Update app.py

app.py

@@ -24,7 +24,7 @@ db_path = os.path.join(os.getcwd(), db_filename)
 if not os.path.exists(db_path):
     db_path = hf_hub_download(repo_id=db_repo, filename=db_filename, repo_type="dataset", use_auth_token=HF_TOKEN)
 
-def find_best_hpo_match(finding, region):
+def find_best_hpo_match(finding, region, threshold):
     """Finds the best HPO match using semantic similarity."""
     query_text = f"{finding} in {region}"
     query_embedding = embedder.encode(query_text)
@@ -44,7 +44,7 @@ def find_best_hpo_match(finding, region):
             best_match = {"hpo_id": hpo_id, "hpo_term": hpo_name}
     
     conn.close()
-    return best_match if best_score > 0.74 else None  # Adjust threshold as needed
+    return best_match if best_score > threshold else None  # Adjust threshold based on user input
 
 
 def get_genes_for_hpo(hpo_id):
@@ -57,9 +57,9 @@ def get_genes_for_hpo(hpo_id):
     return result[0].split(", ") if result else []
 
 
-def get_hpo_for_finding(finding, region):
+def get_hpo_for_finding(finding, region, threshold):
     """Finds the best HPO term and retrieves associated genes."""
-    hpo_match = find_best_hpo_match(finding, region)
+    hpo_match = find_best_hpo_match(finding, region, threshold)
     if hpo_match:
         hpo_match["genes"] = get_genes_for_hpo(hpo_match["hpo_id"])
     else:
@@ -67,28 +67,36 @@ def get_hpo_for_finding(finding, region):
     return hpo_match
 
 
-def hpo_mapper_ui(finding, region):
+def hpo_mapper_ui(finding, region, threshold):
     """Function for Gradio UI to get HPO mappings."""
     if not finding or not region:
         return "Please enter both finding and region.", "", ""
     
-    result = get_hpo_for_finding(finding, region)
+    result = get_hpo_for_finding(finding, region, threshold)
     return result["hpo_id"], result["hpo_term"], ", ".join(result["genes"])
 
 # Create Gradio UI
 demo = gr.Interface(
     fn=hpo_mapper_ui,
-    inputs=[gr.Textbox(label="Finding"), gr.Textbox(label="Region")],
+    inputs=[
+        gr.Textbox(label="Finding"),
+        gr.Textbox(label="Region"),
+        gr.Slider(minimum=0.5, maximum=1.0, step=0.01, value=0.74, label="Threshold")
+    ],
     outputs=[
         gr.Textbox(label="HPO ID"),
         gr.Textbox(label="HPO Term"),
         gr.Textbox(label="Associated Genes")
     ],
     title="HPO Mapper",
-    description="Enter a clinical finding and anatomical region to get the best-matching HPO term and associated genes. Reference:  Application of Generative Artificial Intelligence to Utilise Unstructured Clinical Data for Acceleration of Inflammatory Bowel Disease Research
-Alex Z Kadhim, Zachary Green, Iman Nazari, Jonathan Baker, Michael George, Ashley Heinson, Matt Stammers, Christopher Kipps, R Mark Beattie, James J Ashton, Sarah Ennis
-medRxiv 2025.03.07.25323569; doi: https://doi.org/10.1101/2025.03.07.25323569 "
+    description=(
+        "Enter a clinical finding and anatomical region to get the best-matching HPO term and associated genes.\n\n"
+        "### Reference:\n"
+        "**Application of Generative Artificial Intelligence to Utilise Unstructured Clinical Data for Acceleration of Inflammatory Bowel Disease Research**\n"
+        "Alex Z Kadhim, Zachary Green, Iman Nazari, Jonathan Baker, Michael George, Ashley Heinson, Matt Stammers, Christopher Kipps, R Mark Beattie, James J Ashton, Sarah Ennis\n"
+        "medRxiv 2025.03.07.25323569; [DOI: 10.1101/2025.03.07.25323569](https://doi.org/10.1101/2025.03.07.25323569)"
+    )
 )
 
 if __name__ == "__main__":
-    demo.launch()
+    demo.launch()