NICU Curation Project

Overview

This project focuses on disorders commonly managed in neonatal intensive care units (NICUs), spanning prematurity complications, neonatal critical care, and high-impact genetic diseases that present in the newborn period.

Goals

• Curate NICU-relevant diseases with evidence-backed pathophysiology
• Map neonatal phenotypes to HPO terms
• Annotate treatments with NCIT terms
• Provide PMID-supported evidence for all claims

Target Conditions (NICU Core)

Prematurity / Respiratory

• [ ] Respiratory Distress Syndrome of the Newborn (surfactant deficiency)
• [ ] Bronchopulmonary Dysplasia (chronic lung disease of prematurity)
• [ ] Apnea of Prematurity
• [ ] Transient Tachypnea of the Newborn
• [ ] Meconium Aspiration Syndrome
• [ ] Persistent Pulmonary Hypertension of the Newborn (PPHN)

Neurologic / Brain Injury

• [ ] Hypoxic-Ischemic Encephalopathy (HIE)
• [ ] Intraventricular Hemorrhage (IVH)
• [ ] Periventricular Leukomalacia (PVL)
• [ ] Neonatal Seizures

GI / Nutrition

• [ ] Necrotizing Enterocolitis (NEC)
• [ ] Spontaneous Intestinal Perforation
• [ ] Short Bowel Syndrome (post-NEC or surgical)
• [ ] Feeding Intolerance / Dysmotility (syndrome-level entry if needed)

Infectious

• [ ] Early-Onset Neonatal Sepsis (e.g., GBS, E. coli)
• [ ] Late-Onset Neonatal Sepsis
• [ ] Neonatal Meningitis

Heme / Metabolic / Endocrine

• [ ] Neonatal Hyperbilirubinemia
• [ ] Kernicterus
• [ ] Neonatal Hypoglycemia
• [ ] Anemia of Prematurity
• [ ] Neonatal Polycythemia
• [ ] Congenital Adrenal Hyperplasia
• [ ] Congenital Hypothyroidism

Congenital / Surgical / Cardiac

• [ ] Patent Ductus Arteriosus (PDA)
• [ ] Congenital Diaphragmatic Hernia (CDH)
• [ ] Gastroschisis
• [ ] Omphalocele
• [ ] Esophageal Atresia / Tracheoesophageal Fistula
• [ ] Ductal-Dependent Congenital Heart Disease (TGA, HLHS, etc.)

Target Genetic Diseases (NICU-Relevant)

Chromosomal / Syndromic

• [x] Down syndrome - Down_syndrome.yaml
• [ ] Trisomy 18 (Edwards syndrome)
• [ ] Trisomy 13 (Patau syndrome)
• [x] Wolf-Hirschhorn syndrome - Wolf-Hirschhorn_Syndrome.yaml
• [x] 22q11.2 deletion (DiGeorge syndrome) - 22q11.2_Deletion_Syndrome.yaml - Created 2026-02-03, 85% compliance
• [x] Noonan syndrome - Noonan_Syndrome.yaml

Inborn Errors of Metabolism

• [x] Phenylketonuria (PKU) - Phenylketonuria.yaml
• [x] Maple Syrup Urine Disease - Maple_Syrup_Urine_Disease.yaml
• [ ] Urea cycle disorders (e.g., OTC deficiency)
• [ ] Propionic acidemia
• [ ] Methylmalonic acidemia
• [ ] Isovaleric acidemia
• [ ] Galactosemia
• [x] MCAD deficiency - MCAD_Deficiency.yaml - Created 2026-02-03, 45% compliance (needs evidence)
• [ ] VLCAD deficiency
• [x] Peroxisome biogenesis disorder - Peroxisome_Biogenesis_Disorder.yaml

Neuromuscular / Neurogenetic

• [x] Spinal Muscular Atrophy - Spinal_Muscular_Atrophy.yaml
• [ ] Congenital myotonic dystrophy
• [ ] Congenital myasthenic syndromes

Skeletal Dysplasias

• [x] Thanatophoric dysplasia type 1 - Thanatophoric_Dysplasia_Type_1.yaml
• [x] Thanatophoric dysplasia type 2 - Thanatophoric_Dysplasia_Type_2.yaml
• [x] Achondroplasia - Achondroplasia.yaml
• [x] Hypochondroplasia - Hypochondroplasia.yaml
• [x] SADDAN - SADDAN.yaml

Hematologic / Other Genetic

• [x] G6PD deficiency - Glucose-6-Phosphate_Dehydrogenase_G6PD_Deficiency.yaml
• [x] Gaucher disease - Gaucher_Disease.yaml
• [x] Fabry disease - Fabry_Disease.yaml
• [x] Fanconi anemia - Fanconi_Anemia.yaml
• [x] TARP syndrome - TARP_syndrome.yaml
• [x] Sengers syndrome - Sengers_syndrome.yaml
• [x] CHIME syndrome - CHIME_syndrome.yaml
• [x] HIDEA syndrome - HIDEA_Syndrome.yaml

Curation Workflow

1. Create YAML file in kb/disorders/
2. Validate with just validate <file> and just validate-kb-references <file>
3. Validate terms with just validate-terms <file>
4. Run just qc before committing