Datasets:

yourui
/

hpo_anno

+---
+dataset_info:
+  features:
+  - name: corpus
+    dtype: string
+  - name: ann
+    dtype: string
+  - name: id
+    dtype: string
+  config_name: .
+  splits:
+  - name: train
+    num_bytes: 360668
+    num_examples: 238
+  download_size: 380584
+  dataset_size: 360668
+---

data/GeneReviews.json ADDED Viewed

	@@ -0,0 +1,52 @@

+[
+    {
+        "id": "NBK396257",
+        "corpus": "Summary:\nCLPB (caseinolytic peptidase B) deficiency is characterized by neurologic involvement and neutropenia, which range from severe to mild. To date, a total of 26 individuals from 16 families have been reported.\nDescription:\nThe disease spectrum of CLPB deficiency ranges from severe to moderate to mild as determined by neurologic involvement and neutropenia. Children with neonatal onset or early-infantile onset have severe involvement and may die from complications of their disease, whereas those with late-infantile and early-childhood onset have a milder clinical presentation [Wortmann et al, unpublished data].\nWhile many, but not all, individuals with CLPB deficiency have bilateral congenital or infantile cataracts, their presence is not associated with the severity of the neurologic involvement or neutropenia.\nAlthough no typical dysmorphic features have been reported, secondary dysmorphic features due to muscle involvement and movement disorder can be seen.\nTo date a total of 26 individuals from 16 families with CLPB deficiency have been reported in the literature (n=14). Most have been identified as neonates; all were symptomatic by early childhood.\n",
+        "ann": "72\t94\tneurologic involvement\tHP:0000707\n99\t110\tneutropenia\tHP:0001875\n326\t348\tneurologic involvement\tHP:0000707\n353\t364\tneutropenia\tHP:0001875\n688\t731\tbilateral congenital or infantile cataracts\tHP:0000519\n791\t813\tneurologic involvement\tHP:0000707\n817\t828\tneutropenia\tHP:0001875\n950\t967\tmovement disorder\tHP:0100022"
+    },
+    {
+        "id": "NBK1257",
+        "corpus": "Summary:\nMultiple endocrine neoplasia type 2 (MEN 2) includes the following phenotypes: MEN 2A, FMTC (familial medullary thyroid carcinoma, which may be a variant of MEN 2A), and MEN 2B. All three phenotypes involve high risk for development of medullary carcinoma of the thyroid (MTC); MEN 2A and MEN 2B involve an increased risk for pheochromocytoma; MEN 2A involves an increased risk for parathyroid adenoma or hyperplasia. Additional features in MEN 2B include mucosal neuromas of the lips and tongue, distinctive facies with enlarged lips, ganglioneuromatosis of the gastrointestinal tract, and a marfanoid habitus. MTC typically occurs in early childhood in MEN 2B, early adulthood in MEN 2A, and middle age in FMTC.\nDescription:\nThe endocrine disorders observed in multiple endocrine neoplasia type 2 (MEN 2) are: medullary thyroid carcinoma (MTC) and/or its precursor, C-cell hyperplasia (CCH); pheochromocytoma; and parathyroid adenoma or hyperplasia.\n",
+        "ann": "9\t44\tMultiple endocrine neoplasia type 2\tHP:0100568\n102\t138\tfamilial medullary thyroid carcinoma\tHP:0002865\n245\t279\tmedullary carcinoma of the thyroid\tHP:0002865\n335\t351\tpheochromocytoma\tHP:0002666\n391\t410\tparathyroid adenoma\tHP:0002897\n391\t425\tparathyroid adenoma or hyperplasia\tHP:0008208\n465\t504\tmucosal neuromas of the lips and tongue\tHP:0031023\n506\t524\tdistinctive facies\tHP:0001999\n530\t543\tenlarged lips\tHP:0012471\n545\t564\tganglioneuromatosis\tHP:0025151\n602\t619\tmarfanoid habitus\tHP:0001519\n736\t759\tThe endocrine disorders\tHP:0000818\n772\t807\tmultiple endocrine neoplasia type 2\tHP:0100568\n821\t848\tmedullary thyroid carcinoma\tHP:0002865\n877\t895\tC-cell hyperplasia\tHP:0011781\n903\t919\tpheochromocytoma\tHP:0002666\n925\t944\tparathyroid adenoma\tHP:0002897\n925\t959\tparathyroid adenoma or hyperplasia\tHP:0008208"
+    },
+    {
+        "id": "NBK169825",
+        "corpus": "Summary:\nCASK disorders include a spectrum of phenotypes in both females and males. Two main types of clinical presentation are seen:MICPCH is typically seen in females with moderate-to-severe intellectual disability, progressive microcephaly with or without ophthalmologic anomalies, and sensorineural hearing loss. Most are able to sit independently; 20%-25% attain the ability to walk; language is nearly absent in most. Neurologic features may include axial hypotonia, hypertonia/spasticity of the extremities, and dystonia or other movement disorders. Nearly 40% have seizures by age ten years. Behaviors may include sleep disturbances, hand stereotypies, and self biting.MICPCH in males may occur with or without severe epileptic encephalopathy in addition to severe-to-profound developmental delay. When seizures are present they occur early and may be intractable.In individuals and families with milder (i.e., hypomorphic) pathogenic variants, the clinical phenotype is usually that of XLID with or without nystagmus and additional clinical features. Males have mild-to-severe intellectual disability, with or without nystagmus and other ocular features. Females typically have normal intelligence with some displaying mild-to-severe intellectual disability with or without ocular features.\nDescription:\nCASK disorders are more commonly reported in females and include a spectrum of phenotypes that differs in females and males:\nFemales typically have moderate-to-severe intellectual disability and in most individuals, progressive microcephaly with pontine and cerebellar hypoplasia (MICPCH). Possible findings are ophthalmologic anomalies and sensorineural hearing loss. Females who are relatives of males with the X-linked intellectual disability (XLID) \u00b1 nystagmus phenotype may rarely present with a mild-to-severe intellectual disability phenotype.;In males the spectrum is broad, ranging from severe (intellectual disability and MICPCH, or early-infantile epileptic encephalopathy.\nTo date, 130 individuals (45 males and 85 females) have been identified with a pathogenic variant in CASK. The following description of the phenotypic features associated with this condition is based on these reports.\n",
+        "ann": "174\t216\tmoderate-to-severe intellectual disability\tHP:0002342\n218\t242\tprogressive microcephaly\tHP:0000253\n259\t283\tophthalmologic anomalies\tHP:0000478\n289\t315\tsensorineural hearing loss\tHP:0000407\n389\t414\tlanguage is nearly absent\tHP:0001344\n456\t471\taxial hypotonia\tHP:0008936\n473\t483\thypertonia\tHP:0001276\n484\t494\tspasticity\tHP:0001257\n519\t527\tdystonia\tHP:0001332\n537\t555\tmovement disorders\tHP:0100022\n573\t581\tseizures\tHP:0001250\n622\t640\tsleep disturbances\tHP:0002360\n647\t659\tstereotypies\tHP:0000733\n665\t676\tself biting\tHP:0012169\n726\t750\tepileptic encephalopathy\tHP:0200134\n776\t804\tprofound developmental delay\tHP:0012736\n811\t819\tseizures\tHP:0007359\n1016\t1025\tnystagmus\tHP:0000639\n1071\t1109\tmild-to-severe intellectual disability\tHP:0001256\n1127\t1136\tnystagmus\tHP:0000639\n1228\t1266\tmild-to-severe intellectual disability\tHP:0001256\n1438\t1503\tmoderate-to-severe intellectual disability\tHP:0002342\n1529\t1553\tprogressive microcephaly\tHP:0000253\n1559\t1592\tpontine and cerebellar hypoplasia\tHP:0012110\n1571\t1592\tcerebellar hypoplasia\tHP:0001321\n1654\t1680\tsensorineural hearing loss\tHP:0000407\n1735\t1758\tintellectual disability\tHP:0001249\n1768\t1777\tnystagmus\tHP:0000639\n1814\t1863\tmild-to-severe intellectual disability phenotype\tHP:0001256\n1917\t1940\tintellectual disability\tHP:0001249\n1972\t1996\tepileptic encephalopathy\tHP:0200134\n"
+    },
+    {
+        "id": "NBK1379",
+        "corpus": "Summary:\nSYNE1 deficiency comprises a phenotypic spectrum that ranges from autosomal recessive cerebellar ataxia at the mild end to arthrogryposis multiplex congenita (AMC) at the severe end. SYNE1-deficient cerebellar ataxia, the most commonly recognized manifestation of SYNE1 deficiency to date, is a slowly progressive disorder typically beginning in adulthood (age range 6-45 years). While some individuals have a pure cerebellar syndrome (i.e., cerebellar ataxia, dysarthria, dysmetria, abnormalities in ocular saccades and smooth pursuit), many also have upper motor neuron dysfunction (spasticity, hyperreflexia, Babinski sign) and/or lower motor neuron dysfunction (amyotrophy, reduced reflexes, fasciculations). Most patients develop features of the cerebellar cognitive and affective syndrome (i.e., significant deficits in attention, executive functioning, verbal working memory, and visuospatial/visuoconstructional skills). The two less common phenotypes are SYNE1-deficient childhood-onset multisystem disease (ataxia, upper and lower motor neuron dysfunction, muscle weakness and wasting, intellectual disability) and SYNE1-deficient arthrogryposis multiplex congenita (decreased fetal movements and severe neonatal hypotonia associated with multiple congenital joint contractures including clubfoot).\nDescription:\nThe phenotype and severity of SYNE1 deficiency vary widely and span a spectrum ranging from adult-onset cerebellar ataxia at the milder end to childhood-onset multisystem disease and prenatal-onset arthrogryposis multiplex congenita at the more severe end.\n",
+        "ann": "95\t112\tcerebellar ataxia\tHP:0001251\n132\t166\tarthrogryposis multiplex congenita\tHP:0002804\n208\t225\tcerebellar ataxia\tHP:0001251\n424\t443\tcerebellar syndrome\tHP:0001317\n451\t468\tcerebellar ataxia\tHP:0001251\n470\t480\tdysarthria\tHP:0001260\n482\t491\tdysmetria\tHP:0001310\n493\t525\tabnormalities in ocular saccades\tHP:0000570\n493\t544\tabnormalities in ocular saccades and smooth pursuit\tHP:0000617\n562\t592\tupper motor neuron dysfunction\tHP:0002493\n594\t604\tspasticity\tHP:0001257\n606\t619\thyperreflexia\tHP:0001347\n621\t634\tBabinski sign\tHP:0003487\n643\t673\tlower motor neuron dysfunction\tHP:0002493\n675\t685\tamyotrophy\tHP:0003202\n687\t703\treduced reflexes\tHP:0001265\n705\t719\tfasciculations\tHP:0002380\n811\t844\tsignificant deficits in attention\tHP:0007018\n869\t890\tverbal working memory\tHP:0002354\n896\t935\tvisuospatial/visuoconstructional skills\tHP:0010794\n1026\t1032\tataxia\tHP:0001251\n1034\t1074\tupper and lower motor neuron dysfunction\tHP:0002493\n1044\t1074\tlower motor neuron dysfunction\tHP:0002493\n1076\t1091\tmuscle weakness\tHP:0001324\n1105\t1128\tintellectual disability\tHP:0001249\n1140\t1184\tdeficient arthrogryposis multiplex congenita\tHP:0002804\n1186\t1211\tdecreased fetal movements\tHP:0001558\n1223\t1241\tneonatal hypotonia\tHP:0001319\n1258\t1296\tmultiple congenital joint contractures\tHP:0002804\n1307\t1315\tclubfoot\tHP:0001762\n1435\t1452\tcerebellar ataxia\tHP:0001251\n1523\t1563\tonset arthrogryposis multiplex congenita\tHP:0002804"
+    },
+    {
+        "id": "NBK532447",
+        "corpus": "Summary:\nAbetalipoproteinemia typically presents in infancy with failure to thrive, diarrhea, vomiting, and malabsorption of fat. Hematologic manifestations may include acanthocytosis (irregularly spiculated erythrocytes), anemia, reticulocytosis, and hemolysis with resultant hyperbilirubinemia. Malabsorption of fat-soluble vitamins (A, D, E, and K) can result in an increased international normalized ratio (INR). Untreated individuals may develop atypical pigmentation of the retina that may present with progressive loss of night vision and/or color vision in adulthood. Neuromuscular findings in untreated individuals including progressive loss of deep tendon reflexes, vibratory sense, and proprioception; muscle weakness; dysarthria; and ataxia typically manifest in the first or second decades of life.\nDescription:\nAbetalipoproteinemia typically presents in infancy with failure to thrive, diarrhea, vomiting, and malabsorption of fat. The absence of apo B-containing lipoproteins and resulting deficiency of fat-soluble vitamins lead to multisystem manifestations as the affected individual ages.\nGastrointestinal. Steatorrhea is the primary gastrointestinal manifestation. The severity relates to the fat content of the diet.\nAs affected individuals age they learn to avoid dietary fat, which improves steatorrhea.;Hepatic involvement as identified on laboratory studies is frequently stable over many years and may not evolve to be clinically significant.;Hepatomegaly and hepatic steatosis can be observed, which rarely may progress to steatohepatitis, fibrosis, and cirrhosis.;On a typical diet (e.g., no dietary fat restriction), the intestinal mucosa may have a \"gelee blanche\" or \"white hoar frosting\" appearance on endoscopy.Biopsy of the intestinal epithelium may demonstrate lipid-laden intestinal epithelial cells.\nHematologic manifestations of abetalipoproteinemia include the following:\nAcanthocytosis, defined as irregularly spiculated erythrocytes;Low erythrocyte sedimentation rate;Anemia;Reticulocytosis;Hyperbilirubinemia;Hemolysis;Prolonged INR due to vitamin K deficiency.\nOphthalmologic manifestations of abetalipoproteinemia are variable, with the most prominent being an atypical pigmentation of the retina.\nMany affected individuals are asymptomatic until adulthood, when they experience loss of night vision and/or color vision.;As the disease progresses, affected individuals may experience progressively expanding scotomas.;Without treatment, progression to complete visual loss may occur.;Other rare, typically acquired, ophthalmologic findings include the following:PtosisOphthalmoplegiaCorneal ulcers.\nIt is hypothesized that the possible cause of ptosis and ophthalmoplegia is vitamin E deficiency leading to cranial nerve demyelination. Corneal ulcers may be caused or exacerbated by vitamin A deficiency.\nNeuromuscular. If untreated, neuromuscular manifestations of abetalipoproteinemia secondary to the deficiency of vitamin E typically begin in the first or second decade of life. Symptoms include the following:\nProgressive loss of deep tendon reflexes, vibratory sense, and proprioception;Muscle weakness;Dysarthria;Eventually, a Friedrich's-like ataxia, with a broad base and high stepping gait, can develop in early adulthood in untreated individuals.\nCardiac. Although rare, cardiomegaly can occur after decades, with rare death related to cardiomyopathy reported.\nEndocrinologic. Although rare, both subclinical and overt hypothyroidism have been reported in individuals with abetalipoproteinemia.\nPrognosis. In the past, without high-dose fat-soluble vitamin supplementation, affected individuals would typically not survive past the third decade of life, dying with severe neuromyopathy and respiratory failure. With lifelong high-dose oral fat-soluble vitamin treatment, longevity into the seventh and eighth decade of life, with relatively minimal symptoms, has been reported.\n",
+        "ann": "9\t29\tAbetalipoproteinemia\tHP:0008181\n65\t82\tfailure to thrive\tHP:0001508\n84\t92\tdiarrhea\tHP:0002014\n94\t102\tvomiting\tHP:0002013\n108\t128\tmalabsorption of fat\tHP:0002630\n169\t183\tacanthocytosis\tHP:0001927\n223\t229\tanemia\tHP:0001903\n231\t246\treticulocytosis\tHP:0001923\n277\t295\thyperbilirubinemia\tHP:0002904\n297\t317\tMalabsorption of fat\tHP:0002630\n369\t409\tincreased international normalized ratio\tHP:0008151\n460\t486\tpigmentation of the retina\tHP:0007703\n509\t541\tprogressive loss of night vision\tHP:0007675\n549\t574\tcolor vision in adulthood\tHP:0000551\n646\t674\tloss of deep tendon reflexes\tHP:0001284\n676\t691\tvibratory sense\tHP:0002495\n713\t728\tmuscle weakness\tHP:0001324\n730\t740\tdysarthria\tHP:0001260\n746\t752\tataxia\tHP:0001251\n825\t865\tAbetalipoproteinemia\tHP:0008181\n881\t898\tfailure to thrive\tHP:0001508\n900\t908\tdiarrhea\tHP:0002014\n910\t918\tvomiting\tHP:0002013\n924\t944\tmalabsorption of fat\tHP:0002630\n1126\t1137\tSteatorrhea\tHP:0002570\n1314\t1325\tsteatorrhea\tHP:0002570\n1469\t1481\tHepatomegaly\tHP:0002240\n1486\t1503\thepatic steatosis\tHP:0001397\n1550\t1565\tsteatohepatitis\tHP:0001397\n1581\t1590\tcirrhosis\tHP:0001394\n1867\t1887\tabetalipoproteinemia\tHP:0008181\n1911\t1925\tAcanthocytosis\tHP:0001927\n1974\t2008\tLow erythrocyte sedimentation rate\tHP:0025022\n2009\t2015\tAnemia\tHP:0001903\n2016\t2031\tReticulocytosis\tHP:0001923\n2032\t2050\tHyperbilirubinemia\tHP:0002904\n2061\t2074\tProlonged INR\tHP:0008151\n2082\t2102\tvitamin K deficiency\tHP:0011892\n2137\t2157\tabetalipoproteinemia\tHP:0008181\n2214\t2240\tpigmentation of the retina\tHP:0007703\n2312\t2343\texperience loss of night vision\tHP:0000662\n2351\t2363\tcolor vision\tHP:0000551\n2452\t2460\tscotomas\tHP:0000575\n2505\t2516\tvisual loss\tHP:0000572\n2689\t2695\tptosis\tHP:0000508\n2700\t2715\tophthalmoplegia\tHP:0000602\n2719\t2739\tvitamin E deficiency\tHP:0100513\n2759\t2778\tnerve demyelination\tHP:0011096\n2780\t2794\tCorneal ulcers\tHP:0012804\n2827\t2847\tvitamin A deficiency\tHP:0004905\n2910\t2930\tabetalipoproteinemia\tHP:0008181\n2944\t2971\tthe deficiency of vitamin E\tHP:0100513\n3071\t3099\tloss of deep tendon reflexes\tHP:0001284\n3101\t3116\tvibratory sense \tHP:0002495\n3122\t3136\tproprioception\tHP:0010831\n3137\t3152\tMuscle weakness\tHP:0001324\n3153\t3163\tDysarthria\tHP:0001260\n3195\t3201\tataxia\tHP:0001251\n3225\t3243\thigh stepping gait\tHP:0003376\n3326\t3339\tcardiomegaly\tHP:0001640\n3391\t3405\tcardiomyopathy\tHP:0001638\n3474\t3488\thypothyroidism\tHP:0000821\n3528\t3548\tabetalipoproteinemia\tHP:0008181\n3745\t3764\trespiratory failure\tHP:0002878"
+    },
+    {
+        "id": "NBK321516",
+        "corpus": "Summary:\nNicolaides-Baraitser syndrome (NCBRS) is characterized by sparse scalp hair, prominence of the inter-phalangeal joints and distal phalanges due to decreased subcutaneous fat, characteristic coarse facial features, microcephaly, seizures, and developmental delay / intellectual disability. Seizures are of various types and can be difficult to manage. Developmental delay / intellectual disability (ID) is severe in nearly a half, moderate in a third, and mild in the remainder. Nearly a third never develop speech or language skills.\nDescription:\nThe most common findings in 61 individuals (35 male and 26 female) with Nicolaides-Baraitser syndrome (NCBRS) and a SMARCA2 pathogenic variant are summarized in Table 2.\nEctoderm. Scalp hair is usually sparse at birth and becomes increasingly so with age, particularly in the second decade of life. In some, the sparseness improves with time.\nSkin pigmentation appears to be reduced, although affected individuals do not exhibit true cutaneous albinism.\nPoor subcutaneous fat distribution leads to prominent veins; interphalangeal joints are prominent. The distal phalanges widen with age, becoming oval shaped and broad. Increasing space between the first and second toes can occur over time.\nDelayed tooth eruption is common, often requiring surgical extraction of primary dentition to allow secondary dentition to migrate into place.\nSeizures can be difficult to manage, requiring multiple antiepileptic drugs to achieve reasonable control. The mean and median age of onset of seizures is 24 months and 18 months, respectively. The range is birth to 14 years. Various seizure types have been reported. Regression or lack of developmental progress has been noted with the onset of seizures.\nDevelopmental delay / intellectual disability. Nearly half of affected individuals experience severe developmental delay / intellectual disability (ID) with particular delays in speech and language development. A third exhibit moderate intellectual disability and the remainder have mild ID.\nNearly a third never develop speech or language skills.\nThe mean age for walking independently is 21 months (range: 10 months - 5 years).\nAlthough psychomotor regression is not typical, the high incidence of seizures that progressively worsen has been associated with loss of speech.\nBehavior problems have been reported in at least 19 individuals with some displaying autistic-like features (such as perseveration and hyperacusis). However, a formal clinical diagnosis of autism has not been made in any affected individual reported in the literature.\nGrowth. About half of affected individuals (24/46) have low birth weight and the same proportion experience short stature. None was above the 50th centile for height.\nMicrocephaly tends to be acquired, being noted in almost one third of infants at birth (7/30) and in two thirds (34/52) at follow up.\nOther findings\nCryptorchidism is seen in most males.;Hearing loss has been noted in 4/59 affected individuals. The nature of the hearing loss and age of onset have not been reported.;Visual deficits including myopia and astigmatism have been seen in ten and four affected individuals, respectively.;Congenital heart defects (e.g., atrial septal defect, stenosis of the pulmonary artery, coarctation, patient ductus arteriosus, and double aortic arch) have been reported in six affected persons.\n",
+        "ann": "67\t84\tsparse scalp hair\tHP:0002209\n86\t148\tprominence of the inter-phalangeal joints and distal phalanges\tHP:0006261\n156\t182\tdecreased subcutaneous fat\tHP:0003758\n199\t221\tcharacteristic coarse facial features\tHP:0000280\n223\t235\tmicrocephaly\tHP:0000252\n237\t245\tseizures\tHP:0001250\n251\t270\tdevelopmental delay\tHP:0001263\n273\t296\tintellectual disability\tHP:0001249\n298\t306\tSeizures\tHP:0001250\n360\t379\tDevelopmental delay\tHP:0001263\n382\t405\tintellectual disability\tHP:0001249\n502\t541\tnever develop speech or language skills\tHP:0001344\n736\t764\tScalp hair is usually sparse\tHP:0002209\n899\t924\tSkin pigmentation appears\tHP:0001000\n1000\t1008\talbinism\tHP:0001022\n1010\t1044\tPoor subcutaneous fat distribution\tHP:0007552\n1054\t1069\tprominent veins\tHP:0001015\n1071\t1107\tinterphalangeal joints are prominent\tHP:0006237\n1113\t1135\tdistal phalanges widen\tHP:0009836\n1217\t1248\tsecond toes can occur over time\tHP:0010319\n1250\t1272\tDelayed tooth eruption\tHP:0000684\n1393\t1401\tSeizures\tHP:0001250\n1536\t1544\tseizures\tHP:0001250\n1627\t1634\tseizure\tHP:0001250\n1661\t1705\tRegression or lack of developmental progress\tHP:0001263\n1739\t1747\tseizures\tHP:0001250\n1749\t1768\tDevelopmental delay\tHP:0001263\n1771\t1794\tintellectual disability\tHP:0001249\n1843\t1869\tsevere developmental delay\tHP:0011344\n1872\t1895\tintellectual disability\tHP:0001249\n1906\t1958\tparticular delays in speech and language development\tHP:0000750\n1976\t2008\tmoderate intellectual disability\tHP:0002342\n2188\t2210\tpsychomotor regression\tHP:0002376\n2249\t2257\tseizures\tHP:0001250\n2309\t2323\tloss of speech\tHP:0002371\n2325\t2342\tBehavior problems\tHP:0000708\n2399\t2432\tdisplaying autistic-like features\tHP:0000729\n2442\t2455\tperseveration\tHP:0030223\n2460\t2471\thyperacusis\tHP:0010780\n2514\t2520\tautism\tHP:0000717\n2650\t2666\tlow birth weight\tHP:0001518\n2702\t2715\tshort stature\tHP:0004322\n2761\t2773\tMicrocephaly\tHP:0000252\n2910\t2924\tCryptorchidism\tHP:0000028\n2948\t2960\tHearing loss\tHP:0000365\n3024\t3036\thearing loss\tHP:0000365\n3078\t3093\tVisual deficits\tHP:0100704\n3104\t3110\tmyopia\tHP:0000545\n3115\t3126\tastigmatism\tHP:0000483\n3194\t3218\tCongenital heart defects\tHP:0001627\n3226\t3246\tatrial septal defect\tHP:0001631\n3248\t3280\tstenosis of the pulmonary artery\tHP:0004415\n3282\t3293\tcoarctation\tHP:0001680\n3295\t3320\tpatient ductus arteriosus\tHP:0001643\n3326\t3344\tdouble aortic arch\tHP:0011590"
+    },
+    {
+        "id": "NBK1277",
+        "corpus": "Summary:\nShprintzen-Goldberg syndrome (SGS) is characterized by: delayed motor and cognitive milestones and mild-to-moderate intellectual disability; craniosynostosis of the coronal, sagittal, or lambdoid sutures; distinctive craniofacial features; and musculoskeletal findings including olichostenomelia, arachnodactyly, camptodactyly, pectus excavatum or carinatum, scoliosis, joint hypermobility or contractures, pes planus, foot malposition, and C1-C2 spine malformation. Cardiovascular anomalies may include mitral valve prolapse, secundum atrial septal defect, and aortic root dilatation. Minimal subcutaneous fat, abdominal wall defects, and myopia are also characteristic findings.\nDescription:\nTo date, 44 individuals have been identified with a pathogenic variant in SKI. The following description of the phenotypic features associated with this condition is based on these reports.\nNeurodevelopment. Motor and cognitive milestones are delayed and intellectual disability is usually mild to moderate. To date, three individuals with Shprintzen-Goldberg syndrome (SGS) and a confirmed SKI pathogenic variant were reported to have normal intelligence.\nCraniosynostosis usually involves the coronal, sagittal, or lambdoid sutures. The sutures are fused at birth and craniosynostosis can usually be suspected from the abnormal skull shape. A single suture or multiple sutures may be involved. Information on individuals with SGS who underwent surgery for craniosynostosis in unavailable.\nCharacteristic craniofacial features include hypertelorism, downslanting palpebral fissures, ocular proptosis, high narrow palate, micrognathia, and low-set posteriorly rotated ears. Cleft palate was reported in three of 17 individuals with SGS.\nMusculoskeletal. Arachnodactyly, camptodactyly, pectus deformities, and clubfeet are common features and are present at birth. Joint contractures are often present at birth or in the neonatal period, with the ankle joint most frequently affected.\nCardiovascular. Aortic root dilatation was present in three of 18 affected individuals reported by Carmignac et al one had arterial tortuosity and two had splenic artery aneurysm \u2013 one with spontaneous rupture.\nOcular. Myopia was reported in ten of 19 individuals.\nMinimal subcutaneous fat and/or marfanoid habitus was reported in nine of 20 individuals.\nAbdominal wall defects were reported in 14 of 23 individuals.\nOther\nDural ectasia (5/8 individuals);Chiari 1 malformation (2/3 individuals);Cryptorchidism (1/1 male).\n",
+        "ann": "65\t78\tdelayed motor\tHP:0001270\n108\t148\tmild-to-moderate intellectual disability\tHP:0002342\n150\t181\tcraniosynostosis of the coronal\tHP:0004440\n196\t212\tlambdoid sutures\tHP:0004443\n214\t247\tdistinctive craniofacial features\tHP:0001999\n288\t304\tolichostenomelia\tHP:0001519\n306\t320\tarachnodactyly\tHP:0001166\n322\t335\tcamptodactyly\tHP:0012385\n337\t366\tpectus excavatum or carinatum\tHP:0000766\n368\t377\tscoliosis\tHP:0002650\n379\t398\tjoint hypermobility\tHP:0001382\n402\t414\tcontractures\tHP:0001371\n416\t426\tpes planus\tHP:0001763\n450\t474\tC1-C2 spine malformation\tHP:0008440\n476\t500\tCardiovascular anomalies\tHP:0001626\n513\t534\tmitral valve prolapse\tHP:0001634\n536\t565\tsecundum atrial septal defect\tHP:0001684\n571\t593\taortic root dilatation\tHP:0002616\n595\t619\tMinimal subcutaneous fat\tHP:0003717\n621\t643\tabdominal wall defects\tHP:0010866\n649\t655\tmyopia\tHP:0000545\n921\t953\tcognitive milestones are delayed\tHP:0001263\n958\t997\tintellectual disability is usually mild\tHP:0001256\n1160\t1205\tCraniosynostosis usually involves the coronal\tHP:0004440\n1220\t1236\tlambdoid sutures\tHP:0004443\n1273\t1176\tcraniosynostosis\tHP:0001363\n1324\t1344\tabnormal skull shape\tHP:0002678\n1461\t1477\tcraniosynostosis\tHP:0001363\n1539\t1552\thypertelorism\tHP:0000316\n1554\t1585\tdownslanting palpebral fissures\tHP:0000494\n1587\t1603\tocular proptosis\tHP:0000520\n1605\t1623\thigh narrow palate\tHP:0002705\n1625\t1637\tmicrognathia\tHP:0000347\n1643\t1675\tlow-set posteriorly rotated ears\tHP:0000368\n1677\t1689\tCleft palate\tHP:0000175\n1757\t1771\tArachnodactyly\tHP:0001166\n1773\t1786\tcamptodactyly\tHP:0012385\n1788\t1806\tpectus deformities\tHP:0000766\n1812\t1820\tclubfeet\tHP:0001762\n1867\t1885\tJoint contractures\tHP:0001371\n2003\t2037\tAortic root dilatation was present\tHP:0002616\n2110\t2129\tarterial tortuosity\tHP:0005116\n2206\t2212\tMyopia\tHP:0000545\n2252\t2276\tMinimal subcutaneous fat\tHP:0003717\n2284\t2301\tmarfanoid habitus\tHP:0001519\n2342\t2364\tAbdominal wall defects\tHP:0010866\n2410\t2423\tDural ectasia\tHP:0100775\n2442\t2463\tChiari 1 malformation\tHP:0002308\n2482\t2496\tCryptorchidism\tHP:0000028"
+    },
+    {
+        "id": "NBK148668",
+        "corpus": "Summary:\nThe phenotypic spectrum of mucopolysaccharidosis IVA (MPS IVA) is a continuum that ranges from a severe and rapidly progressive early-onset form to a slowly progressive later-onset form. Children with MPS IVA have no distinctive clinical findings at birth. The severe form is usually apparent between ages one and three years, often first manifesting as kyphoscoliosis, knock-knee (genu valgum), and pectus carinatum; the slowly progressive form may not become evident until late childhood or adolescence often first manifesting as hip problems (pain, stiffness, and Legg Perthes disease). Progressive bone and joint involvement leads to short stature, and eventually to disabling pain and arthritis. Involvement of other organ systems can lead to significant morbidity, including respiratory compromise, obstructive sleep apnea, valvular heart disease, hearing impairment, visual impairment from corneal clouding, dental abnormalities, and hepatomegaly. Compression of the spinal cord is a common complication that results in neurologic impairment. Children with MPS IVA have normal intellectual abilities at the outset of the disease.\nDescription:\nMucopolysaccharidosis type IVA (MPS IVA) comprises a clinical continuum ranging from a severe and rapidly progressive form to a slowly progressive form. In the past, the two forms were distinguished by height, the subjective assessment of severity of bone deformity, and survival; however, neither clinical nor biochemical findings can provide clear distinctions between the two forms and, thus, the MPS IVA phenotype should be considered a continuum from severe to slowly progressive.\nAffected children have no distinctive clinical findings at birth. The severe form is usually apparent between ages one and three years. The slowly progressive form may not become evident until late childhood or adolescence.\nIn both forms, the initial presentations vary and may be a single finding or several findings. Kyphoscoliosis, knock-knee (genu valgum) (Figure 5), and pectus carinatum (Figure 3 and Figure 4) are the most common initial manifestations of the severe form.\nBecause descriptions of the natural history of MPS IV published in the past may not have distinguished between MPS IVA (Morquio syndrome type A; accounting for >95% of affected individuals) and MPS IVB (Morquio syndrome type B; <5% of affected individuals), the following information is relevant to both MPS IVA and MPS IVB.\nWhile the skeletal findings of MPS IVA are the hallmark findings, involvement of other organ systems can lead to significant morbidity, including respiratory compromise, obstructive sleep apnea, valvular heart disease, hearing impairment, corneal clouding, dental abnormalities, and hepatomegaly. Compression of the spinal cord results in neurologic involvement especially when disease is recognized later in life.\nCoarse facial features are also present but milder than in other mucopolysaccharidoses (see Differential Diagnosis).\nChildren with MPS IVA typically have normal intellectual ability.\nLigamentous laxity and joint hypermobility are distinctive features of MPS IVA, and are rare among other storage disorders.\n",
+        "ann": "363\t377\tkyphoscoliosis\tHP:0002751\n379\t389\tknock-knee\tHP:0002857\n391\t402\tgenu valgum\tHP:0002857\n409\t425\tpectus carinatum\tHP:0000768\n555\t559\tpain\tHP:0012531\n576\t596\tLegg Perthes disease\tHP:0005743\n647\t660\tshort stature\tHP:0004322\n690\t694\tpain\tHP:0012531\n699\t708\tarthritis\tHP:0001369\n790\t812\trespiratory compromise\tHP:0002093\n814\t837\tobstructive sleep apnea\tHP:0002870\n839\t861\tvalvular heart disease\tHP:0001654\n863\t881\thearing impairment\tHP:0000365\n883\t900\tvisual impairment\tHP:0000505\n906\t922\tcorneal clouding\tHP:0007957\n924\t944\tdental abnormalities\tHP:0000164\n950\t962\thepatomegaly\tHP:0002240\n964\t994\tCompression of the spinal cord\tHP:0002176\n1964\t1978\tKyphoscoliosis\tHP:0002751\n1980\t1990\tknock-knee\tHP:0002857\n1992\t2003\tgenu valgum\tHP:0002857\n2021\t2037\tpectus carinatum\tHP:0000768\n2596\t2618\trespiratory compromise\tHP:0002093\n2620\t2643\tobstructive sleep apnea\tHP:0002870\n2645\t2667\tvalvular heart disease\tHP:0001654\n2669\t2687\thearing impairment\tHP:0000365\n2689\t2705\tcorneal clouding\tHP:0007957\n2707\t2727\tdental abnormalities\tHP:0000164\n2733\t2745\thepatomegaly\tHP:0002240\n2747\t2777\tCompression of the spinal cord\tHP:0002176\n2789\t2811\tneurologic involvement\tHP:0000707\n2865\t2887\tCoarse facial features\tHP:0000280\n3048\t3066\tLigamentous laxity\tHP:0001388\n3071\t3090\tjoint hypermobility\tHP:0001382"
+    },
+    {
+        "id": "NBK550349",
+        "corpus": "Summary:\nFructose-1,6-bisphosphatase (FBP1) deficiency is characterized by episodic acute crises of lactic acidosis and ketotic hypoglycemia, manifesting as hyperventilation, apneic spells, seizures, and/or coma. Acute crises are most common in early childhood; nearly half of affected children have hypoglycemia in the neonatal period (especially the first 4 days) resulting from deficient glycogen stores. Factors known to trigger episodes include fever, fasting, decreased oral intake, vomiting, infections, and ingestion of large amounts of fructose.In untreated individuals, symptoms worsen progressively as continued catabolism leads to multiorgan failure (especially liver, brain, and later heart). Morbidity and mortality are high. Sepsis, blindness, and Reye syndrome-like presentation have been reported.In between acute episodes, children are asymptomatic. While the majority of affected children have normal growth and psychomotor development, a few have intellectual disability, presumably due to early and prolonged hypoglycemia.\nDescription:\nThe manifestations of fructose-1,6-bisphosphatase (FBP1) deficiency are generally episodic due to lactic acidosis and ketotic hypoglycemia, which are often triggered by fasting or febrile infections. The episodes of acute crisis are most frequent in early life \u2013 neonatal period, infancy, and early childhood \u2013 and subsequently decrease in frequency. In FBP1 deficiency, several metabolic derangements can occur with or without hypoglycemia.\nClassically, FBP1 deficiency manifests in the first year of life. Nearly half of affected infants present within the first four days of life with an acute crisis. Neonatal presentation results from hypoglycemia due to deficient glycogen stores.\nAcute crises are characterized by episodes of hyperventilation, apneic spells, seizures, and/or coma, often with hepatomegaly. Muscular hypotonia may also be present. This may be associated with transient liver dysfunction (transaminitis), which does not require specific treatment. With age, the frequency of attacks decreases and episodes are characterized by irritability, somnolence, hypotonia, and dyspnea.\nFactors known to trigger episodes include fever, fasting, decreased oral intake, vomiting, infections, and ingestion of large amounts of fructose. Episodes tend to be recurrent. Often four to five episodes occur before the correct diagnosis is established.\nIn between crises, children are asymptomatic and the majority experience normal growth and psychomotor development.\nIn untreated individuals, symptoms worsen progressively as continued catabolism leads to multiorgan failure (especially liver, brain, and later heart). Morbidity and mortality are high. Sepsis, blindness, and Reye syndrome-like presentation have been reported.\n",
+        "ann": "100\t115\tlactic acidosis\tHP:0003128\n120\t140\tketotic hypoglycemia\tHP:0012734\n157\t173\thyperventilation\tHP:0002883\n175\t188\tapneic spells\tHP:0002104\n190\t198\tseizures\tHP:0001250\n207\t211\tcoma\tHP:0001259\n300\t312\thypoglycemia\tHP:0001943\n450\t455\tfever\tHP:0001945\n489\t497\tvomiting\tHP:0002013\n740\t746\tSepsis\tHP:0100806\n748\t757\tblindness\tHP:0000618\n763\t794\tReye syndrome-like presentation\tHP:0006582\n967\t990\tintellectual disability\tHP:0001249\n1020\t1042\tprolonged hypoglycemia\tHP:0001943\n1155\t1170\tlactic acidosis\tHP:0003128\n1175\t1195\tketotic hypoglycemia\tHP:0012734\n1436\t1458\tmetabolic derangements\tHP:0001939\n1485\t1497\thypoglycemia\tHP:0001943\n1697\t1709\thypoglycemia\tHP:0001943\n1790\t1806\thyperventilation\tHP:0002883\n1808\t1821\tapneic spells\tHP:0002104\n1823\t1831\tseizures\tHP:0001250\n1840\t1844\tcoma\tHP:0001259\n1857\t1869\thepatomegaly\tHP:0002240\n1871\t1889\tMuscular hypotonia\tHP:0001252\n1939\t1966\ttransient liver dysfunction\tHP:0001410\n2106\t2118\tirritability\tHP:0000737\n2120\t2130\tsomnolence\tHP:0001262\n2132\t2141\thypotonia\tHP:0001290\n2147\t2154\tdyspnea\tHP:0002094\n2198\t2203\tfever\tHP:0001945\n2237\t2245\tvomiting\tHP:0002013\n2715\t2721\tSepsis\tHP:0100806\n2723\t2732\tblindness\tHP:0000618\n2738\t2769\tReye syndrome-like presentation\tHP:0006582"
+    },
+    {
+        "id": "NBK164500",
+        "corpus": "Summary:\nGLB1-related disorders comprise two phenotypically distinct lysosomal storage disorders: GM1 gangliosidosis and mucopolysaccharidosis type IVB (MPS IVB).GM1 gangliosidosis includes phenotypes that range from severe to mild. Type I (infantile) begins before age one year; progressive central nervous system dysfunction leads to spasticity, deafness, blindness, and decerebrate rigidity. Life expectancy is two to three years. Type II can be subdivided into the late-infantile form and juvenile form. Type II, late-infantile form begins between ages one and three years; life expectancy is five to ten years. Type II, juvenile form begins between ages three and ten years with insidious plateauing of motor and cognitive development followed by slow regression. Type II may or may not include skeletal dysplasia. Type III begins in the second to third decade with extrapyramidal signs, gait disturbance, and cardiomyopathy; and can be misidentified as Parkinson disease. Intellectual impairment is common late in the disease; skeletal involvement includes short stature, kyphosis, and scoliosis of varying severity.MPS IVB is characterized by skeletal changes, including short stature and skeletal dysplasia. Affected children have no distinctive clinical findings at birth. The severe form is usually apparent between ages one and three years, and the attenuated form in late childhood or adolescence. In addition to skeletal involvement, significant morbidity can result from respiratory compromise, obstructive sleep apnea, valvular heart disease, hearing impairment, corneal clouding, and spinal cord compression. Intellect is normal unless spinal cord compression leads to central nervous system compromise.\nDescription:\nGLB1-related disorders comprise two phenotypically distinct disorders: GM1 gangliosidosis and mucopolysaccharidosis type IVB (MPS IVB).\n",
+        "ann": "69\t96\tlysosomal storage disorders\tHP:0004356\n98\t116\tGM1 gangliosidosis\tHP:0020160\n336\t346\tspasticity\tHP:0001257\n348\t356\tdeafness\tHP:0000365\n358\t367\tblindness\tHP:0000618\n373\t393\tdecerebrate rigidity\tHP:0025013\n718\t739\tcognitive development\tHP:0001263\n800\t818\tskeletal dysplasia\tHP:0002652\n871\t891\textrapyramidal signs\tHP:0002071\n893\t909\tgait disturbance\tHP:0001288\n915\t929\tcardiomyopathy\tHP:0001638\n978\t1011\tIntellectual impairment is common\tHP:0100543\n1063\t1076\tshort stature\tHP:0004322\n1078\t1086\tkyphosis\tHP:0002808\n1092\t1101\tscoliosis\tHP:0002650\n1178\t1191\tshort stature\tHP:0004322\n1196\t1214\tskeletal dysplasia\tHP:0002652\n1485\t1507\trespiratory compromise\tHP:0002093\n1509\t1532\tobstructive sleep apnea\tHP:0002870\n1534\t1556\tvalvular heart disease\tHP:0001654\n1558\t1576\thearing impairment\tHP:0000365\n1578\t1594\tcorneal clouding\tHP:0007957\n1600\t1623\tspinal cord compression\tHP:0002176\n1652\t1675\tspinal cord compression\tHP:0002176\n1685\t1718\tcentral nervous system compromise\tHP:0000707\n1806\t1824\tGM1 gangliosidosis\tHP:0020160"
+    }
+]

hpo_anno.py ADDED Viewed

	@@ -0,0 +1,95 @@

+"""
+Author: yourui
+Date: 2023-07-10
+Copyright (c) 2023 by yourui, Inc. All Rights Reserved.
+"""
+# Copyright 2020 The HuggingFace Datasets Authors and the current dataset script contributor.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+import json
+import os
+import datasets
+import pandas as pd
+logger = datasets.logging.get_logger(__name__)
+_CITATION = """\
+CITATION
+"""
+_DESCRIPTION = """\
+DESCRIPTION
+"""
+_HOMEPAGE = "HOMEPAGE"
+_LICENSE = ""
+_DATA_URL = r"https://huggingface.co/datasets/yourui/hpo_anno/resolve/main/data/"
+task_list = [
+    "GeneReviews"
+]
+class HPOAnnoConfig(datasets.BuilderConfig):
+    def __init__(self, **kwargs):
+        super().__init__(version=datasets.Version("1.0.0"), **kwargs)
+class HPOAnno(datasets.GeneratorBasedBuilder):
+    BUILDER_CONFIGS = [
+        HPOAnnoConfig(
+            name=task_name,
+        )
+        for task_name in task_list
+    ]
+    def _info(self):
+        features = datasets.Features(
+            {
+                "id":datasets.Value("string"),
+                "corpus": datasets.Value("string"),
+                "ann": datasets.Value("string"),
+            }
+        )
+        return datasets.DatasetInfo(
+            description=_DESCRIPTION,
+            features=features,
+            homepage=_HOMEPAGE,
+            license=_LICENSE,
+            citation=_CITATION,
+        )
+    def _split_generators(self, dl_manager):
+        fileurls = [os.path.join(_DATA_URL, task_name+".json") for task_name in task_list]
+        local_datafiles = dl_manager.download_and_extract(fileurls)
+        return [
+            datasets.SplitGenerator(name=datasets.Split.TRAIN, gen_kwargs={"filenames":task_list ,"local_datafiles": local_datafiles}),
+        ]
+    def _generate_examples(self, filepath):
+        logger.info("generating examples from = %s", filepath)
+        key = 0
+        with open(filepath, encoding="utf-8") as f:
+            obj = json.load(f)
+            for item in obj:
+                yield key, {
+                    "id": item["id"],
+                    "corpus":  item["corpus"],
+                    "ann": item["ann"]
+                }
+                key += 1