPrefix": "http://purl.obolibrary.org/obo/GENO_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "06/01/23", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "omim", + "name": "An Online Catalog of Human Genes and Genetic Disorders", + "url": "https://www.omim.org", + "version": "January 4, 2023", + "namespacePrefix": "OMIM", + "iriPrefix": "https://www.omim.org/entry/" + }, + { + "id": "so", + "name": "Sequence types and features ontology", + "url": "http://purl.obolibrary.org/obo/so.obo", + "version": "2021-11-22", + "namespacePrefix": "SO", + "iriPrefix": "http://purl.obolibrary.org/obo/SO_" + }, + { + "id": "hp", + "name": "human phenotype ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2024-12-12", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + } + ], + "phenopacketSchemaVersion": "2.0", + "externalReferences": [ + { + "id": "PMID:36256512", + "reference": "https://pubmed.ncbi.nlm.nih.gov/36256512", + "description": "Phenotypic continuum of NFU1-related disorders" + } + ] + } +} \ No newline at end of file diff --git a/notebooks/NFU1/phenopackets/PMID_36256512_F4-II4.json b/notebooks/NFU1/phenopackets/PMID_36256512_F4-II4.json new file mode 100644 index 00000000..88b4eb6d --- /dev/null +++ b/notebooks/NFU1/phenopackets/PMID_36256512_F4-II4.json @@ -0,0 +1,220 @@ +{ + "id": "PMID_36256512_F4_II_4", + "subject": { + "id": "F4-II:4 ", + "timeAtLastEncounter": { + "age": { + "iso8601duration": "P2Y" + } + }, + "vitalStatus": { + "status": "DECEASED", + "timeOfDeath": { + "age": { + "iso8601duration": "P2Y" + } + } + }, + "sex": "FEMALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0010550", + "label": "Paraplegia" + }, + "onset": { + "age": { + "iso8601duration": "P2Y9M" + } + } + }, + { + "type": { + "id": "HP:0002376", + "label": "Developmental regression" + } + }, + { + "type": { + "id": "HP:0031936", + "label": "Delayed ability to walk" + } + }, + { + "type": { + "id": "HP:0001276", + "label": "Hypertonia" + } + }, + { + "type": { + "id": "HP:0001348", + "label": "Brisk reflexes" + } + }, + { + "type": { + "id": "HP:0011449", + "label": "Knee clonus" + } + }, + { + "type": { + "id": "HP:0011448", + "label": "Ankle clonus" + } + }, + { + "type": { + "id": "HP:0002066", + "label": "Gait ataxia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0003128", + "label": "Lactic acidosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0003487", + "label": "Babinski sign" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001762", + "label": "Talipes equinovarus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0009830", + "label": "Peripheral neuropathy" + }, + "excluded": true + } + ], + "interpretations": [ + { + "id": "F4-II:4 ", + "progressStatus": "SOLVED", + "diagnosis": { + "disease": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "genomicInterpretations": [ + { + "subjectOrBiosampleId": "F4-II:4 ", + "interpretationStatus": "CAUSATIVE", + "variantInterpretation": { + "variationDescriptor": { + "id": "var_VOLSOfckDsHOqwSjqDnpkrjMW", + "geneContext": { + "valueId": "HGNC:16287", + "symbol": "NFU1" + }, + "expressions": [ + { + "syntax": "hgvs.c", + "value": "NM_001002755.4:c.362T>C" + }, + { + "syntax": "hgvs.g", + "value": "NC_000002.12:g.69419545A>G" + } + ], + "vcfRecord": { + "genomeAssembly": "hg38", + "chrom": "chr2", + "pos": "69419545", + "ref": "A", + "alt": "G" + }, + "moleculeContext": "genomic", + "allelicState": { + "id": "GENO:0000136", + "label": "homozygous" + } + } + } + } + ] + } + } + ], + "diseases": [ + { + "term": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "onset": { + "age": { + "iso8601duration": "P2Y9M" + } + } + } + ], + "metaData": { + "created": "2025-01-08T13:24:32.120321035Z", + "createdBy": "ORCID:0000-0002-0736-9199", + "resources": [ + { + "id": "geno", + "name": "Genotype Ontology", + "url": "http://purl.obolibrary.org/obo/geno.owl", + "version": "2022-03-05", + "namespacePrefix": "GENO", + "iriPrefix": "http://purl.obolibrary.org/obo/GENO_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "06/01/23", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "omim", + "name": "An Online Catalog of Human Genes and Genetic Disorders", + "url": "https://www.omim.org", + "version": "January 4, 2023", + "namespacePrefix": "OMIM", + "iriPrefix": "https://www.omim.org/entry/" + }, + { + "id": "so", + "name": "Sequence types and features ontology", + "url": "http://purl.obolibrary.org/obo/so.obo", + "version": "2021-11-22", + "namespacePrefix": "SO", + "iriPrefix": "http://purl.obolibrary.org/obo/SO_" + }, + { + "id": "hp", + "name": "human phenotype ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2024-12-12", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + } + ], + "phenopacketSchemaVersion": "2.0", + "externalReferences": [ + { + "id": "PMID:36256512", + "reference": "https://pubmed.ncbi.nlm.nih.gov/36256512", + "description": "Phenotypic continuum of NFU1-related disorders" + } + ] + } +} \ No newline at end of file diff --git a/notebooks/NFU1/phenopackets/PMID_36256512_F4-II5.json b/notebooks/NFU1/phenopackets/PMID_36256512_F4-II5.json new file mode 100644 index 00000000..75aa13d5 --- /dev/null +++ b/notebooks/NFU1/phenopackets/PMID_36256512_F4-II5.json @@ -0,0 +1,249 @@ +{ + "id": "PMID_36256512_F4_II_5", + "subject": { + "id": "F4-II:5 ", + "timeAtLastEncounter": { + "age": { + "iso8601duration": "P6Y" + } + }, + "vitalStatus": { + "status": "ALIVE" + }, + "sex": "FEMALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0010550", + "label": "Paraplegia" + }, + "onset": { + "age": { + "iso8601duration": "P11M" + } + } + }, + { + "type": { + "id": "HP:0001276", + "label": "Hypertonia" + } + }, + { + "type": { + "id": "HP:0001348", + "label": "Brisk reflexes" + } + }, + { + "type": { + "id": "HP:0011449", + "label": "Knee clonus" + } + }, + { + "type": { + "id": "HP:0011448", + "label": "Ankle clonus" + } + }, + { + "type": { + "id": "HP:0034295", + "label": "Reduced cerebral white matter volume" + } + }, + { + "type": { + "id": "HP:0002079", + "label": "Hypoplasia of the corpus callosum" + } + }, + { + "type": { + "id": "HP:0002280", + "label": "Enlarged cisterna magna" + } + }, + { + "type": { + "id": "HP:0002066", + "label": "Gait ataxia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001263", + "label": "Global developmental delay" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0003128", + "label": "Lactic acidosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002376", + "label": "Developmental regression" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0003487", + "label": "Babinski sign" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011096", + "label": "Peripheral demyelination" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001298", + "label": "Encephalopathy" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001762", + "label": "Talipes equinovarus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0009830", + "label": "Peripheral neuropathy" + }, + "excluded": true + } + ], + "interpretations": [ + { + "id": "F4-II:5 ", + "progressStatus": "SOLVED", + "diagnosis": { + "disease": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "genomicInterpretations": [ + { + "subjectOrBiosampleId": "F4-II:5 ", + "interpretationStatus": "CAUSATIVE", + "variantInterpretation": { + "variationDescriptor": { + "id": "var_VOLSOfckDsHOqwSjqDnpkrjMW", + "geneContext": { + "valueId": "HGNC:16287", + "symbol": "NFU1" + }, + "expressions": [ + { + "syntax": "hgvs.c", + "value": "NM_001002755.4:c.362T>C" + }, + { + "syntax": "hgvs.g", + "value": "NC_000002.12:g.69419545A>G" + } + ], + "vcfRecord": { + "genomeAssembly": "hg38", + "chrom": "chr2", + "pos": "69419545", + "ref": "A", + "alt": "G" + }, + "moleculeContext": "genomic", + "allelicState": { + "id": "GENO:0000136", + "label": "homozygous" + } + } + } + } + ] + } + } + ], + "diseases": [ + { + "term": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "onset": { + "age": { + "iso8601duration": "P11M" + } + } + } + ], + "metaData": { + "created": "2025-01-08T13:24:32.120782136Z", + "createdBy": "ORCID:0000-0002-0736-9199", + "resources": [ + { + "id": "geno", + "name": "Genotype Ontology", + "url": "http://purl.obolibrary.org/obo/geno.owl", + "version": "2022-03-05", + "namespacePrefix": "GENO", + "iriPrefix": "http://purl.obolibrary.org/obo/GENO_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "06/01/23", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "omim", + "name": "An Online Catalog of Human Genes and Genetic Disorders", + "url": "https://www.omim.org", + "version": "January 4, 2023", + "namespacePrefix": "OMIM", + "iriPrefix": "https://www.omim.org/entry/" + }, + { + "id": "so", + "name": "Sequence types and features ontology", + "url": "http://purl.obolibrary.org/obo/so.obo", + "version": "2021-11-22", + "namespacePrefix": "SO", + "iriPrefix": "http://purl.obolibrary.org/obo/SO_" + }, + { + "id": "hp", + "name": "human phenotype ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2024-12-12", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + } + ], + "phenopacketSchemaVersion": "2.0", + "externalReferences": [ + { + "id": "PMID:36256512", + "reference": "https://pubmed.ncbi.nlm.nih.gov/36256512", + "description": "Phenotypic continuum of NFU1-related disorders" + } + ] + } +} \ No newline at end of file diff --git a/notebooks/NFU1/phenopackets/PMID_36256512_F4-II6.json b/notebooks/NFU1/phenopackets/PMID_36256512_F4-II6.json new file mode 100644 index 00000000..79d36fb9 --- /dev/null +++ b/notebooks/NFU1/phenopackets/PMID_36256512_F4-II6.json @@ -0,0 +1,258 @@ +{ + "id": "PMID_36256512_F4_II_6", + "subject": { + "id": "F4-II:6 ", + "timeAtLastEncounter": { + "age": { + "iso8601duration": "P2Y6M" + } + }, + "vitalStatus": { + "status": "DECEASED", + "timeOfDeath": { + "age": { + "iso8601duration": "P2Y6M" + } + } + }, + "sex": "FEMALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0010550", + "label": "Paraplegia" + }, + "onset": { + "age": { + "iso8601duration": "P1Y" + } + } + }, + { + "type": { + "id": "HP:0001263", + "label": "Global developmental delay" + } + }, + { + "type": { + "id": "HP:0002376", + "label": "Developmental regression" + } + }, + { + "type": { + "id": "HP:0031936", + "label": "Delayed ability to walk" + } + }, + { + "type": { + "id": "HP:0001276", + "label": "Hypertonia" + } + }, + { + "type": { + "id": "HP:0001348", + "label": "Brisk reflexes" + } + }, + { + "type": { + "id": "HP:0011449", + "label": "Knee clonus" + } + }, + { + "type": { + "id": "HP:0011448", + "label": "Ankle clonus" + } + }, + { + "type": { + "id": "HP:0034295", + "label": "Reduced cerebral white matter volume" + } + }, + { + "type": { + "id": "HP:0002079", + "label": "Hypoplasia of the corpus callosum" + } + }, + { + "type": { + "id": "HP:0002280", + "label": "Enlarged cisterna magna" + } + }, + { + "type": { + "id": "HP:0002066", + "label": "Gait ataxia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0003128", + "label": "Lactic acidosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0003487", + "label": "Babinski sign" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011096", + "label": "Peripheral demyelination" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001298", + "label": "Encephalopathy" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001762", + "label": "Talipes equinovarus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0009830", + "label": "Peripheral neuropathy" + }, + "excluded": true + } + ], + "interpretations": [ + { + "id": "F4-II:6 ", + "progressStatus": "SOLVED", + "diagnosis": { + "disease": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "genomicInterpretations": [ + { + "subjectOrBiosampleId": "F4-II:6 ", + "interpretationStatus": "CAUSATIVE", + "variantInterpretation": { + "variationDescriptor": { + "id": "var_VOLSOfckDsHOqwSjqDnpkrjMW", + "geneContext": { + "valueId": "HGNC:16287", + "symbol": "NFU1" + }, + "expressions": [ + { + "syntax": "hgvs.c", + "value": "NM_001002755.4:c.362T>C" + }, + { + "syntax": "hgvs.g", + "value": "NC_000002.12:g.69419545A>G" + } + ], + "vcfRecord": { + "genomeAssembly": "hg38", + "chrom": "chr2", + "pos": "69419545", + "ref": "A", + "alt": "G" + }, + "moleculeContext": "genomic", + "allelicState": { + "id": "GENO:0000136", + "label": "homozygous" + } + } + } + } + ] + } + } + ], + "diseases": [ + { + "term": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "onset": { + "age": { + "iso8601duration": "P1Y" + } + } + } + ], + "metaData": { + "created": "2025-01-08T13:24:32.121264934Z", + "createdBy": "ORCID:0000-0002-0736-9199", + "resources": [ + { + "id": "geno", + "name": "Genotype Ontology", + "url": "http://purl.obolibrary.org/obo/geno.owl", + "version": "2022-03-05", + "namespacePrefix": "GENO", + "iriPrefix": "http://purl.obolibrary.org/obo/GENO_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "06/01/23", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "omim", + "name": "An Online Catalog of Human Genes and Genetic Disorders", + "url": "https://www.omim.org", + "version": "January 4, 2023", + "namespacePrefix": "OMIM", + "iriPrefix": "https://www.omim.org/entry/" + }, + { + "id": "so", + "name": "Sequence types and features ontology", + "url": "http://purl.obolibrary.org/obo/so.obo", + "version": "2021-11-22", + "namespacePrefix": "SO", + "iriPrefix": "http://purl.obolibrary.org/obo/SO_" + }, + { + "id": "hp", + "name": "human phenotype ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2024-12-12", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + } + ], + "phenopacketSchemaVersion": "2.0", + "externalReferences": [ + { + "id": "PMID:36256512", + "reference": "https://pubmed.ncbi.nlm.nih.gov/36256512", + "description": "Phenotypic continuum of NFU1-related disorders" + } + ] + } +} \ No newline at end of file diff --git a/notebooks/NFU1/phenopackets/PMID_36256512_F5-II1.json b/notebooks/NFU1/phenopackets/PMID_36256512_F5-II1.json new file mode 100644 index 00000000..7fe7008a --- /dev/null +++ b/notebooks/NFU1/phenopackets/PMID_36256512_F5-II1.json @@ -0,0 +1,277 @@ +{ + "id": "PMID_36256512_F5_II_1", + "subject": { + "id": "F5-II:1 ", + "timeAtLastEncounter": { + "age": { + "iso8601duration": "P6M" + } + }, + "vitalStatus": { + "status": "DECEASED", + "timeOfDeath": { + "age": { + "iso8601duration": "P6M" + } + } + }, + "sex": "FEMALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0001945", + "label": "Fever" + }, + "onset": { + "age": { + "iso8601duration": "P5M" + } + } + }, + { + "type": { + "id": "HP:0001252", + "label": "Hypotonia" + }, + "onset": { + "age": { + "iso8601duration": "P5M" + } + } + }, + { + "type": { + "id": "HP:0002878", + "label": "Respiratory failure" + }, + "onset": { + "age": { + "iso8601duration": "P5M" + } + } + }, + { + "type": { + "id": "HP:0001941", + "label": "Acidosis" + }, + "onset": { + "age": { + "iso8601duration": "P5M" + } + } + }, + { + "type": { + "id": "HP:0002376", + "label": "Developmental regression" + } + }, + { + "type": { + "id": "HP:0001348", + "label": "Brisk reflexes" + } + }, + { + "type": { + "id": "HP:0034295", + "label": "Reduced cerebral white matter volume" + } + }, + { + "type": { + "id": "HP:0002066", + "label": "Gait ataxia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001276", + "label": "Hypertonia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011449", + "label": "Knee clonus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011448", + "label": "Ankle clonus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0003487", + "label": "Babinski sign" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002079", + "label": "Hypoplasia of the corpus callosum" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011096", + "label": "Peripheral demyelination" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002280", + "label": "Enlarged cisterna magna" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001298", + "label": "Encephalopathy" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001762", + "label": "Talipes equinovarus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0009830", + "label": "Peripheral neuropathy" + }, + "excluded": true + } + ], + "interpretations": [ + { + "id": "F5-II:1 ", + "progressStatus": "SOLVED", + "diagnosis": { + "disease": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "genomicInterpretations": [ + { + "subjectOrBiosampleId": "F5-II:1 ", + "interpretationStatus": "CAUSATIVE", + "variantInterpretation": { + "variationDescriptor": { + "id": "var_VOLSOfckDsHOqwSjqDnpkrjMW", + "geneContext": { + "valueId": "HGNC:16287", + "symbol": "NFU1" + }, + "expressions": [ + { + "syntax": "hgvs.c", + "value": "NM_001002755.4:c.362T>C" + }, + { + "syntax": "hgvs.g", + "value": "NC_000002.12:g.69419545A>G" + } + ], + "vcfRecord": { + "genomeAssembly": "hg38", + "chrom": "chr2", + "pos": "69419545", + "ref": "A", + "alt": "G" + }, + "moleculeContext": "genomic", + "allelicState": { + "id": "GENO:0000136", + "label": "homozygous" + } + } + } + } + ] + } + } + ], + "diseases": [ + { + "term": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "onset": { + "age": { + "iso8601duration": "P5M" + } + } + } + ], + "metaData": { + "created": "2025-01-08T13:24:32.121779918Z", + "createdBy": "ORCID:0000-0002-0736-9199", + "resources": [ + { + "id": "geno", + "name": "Genotype Ontology", + "url": "http://purl.obolibrary.org/obo/geno.owl", + "version": "2022-03-05", + "namespacePrefix": "GENO", + "iriPrefix": "http://purl.obolibrary.org/obo/GENO_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "06/01/23", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "omim", + "name": "An Online Catalog of Human Genes and Genetic Disorders", + "url": "https://www.omim.org", + "version": "January 4, 2023", + "namespacePrefix": "OMIM", + "iriPrefix": "https://www.omim.org/entry/" + }, + { + "id": "so", + "name": "Sequence types and features ontology", + "url": "http://purl.obolibrary.org/obo/so.obo", + "version": "2021-11-22", + "namespacePrefix": "SO", + "iriPrefix": "http://purl.obolibrary.org/obo/SO_" + }, + { + "id": "hp", + "name": "human phenotype ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2024-12-12", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + } + ], + "phenopacketSchemaVersion": "2.0", + "externalReferences": [ + { + "id": "PMID:36256512", + "reference": "https://pubmed.ncbi.nlm.nih.gov/36256512", + "description": "Phenotypic continuum of NFU1-related disorders" + } + ] + } +} \ No newline at end of file diff --git a/notebooks/NFU1/phenopackets/PMID_36256512_F5-II2.json b/notebooks/NFU1/phenopackets/PMID_36256512_F5-II2.json new file mode 100644 index 00000000..72876dc6 --- /dev/null +++ b/notebooks/NFU1/phenopackets/PMID_36256512_F5-II2.json @@ -0,0 +1,249 @@ +{ + "id": "PMID_36256512_F5_II_2", + "subject": { + "id": "F5-II:2 ", + "timeAtLastEncounter": { + "age": { + "iso8601duration": "P4Y7M" + } + }, + "vitalStatus": { + "status": "ALIVE" + }, + "sex": "MALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0010550", + "label": "Paraplegia" + }, + "onset": { + "age": { + "iso8601duration": "P1Y2M" + } + } + }, + { + "type": { + "id": "HP:0002376", + "label": "Developmental regression" + } + }, + { + "type": { + "id": "HP:0031936", + "label": "Delayed ability to walk" + } + }, + { + "type": { + "id": "HP:0001276", + "label": "Hypertonia" + } + }, + { + "type": { + "id": "HP:0001348", + "label": "Brisk reflexes" + } + }, + { + "type": { + "id": "HP:0034295", + "label": "Reduced cerebral white matter volume" + } + }, + { + "type": { + "id": "HP:0002079", + "label": "Hypoplasia of the corpus callosum" + } + }, + { + "type": { + "id": "HP:0002280", + "label": "Enlarged cisterna magna" + } + }, + { + "type": { + "id": "HP:0002066", + "label": "Gait ataxia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0003128", + "label": "Lactic acidosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011449", + "label": "Knee clonus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011448", + "label": "Ankle clonus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0003487", + "label": "Babinski sign" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011096", + "label": "Peripheral demyelination" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001298", + "label": "Encephalopathy" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001762", + "label": "Talipes equinovarus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0009830", + "label": "Peripheral neuropathy" + }, + "excluded": true + } + ], + "interpretations": [ + { + "id": "F5-II:2 ", + "progressStatus": "SOLVED", + "diagnosis": { + "disease": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "genomicInterpretations": [ + { + "subjectOrBiosampleId": "F5-II:2 ", + "interpretationStatus": "CAUSATIVE", + "variantInterpretation": { + "variationDescriptor": { + "id": "var_VOLSOfckDsHOqwSjqDnpkrjMW", + "geneContext": { + "valueId": "HGNC:16287", + "symbol": "NFU1" + }, + "expressions": [ + { + "syntax": "hgvs.c", + "value": "NM_001002755.4:c.362T>C" + }, + { + "syntax": "hgvs.g", + "value": "NC_000002.12:g.69419545A>G" + } + ], + "vcfRecord": { + "genomeAssembly": "hg38", + "chrom": "chr2", + "pos": "69419545", + "ref": "A", + "alt": "G" + }, + "moleculeContext": "genomic", + "allelicState": { + "id": "GENO:0000136", + "label": "homozygous" + } + } + } + } + ] + } + } + ], + "diseases": [ + { + "term": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "onset": { + "age": { + "iso8601duration": "P1Y2M" + } + } + } + ], + "metaData": { + "created": "2025-01-08T13:24:32.122424125Z", + "createdBy": "ORCID:0000-0002-0736-9199", + "resources": [ + { + "id": "geno", + "name": "Genotype Ontology", + "url": "http://purl.obolibrary.org/obo/geno.owl", + "version": "2022-03-05", + "namespacePrefix": "GENO", + "iriPrefix": "http://purl.obolibrary.org/obo/GENO_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "06/01/23", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "omim", + "name": "An Online Catalog of Human Genes and Genetic Disorders", + "url": "https://www.omim.org", + "version": "January 4, 2023", + "namespacePrefix": "OMIM", + "iriPrefix": "https://www.omim.org/entry/" + }, + { + "id": "so", + "name": "Sequence types and features ontology", + "url": "http://purl.obolibrary.org/obo/so.obo", + "version": "2021-11-22", + "namespacePrefix": "SO", + "iriPrefix": "http://purl.obolibrary.org/obo/SO_" + }, + { + "id": "hp", + "name": "human phenotype ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2024-12-12", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + } + ], + "phenopacketSchemaVersion": "2.0", + "externalReferences": [ + { + "id": "PMID:36256512", + "reference": "https://pubmed.ncbi.nlm.nih.gov/36256512", + "description": "Phenotypic continuum of NFU1-related disorders" + } + ] + } +} \ No newline at end of file diff --git a/notebooks/NFU1/phenopackets/PMID_36256512_F6-II2.json b/notebooks/NFU1/phenopackets/PMID_36256512_F6-II2.json new file mode 100644 index 00000000..d131a208 --- /dev/null +++ b/notebooks/NFU1/phenopackets/PMID_36256512_F6-II2.json @@ -0,0 +1,284 @@ +{ + "id": "PMID_36256512_F6_II_2", + "subject": { + "id": "F6-II:2 ", + "timeAtLastEncounter": { + "age": { + "iso8601duration": "P3Y" + } + }, + "vitalStatus": { + "status": "DECEASED", + "timeOfDeath": { + "age": { + "iso8601duration": "P3Y" + } + } + }, + "sex": "MALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0001288", + "label": "Gait disturbance" + }, + "onset": { + "age": { + "iso8601duration": "P1Y" + } + } + }, + { + "type": { + "id": "HP:0007020", + "label": "Progressive spastic paraplegia" + }, + "onset": { + "age": { + "iso8601duration": "P1Y" + } + } + }, + { + "type": { + "id": "HP:0003128", + "label": "Lactic acidosis" + } + }, + { + "type": { + "id": "HP:0002376", + "label": "Developmental regression" + } + }, + { + "type": { + "id": "HP:0001348", + "label": "Brisk reflexes" + } + }, + { + "type": { + "id": "HP:0011449", + "label": "Knee clonus" + } + }, + { + "type": { + "id": "HP:0011448", + "label": "Ankle clonus" + } + }, + { + "type": { + "id": "HP:0003487", + "label": "Babinski sign" + } + }, + { + "type": { + "id": "HP:0034295", + "label": "Reduced cerebral white matter volume" + } + }, + { + "type": { + "id": "HP:0002079", + "label": "Hypoplasia of the corpus callosum" + } + }, + { + "type": { + "id": "HP:0002280", + "label": "Enlarged cisterna magna" + } + }, + { + "type": { + "id": "HP:0002066", + "label": "Gait ataxia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000486", + "label": "Strabismus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000639", + "label": "Nystagmus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000648", + "label": "Optic atrophy" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000508", + "label": "Ptosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000544", + "label": "External ophthalmoplegia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011096", + "label": "Peripheral demyelination" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001298", + "label": "Encephalopathy" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001762", + "label": "Talipes equinovarus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0009830", + "label": "Peripheral neuropathy" + }, + "excluded": true + } + ], + "interpretations": [ + { + "id": "F6-II:2 ", + "progressStatus": "SOLVED", + "diagnosis": { + "disease": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "genomicInterpretations": [ + { + "subjectOrBiosampleId": "F6-II:2 ", + "interpretationStatus": "CAUSATIVE", + "variantInterpretation": { + "variationDescriptor": { + "id": "var_VOLSOfckDsHOqwSjqDnpkrjMW", + "geneContext": { + "valueId": "HGNC:16287", + "symbol": "NFU1" + }, + "expressions": [ + { + "syntax": "hgvs.c", + "value": "NM_001002755.4:c.362T>C" + }, + { + "syntax": "hgvs.g", + "value": "NC_000002.12:g.69419545A>G" + } + ], + "vcfRecord": { + "genomeAssembly": "hg38", + "chrom": "chr2", + "pos": "69419545", + "ref": "A", + "alt": "G" + }, + "moleculeContext": "genomic", + "allelicState": { + "id": "GENO:0000136", + "label": "homozygous" + } + } + } + } + ] + } + } + ], + "diseases": [ + { + "term": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "onset": { + "age": { + "iso8601duration": "P1Y" + } + } + } + ], + "metaData": { + "created": "2025-01-08T13:24:32.122959852Z", + "createdBy": "ORCID:0000-0002-0736-9199", + "resources": [ + { + "id": "geno", + "name": "Genotype Ontology", + "url": "http://purl.obolibrary.org/obo/geno.owl", + "version": "2022-03-05", + "namespacePrefix": "GENO", + "iriPrefix": "http://purl.obolibrary.org/obo/GENO_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "06/01/23", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "omim", + "name": "An Online Catalog of Human Genes and Genetic Disorders", + "url": "https://www.omim.org", + "version": "January 4, 2023", + "namespacePrefix": "OMIM", + "iriPrefix": "https://www.omim.org/entry/" + }, + { + "id": "so", + "name": "Sequence types and features ontology", + "url": "http://purl.obolibrary.org/obo/so.obo", + "version": "2021-11-22", + "namespacePrefix": "SO", + "iriPrefix": "http://purl.obolibrary.org/obo/SO_" + }, + { + "id": "hp", + "name": "human phenotype ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2024-12-12", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + } + ], + "phenopacketSchemaVersion": "2.0", + "externalReferences": [ + { + "id": "PMID:36256512", + "reference": "https://pubmed.ncbi.nlm.nih.gov/36256512", + "description": "Phenotypic continuum of NFU1-related disorders" + } + ] + } +} \ No newline at end of file diff --git a/notebooks/NFU1/phenopackets/PMID_36256512_F6-II3.json b/notebooks/NFU1/phenopackets/PMID_36256512_F6-II3.json new file mode 100644 index 00000000..d443b97c --- /dev/null +++ b/notebooks/NFU1/phenopackets/PMID_36256512_F6-II3.json @@ -0,0 +1,264 @@ +{ + "id": "PMID_36256512_F6_II_3", + "subject": { + "id": "F6-II:3 ", + "timeAtLastEncounter": { + "age": { + "iso8601duration": "P2Y3M" + } + }, + "vitalStatus": { + "status": "ALIVE" + }, + "sex": "MALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0002061", + "label": "Lower limb spasticity" + }, + "onset": { + "age": { + "iso8601duration": "P10M" + } + } + }, + { + "type": { + "id": "HP:0003128", + "label": "Lactic acidosis" + } + }, + { + "type": { + "id": "HP:0002376", + "label": "Developmental regression" + } + }, + { + "type": { + "id": "HP:0001348", + "label": "Brisk reflexes" + } + }, + { + "type": { + "id": "HP:0011449", + "label": "Knee clonus" + } + }, + { + "type": { + "id": "HP:0011448", + "label": "Ankle clonus" + } + }, + { + "type": { + "id": "HP:0003487", + "label": "Babinski sign" + } + }, + { + "type": { + "id": "HP:0002066", + "label": "Gait ataxia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000486", + "label": "Strabismus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000639", + "label": "Nystagmus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000648", + "label": "Optic atrophy" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000508", + "label": "Ptosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000544", + "label": "External ophthalmoplegia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002079", + "label": "Hypoplasia of the corpus callosum" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011096", + "label": "Peripheral demyelination" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002280", + "label": "Enlarged cisterna magna" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001298", + "label": "Encephalopathy" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001762", + "label": "Talipes equinovarus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0009830", + "label": "Peripheral neuropathy" + }, + "excluded": true + } + ], + "interpretations": [ + { + "id": "F6-II:3 ", + "progressStatus": "SOLVED", + "diagnosis": { + "disease": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "genomicInterpretations": [ + { + "subjectOrBiosampleId": "F6-II:3 ", + "interpretationStatus": "CAUSATIVE", + "variantInterpretation": { + "variationDescriptor": { + "id": "var_VOLSOfckDsHOqwSjqDnpkrjMW", + "geneContext": { + "valueId": "HGNC:16287", + "symbol": "NFU1" + }, + "expressions": [ + { + "syntax": "hgvs.c", + "value": "NM_001002755.4:c.362T>C" + }, + { + "syntax": "hgvs.g", + "value": "NC_000002.12:g.69419545A>G" + } + ], + "vcfRecord": { + "genomeAssembly": "hg38", + "chrom": "chr2", + "pos": "69419545", + "ref": "A", + "alt": "G" + }, + "moleculeContext": "genomic", + "allelicState": { + "id": "GENO:0000136", + "label": "homozygous" + } + } + } + } + ] + } + } + ], + "diseases": [ + { + "term": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "onset": { + "age": { + "iso8601duration": "P10M" + } + } + } + ], + "metaData": { + "created": "2025-01-08T13:24:32.123540878Z", + "createdBy": "ORCID:0000-0002-0736-9199", + "resources": [ + { + "id": "geno", + "name": "Genotype Ontology", + "url": "http://purl.obolibrary.org/obo/geno.owl", + "version": "2022-03-05", + "namespacePrefix": "GENO", + "iriPrefix": "http://purl.obolibrary.org/obo/GENO_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "06/01/23", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "omim", + "name": "An Online Catalog of Human Genes and Genetic Disorders", + "url": "https://www.omim.org", + "version": "January 4, 2023", + "namespacePrefix": "OMIM", + "iriPrefix": "https://www.omim.org/entry/" + }, + { + "id": "so", + "name": "Sequence types and features ontology", + "url": "http://purl.obolibrary.org/obo/so.obo", + "version": "2021-11-22", + "namespacePrefix": "SO", + "iriPrefix": "http://purl.obolibrary.org/obo/SO_" + }, + { + "id": "hp", + "name": "human phenotype ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2024-12-12", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + } + ], + "phenopacketSchemaVersion": "2.0", + "externalReferences": [ + { + "id": "PMID:36256512", + "reference": "https://pubmed.ncbi.nlm.nih.gov/36256512", + "description": "Phenotypic continuum of NFU1-related disorders" + } + ] + } +} \ No newline at end of file diff --git a/notebooks/NFU1/phenopackets/PMID_36256512_F7-II1.json b/notebooks/NFU1/phenopackets/PMID_36256512_F7-II1.json new file mode 100644 index 00000000..2226a991 --- /dev/null +++ b/notebooks/NFU1/phenopackets/PMID_36256512_F7-II1.json @@ -0,0 +1,250 @@ +{ + "id": "PMID_36256512_F7_II_1", + "subject": { + "id": "F7-II:1 ", + "timeAtLastEncounter": { + "age": { + "iso8601duration": "P10Y" + } + }, + "vitalStatus": { + "status": "ALIVE" + }, + "sex": "MALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0010550", + "label": "Paraplegia" + }, + "onset": { + "age": { + "iso8601duration": "P3M" + } + } + }, + { + "type": { + "id": "HP:0031936", + "label": "Delayed ability to walk" + } + }, + { + "type": { + "id": "HP:0001276", + "label": "Hypertonia" + } + }, + { + "type": { + "id": "HP:0001348", + "label": "Brisk reflexes" + } + }, + { + "type": { + "id": "HP:0002079", + "label": "Hypoplasia of the corpus callosum" + } + }, + { + "type": { + "id": "HP:0002280", + "label": "Enlarged cisterna magna" + } + }, + { + "type": { + "id": "HP:0001762", + "label": "Talipes equinovarus" + } + }, + { + "type": { + "id": "HP:0002066", + "label": "Gait ataxia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0003128", + "label": "Lactic acidosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002376", + "label": "Developmental regression" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011449", + "label": "Knee clonus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011448", + "label": "Ankle clonus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0003487", + "label": "Babinski sign" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0034295", + "label": "Reduced cerebral white matter volume" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011096", + "label": "Peripheral demyelination" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001298", + "label": "Encephalopathy" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0009830", + "label": "Peripheral neuropathy" + }, + "excluded": true + } + ], + "interpretations": [ + { + "id": "F7-II:1 ", + "progressStatus": "SOLVED", + "diagnosis": { + "disease": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "genomicInterpretations": [ + { + "subjectOrBiosampleId": "F7-II:1 ", + "interpretationStatus": "CAUSATIVE", + "variantInterpretation": { + "variationDescriptor": { + "id": "var_vlWqyyqDTmrdYgizSMhTykUKm", + "geneContext": { + "valueId": "HGNC:16287", + "symbol": "NFU1" + }, + "expressions": [ + { + "syntax": "hgvs.c", + "value": "NM_001002755.4:c.295C>G" + }, + { + "syntax": "hgvs.g", + "value": "NC_000002.12:g.69423589G>C" + } + ], + "vcfRecord": { + "genomeAssembly": "hg38", + "chrom": "chr2", + "pos": "69423589", + "ref": "G", + "alt": "C" + }, + "moleculeContext": "genomic", + "allelicState": { + "id": "GENO:0000136", + "label": "homozygous" + } + } + } + } + ] + } + } + ], + "diseases": [ + { + "term": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "onset": { + "age": { + "iso8601duration": "P3M" + } + } + } + ], + "metaData": { + "created": "2025-01-08T13:24:32.124045133Z", + "createdBy": "ORCID:0000-0002-0736-9199", + "resources": [ + { + "id": "geno", + "name": "Genotype Ontology", + "url": "http://purl.obolibrary.org/obo/geno.owl", + "version": "2022-03-05", + "namespacePrefix": "GENO", + "iriPrefix": "http://purl.obolibrary.org/obo/GENO_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "06/01/23", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "omim", + "name": "An Online Catalog of Human Genes and Genetic Disorders", + "url": "https://www.omim.org", + "version": "January 4, 2023", + "namespacePrefix": "OMIM", + "iriPrefix": "https://www.omim.org/entry/" + }, + { + "id": "so", + "name": "Sequence types and features ontology", + "url": "http://purl.obolibrary.org/obo/so.obo", + "version": "2021-11-22", + "namespacePrefix": "SO", + "iriPrefix": "http://purl.obolibrary.org/obo/SO_" + }, + { + "id": "hp", + "name": "human phenotype ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2024-12-12", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + } + ], + "phenopacketSchemaVersion": "2.0", + "externalReferences": [ + { + "id": "PMID:36256512", + "reference": "https://pubmed.ncbi.nlm.nih.gov/36256512", + "description": "Phenotypic continuum of NFU1-related disorders" + } + ] + } +} \ No newline at end of file diff --git a/notebooks/NFU1/phenopackets/PMID_36256512_F7-II2.json b/notebooks/NFU1/phenopackets/PMID_36256512_F7-II2.json new file mode 100644 index 00000000..e6befd60 --- /dev/null +++ b/notebooks/NFU1/phenopackets/PMID_36256512_F7-II2.json @@ -0,0 +1,252 @@ +{ + "id": "PMID_36256512_F7_II_2", + "subject": { + "id": "F7-II:2 ", + "timeAtLastEncounter": { + "age": { + "iso8601duration": "P6Y" + } + }, + "vitalStatus": { + "status": "ALIVE" + }, + "sex": "MALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0010550", + "label": "Paraplegia" + }, + "onset": { + "age": { + "iso8601duration": "P3M" + } + } + }, + { + "type": { + "id": "HP:0031936", + "label": "Delayed ability to walk" + } + }, + { + "type": { + "id": "HP:0001276", + "label": "Hypertonia" + } + }, + { + "type": { + "id": "HP:0001348", + "label": "Brisk reflexes" + } + }, + { + "type": { + "id": "HP:0001762", + "label": "Talipes equinovarus" + } + }, + { + "type": { + "id": "HP:0002066", + "label": "Gait ataxia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0003128", + "label": "Lactic acidosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002376", + "label": "Developmental regression" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011449", + "label": "Knee clonus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011448", + "label": "Ankle clonus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0003487", + "label": "Babinski sign" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0034295", + "label": "Reduced cerebral white matter volume" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002079", + "label": "Hypoplasia of the corpus callosum" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011096", + "label": "Peripheral demyelination" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002280", + "label": "Enlarged cisterna magna" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001298", + "label": "Encephalopathy" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0009830", + "label": "Peripheral neuropathy" + }, + "excluded": true + } + ], + "interpretations": [ + { + "id": "F7-II:2 ", + "progressStatus": "SOLVED", + "diagnosis": { + "disease": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "genomicInterpretations": [ + { + "subjectOrBiosampleId": "F7-II:2 ", + "interpretationStatus": "CAUSATIVE", + "variantInterpretation": { + "variationDescriptor": { + "id": "var_vlWqyyqDTmrdYgizSMhTykUKm", + "geneContext": { + "valueId": "HGNC:16287", + "symbol": "NFU1" + }, + "expressions": [ + { + "syntax": "hgvs.c", + "value": "NM_001002755.4:c.295C>G" + }, + { + "syntax": "hgvs.g", + "value": "NC_000002.12:g.69423589G>C" + } + ], + "vcfRecord": { + "genomeAssembly": "hg38", + "chrom": "chr2", + "pos": "69423589", + "ref": "G", + "alt": "C" + }, + "moleculeContext": "genomic", + "allelicState": { + "id": "GENO:0000136", + "label": "homozygous" + } + } + } + } + ] + } + } + ], + "diseases": [ + { + "term": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "onset": { + "age": { + "iso8601duration": "P3M" + } + } + } + ], + "metaData": { + "created": "2025-01-08T13:24:32.124588966Z", + "createdBy": "ORCID:0000-0002-0736-9199", + "resources": [ + { + "id": "geno", + "name": "Genotype Ontology", + "url": "http://purl.obolibrary.org/obo/geno.owl", + "version": "2022-03-05", + "namespacePrefix": "GENO", + "iriPrefix": "http://purl.obolibrary.org/obo/GENO_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "06/01/23", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "omim", + "name": "An Online Catalog of Human Genes and Genetic Disorders", + "url": "https://www.omim.org", + "version": "January 4, 2023", + "namespacePrefix": "OMIM", + "iriPrefix": "https://www.omim.org/entry/" + }, + { + "id": "so", + "name": "Sequence types and features ontology", + "url": "http://purl.obolibrary.org/obo/so.obo", + "version": "2021-11-22", + "namespacePrefix": "SO", + "iriPrefix": "http://purl.obolibrary.org/obo/SO_" + }, + { + "id": "hp", + "name": "human phenotype ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2024-12-12", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + } + ], + "phenopacketSchemaVersion": "2.0", + "externalReferences": [ + { + "id": "PMID:36256512", + "reference": "https://pubmed.ncbi.nlm.nih.gov/36256512", + "description": "Phenotypic continuum of NFU1-related disorders" + } + ] + } +} \ No newline at end of file diff --git a/notebooks/NFU1/phenopackets/PMID_36256512_F8-II5.json b/notebooks/NFU1/phenopackets/PMID_36256512_F8-II5.json new file mode 100644 index 00000000..614178a8 --- /dev/null +++ b/notebooks/NFU1/phenopackets/PMID_36256512_F8-II5.json @@ -0,0 +1,246 @@ +{ + "id": "PMID_36256512_F8_II_5", + "subject": { + "id": "F8-II:5", + "timeAtLastEncounter": { + "age": { + "iso8601duration": "P7Y7M" + } + }, + "vitalStatus": { + "status": "ALIVE" + }, + "sex": "MALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0002359", + "label": "Frequent falls" + }, + "onset": { + "age": { + "iso8601duration": "P1Y6M" + } + } + }, + { + "type": { + "id": "HP:0002376", + "label": "Developmental regression" + } + }, + { + "type": { + "id": "HP:0001276", + "label": "Hypertonia" + } + }, + { + "type": { + "id": "HP:0001348", + "label": "Brisk reflexes" + } + }, + { + "type": { + "id": "HP:0002066", + "label": "Gait ataxia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0003128", + "label": "Lactic acidosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000486", + "label": "Strabismus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000639", + "label": "Nystagmus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000648", + "label": "Optic atrophy" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000508", + "label": "Ptosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000544", + "label": "External ophthalmoplegia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011449", + "label": "Knee clonus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011448", + "label": "Ankle clonus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0003487", + "label": "Babinski sign" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001762", + "label": "Talipes equinovarus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0009830", + "label": "Peripheral neuropathy" + }, + "excluded": true + } + ], + "interpretations": [ + { + "id": "F8-II:5", + "progressStatus": "SOLVED", + "diagnosis": { + "disease": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "genomicInterpretations": [ + { + "subjectOrBiosampleId": "F8-II:5", + "interpretationStatus": "CAUSATIVE", + "variantInterpretation": { + "variationDescriptor": { + "id": "var_hlQELcFpgXphXETVLsVvPrZtL", + "geneContext": { + "valueId": "HGNC:16287", + "symbol": "NFU1" + }, + "expressions": [ + { + "syntax": "hgvs.c", + "value": "NM_001002755.4:c.263T>C" + }, + { + "syntax": "hgvs.g", + "value": "NC_000002.12:g.69423621A>G" + } + ], + "vcfRecord": { + "genomeAssembly": "hg38", + "chrom": "chr2", + "pos": "69423621", + "ref": "A", + "alt": "G" + }, + "moleculeContext": "genomic", + "allelicState": { + "id": "GENO:0000136", + "label": "homozygous" + } + } + } + } + ] + } + } + ], + "diseases": [ + { + "term": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "onset": { + "age": { + "iso8601duration": "P1Y6M" + } + } + } + ], + "metaData": { + "created": "2025-01-08T13:24:32.125123023Z", + "createdBy": "ORCID:0000-0002-0736-9199", + "resources": [ + { + "id": "geno", + "name": "Genotype Ontology", + "url": "http://purl.obolibrary.org/obo/geno.owl", + "version": "2022-03-05", + "namespacePrefix": "GENO", + "iriPrefix": "http://purl.obolibrary.org/obo/GENO_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "06/01/23", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "omim", + "name": "An Online Catalog of Human Genes and Genetic Disorders", + "url": "https://www.omim.org", + "version": "January 4, 2023", + "namespacePrefix": "OMIM", + "iriPrefix": "https://www.omim.org/entry/" + }, + { + "id": "so", + "name": "Sequence types and features ontology", + "url": "http://purl.obolibrary.org/obo/so.obo", + "version": "2021-11-22", + "namespacePrefix": "SO", + "iriPrefix": "http://purl.obolibrary.org/obo/SO_" + }, + { + "id": "hp", + "name": "human phenotype ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2024-12-12", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + } + ], + "phenopacketSchemaVersion": "2.0", + "externalReferences": [ + { + "id": "PMID:36256512", + "reference": "https://pubmed.ncbi.nlm.nih.gov/36256512", + "description": "Phenotypic continuum of NFU1-related disorders" + } + ] + } +} \ No newline at end of file diff --git a/notebooks/NFU1/phenopackets/PMID_36256512_F8-II6.json b/notebooks/NFU1/phenopackets/PMID_36256512_F8-II6.json new file mode 100644 index 00000000..87fef657 --- /dev/null +++ b/notebooks/NFU1/phenopackets/PMID_36256512_F8-II6.json @@ -0,0 +1,246 @@ +{ + "id": "PMID_36256512_F8_II_6", + "subject": { + "id": "F8-II:6", + "timeAtLastEncounter": { + "age": { + "iso8601duration": "P6Y6M" + } + }, + "vitalStatus": { + "status": "ALIVE" + }, + "sex": "MALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0002359", + "label": "Frequent falls" + }, + "onset": { + "age": { + "iso8601duration": "P1Y6M" + } + } + }, + { + "type": { + "id": "HP:0002376", + "label": "Developmental regression" + } + }, + { + "type": { + "id": "HP:0001276", + "label": "Hypertonia" + } + }, + { + "type": { + "id": "HP:0001348", + "label": "Brisk reflexes" + } + }, + { + "type": { + "id": "HP:0002066", + "label": "Gait ataxia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0003128", + "label": "Lactic acidosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000486", + "label": "Strabismus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000639", + "label": "Nystagmus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000648", + "label": "Optic atrophy" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000508", + "label": "Ptosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000544", + "label": "External ophthalmoplegia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011449", + "label": "Knee clonus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011448", + "label": "Ankle clonus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0003487", + "label": "Babinski sign" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001762", + "label": "Talipes equinovarus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0009830", + "label": "Peripheral neuropathy" + }, + "excluded": true + } + ], + "interpretations": [ + { + "id": "F8-II:6", + "progressStatus": "SOLVED", + "diagnosis": { + "disease": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "genomicInterpretations": [ + { + "subjectOrBiosampleId": "F8-II:6", + "interpretationStatus": "CAUSATIVE", + "variantInterpretation": { + "variationDescriptor": { + "id": "var_hlQELcFpgXphXETVLsVvPrZtL", + "geneContext": { + "valueId": "HGNC:16287", + "symbol": "NFU1" + }, + "expressions": [ + { + "syntax": "hgvs.c", + "value": "NM_001002755.4:c.263T>C" + }, + { + "syntax": "hgvs.g", + "value": "NC_000002.12:g.69423621A>G" + } + ], + "vcfRecord": { + "genomeAssembly": "hg38", + "chrom": "chr2", + "pos": "69423621", + "ref": "A", + "alt": "G" + }, + "moleculeContext": "genomic", + "allelicState": { + "id": "GENO:0000136", + "label": "homozygous" + } + } + } + } + ] + } + } + ], + "diseases": [ + { + "term": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "onset": { + "age": { + "iso8601duration": "P1Y6M" + } + } + } + ], + "metaData": { + "created": "2025-01-08T13:24:32.125625133Z", + "createdBy": "ORCID:0000-0002-0736-9199", + "resources": [ + { + "id": "geno", + "name": "Genotype Ontology", + "url": "http://purl.obolibrary.org/obo/geno.owl", + "version": "2022-03-05", + "namespacePrefix": "GENO", + "iriPrefix": "http://purl.obolibrary.org/obo/GENO_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "06/01/23", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "omim", + "name": "An Online Catalog of Human Genes and Genetic Disorders", + "url": "https://www.omim.org", + "version": "January 4, 2023", + "namespacePrefix": "OMIM", + "iriPrefix": "https://www.omim.org/entry/" + }, + { + "id": "so", + "name": "Sequence types and features ontology", + "url": "http://purl.obolibrary.org/obo/so.obo", + "version": "2021-11-22", + "namespacePrefix": "SO", + "iriPrefix": "http://purl.obolibrary.org/obo/SO_" + }, + { + "id": "hp", + "name": "human phenotype ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2024-12-12", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + } + ], + "phenopacketSchemaVersion": "2.0", + "externalReferences": [ + { + "id": "PMID:36256512", + "reference": "https://pubmed.ncbi.nlm.nih.gov/36256512", + "description": "Phenotypic continuum of NFU1-related disorders" + } + ] + } +} \ No newline at end of file diff --git a/notebooks/NFU1/phenopackets/PMID_36256512_F9-II1.json b/notebooks/NFU1/phenopackets/PMID_36256512_F9-II1.json new file mode 100644 index 00000000..6513d0d5 --- /dev/null +++ b/notebooks/NFU1/phenopackets/PMID_36256512_F9-II1.json @@ -0,0 +1,268 @@ +{ + "id": "PMID_36256512_F9_II_1", + "subject": { + "id": "F9-II:1 ", + "timeAtLastEncounter": { + "age": { + "iso8601duration": "P12Y" + } + }, + "vitalStatus": {}, + "sex": "MALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0002376", + "label": "Developmental regression" + } + }, + { + "type": { + "id": "HP:0000508", + "label": "Ptosis" + } + }, + { + "type": { + "id": "HP:0009830", + "label": "Peripheral neuropathy" + } + }, + { + "type": { + "id": "HP:0002066", + "label": "Gait ataxia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0003128", + "label": "Lactic acidosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000486", + "label": "Strabismus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000639", + "label": "Nystagmus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000648", + "label": "Optic atrophy" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000544", + "label": "External ophthalmoplegia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0034295", + "label": "Reduced cerebral white matter volume" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002079", + "label": "Hypoplasia of the corpus callosum" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0011096", + "label": "Peripheral demyelination" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002280", + "label": "Enlarged cisterna magna" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001298", + "label": "Encephalopathy" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001762", + "label": "Talipes equinovarus" + }, + "excluded": true + } + ], + "interpretations": [ + { + "id": "F9-II:1 ", + "progressStatus": "SOLVED", + "diagnosis": { + "disease": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "genomicInterpretations": [ + { + "subjectOrBiosampleId": "F9-II:1 ", + "interpretationStatus": "CAUSATIVE", + "variantInterpretation": { + "variationDescriptor": { + "id": "var_hRsxjsMycpNuKbdKUlOTBGYPv", + "geneContext": { + "valueId": "HGNC:16287", + "symbol": "NFU1" + }, + "expressions": [ + { + "syntax": "hgvs.c", + "value": "NM_001002755.4:c.548C>G" + }, + { + "syntax": "hgvs.g", + "value": "NC_000002.12:g.69400536G>C" + } + ], + "vcfRecord": { + "genomeAssembly": "hg38", + "chrom": "chr2", + "pos": "69400536", + "ref": "G", + "alt": "C" + }, + "moleculeContext": "genomic", + "allelicState": { + "id": "GENO:0000135", + "label": "heterozygous" + } + } + } + }, + { + "subjectOrBiosampleId": "F9-II:1 ", + "interpretationStatus": "CAUSATIVE", + "variantInterpretation": { + "variationDescriptor": { + "id": "var_umwWlfSAhhWeqdQHJoPUspywm", + "geneContext": { + "valueId": "HGNC:16287", + "symbol": "NFU1" + }, + "expressions": [ + { + "syntax": "hgvs.c", + "value": "NM_001002755.4:c.629G>T" + }, + { + "syntax": "hgvs.g", + "value": "NC_000002.12:g.69400455C>A" + } + ], + "vcfRecord": { + "genomeAssembly": "hg38", + "chrom": "chr2", + "pos": "69400455", + "ref": "C", + "alt": "A" + }, + "moleculeContext": "genomic", + "allelicState": { + "id": "GENO:0000135", + "label": "heterozygous" + } + } + } + } + ] + } + } + ], + "diseases": [ + { + "term": { + "id": "OMIM:620938", + "label": "Spastic paraplegia 93, autosomal recessive" + }, + "onset": { + "age": { + "iso8601duration": "P2Y" + } + } + } + ], + "metaData": { + "created": "2025-01-08T13:24:32.126104116Z", + "createdBy": "ORCID:0000-0002-0736-9199", + "resources": [ + { + "id": "geno", + "name": "Genotype Ontology", + "url": "http://purl.obolibrary.org/obo/geno.owl", + "version": "2022-03-05", + "namespacePrefix": "GENO", + "iriPrefix": "http://purl.obolibrary.org/obo/GENO_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "06/01/23", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "omim", + "name": "An Online Catalog of Human Genes and Genetic Disorders", + "url": "https://www.omim.org", + "version": "January 4, 2023", + "namespacePrefix": "OMIM", + "iriPrefix": "https://www.omim.org/entry/" + }, + { + "id": "so", + "name": "Sequence types and features ontology", + "url": "http://purl.obolibrary.org/obo/so.obo", + "version": "2021-11-22", + "namespacePrefix": "SO", + "iriPrefix": "http://purl.obolibrary.org/obo/SO_" + }, + { + "id": "hp", + "name": "human phenotype ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2024-12-12", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + } + ], + "phenopacketSchemaVersion": "2.0", + "externalReferences": [ + { + "id": "PMID:36256512", + "reference": "https://pubmed.ncbi.nlm.nih.gov/36256512", + "description": "Phenotypic continuum of NFU1-related disorders" + } + ] + } +} \ No newline at end of file