Digestive System Phenotypes

This collection consists of phenotypic cohort definitions for patients with diseases affecting the gastrointestinal tract and accessory organs, such as the liver, pancreas, and gallbladder. These conditions include inflammatory diseases (e.g., Crohn’s disease), infections (e.g., Helicobacter pylori gastritis), functional disorders (e.g., irritable bowel syndrome), and structural abnormalities (e.g., biliary atresia). Phenotype definitions may incorporate diagnostic codes, endoscopic or imaging procedures, laboratory tests (e.g., liver function panels, stool inflammatory markers), medication usage (e.g., proton pump inhibitors, immunosuppressants), and clinical notes. Example phenotypes in this domain include “Pediatric Inflammatory Bowel Disease,” which might require diagnosis codes alongside endoscopy or pathology confirmation, and “Acute Pancreatitis,” defined by clinical presentation, serum lipase levels, and radiologic evidence of pancreatic inflammation.