Merge pull request #38 from monarch-initiative/turkish

more cases

.gitignore

@@ -26,3 +26,4 @@ replay_pid*
 /data/
 /prompts/
 /fenominal-mined.txt
+/p2p_test.txt

docs/cases/PMID_20089953.txt

@@ -0,0 +1,25 @@
+[source]
+pmid = PMID:20089953
+title = Lack of cyclophilin B in osteogenesis imperfecta with normal collagen folding
+[diagnosis]
+disease_id = OMIM:259440
+disease_label = Osteogenesis imperfecta, type IX
+[text]
+The proband (Patient III-4) was a 4-year-old girl who was delivered at term by cesarean
+section owing to the breech position. She weighed 2720 g (6 lb) (10th percentile) at
+birth and had a wide anterior fontanelle; bilateral fractures of the humeri, radii,
+ulnae, femora, and tibiae were noted on radiographs. She was able to sit independently
+at the age of 2.75 years and was able to walk at the age of 3.5 years with the use of
+long leg braces and a walker. Postnatal fractures began to occur when she reached 6
+months of age; she sustained six long-bone fractures and underwent four lower-extremity
+osteotomy procedures. Her growth curve fell below normal by the age of 6 months.
+At 28 months of age, her weight and length were both at the 50th percentile for a
+normal 9-month-old girl. She had generalized, moderate ligamentous laxity, triangular
+facies with a high-bossed forehead, and proptosis. An umbilical hernia was noted at
+the age of 5 months. She had bilateral pes planus. Skeletal radiographs obtained when
+she was a newborn revealed osteoporotic long bones, with undertubulation and bowing of
+the femora and tibiae (Figure 1B, top row). By the age of 15 months, the vertebral
+bodies of T11 through L2 showed substantial anterior compression. At 33 months,
+long-bone undertubulation had improved but was still present in the femoral metaphyses.
+The z score for L1 to L4 on dual-energy x-ray absorptiometry (DXA) was −3.9 at the age
+of 3.5 years.

docs/cases/PMID_23311634.txt

@@ -0,0 +1,67 @@
+[source]
+pmid = PMID:23311634
+title = Identification of novel mutation in cathepsin C gene causing Papillon-Lefèvre Syndrome in Mexican patients
+[diagnosis]
+disease_id = OMIM:245000
+disease_label = Papillon-Lefevre syndrome
+[text]
+A male infant with congenital ichthyosis, presented as collodion baby phenotype,
+was transferred to a department of neonatal intensive care (level III) at the
+age of 11 weeks for further diagnosis.
+He was born at 33 weeks' gestation to a 34-year-old gravida 2, para 2, healthy woman.
+He was delivered by caesarean section, his birth weight was 1245g (3c, Z score −1,9)
+(Fenton and Kim, 2013), head circumference 28cm (3–10 c, Z score −1,5), and an Apgar score
+of eight in the first and fifth minute. The pregnancy was complicated by intrauterine
+growth restriction and the premature rupture of membranes. The woman's first child is
+a 7-year-old healthy girl. The family history was negative for any congenital
+disorders.
+A physical examination after delivery revealed thick scales all over the body,
+a lack of hair and dysmorphic features including microphthalmia, hypotelorism,
+trigonocephaly, low-set ears, natal teeth, bilateral cryptorchidism and pes planus
+(Fig. 1).
+The patient's history preceding the transfer included congenital pneumonia requiring
+mechanical ventilation, oxygeno-dependance till the 67th day of life, secondary
+infections, anaemia and failure to thrive.
+At admission to the NICU, apart from the above-mentioned features, physical examination
+revealed ectropion, eclabium, hypertonia, multiple constriction bands over fingers and
+hyperkeratotic scales over nails. The patient's weight was 1735g (««3c, Z score −6,4)
+and laboratory tests showed multiple metabolic abnormalities including hypoproteinaemia,
+hypoalbuminemia, hypocalcaemia and hypophosphatemia. Enteral feeding appeared to be
+ineffective due to vomiting. Parenteral nutrition via a central venous catheter was
+introduced to provide the optimal caloric intake and to supplement for deficiencies.
+Hypertrophic pyloric stenosis was identified to be the cause of feeding problems.
+Nonetheless, the surgical treatment had to be postponed as the infant developed systemic
+infection, at first bacterial, then fungal (Candida albicans) which led to multiorgan
+failure with: renal failure, thrombocytopenia, anaemia, coagulopathy and respiratory
+failure requiring a high frequency oscillatory ventilation for four weeks. The fungal
+sepsis was treated with micafungin and amphotericin B for 50 days. The infant's condition
+improved, and he was assessed as fit for surgery which would enable enteral feeding.
+A laparotomy revealed slightly hypertrophic pylorus, adhesions obstructing the distal
+part of duodenum and Meckel's diverticulum which were removed.
+During further hospitalisation, the patient developed catheter-related sepsis three times.
+In two instances, blood cultures were positive for Staphylococcus haemolitycus and in
+one case for Klebsiella pneumoniae. The latter resulted in respiratory failure requiring
+mechanical ventilation for a number of days. After this, the patient remained
+oxygen-dependant.
+Although infections were treated according to antibiograms and central venous catheters
+were replaced every time, the biochemical markers of infection never reached normal
+limits. Hepatosplenomegaly was palpable on physical examination. Permanent lymphopenia,
+neutropenia and thrombocytopenia were present on a complete blood count. Immunological
+tests were inconclusive for any primary immune deficiency (Table 1). The patient's
+proneness to infection seemed to be due to his skin condition, hospitalisation in the
+ICU, and colonization by drug resistant bacterial strains.
+As for the infant's skin, a daily bath in potassium permanganate solution was followed
+by the mechanical removal of scales and regular application of sterile silicone
+lubricant prepared in the hospital's pharmacy. Dexpanthenol gel was applied topically
+on the eyes to protect the cornea. The skin condition had only slightly improved
+following this management.
+When enteral feedings were restored, a hypercaloric formula was introduced.
+Nevertheless, the infant was not gaining weight and cachexia continued to progress.
+He also continued to have hypocalcaemia and hypophosphatemia despite oral s
+upplementation.
+Regarding his neurological evaluation, MRI scan was conducted because of trigonocephaly.
+The examination showed delayed myelination, dilated ventricles, and structural
+alterations of frontal lobes.
+In terms of genetic diagnosis, new generation sequencing was the first to be performed
+with the results being negative (Table 2).
+

docs/cases/PMID_28757203.txt

@@ -0,0 +1,25 @@
+[source]
+pmid = PMID:28757203
+title = Biallelic Mutations in LIPT2 Cause a Mitochondrial Lipoylation Defect Associated with Severe Neonatal Encephalopathy
+[diagnosis]
+disease_id = OMIM:617668
+disease_label = Encephalopathy, neonatal severe, with lactic acidosis and brain abnormalities
+[text]
+Individual 1 (P1), a boy, was the first child of non-consanguineous parents of French (mother) and Ivory
+Coast (father) origin. He was born after an uneventful pregnancy and spontaneous delivery at term with
+normal birth parameters (body weight 3,750 g, length 51 cm, head circumference 35 cm). Apgar scores
+were 9/10/10. From birth on, he presented with truncal hypotonia, spastic tetraparesis, and dystonia.
+Brain MRI showed marked supra-tentorial cortical atrophy with ventricular dilatation as well as bifrontal white matter abnormalities and delayed myelination (Figure 1Amiddle). MRS spectroscopy with
+a long TE (144) showed a lactate peak (Figure 1B). This clinical and radiological presentation led us to
+suspect a mitochondrial disease. At age 2.5 years, the affected individual was bed- and wheelchair-bound
+with no head control. He could neither sit unaided nor speak or understand simple orders. He was
+otherwise fully conscious and alert, and he could smile at times and follow with his eyes. His weight
+was -2.5 SD, his length was at the median, and his head circumference (HC) was -4 SD. Major
+swallowing difficulties led to gastrostomy. At the age of 3 years, he developed complex epilepsy treated
+by oxcarbazepine (Trileptal®), clobazam (Urbanyl®), and topiramate (Epitomax®).
+Electroencephalography at the age of 7 years showed in the awake state, an absence of occipital alpha
+rhythm, polyrhythmic background activity with diffuse alpha, theta and rare delta rhythms, multifocal
+spikes and sharp waves, sometimes in bursts or rhythmic sequences, with right posterior predominance
+(Figure S3A). Cardiac ultrasonography, audiological and ophthalmological examination were normal.
+At the age of 7 years and 9 months, the ventricular dilatation and sub-tentorial cortical atrophy were
+increased. No episodes of metabolic decompensation have been documented.

docs/cases/PMID_28841907.txt

@@ -0,0 +1,40 @@
+[source]
+pmid = PMID:28841907
+title = A novel mutation in the COL2A1 gene in a patient with Stickler syndrome type 1: a case report and review of the literature
+[diagnosis]
+disease_id = OMIM:108300
+disease_label = Stickler syndrome, type I
+[text]
+A 24-month-old Japanese boy was referred to our hospital for evaluation of his
+short stature. He was born at a gestational age of 38 weeks and 4 days and had a
+submucous cleft palate and micrognathia. His birth weight was 3225 g
+(+0.53 standard deviation (SD) of average Japanese male infants), and his birth length
+was 45 cm (−1.80 SD). His submucous cleft palate was repaired at 18 months of age.
+Tympanostomy tubes were placed at the same time for secretory otitis media.
+Auditory brainstem response testing showed normal findings. At 22 months, he was found to
+have bilateral leukocoria. Phacoemulsification and anterior vitrectomy for bilateral
+lens opacities were performed at another hospital. He was considered to have
+Pierre Robin sequence, but the association with the ophthalmic symptoms was not
+investigated. He received speech therapy for speech delay.
+At presentation, the patient weighed 11.6 kg (−0.33 SD) with a height of 79.1 cm
+(−2.52 SD). His arm span was 79 cm, and his sitting height was 48.5 cm
+(sitting height/height ratio 0.61). He showed ocular hypertelorism;
+prominent eyes due to shallow eye sockets; a flat midface with a depressed nasal bridge;
+anteverted nares; micrognathia; low-set ears; and limitations in bilateral elbow flexion;
+but no hypotonia, hyperextensible joints, or joint pain. All other family members,
+which included his parents and two brothers, were healthy.
+His parents are not consanguineous. His father’s height was 182 cm
+(+1.93 SD of average Japanese adult men), and his mother’s height was 147 cm
+(−2.09 SD of average Japanese adult women).
+Radiographs showed thickening of the calvaria, widening of the distal humeral metaphysis,
+lack of femoral head ossification, deformity of the femoral neck,
+and distal femoral and proximal tibial epiphyseal ossification centers.
+Serum insulin-like growth factor-1 was 20.17 nmol/L (154 ng/ml)
+(normal range 2.36–20.17 nmol/L [18–154 ng/ml]).
+An L-arginine stimulation test for growth hormone (0.5 g/kg arginine) showed a peak
+growth hormone level of 16.4 ng/ml. A luteinizing hormone-releasing
+hormone/thyrotropin-releasing hormone stimulation test
+(3 μg/kg luteinizing hormone-releasing hormone; 10 μg/kg thyrotropin-releasing hormone)
+showed prepubertal and normal thyroid-stimulating hormone responses.
+His karyotype was 46,XY. A brain magnetic resonance imaging scan showed no abnormalities.
+Echocardiography showed no evidence of mitral valve prolapse.

docs/cases/PMID_29575628.txt

@@ -0,0 +1,46 @@
+[source]
+pmid = PMID:29575628
+title = Congenital sodium diarrhea and chorioretinal coloboma with optic disc coloboma in a patient with biallelic SPINT2 mutations, including p.(Tyr163Cys)
+[diagnosis]
+disease_id = OMIM:270420
+disease_label = Diarrhea 3, secretory sodium, congenital, syndromic
+[text]
+A two-month-old male with failure to thrive, hyponatremia, hypovolemia,
+and cleft lip and palate was referred to the ophthalmology service for evaluation.
+He was born to healthy, unrelated parents and had three unaffected siblings.
+A cleft lip was noted on prenatal ultrasound and a repeat ultrasound confirmed
+bilateral cleft lip and palate. Fetal echocardiogram was normal. The remainder of
+the pregnancy was uncomplicated and he was born at 39 weeks via spontaneous vaginal
+delivery with a birthweight of 2,953 grams (10–25th centile). He spent two days in
+the hospital before being discharged home. At seven weeks of age, he was hospitalized
+for dehydration and electrolyte abnormalities after seven days of vomiting and diarrhea.
+An orogastric tube was placed to supplement his oral feeds. However, two weeks later,
+he was readmitted for emesis and discomfort with feeds. Given his recurrent episodes
+of failure to thrive and his cleft lip and palate, the decision was made to supplement
+his parenteral nutrition with enteral nutrition through a gastrostomy tube.
+On examination at two months of life, weight was 3.88 kilograms (<2nd centile),
+length was 57 centimeters (25th centile) and occipitofrontal circumference was 39
+centimeters (50th centile). Craniofacial features included a prominent and square
+forehead, a prominent occiput, bilateral preauricular pits, and bilateral cleft lip
+and palate with distortion of the nares (Figure 1). He was light averse in both eyes,
+but had normal intraocular pressures by palpation. The anterior segment appeared normal,
+but he had a large chorioretinal coloboma involving the optic nerve and macula in
+his left eye (Figure 2). On review in ophthalmology clinic six months later, his
+mother reported he was sensitive to light. At this time, he was noted to fix and
+follow with each eye. He had normal pupillary responses and intraocular pressures
+of 9 mmHg in each eye by iCare. He demonstrated an intermittent left exotropia
+with grossly full extraocular movements. The anterior segment was notable for
+irregularity of the corneal surface with significant punctate staining of both
+corneas when examined with fluorescein eye drops and cobalt blue light. Although
+there were diffuse punctate epithelial erosions in both eyes, there were no
+frank epithelial defects. The right fundus was normal and the left fundus
+demonstrated the same extensive optic disc coloboma, unchanged from prior examination.
+A cycloplegic refraction was also performed and revealed +2.00 sphere/+1.00
+cylinder × 090 for the right eye and +0.50 diopter sphere for the left.
+Pathologic analysis of the duodenum demonstrated unremarkable small intestinal mucosa
+with an intact brush border. Electron microscopy verified an intact unremarkable
+surface epithelium, without evidence of tufting or microvillus inclusions, although
+it can be difficult to detect the characteristic “tufts” associated with tufting
+enteropathy on routine biopsies of the small bowel. The cell junctions between
+the surface epithelial cells were intact and of normal configuration and the
+epithelial cell organelles were of normal morphology.

docs/cases/PMID_30243293.txt

@@ -0,0 +1,8 @@
+[source]
+pmid = PMID:30243293
+title = A case report: autosomal recessive Myotonia congenita caused by a novel splice mutation (c.1401 + 1G > A) in CLCN1 gene of a Chinese Han patient
+[diagnosis]
+disease_id = OMIM:160800
+disease_label = Myotonia congenita, dominant
+[text]
+A 21-year-old man complained of transient muscle stiffness since 10 years. He experienced difficulty in initiating movement and felt muscle weakness after rest. However the symptoms typically improved after repeated contraction (warm-up phenomenon). The symptoms tended to aggravate during cold weather. He was unable to open his eyes immediately after washing his face with cold water. He had non-consanguineous parents and there was no significant family history. Further, the patient showed normal growth and development. Medical examination showed generalized muscle hypertrophy and normal muscle strength as assessed with the Medical Research Council (MRC) sum score. Deep tendon reflexes were attenuated. No nerve dysfunction or sensory deficit was noted. The serum creatine kinase level was 2-fold higher than the upper limit of the normal reference level. Electromyogram showed myotonic discharges. Biceps muscle biopsy specimen was obtained after written informed consent of the patient. The specimen was precooled with isopentane and frozen in liquid nitrogen. A section of muscle biopsy specimen was stained with hematoxylin-eosin (HE) and modified Gomori’s trichrome (MGT). Activity of oxidative enzymes such as succinate dehydrogenase (SDH), NADH-tetrazolium reductase (NADH-TR), and cytochrome c oxidase (COX) were normal.

src/main/java/org/monarchinitiative/phenopacket2prompt/cmd/TestDriveCommand.java

@@ -279,7 +279,7 @@ private String createPrompts(List<PpktIndividual> individualList, PromptGenerato
         StringBuilder sb = new StringBuilder();
         for (PpktIndividual individual : individualList) {
             if (individual.hasExcludedPhenotypeFeatureAtOnset() ||individual.hasObservedPhenotypeFeatureAtOnset()) {
-                String prompt = generator.createPrompt(individual);
+                String prompt = generator.createPromptWithoutHeader(individual);
                 sb.append(prompt).append("\n\n");
             } else {
                 System.err.println("[WARN] No HPO terms found for " + individual.getPhenopacketId());

src/main/java/org/monarchinitiative/phenopacket2prompt/output/impl/spanish/PpktPhenotypicfeatureSpanish.java

@@ -119,10 +119,10 @@ public String featuresAtOnset(String personString, List<OntologyTerm> ontologyTe
         var observedStr = getCommaList(observedSpanish);
         var excludedStr = getCommaList(excludedSpanish);
         if (!observed.isEmpty() && ! excluded.isEmpty()) {
-            return String.format("%s presentó los siguientes síntomas: %s. Por el contrario, se %s los siguientes síntomas: %s.",
+            return String.format("%s presentó los siguientes síntomas: %s. Por el contrario, se %s: %s.",
                     personString,
                     observedStr,
-                    excluded.size()>1? "excluyeron":"excluyeró",
+                    excluded.size()>1? "excluyeron los siguientes síntomas":"excluyeró el siguiente síntoma",
                     excludedStr);
         } else if (!observed.isEmpty()) {
             return String.format("%s presentó los siguientes síntomas: %s.", personString, observedStr);