Autoimmune Diseases Curation Project
Overview
Comprehensive curation of autoimmune diseases for the dismech knowledge base, covering diverse autoimmune mechanisms including organ-specific, systemic, and autoinflammatory conditions.
This is an evergreen project: beyond the initial diseases, "Other" expansion categories capture related conditions that share autoimmune mechanisms and can be unfolded as curation continues.
Existing Autoimmune Diseases in KB (14)
These are already in the knowledge base and may benefit from enhancement:
| Disease | File | Status |
|---|---|---|
| Hashimoto's Thyroiditis | Hashimotos_Thyroiditis.yaml | ✓ Curated |
| Graves' Disease | Graves_Disease.yaml | ✅ Enhanced (81.9%) |
| Celiac Disease | Celiac_Disease.yaml | ✓ Curated |
| Multiple Sclerosis | Multiple_Sclerosis.yaml | ✅ Enhanced (92.0%) |
| Rheumatoid Arthritis | Rheumatoid_Arthritis.yaml | ✅ Enhanced (87.6%) |
| Systemic Lupus Erythematosus | Systemic_Lupus_Erythematosus.yaml | ✅ Enhanced (79.4%) |
| Type 1 Diabetes | Type_I_Diabetes.yaml | ✅ Enhanced (60.2%) |
| Psoriasis | Psoriasis.yaml | ✓ Curated |
| Ulcerative Colitis | Ulcerative_Colitis.yaml | ✓ Curated |
| Crohn's Disease | Crohn_Disease.yaml | ✅ Enhanced (76.2%) |
| Vitiligo | Vitiligo.yaml | ✅ Enhanced (86.7%) |
| Addison's Disease | Addisons_Disease.yaml | ✅ Enhanced (77.7%) |
| Antiphospholipid Syndrome | Antiphospholipid_Syndrome.yaml | Needs review (89.8%) |
| Stiff Person Syndrome | Stiff_Person_Syndrome.yaml | ✅ Complete (100%) |
New Autoimmune Diseases to Curate (20)
Systemic Autoimmune Diseases
| Disease | File | Status | Evidence Items |
|---|---|---|---|
| Sjögren's Syndrome | Sjogrens_Syndrome.yaml | ✅ Complete | 9 |
| Scleroderma (Systemic Sclerosis) | Systemic_Sclerosis.yaml | ✅ Complete | 6 |
| Mixed Connective Tissue Disease | Mixed_Connective_Tissue_Disease.yaml | ✅ Complete | 9 |
| Dermatomyositis | Dermatomyositis.yaml | ✅ Complete | 12 |
| Polymyositis | Polymyositis.yaml | ✅ Complete | 11 |
| Other systemic autoimmune | — | [ ] | e.g. adult Still disease, relapsing polychondritis |
Neurological Autoimmune Diseases
| Disease | File | Status | Evidence Items |
|---|---|---|---|
| Myasthenia Gravis | Myasthenia_Gravis.yaml | ✅ Complete | 9 |
| Guillain-Barré Syndrome | Guillain_Barre_Syndrome.yaml | ✅ Complete | 7 |
| CIDP | Chronic_Inflammatory_Demyelinating_Polyneuropathy.yaml | ✅ Complete | 6 |
| Other neurological autoimmune | — | [ ] | e.g. autoimmune encephalitis, neuromyelitis optica, ADEM |
Musculoskeletal Autoimmune Diseases
| Disease | File | Status | Evidence Items |
|---|---|---|---|
| Ankylosing Spondylitis | Ankylosing_Spondylitis.yaml | ✅ Complete | 9 |
| Other spondyloarthropathies | — | [ ] | e.g. psoriatic arthritis, reactive arthritis, enteropathic arthritis |
Hepatobiliary Autoimmune Diseases
| Disease | File | Status | Evidence Items |
|---|---|---|---|
| Primary Biliary Cholangitis | Primary_Biliary_Cholangitis.yaml | ✅ Complete | 9 |
| Autoimmune Hepatitis | Autoimmune_Hepatitis.yaml | ✅ Complete | 6 |
| Primary Sclerosing Cholangitis | Primary_Sclerosing_Cholangitis.yaml | ✅ Complete | 7 |
| Other hepatobiliary autoimmune | — | [ ] | e.g. IgG4-related cholangitis, overlap syndromes |
Vasculitis
| Disease | File | Status | Evidence Items |
|---|---|---|---|
| Giant Cell Arteritis | Giant_Cell_Arteritis.yaml | ✅ Complete | 9 |
| Granulomatosis with Polyangiitis | Granulomatosis_with_Polyangiitis.yaml | ✅ Complete | 10 |
| Behçet's Disease | Behcets_Disease.yaml | ✅ Complete | 6 |
| Other large vessel vasculitis | — | [ ] | e.g. Takayasu arteritis |
| Other small vessel vasculitis | — | [ ] | e.g. microscopic polyangiitis, eosinophilic GPA, anti-GBM disease |
Dermatological Autoimmune Diseases
| Disease | File | Status | Evidence Items |
|---|---|---|---|
| Pemphigus Vulgaris | Pemphigus_Vulgaris.yaml | ✅ Complete | 7 |
| Alopecia Areata | Alopecia_Areata.yaml | ✅ Complete | 10 |
| Other bullous autoimmune | — | [ ] | e.g. bullous pemphigoid, dermatitis herpetiformis, epidermolysis bullosa acquisita |
Hematological Autoimmune Diseases
| Disease | File | Status | Evidence Items |
|---|---|---|---|
| Autoimmune Hemolytic Anemia | Autoimmune_Hemolytic_Anemia.yaml | ✅ Complete | 7 |
| Immune Thrombocytopenia (ITP) | Immune_Thrombocytopenia.yaml | ✅ Complete | 7 |
| Other hematological autoimmune | — | [ ] | e.g. autoimmune neutropenia, Evans syndrome, TTP |
Renal Autoimmune Diseases
| Disease | File | Status | Evidence Items |
|---|---|---|---|
| IgA Nephropathy | IgA_Nephropathy.yaml | ✅ Complete | 7 |
| Other renal autoimmune | — | [ ] | e.g. membranous nephropathy, lupus nephritis, anti-GBM nephritis |
Progress
- Existing (enhancement): 9/10 (90%) - Only Antiphospholipid Syndrome remains
- New diseases: 20/20 (100%) ✅
- Evidence enhancement: 20/20 (100%) ✅ - 153 total evidence items added
Key Autoimmune Mechanisms to Cover
- Antibody-mediated - autoantibodies targeting self-antigens (e.g., anti-AChR in MG, anti-dsDNA in SLE)
- T cell-mediated - autoreactive T cells attacking tissues (e.g., MS, T1D)
- Immune complex deposition - circulating immune complexes causing tissue damage
- Complement activation - complement-mediated tissue destruction
- Cytokine dysregulation - aberrant inflammatory cytokine production
- Molecular mimicry - cross-reactivity between pathogen and self-antigens
- Epitope spreading - expansion of autoimmune response to additional self-antigens
Common Autoantibodies to Document
- ANA (antinuclear antibodies)
- Anti-dsDNA
- Anti-Ro/SSA, Anti-La/SSB
- ANCA (anti-neutrophil cytoplasmic antibodies)
- Anti-CCP (anti-cyclic citrullinated peptide)
- Anti-TPO, Anti-thyroglobulin
- Anti-AChR (acetylcholine receptor)
- Anti-GAD65
STATUS
New Diseases (20/20 Complete)
- [x] Sjögren's Syndrome
- [x] Systemic Sclerosis
- [x] Mixed Connective Tissue Disease
- [x] Dermatomyositis
- [x] Polymyositis
- [x] Myasthenia Gravis
- [x] Guillain-Barré Syndrome
- [x] CIDP
- [x] Ankylosing Spondylitis
- [x] Primary Biliary Cholangitis
- [x] Autoimmune Hepatitis
- [x] Primary Sclerosing Cholangitis
- [x] Giant Cell Arteritis
- [x] Granulomatosis with Polyangiitis
- [x] Behçet's Disease
- [x] Pemphigus Vulgaris
- [x] Alopecia Areata
- [x] Autoimmune Hemolytic Anemia
- [x] Immune Thrombocytopenia
- [x] IgA Nephropathy
Existing Diseases Needing Enhancement (9/10)
- [x] Graves' Disease (77.7% -> 81.9% compliance)
- [x] Multiple Sclerosis (86.6% -> 92.0% compliance)
- [x] Rheumatoid Arthritis (83.0% -> 87.6% compliance)
- [x] Systemic Lupus Erythematosus (77.6% -> 79.4% compliance)
- [x] Type 1 Diabetes (53.7% -> 60.2% compliance)
- [x] Crohn's Disease (75.2% -> 76.2% compliance)
- [x] Vitiligo (80.0% -> 86.7% compliance)
- [x] Addison's Disease (73.4% -> 77.7% compliance)
- [ ] Antiphospholipid Syndrome (89.8% compliance)
- [x] Stiff Person Syndrome (100% compliance - done)
Expansion Categories
- [ ] Other systemic autoimmune; e.g. adult Still disease, relapsing polychondritis
- [ ] Other neurological autoimmune; e.g. autoimmune encephalitis, neuromyelitis optica, ADEM
- [ ] Other spondyloarthropathies; e.g. psoriatic arthritis, reactive arthritis
- [ ] Other hepatobiliary autoimmune; e.g. IgG4-related cholangitis, overlap syndromes
- [ ] Other large vessel vasculitis; e.g. Takayasu arteritis
- [ ] Other small vessel vasculitis; e.g. microscopic polyangiitis, eosinophilic GPA
- [ ] Other bullous autoimmune; e.g. bullous pemphigoid, dermatitis herpetiformis
- [ ] Other hematological autoimmune; e.g. autoimmune neutropenia, Evans syndrome, TTP
- [ ] Other renal autoimmune; e.g. membranous nephropathy, lupus nephritis
NOTES
2025-12-18 (Session 3)
Enhanced 5 existing autoimmune disease files: - Graves' Disease: 77.7% -> 81.9% - Added evidence for CTLA4 (PMID:10404810) - Added evidence for PTPN22 (PMID:33103521) - Added evidence for CD40 (PMID:12593727) - Added evidence for TSHR (PMID:27231040) - Systemic Lupus Erythematosus: 77.6% -> 79.4% - Added evidence for Anifrolumab (PMID:28130918) - Added evidence for Belimumab (PMID:22127708) - Vitiligo: 80.0% -> 86.7% - Added evidence for IFIH1 (PMID:22561518) - Added evidence for BACH2 (PMID:22561518) - Added evidence for IRF4 (PMID:27723757) - Added evidence for FOXP3 (PMID:33181260) - Rheumatoid Arthritis: 83.0% -> 87.6% - Added evidence for JAK/STAT Signaling (PMID:35367240) - Added evidence for PADI4 (PMID:17893996) - Multiple Sclerosis: 86.6% -> 92.0% - Added evidence for IL7R (PMID:17660530) - Added evidence for IL2RA (PMID:17660530)
All additions passed validation (schema, term, and reference checks).
2025-12-18 (Session 2)
Enhanced 3 existing autoimmune disease files: - Type 1 Diabetes: 53.7% -> 60.2% (66.4% weighted) - Added evidence for interferon-driven beta cell response (PMID:38409439) - Added evidence for HLA-DQ2 (PMID:22184118) - Added evidence for PTPN22 (PMID:15734872) - Added evidence for IL2RA (PMID:22461703) - Added evidence for CTLA4 (PMID:9353155) - Added evidence for Teplizumab (PMID:36877454) - Added evidence for CGM (PMID:34872983) - Addison's Disease: 73.4% -> 77.7% (81.5% weighted) - Added evidence for CYP21A2 autoantigen (PMID:34665570) - Added evidence for HLA-DR3-DQ2/DR4-DQ8 (PMID:12392510) - Added evidence for CTLA4 (PMID:26204230) - Added evidence for PTPN22 (PMID:18301444) - Crohn's Disease: 75.2% -> 76.2% (79.8% weighted) - Added evidence for autophagy/Paneth cell dysfunction (PMID:18849966)
All additions passed validation (schema, term, and reference checks).
2025-12-18 (Session 1)
- QC validation completed: All 114 disorder files pass validation
- All 20 new autoimmune diseases validated successfully with schema, term, and reference checks
- Compliance analysis performed:
- New diseases: 55-72% compliance (pathophysiology evidence strong at 92-97%, but phenotypes/treatments evidence lower)
- Term mappings: 100% for all new files
- Main gap: Evidence coverage for phenotypes (~13-30%) and treatments (~9-11%)
- Existing diseases review:
- Type I Diabetes needs most work (53.7%)
- Stiff Person Syndrome is complete (100%)
- Others range 73-90%
- Next steps for enhancement: Add evidence items to phenotypes, treatments, and biochemical sections