German translations

docs/cases/PMID_30012084.txt

@@ -0,0 +1,19 @@
+[source]
+pmid = PMID:30012084
+title = The most 5' truncating homozygous mutation of WNT1 in siblings with osteogenesis imperfecta with a variable degree of brain anomalies: a case report
+[diagnosis]
+disease_id = OMIM:615220
+disease_label = Osteogenesis imperfecta, type XV
+[text]
+A 14-year-old Thai girl was born via cesarean section due to premature rupture of the membrane with a birth weight of 2500 g.
+She is the first child of a consanguineous (second-degree relatives) couple. Both parents are healthy and have never had fractures.
+During her first year of life, she had delayed motor development and growth failure. At one year of age, she could not sit by
+herself and weighed 7.5 kg (< 3rd centile). She presented to our hospital at 14 months of age with fractures of both femora
+without a history of significant trauma. She was found to have ptosis of both eyes with normal teeth but no blue sclerae.
+She was small for her age. Her weight was 7.8 kg (3rd centile) and her length was 68 cm (< 3rd centile). Skeletal survey
+showed diffuse osteopenia, multiple healed fractures of the right humoral shaft, both tibiae and fibulae. Spine radiograph showed
+flattening and indentation of vertebral bodies (Fig. 1).
+Radiological features of the proband. Imaging of the thoracic and lumbar spines at 14 months of age, (a) the
+antero-posterior and (b) lateral views revealed depressed multiple vertebrae.
+Figures c-f showed imaging at 14 years of age of upper extremities (c-d) and lower extremities (e-f) revealing deformities
+of humeri, left ulna and radius, right tibia and fibula, left tibia and fibula, respectively

docs/cases/PMID_30509212.txt

@@ -0,0 +1,24 @@
+[source]
+pmid = PMID:30509212
+title = Novel KDM6A splice-site mutation in kabuki syndrome with congenital hydrocephalus: a case report
+[diagnosis]
+disease_id = OMIM:300867
+disease_label = Kabuki syndrome 2
+[text]
+A 2 months and 13 days old male was hospitalized in the neonatology department of our hospital for postnatal growth retardation
+on 20 February, 2017. The infant was spontaneous breech delivery at the 36th week plus 1 day of gestation with a
+weight of 2.8 kg and head circumference of 31 cm. The Apgar scores of the infant all were 8 at 1, 5, and 10 min.
+The infant was the third child of a 29-year-old mother who had fewer dysmorphic features and had two unaffected older sisters.
+Before the infant was born, magnetic resonance imaging (MRI) results showed that enlarged lateral ventricles (Fig. 1),
+this indicated congenital hydrocephalus.
+After admission to our hospital, physical examination showed that the patient’s growth and development level was of
+below the normal range 3rd centiles at height (~52 cm), weight (~2.9 kg) and head circumference (~33.5 cm) in accordance
+with the new WHO (2006) Child growth standards [13], suggesting postnatal onset of growth retardation.
+The patient had an inability to lift the head and weak crying. The patient couldn’t amuse by physician, and couldn’t accomplish
+the tests of audio and visual tracking. However, The patient presented with recognizable facial features,
+including sparse eyebrows (Fig. 2a), a depressed nasal tip (Fig. 2b), long palpebral fissures with eversion of
+the lateral part of the lower eyelid (Fig. 2c), large prominent ears with low set ears (Fig. 2d), micrognathia (Fig. 2e),
+gingival thickening and a high palate with cleft (Fig. 2f). In addition, head computed tomography (CT) scan revealed
+hydrocephalus (Fig. 3), ultrasonography showed developmental dysplasia of hip (Fig. 4).
+The results of cardiopulmonary and hepatolienal examination were normal. The patient had hypotonia, no pathological reflex.
+Liver and kidney functions, thyroid function, blood counts, electrolytes were normal.

docs/cases/PMID_30643655.txt

@@ -0,0 +1,10 @@
+[source]
+pmid = PMID:30643655
+title = Exome Sequencing: Mutilating Sensory Neuropathy with Spastic Paraplegia due to a Mutation in FAM134B Gene
+[diagnosis]
+disease_id = OMIM:613115
+disease_label = Neuropathy, hereditary sensory and autonomic, type IIB
+[text]
+Family 2: A 15-year-old boy (F2: IV: 1) presented with a history of frequent falls, unsteadiness, and pain insensitivity from an early age of 4 years [Figure 1(a)]. During the 5-year follow-up, he was hospitalized multiple times due to skin ulcers and osteomyelitis affecting his feet and toes. There was mild spasticity in the lower limbs with minimal pyramidal weakness (MRC4). Tendon reflexes were exaggerated with negative extensor response.
+
+Touch, pinprick, temperature and vibration revealed mild impairment in the distal part of the lower extremities for all the affected’s from family 1 while it was normal for family 2. In both families, applying strong pressure to the Achilles tendon or touching the exposed bony areas was not followed by an adequate pain reflex. Neurophysiological findings were normal or mildly abnormal in family 1 in the early stages but follow-up studies revealed sensory axonal polyneuropathy predominantly in the lower limbs while it was normal for family 2. Sympathetic skin response and beat to beat variation were also found to be normal for family 2 but abnormal in family 1 indicating involvement of the autonomic nervous system. Cerebral MRI as well as other hematological and biochemical investigations was normal

src/main/java/org/monarchinitiative/phenopacket2prompt/model/HpoOnsetAge.java

@@ -15,12 +15,19 @@ public final class HpoOnsetAge implements PhenopacketAge {
     private final int totalDays;
 
 
-    /**
-     * One of Antenatal onset HP:0030674; Fetal onset HP:0011461; Late first trimester onset HP:0034199;
-     * Third trimester onset HP:0034197; Second trimester onset HP:0034198; Embryonal onset HP:0011460
+
+    private final static TermId antenatalOnset = TermId.of("HP:0030674");
+    private final static TermId fetalOnset = TermId.of("HP:0011461");
+    private final static TermId lateFirstTrimesterOnset = TermId.of("HP:0034199");
+    private final static TermId secondTrimesterOnset = TermId.of("HP:0034198");
+    private final static TermId thirdTrimesterOnset = TermId.of("HP:0034197");
+
+    private final static TermId embryonalOnset = TermId.of("HP:0011460");
+    /** Note we are including antenatal in fetal, because this is almost certainly what is meant if embryonal is not
+     * specifically indicated
      */
-    private final static Set<TermId> fetalIds = Set.of(TermId.of(" HP:0030674"), TermId.of("HP:0011461"), TermId.of("HP:0034199"),
-            TermId.of("HP:0034197"), TermId.of("HP:0034198"), TermId.of("HP:0011460*"));
+    private final static Set<TermId> fetalIds = Set.of(antenatalOnset, fetalOnset,
+            lateFirstTrimesterOnset, secondTrimesterOnset, thirdTrimesterOnset);
 
     public static HpoOnsetAge congenital() {
         return new HpoOnsetAge(congenitalOnset.getValue(), "Congenital onset");
@@ -150,4 +157,10 @@ public boolean equals(Object obj) {
         return iso.totalDays() == totalDays();
     }
 
+
+    @Override
+    public String toString() {
+        return String.format("[HpoOnsetAge]: %s (%s)", this.label, this.tid.getValue());
+    }
+
 }

src/main/java/org/monarchinitiative/phenopacket2prompt/output/PPKtBuildingBlockGenerator.java → src/main/java/org/monarchinitiative/phenopacket2prompt/output/BuildingBlockGenerator.java

@@ -7,7 +7,7 @@
  * Provide the "building blocks" (i.e., text fragments) needed to generate the
  * texts in the various languages.
  */
-public interface PPKtBuildingBlockGenerator {
+public interface BuildingBlockGenerator {
 
     // days, months, years -- format singular and plural forms
     String days(int d);

src/main/java/org/monarchinitiative/phenopacket2prompt/output/impl/english/PPKtEnglishBuildingBlocks.java → src/main/java/org/monarchinitiative/phenopacket2prompt/output/impl/english/EnglishBuildingBlocks.java

@@ -1,12 +1,12 @@
 package org.monarchinitiative.phenopacket2prompt.output.impl.english;
 
 import org.monarchinitiative.phenopacket2prompt.model.Iso8601Age;
-import org.monarchinitiative.phenopacket2prompt.output.PPKtBuildingBlockGenerator;
+import org.monarchinitiative.phenopacket2prompt.output.BuildingBlockGenerator;
 
 import java.util.ArrayList;
 import java.util.List;
 
-public class PPKtEnglishBuildingBlocks implements PPKtBuildingBlockGenerator {
+public class EnglishBuildingBlocks implements BuildingBlockGenerator {
 
 
     @Override

src/main/java/org/monarchinitiative/phenopacket2prompt/output/impl/english/PpktIndividualEnglish.java

@@ -2,13 +2,12 @@
 
 import org.monarchinitiative.phenol.base.PhenolRuntimeException;
 import org.monarchinitiative.phenopacket2prompt.model.*;
-import org.monarchinitiative.phenopacket2prompt.output.PPKtBuildingBlockGenerator;
+import org.monarchinitiative.phenopacket2prompt.output.BuildingBlockGenerator;
 import org.monarchinitiative.phenopacket2prompt.output.PPKtIndividualInfoGenerator;
 
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Optional;
-import java.util.Set;
 
 
 /**
@@ -32,17 +31,17 @@
  */
 public class PpktIndividualEnglish implements PPKtIndividualInfoGenerator {
 
-    private final PPKtBuildingBlockGenerator buildBlocks;
+    private final BuildingBlockGenerator buildBlocks;
 
     public PpktIndividualEnglish() {
-        buildBlocks = new PPKtEnglishBuildingBlocks();
+        buildBlocks = new EnglishBuildingBlocks();
     }
 
     /**
      * We begin our description with a sentence
      *
-     * @param individual
-     * @return
+     * @param individual the individual for whom we are creating a diagnostic prompt
+     * @return complete prompt for an LLM
      */
     public String getIndividualDescription(PpktIndividual individual) {
         if (individual.annotationCount() == 0) {
@@ -117,10 +116,12 @@ private String nameOfLifeStage(HpoOnsetAge hpoOnsetTermAge) {
             return "an " +buildBlocks.adolescentChild();
         } else if (hpoOnsetTermAge.isNeonate()) {
             return "a " +buildBlocks.newborn();
-        } else if (hpoOnsetTermAge.isAdult()) {
+        } else if (hpoOnsetTermAge.isYoungAdult()) {
+            return "a young adult"; // +buildBlocks.asYoungAdult();
+        }  else if (hpoOnsetTermAge.isAdult()) {
             return "an " +buildBlocks.adult();
         } else {
-            throw new PhenolRuntimeException("Could not identify life stage name for HpoOnsetAge " + hpoOnsetTermAge);
+            throw new PhenolRuntimeException("Could not identify life stage name for HpoOnsetAge " + hpoOnsetTermAge.toString());
         }
     }
 
@@ -295,4 +296,5 @@ public String atAgeForVignette(PhenopacketAge ppktAge) {
     }
 
 
+
 }