Merge pull request #31 from monarch-initiative/textmining

Textmining

.gitignore

@@ -25,3 +25,4 @@ replay_pid*
 /.idea/
 /data/
 /prompts/
+/fenominal-mined.txt

docs/cases/PMID_15673476.txt

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+[source]
+pmid = PMID:15673476
+title = A novel heterozygous missense mutation in the UMOD gene responsible for Familial Juvenile Hyperuricemic Nephropathy
+[diagnosis]
+disease_id = OMIM:162000
+disease_label = Tubulointerstitial kidney disease, autosomal dominant, 1
+[text]
+The proband is an affected female who was first evaluated at the age of 24, when she presented with a gout attack and hyperuricemia.
+ At age 27 she was told having renal failure. However, a renal biopsy was not performed.
+ At age 44, serum creatinine was 2.8 mg/dl and ultrasound imaging detected numerous renal cysts.
+ Renal disease slowly progressed and the patient reached ESRD when she was 49 years old.
+ Her father died at the age of 55 from ESRD and suffered from hyperuricemia and gout.
+ The proband's only son is also affected. At the age of 18 years he had a gout attack.
+ On the initial evaluation, serum uric acid was 15 mg/dl and serum creatinine 1.6 mg/dl.
+ Renal cysts were also detected on ultrasound examination.

docs/cases/PMID_16962354.txt

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+[source]
+pmid = PMID:16962354
+title = Functional analysis of mutations in TGIF associated with holoprosencephaly
+[diagnosis]
+disease_id = OMIM:142946
+disease_label = Holoprosencephaly 4
+[text]
+A male proband presenting with lobar holoprosencephaly, atypical ventricles with small frontal horns,
+hypothalamic and caudate fusion, diabetes insipidus, seizures,
+premaxillary agenesis, microcephaly, absent nasal root and septum with a
+depressed nasal tip (Fig. 1A and B).

docs/cases/PMID_17661815.txt

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+[source]
+pmid = PMID:17661815
+title = Familial CHARGE syndrome because of CHD7 mutation: clinical intra- and interfamilial variability
+[diagnosis]
+disease_id = OMIM:214800
+disease_label = CHARGE syndrome
+[text]
+Patient A III-2 is the second boy of non-consanguineous French parents, respectively, aged 30 and 29 years, at the time of conception.
+The pregnancy was characterized by polyhydramnios from the 26th week of gestation.
+Delivery took place after 38 weeks by caesarean section with normal birth weight (BW) (3025 g, 50th centile), birth length (BL)
+(48 cm, 25th centile) and head circumference (OFC) (34.5 cm, 50th centile). MCA noted at birth included esophageal atresia with tracheoesophageal fistula,
+bilateral cleft lip and palate, large ventricular septal defect, dextroposition of aorta, atresia of the brachiocephalic trunk,
+malacia of the right main bronchus, costovertebral abnormalities (bifid fourth dorsal vertebrae, duplication of the fourth right rib,
+and spina bifida occulta from the seventh to the ninth dorsal vertebrae) and left cryptorchidism.
+Axial control acquisition was delayed as he sat at the age of 11 months, walked at 22 months.
+Balance problems persisted for several years. Recurrent otitis media, responsible for conductive hearing loss,
+required bilateral tympanostomy tubes. First words were delayed till 30 months. Learning disabilities and writing difficulties
+were confirmed when he was 8 year. When referred to the genetic department at the age of 15 years,
+he was 151 cm tall (−2 SD ), weighted 40 kg (−2 SD), and had an OFC of 52 cm (−2 SD).
+At that time, he had a long face with prominent chin, small mouth, high nasal bridge and triangular shape of right concha
+(Fig. 1). He had postural instability. Vestibular testing showed absence of response on canal function test with residual otolith
+function and residual left vestibulospinal responses on vestibular evoked myogenic potential test.
+Magnetic resonance imaging (MRI) examination showed hypoplastic superior and lateral semicircular canals (SCC) in the right ear
+and aplastic superior and hypoplastic lateral SCC in the left ear (Fig. 2). The vestibulae and the cochleae were normal.
+Facial and vestibulo-cochlear nerves were present on both sides. Brain MRI revealed a hypoplastic internal left carotid artery.
+There was no evidence for arhinencephaly. He had mild convergent strabismus, discrete myopia and posterior embryotoxon.
+Funduscopic examination revealed hypoplastic papillae. Using WISC IV scale at age 15 years his verbal conceptual index (VCI) was 78,
+perceptual reasoning index (PRI) 58, working memory index (WMI) 62 and processing speed index (PSI) 81.
+[text]
+Patient B III-1 is the first child from healthy unrelated Caucasian parents. Mother and father were both 26 years old at time of conception.
+Cerebral ventricular dilatation was suspected on pre-natal ultrasound but not confirmed by fetal cerebral MRI.
+Fetal karyotype was normal (46, XY). Premature labor occurred and delivery took place at a gestational age of 35 weeks.
+BW was 2050 g (third centile); BL 46.5 cm (50th centile) and OFC 34 cm (90th centile). He had cup-shaped ears with missing earlobes,
+right facial palsy, bifid uvula and mild retrognathism (Fig. 4) with associated cryptorchidism and global hypotonia.
+Swallowing difficulties with poor feeding were noted. Laryngoscopy revealed left vocal cord palsy.
+An atrial septal defect was diagnosed by echocardiography. Fundoscopy showed right retinal coloboma.
+Brainstem electric response audiometry identified a sensorineural deafness, visual evoked potentials were in the normal range.
+Metabolic work-up did not show any anomaly. This boy died on day 19 after refractory convulsive episodes starting on day 4.
+Encephalopathy and hydrocephaly were subsequently noted, as post-natal cerebral MRI (day 7) showed quadriventricular enlargement
+because of bloody effusion in occipital horns without any underlying vascular malformation. On autopsy,
+brain external examination revealed the absence of olfactory bulbs with a thin corpus callosum.
+On microscopic exam, cranial nerve roots were normal. Deep cerebellar heterotopia was present.
+Complete macroscopic and microscopic examinations were otherwise normal except for the presence of testis in the inguinal canals.

docs/cases/PMID_19208399.txt

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+[source]
+pmid = PMID:19208399
+title = A novel mutation in the VCP gene (G157R) in a German family with inclusion-body myopathy with Paget disease of bone and frontotemporal dementia
+[diagnosis]
+disease_id = OMIM:167320
+disease_label = Inclusion body myopathy with early-onset Paget disease and frontotemporal dementia 1
+[text]
+Patient II-3. At the age of 41 years, the
+male index patient developed slowly progressive symmetric muscle weakness, which started in the proximal upper limb muscles
+but is now most pronounced in the proximal leg muscles. Three years
+after onset he noticed increasing hearing impairment and bone pain. Elevated plasma levels of the
+bone-specific alkaline phosphatase isoenzyme (168 g/L, normal 8 –17) in combination with typical
+changes on a 99mTc total body bone scan suggested
+a diagnosis of PDB. Biphosphonate treatment was
+initiated and led to improvement of bone pain and a
+marked reduction of alkaline phosphatase.
+The muscle weakness, however, continued to increase, and
+eventually the patient became unable to walk more
+than 30 meters unaided. On examination, there was
+proximal weakness and atrophy of the limb muscles
+with bilateral scapular winging and a positive Trendelenburg sign. He had a waddling gait and required
+the support of two crutches. The patient’s wife had
+recently noticed an impaired capability of her husband to recognize faces of persons known to him. In
+addition, he had become apathetic and had lost
+interest in previous hobbies. Plasma creatine kinase
+(CK) levels were mildly elevated. Nerve conduction
+studies were normal, but electromyographic studies
+showed moderate myopathic changes with fibrillation potentials and polyphasic small-amplitude,
+short-duration motor unit potentials. Neuropsychological evaluation (DemTect, frontal assessment battery)
+ did not show significant cognitive impairment. Audiometry revealed moderate left-sided
+perceptive deafness of 50 dB HL. Cranial magnetic
+resonance imaging (MRI) showed bony changes typical of Paget disease, but no evidence of auditory
+nerve compression due to Paget disease. Intracranial
+findings were normal without signs of frontal lobe
+atrophy. A muscle biopsy from the quadriceps muscle revealed moderate histopathological changes
+consisting of angulated and atrophic fibers with a
+few inclusion bodies, but no rimmed vacuoles. The
+inclusions were ubiquitin-positive, but they were negative for beta-amyloid. Ubiquitin-positive inclusions
+could also be demonstrated in the nucleus of myocytes, endothelial cells, and fibroblasts.

docs/cases/PMID_20149460.txt

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+[source]
+pmid = PMID:20149460
+title = A novel mutation in the signal transducer and activator of transcription 3 (STAT3) gene, in hyper-IgE syndrome
+[diagnosis]
+disease_id = OMIM:147060
+disease_label = Hyper-IgE syndrome 1, autosomal dominant, with recurrent infections
+[text]
+A 12-year-old Greek girl was admitted because of fever, and cough for a week. Her parents were not consanguineous.
+She had no remarkable perinatal problems and had been vaccinated as scheduled. She had a history of atopic dermatitis since 6 months of age.
+Past medical history also revealed recurrent infections, including multiple episodes of skin abscesses and pneumonia.
+She had a history of two hospitalizations for pneumonia with cyst formation in the right lung and numerous visits at the
+clinic for the treatment of skin abscesses caused by Staphyloccocus aureus. Family history revealed no members with relevant allergic or immunologic diseases.
+On physical examination, her height was 118 cm (under the 5th percentile), and her weight was 25.8 kg (under the 5th percentile).
+She had coarse facial features with facial asymmetry, and prominent forehead. She was also diagnosed with scoliosis with maximal curvature of 14°.
+Complete blood cell counts demonstrated a high total eosinophil count (max 4000 cells/μl).
+The serum IgE level was increased at 74.000 IU/ml. All other laboratory data examined, such as serum immunoglobulin level,
+the oxidative burst of granulocytes and complement components, were normal with the exception of slightly increased IgD titer (300 mg/l).
+Lymphocyte subset analyses revealed normal levels of both CD4+ and CD8+ T cells (883 and 850 cells/μl, respectively).

docs/cases/PMID_20932317.txt

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+[source]
+pmid = PMID:20932317
+title = Frameshift mutation hotspot identified in Smith-Magenis syndrome: case report and review of literature
+[diagnosis]
+disease_id = OMIM:182290
+disease_label = Smith-Magenis syndrome
+[text]
+Case 1
+SMS324 is an 18-year-old male who was delivered at 38 weeks gestation following premature labor and antepartum haemorrhage.
+His birth weight was 2,750 g (10th-50th centile). While his neonatal period was complicated by gastroesophageal reflux
+and failure to thrive, he was admitted to the hospital at 1 year of age for being considerably overweight, with fat folds
+on his arms and legs. He spoke his first words at 6 months and walked at 12 months. His medical history includes two
+episodes of severe asthma, petit mal seizures between the ages of 5-10 y and three spontaneous pneumothoraces (SP).
+He had a square shaped face, upslanting palpebral fissures, down turned mouth, inverted upper lip, and synophrys (Fig. 1A).
+Other physical anomalies included brachydactyly, bilateral fifth finger clinodactyly with
+a small middle phalanx of his fifth fingers, and pes planus. At 16 years of age, height was 163 cm (< 3rd centile),
+head circumference was 54 cm, and he presented with relative truncal obesity.
+Behaviorally, SMS324 exhibited head-banging and rage attacks starting at age 3.
+At age 16, he continues to have recurrent episodes of rage attacks, anxiety, and obsessional behavior.
+He has never slept through the night, with recurrent 3 a.m. wakenings.
+Apart from finger chewing, he exhibits no self-injurious behaviors, self hugging, onychotillomania or polyembolokomania.
+He has had a persistent history of sleep disturbance.
+A formal developmental assessment indicated a mild global developmental delay.
+He was initially diagnosed with attention deficit disorder;
+however, a later assessment indicated this diagnosis was incorrect.
+He was initially mainstreamed in a regular classroom at school but at age 16 now functions in an OI classroom with supervision.