Chronic Disease Curation Project

Overview

This project aims to curate comprehensive pathophysiology entries for major chronic diseases in the Disorder Mechanisms Knowledge Base. Chronic diseases represent long-term conditions that require ongoing management and significantly impact quality of life.

This is an evergreen project: beyond the initial phases, "Other" expansion categories capture related conditions that share mechanisms and can be unfolded as curation continues.

Goals

• Document disease mechanisms with evidence-backed pathophysiology
• Map phenotypes to HPO terms
• Annotate treatments with NCIT terms
• Provide PMID-supported evidence for all claims

Target Diseases - Phase 1 (Complete)

• [x] Type 2 Diabetes Mellitus - Type_2_Diabetes_Mellitus.yaml
• [x] Hypertension - Essential_Hypertension.yaml
• [x] Chronic Obstructive Pulmonary Disease (COPD) - Chronic_Obstructive_Pulmonary_Disease.yaml
• [x] Coronary Artery Disease - Coronary_Artery_Disease.yaml
• [x] Chronic Kidney Disease - Chronic_Kidney_Disease.yaml
• [x] Heart Failure - Heart_Failure.yaml
• [x] Osteoarthritis - Osteoarthritis.yaml
• [x] Rheumatoid Arthritis - Rheumatoid_Arthritis.yaml
• [x] Asthma - Asthma.yaml
• [x] Inflammatory Bowel Disease - Crohn_Disease.yaml (Ulcerative Colitis pending)
• [x] Alzheimer's Disease - Alhzeimer_Disease.yaml
• [x] Parkinson's Disease - Parkinsons_Disease.yaml
• [x] Multiple Sclerosis - Multiple_Sclerosis.yaml
• [x] Systemic Lupus Erythematosus - Systemic_Lupus_Erythematosus.yaml
• [x] Chronic Liver Disease / Cirrhosis - Liver_Cirrhosis.yaml
• [x] Atrial Fibrillation - Atrial_Fibrillation.yaml
• [x] Obesity - Obesity.yaml
• [x] Depression (Major Depressive Disorder) - Major_Depressive_Disorder.yaml
• [x] Epilepsy - Epilepsy.yaml
• [x] Psoriasis - Psoriasis.yaml

Target Diseases - Phase 2 (Complete)

Endocrine/Metabolic

• [x] Hypothyroidism (Hashimoto's Thyroiditis) - Hashimotos_Thyroiditis.yaml
• [x] Polycystic Ovary Syndrome (PCOS) - Polycystic_Ovary_Syndrome.yaml
• [x] Gout - Gout.yaml
• [ ] Other endocrine/metabolic; e.g. Cushing syndrome, acromegaly, hyperparathyroidism

Musculoskeletal

• [x] Osteoporosis - Osteoporosis.yaml
• [x] Fibromyalgia - Fibromyalgia.yaml
• [ ] Other musculoskeletal; e.g. Paget disease, osteogenesis imperfecta, ankylosing spondylitis

Gastrointestinal

• [x] Gastroesophageal Reflux Disease (GERD) - Gastroesophageal_Reflux_Disease.yaml
• [x] Irritable Bowel Syndrome (IBS) - Irritable_Bowel_Syndrome.yaml
• [x] Ulcerative Colitis - Ulcerative_Colitis.yaml
• [x] Celiac Disease - Celiac_Disease.yaml
• [x] Chronic Pancreatitis - Chronic_Pancreatitis.yaml
• [ ] Other gastrointestinal; e.g. Barrett esophagus, diverticular disease, chronic constipation

Psychiatric/Neurological

• [x] Bipolar Disorder - Bipolar_Disorder.yaml
• [x] Generalized Anxiety Disorder - Generalized_Anxiety_Disorder.yaml
• [x] Migraine - Migraine.yaml
• [ ] Other psychiatric; e.g. schizophrenia, OCD, PTSD, eating disorders
• [ ] Other neurological; e.g. ALS, Huntington disease, essential tremor, neuropathies

Cardiovascular

• [x] Peripheral Artery Disease - Peripheral_Artery_Disease.yaml
• [ ] Other cardiovascular; e.g. cardiomyopathies, valvular heart disease, aortic aneurysm

Respiratory

• [x] Obstructive Sleep Apnea - Obstructive_Sleep_Apnea.yaml
• [ ] Other respiratory; e.g. pulmonary fibrosis, bronchiectasis, pulmonary hypertension

Reproductive/Urological

• [x] Endometriosis - Endometriosis.yaml
• [x] Benign Prostatic Hyperplasia - Benign_Prostatic_Hyperplasia.yaml
• [ ] Other reproductive/urological; e.g. chronic pelvic pain, interstitial cystitis, male infertility

Ophthalmological

• [x] Glaucoma - Glaucoma.yaml
• [x] Age-related Macular Degeneration - Age_Related_Macular_Degeneration.yaml
• [ ] Other ophthalmological; e.g. diabetic retinopathy, cataracts, dry eye disease

Hematological

• [x] Sickle Cell Disease - Sickle_Cell_Disease.yaml
• [ ] Other hematological; e.g. thalassemias, hemophilia, myelodysplastic syndromes

Curation Workflow

1. Research disease pathophysiology using primary literature
2. Create YAML file in kb/disorders/
3. Validate with just validate and just validate-kb-references
4. Run just qc before committing

STATUS

Phase 1: 20/20 (100%) Complete Phase 2: 20/20 (100%) Complete Core diseases: 40/40 (100%)

Both phases complete. All 40 target chronic diseases have been curated with: - Evidence-backed pathophysiology mechanisms - HPO phenotype annotations - PMID-supported evidence items - Schema-validated YAML files

Expansion Categories

• [ ] Other endocrine/metabolic; e.g. Cushing syndrome, acromegaly, hyperparathyroidism
• [ ] Other musculoskeletal; e.g. Paget disease, osteogenesis imperfecta
• [ ] Other gastrointestinal; e.g. Barrett esophagus, diverticular disease
• [ ] Other psychiatric; e.g. schizophrenia, OCD, PTSD, eating disorders
• [ ] Other neurological; e.g. ALS, Huntington disease, essential tremor
• [ ] Other cardiovascular; e.g. cardiomyopathies, valvular heart disease
• [ ] Other respiratory; e.g. pulmonary fibrosis, bronchiectasis, pulmonary hypertension
• [ ] Other reproductive/urological; e.g. chronic pelvic pain, interstitial cystitis
• [ ] Other ophthalmological; e.g. diabetic retinopathy, cataracts, dry eye disease
• [ ] Other hematological; e.g. thalassemias, hemophilia, myelodysplastic syndromes

NOTES

2025-12-17

Initial status review completed. Cross-referenced target diseases against existing KB files: - 7 of 20 target diseases already have entries - Identified priority queue starting with Type 2 Diabetes (highest prevalence chronic disease) - Note: Alzheimer file has typo in name (Alhzeimer_Disease.yaml)

2025-12-17 (later)

Bulk curation completed for 13 remaining diseases:

Workflow used: 1. Created initial YAML files with complete structure 2. Ran deep research (falcon) for all 13 diseases 3. Enhanced with PMID-backed evidence items 4. Validated all files against schema

All files pass just validate checks.

2025-12-18

Phase 2 bulk curation completed for 20 additional chronic diseases:

Workflow: 1. Created 20 initial YAML files with MONDO IDs and basic structure 2. Ran deep research (falcon) for all 20 diseases 3. Enhanced with PMID-backed evidence items using parallel agents 4. Validated all files against schema

All 20 files pass just validate checks with schema, term, and reference validation.