Merge pull request #174 from monarch-initiative/generate-pages-20260122-223401

📄 Regenerate pages and dashboard (2026-01-22)

Author: dragon-ai-agent

app/data.js

@@ -11563,6 +11563,75 @@ window.searchData = [
     "num_genes": 1,
     "num_treatments": 4
   },
+  {
+    "name": "Pouchitis",
+    "disease_id": "MONDO:0005312",
+    "category": "Complex",
+    "parents": [
+      "Inflammatory Bowel Disease",
+      "Postoperative Complications"
+    ],
+    "subtypes": [],
+    "description": "Altered gut microbiome composition in the ileal pouch, with decreased microbial diversity and shifts toward pathogenic bacterial species. The pouch environment lacks normal colonic bacteria and experiences reduced butyrate-producing bacteria, leading to an imbalanced microbial ecosystem that triggers inflammation.\n",
+    "pathophysiology": [
+      "Bacterial Dysbiosis",
+      "Mucosal Immune Dysregulation",
+      "Epithelial Barrier Dysfunction",
+      "NOD2 Genetic Susceptibility"
+    ],
+    "cell_types": [
+      "neutrophil",
+      "dendritic cell",
+      "T cell",
+      "intestinal epithelial cell"
+    ],
+    "cell_type_ids": [
+      "CL:0000775",
+      "CL:0000451",
+      "CL:0000084",
+      "CL:0002563"
+    ],
+    "biological_processes": [
+      "inflammatory response",
+      "cytokine production",
+      "bicellular tight junction assembly"
+    ],
+    "phenotypes": [
+      "Increased Stool Frequency",
+      "Abdominal Pain",
+      "Rectal Bleeding",
+      "Urgency",
+      "Fever"
+    ],
+    "phenotype_categories": [],
+    "phenotype_ids": [
+      "HP:0002014",
+      "HP:0002027",
+      "HP:0002573",
+      "HP:0012701",
+      "HP:0001945"
+    ],
+    "frequencies": [],
+    "genes": [],
+    "treatments": [
+      "Antibiotic Therapy",
+      "Probiotic Therapy",
+      "Anti-inflammatory Medications",
+      "Immunosuppressive Therapy"
+    ],
+    "environmental": [
+      "Prior Ulcerative Colitis",
+      "Surgical Factors",
+      "NSAID Use"
+    ],
+    "biochemical": [],
+    "source_file": "Pouchitis.yaml",
+    "page_url": "../pages/disorders/Pouchitis.html",
+    "num_phenotypes": 5,
+    "num_pathophysiology": 4,
+    "num_genes": 0,
+    "num_treatments": 4
+  },
   {
     "name": "Primary Biliary Cholangitis",
     "disease_id": "MONDO:0005388",

dashboard/index.html

@@ -110,21 +110,21 @@
     <div class="container">
         <header>
             <h1>QC Dashboard - Multi-File Comparison</h1>
-            <p class="subtitle">166 files analyzed (sorted by compliance, lowest first)</p>
+            <p class="subtitle">167 files analyzed (sorted by compliance, lowest first)</p>
         </header>
 
         <section class="summary-cards">
             <div class="card">
                 <h3>Files Analyzed</h3>
-                <div class="value">166</div>
+                <div class="value">167</div>
             </div>
             <div class="card">
                 <h3>Average Compliance</h3>
                 <div class="value bad">74.4%</div>
             </div>
             <div class="card">
                 <h3>Total Checks</h3>
-                <div class="value">6988/9389</div>
+                <div class="value">7013/9425</div>
             </div>
             <div class="card">
                 <h3>Total Violations</h3>
@@ -569,6 +569,12 @@ <h2>All Files (Sorted by Priority)</h2>
                 <td>74.2%</td>
                 <td>54/81</td>
                 <td>1</td>
+            </tr><tr class="">
+                <td><code>Pouchitis.yaml</code></td>
+                <td class="bad">69.4%</td>
+                <td>79.5%</td>
+                <td>25/36</td>
+                <td></td>
             </tr><tr class="">
                 <td><code>Beta_Mannosidosis.yaml</code></td>
                 <td class="bad">69.6%</td>
@@ -1193,7 +1199,7 @@ <h2>All Files (Sorted by Priority)</h2>
         </section>
 
         <footer>
-            <p>Generated by <a href="https://github.com/linkml/linkml-data-qc">linkml-data-qc</a> on 2026-01-22 17:01</p>
+            <p>Generated by <a href="https://github.com/linkml/linkml-data-qc">linkml-data-qc</a> on 2026-01-22 22:34</p>
         </footer>
     </div>
 </body>

dashboard/reports.json

@@ -503,6 +503,14 @@
     "total_populated": 54,
     "violations": 1
   },
+  {
+    "file": "Pouchitis.yaml",
+    "global_compliance": 69.44444444444444,
+    "weighted_compliance": 79.45205479452055,
+    "total_checks": 36,
+    "total_populated": 25,
+    "violations": 0
+  },
   {
     "file": "Beta_Mannosidosis.yaml",
     "global_compliance": 69.56521739130434,

pages/disorders/ATTR_Amyloidosis.html

@@ -1171,16 +1171,16 @@ <h2 class="card-title">Causal Graph</h2>
 
             <div class="mermaid-container">
                 <pre class="mermaid">graph TD
-    Cardiomyopathy[&#34;Cardiomyopathy&#34;]
-    Heart_Failure[&#34;Heart Failure&#34;]
     Cardiac_and_Neurological_Dysfunction[&#34;Cardiac and Neurological Dysfunction&#34;]
     Autonomic_Dysfunction[&#34;Autonomic Dysfunction&#34;]
     Amyloid_Fibril_Formation[&#34;Amyloid Fibril Formation&#34;]
-    Orthostatic_Hypotension[&#34;Orthostatic Hypotension&#34;]
-    Arrhythmias[&#34;Arrhythmias&#34;]
-    Peripheral_Neuropathy[&#34;Peripheral Neuropathy&#34;]
-    Sensory_Loss[&#34;Sensory Loss&#34;]
     Numbness_and_Tingling[&#34;Numbness and Tingling&#34;]
+    Heart_Failure[&#34;Heart Failure&#34;]
+    Sensory_Loss[&#34;Sensory Loss&#34;]
+    Peripheral_Neuropathy[&#34;Peripheral Neuropathy&#34;]
+    Arrhythmias[&#34;Arrhythmias&#34;]
+    Cardiomyopathy[&#34;Cardiomyopathy&#34;]
+    Orthostatic_Hypotension[&#34;Orthostatic Hypotension&#34;]
 
     Amyloid_Fibril_Formation -.-&gt; Cardiac_and_Neurological_Dysfunction
     Peripheral_Neuropathy --&gt; Sensory_Loss
@@ -1190,16 +1190,16 @@ <h2 class="card-title">Causal Graph</h2>
     Cardiomyopathy --&gt; Arrhythmias
     Cardiomyopathy --&gt; Orthostatic_Hypotension
 
-    style Cardiomyopathy fill:#fef3c7
-    style Heart_Failure fill:#fef3c7
     style Cardiac_and_Neurological_Dysfunction fill:#fee2e2,stroke:#dc2626,stroke-dasharray: 5 5
     style Autonomic_Dysfunction fill:#fef3c7
     style Amyloid_Fibril_Formation fill:#dbeafe
-    style Orthostatic_Hypotension fill:#fef3c7
-    style Arrhythmias fill:#fef3c7
-    style Peripheral_Neuropathy fill:#fef3c7
+    style Numbness_and_Tingling fill:#fef3c7
+    style Heart_Failure fill:#fef3c7
     style Sensory_Loss fill:#fef3c7
-    style Numbness_and_Tingling fill:#fef3c7</pre>
+    style Peripheral_Neuropathy fill:#fef3c7
+    style Arrhythmias fill:#fef3c7
+    style Cardiomyopathy fill:#fef3c7
+    style Orthostatic_Hypotension fill:#fef3c7</pre>
             </div>
         </div>
 

pages/disorders/Addison's_Disease.html

@@ -1023,14 +1023,14 @@ <h2 class="card-title">Causal Graph</h2>
 
             <div class="mermaid-container">
                 <pre class="mermaid">graph TD
-    Hyponatremia[&#34;Hyponatremia&#34;]
-    Polygenic_Susceptibility[&#34;Polygenic Susceptibility&#34;]
+    Reduced_Aldosterone_Production[&#34;Reduced Aldosterone Production&#34;]
+    Autoimmune_Adrenalitis[&#34;Autoimmune Adrenalitis&#34;]
     Weight_Loss[&#34;Weight Loss&#34;]
     Reduced_Cortisol_Production[&#34;Reduced Cortisol Production&#34;]
-    Autoimmune_Adrenalitis[&#34;Autoimmune Adrenalitis&#34;]
-    Hyperkalemia[&#34;Hyperkalemia&#34;]
-    Reduced_Aldosterone_Production[&#34;Reduced Aldosterone Production&#34;]
+    Hyponatremia[&#34;Hyponatremia&#34;]
+    Polygenic_Susceptibility[&#34;Polygenic Susceptibility&#34;]
     Hypoglycemia[&#34;Hypoglycemia&#34;]
+    Hyperkalemia[&#34;Hyperkalemia&#34;]
 
     Autoimmune_Adrenalitis --&gt; Reduced_Cortisol_Production
     Autoimmune_Adrenalitis --&gt; Reduced_Aldosterone_Production
@@ -1040,14 +1040,14 @@ <h2 class="card-title">Causal Graph</h2>
     Reduced_Aldosterone_Production --&gt; Hyperkalemia
     Polygenic_Susceptibility --&gt; Autoimmune_Adrenalitis
 
-    style Hyponatremia fill:#fef3c7
-    style Polygenic_Susceptibility fill:#dbeafe
+    style Reduced_Aldosterone_Production fill:#dbeafe
+    style Autoimmune_Adrenalitis fill:#dbeafe
     style Weight_Loss fill:#fef3c7
     style Reduced_Cortisol_Production fill:#dbeafe
-    style Autoimmune_Adrenalitis fill:#dbeafe
-    style Hyperkalemia fill:#fef3c7
-    style Reduced_Aldosterone_Production fill:#dbeafe
-    style Hypoglycemia fill:#fef3c7</pre>
+    style Hyponatremia fill:#fef3c7
+    style Polygenic_Susceptibility fill:#dbeafe
+    style Hypoglycemia fill:#fef3c7
+    style Hyperkalemia fill:#fef3c7</pre>
             </div>
         </div>
 

pages/disorders/Alzheimer's_Disease.html

@@ -886,14 +886,14 @@ <h2 class="card-title">Causal Graph</h2>
             <div class="mermaid-container">
                 <pre class="mermaid">graph TD
     Cognitive_Decline[&#34;Cognitive Decline&#34;]
+    Neuronal_Death[&#34;Neuronal Death&#34;]
+    Amyloid_Beta_Plaque_Formation[&#34;Amyloid-Beta Plaque Formation&#34;]
     Neuroinflammation[&#34;Neuroinflammation&#34;]
-    Memory_Impairment[&#34;Memory Impairment&#34;]
     Brain_Atrophy[&#34;Brain Atrophy&#34;]
-    Amyloid_Beta_Plaque_Formation[&#34;Amyloid-Beta Plaque Formation&#34;]
-    Synaptic_Dysfunction[&#34;Synaptic Dysfunction&#34;]
-    Dementia[&#34;Dementia&#34;]
+    Memory_Impairment[&#34;Memory Impairment&#34;]
     Neurofibrillary_Tangle_Formation[&#34;Neurofibrillary Tangle Formation&#34;]
-    Neuronal_Death[&#34;Neuronal Death&#34;]
+    Dementia[&#34;Dementia&#34;]
+    Synaptic_Dysfunction[&#34;Synaptic Dysfunction&#34;]
 
     Amyloid_Beta_Plaque_Formation --&gt; Synaptic_Dysfunction
     Amyloid_Beta_Plaque_Formation --&gt; Neuroinflammation
@@ -906,14 +906,14 @@ <h2 class="card-title">Causal Graph</h2>
     Neuronal_Death --&gt; Dementia
 
     style Cognitive_Decline fill:#fee2e2,stroke:#dc2626,stroke-dasharray: 5 5
+    style Neuronal_Death fill:#dbeafe
+    style Amyloid_Beta_Plaque_Formation fill:#dbeafe
     style Neuroinflammation fill:#dbeafe
-    style Memory_Impairment fill:#fef3c7
     style Brain_Atrophy fill:#fee2e2,stroke:#dc2626,stroke-dasharray: 5 5
-    style Amyloid_Beta_Plaque_Formation fill:#dbeafe
-    style Synaptic_Dysfunction fill:#dbeafe
-    style Dementia fill:#fef3c7
+    style Memory_Impairment fill:#fef3c7
     style Neurofibrillary_Tangle_Formation fill:#dbeafe
-    style Neuronal_Death fill:#dbeafe</pre>
+    style Dementia fill:#fef3c7
+    style Synaptic_Dysfunction fill:#dbeafe</pre>
             </div>
         </div>
 

pages/disorders/Antiphospholipid_Syndrome.html

@@ -1378,15 +1378,15 @@ <h2 class="card-title">Causal Graph</h2>
             <div class="mermaid-container">
                 <pre class="mermaid">graph TD
     Stroke[&#34;Stroke&#34;]
-    Deep_Vein_Thrombosis[&#34;Deep Vein Thrombosis&#34;]
     Pulmonary_Embolism[&#34;Pulmonary Embolism&#34;]
+    Deep_Vein_Thrombosis[&#34;Deep Vein Thrombosis&#34;]
 
     Deep_Vein_Thrombosis --&gt; Pulmonary_Embolism
     Deep_Vein_Thrombosis --&gt; Stroke
 
     style Stroke fill:#fef3c7
-    style Deep_Vein_Thrombosis fill:#fef3c7
-    style Pulmonary_Embolism fill:#fef3c7</pre>
+    style Pulmonary_Embolism fill:#fef3c7
+    style Deep_Vein_Thrombosis fill:#fef3c7</pre>
             </div>
         </div>
 

pages/disorders/Asthma.html

@@ -1515,21 +1515,21 @@ <h2 class="card-title">Causal Graph</h2>
 
             <div class="mermaid-container">
                 <pre class="mermaid">graph TD
-    Bronchoconstriction[&#34;Bronchoconstriction&#34;]
-    Airway_Inflammation[&#34;Airway Inflammation&#34;]
     Respiratory_Distress[&#34;Respiratory Distress&#34;]
-    Wheezing[&#34;Wheezing&#34;]
+    Airway_Inflammation[&#34;Airway Inflammation&#34;]
     Reduced_Exercise_Tolerance[&#34;Reduced Exercise Tolerance&#34;]
+    Wheezing[&#34;Wheezing&#34;]
+    Bronchoconstriction[&#34;Bronchoconstriction&#34;]
 
     Airway_Inflammation --&gt; Bronchoconstriction
     Wheezing --&gt; Respiratory_Distress
     Wheezing --&gt; Reduced_Exercise_Tolerance
 
-    style Bronchoconstriction fill:#dbeafe
-    style Airway_Inflammation fill:#dbeafe
     style Respiratory_Distress fill:#fef3c7
+    style Airway_Inflammation fill:#dbeafe
+    style Reduced_Exercise_Tolerance fill:#fef3c7
     style Wheezing fill:#fef3c7
-    style Reduced_Exercise_Tolerance fill:#fef3c7</pre>
+    style Bronchoconstriction fill:#dbeafe</pre>
             </div>
         </div>
 

pages/disorders/Bacterial_meningitis.html

@@ -1282,18 +1282,18 @@ <h2 class="card-title">Causal Graph</h2>
             <div class="mermaid-container">
                 <pre class="mermaid">graph TD
     Focal_Neurological_Deficits[&#34;Focal Neurological Deficits&#34;]
-    Seizures[&#34;Seizures&#34;]
-    Altered_Mental_Status[&#34;Altered Mental Status&#34;]
     Increased_Intracranial_Pressure[&#34;Increased Intracranial Pressure&#34;]
+    Altered_Mental_Status[&#34;Altered Mental Status&#34;]
+    Seizures[&#34;Seizures&#34;]
 
     Increased_Intracranial_Pressure --&gt; Altered_Mental_Status
     Increased_Intracranial_Pressure --&gt; Seizures
     Increased_Intracranial_Pressure --&gt; Focal_Neurological_Deficits
 
     style Focal_Neurological_Deficits fill:#fef3c7
-    style Seizures fill:#fef3c7
+    style Increased_Intracranial_Pressure fill:#dbeafe
     style Altered_Mental_Status fill:#fef3c7
-    style Increased_Intracranial_Pressure fill:#dbeafe</pre>
+    style Seizures fill:#fef3c7</pre>
             </div>
         </div>
 

pages/disorders/Bronchiectasis.html

@@ -925,16 +925,16 @@ <h2 class="card-title">Causal Graph</h2>
 
             <div class="mermaid-container">
                 <pre class="mermaid">graph TD
+    Airway_Dilation[&#34;Airway Dilation&#34;]
     Chronic_Infection_and_Inflammation[&#34;Chronic Infection and Inflammation&#34;]
     Impaired_Mucociliary_Clearance[&#34;Impaired Mucociliary Clearance&#34;]
-    Airway_Dilation[&#34;Airway Dilation&#34;]
 
     Chronic_Infection_and_Inflammation --&gt; Airway_Dilation
     Airway_Dilation --&gt; Impaired_Mucociliary_Clearance
 
+    style Airway_Dilation fill:#dbeafe
     style Chronic_Infection_and_Inflammation fill:#dbeafe
-    style Impaired_Mucociliary_Clearance fill:#dbeafe
-    style Airway_Dilation fill:#dbeafe</pre>
+    style Impaired_Mucociliary_Clearance fill:#dbeafe</pre>
             </div>
         </div>