update

app.py

@@ -6,41 +6,77 @@ import json
 from utils import format_chat, append_to_sheet, read_sheet_to_df
 import random
 
+# Load tool lists
+fda_drug_labeling_tools_path = "fda_drug_labeling_tools.json"
+monarch_tools_path = "monarch_tools.json"
+opentarget_tools_path = "opentarget_tools.json"
+
+try:
+    with open(fda_drug_labeling_tools_path, 'r') as f:
+        fda_data = json.load(f)
+        fda_drug_labeling_tools_list = [item['name'] for item in fda_data if 'name' in item]
+except Exception as e:
+    print(f"Error processing {fda_drug_labeling_tools_path}: {e}")
+    fda_drug_labeling_tools_list = ["Error loading FDA tools"]
+
+try:
+    with open(monarch_tools_path, 'r') as f:
+        monarch_data = json.load(f)
+        monarch_tools_list = [item['name'] for item in monarch_data if 'name' in item]
+except Exception as e:
+    print(f"Error processing {monarch_tools_path}: {e}")
+    monarch_tools_list = ["Error loading Monarch tools"]
+
+try:
+    with open(opentarget_tools_path, 'r') as f:
+        opentarget_data = json.load(f)
+        opentarget_tools_list = [item['name'] for item in opentarget_data if 'name' in item]
+except Exception as e:
+    print(f"Error processing {opentarget_tools_path}: {e}")
+    opentarget_tools_list = ["Error loading OpenTarget tools"]
+
+#for labeling the different tool calls in format_chat
+tool_database_labels = {
+    "**from approved FDA drug labels**": fda_drug_labeling_tools_list,
+    "**from the Monarch Initiative databases**": monarch_tools_list,
+    "**from the Open Targets database**": opentarget_tools_list,
+}
+
 # Define the six evaluation criteria as a list of dictionaries.
 criteria = [
     {
         "label": "Problem Resolution",
         "text": (
             "Problem Resolution: Did the model effectively solve the problem?",
-            "1️⃣ Did Not Solve the Problem at All<br>2️⃣ Attempted to Solve but Largely Incorrect or Incomplete<br>3️⃣ Partially Solved the Problem, but with Limitations<br>4️⃣ Mostly Solved the Problem, with Minor Issues<br>5️⃣ Completely and Effectively Solved the Problem"
+            "1️⃣ Did Not Solve the Problem at All. 2️⃣ Attempted to Solve but Largely Incorrect or Incomplete. 3️⃣ Partially Solved the Problem, but with Limitations. 4️⃣ Mostly Solved the Problem, with Minor Issues. 5️⃣ Completely and Effectively Solved the Problem."
         )
     },
     {
         "label": "Helpfulness",
         "text": (
             "Helpfulness: Was the answer and reasoning provided helpful in addressing the question?",
-            "1️⃣ Not Helpful at All<br>2️⃣ Slightly Helpful, but Largely Insufficient<br>3️⃣ Moderately Helpful, but Needs Improvement<br>4️⃣ Helpful and Mostly Clear, with Minor Issues<br>5️⃣ Extremely Helpful and Comprehensive"
+            "1️⃣ Not Helpful at All. 2️⃣ Slightly Helpful, but Largely Insufficient. 3️⃣ Moderately Helpful, but Needs Improvement. 4️⃣ Helpful and Mostly Clear, with Minor Issues. 5️⃣ Extremely Helpful and Comprehensive."
         )
     },
     {
         "label": "Scientific Consensus",
         "text": (
-            "Scientific and Clinical Consensus: Does the answer align with established scientific and clinical consensus?",
-            "1️⃣ Completely Misaligned with Scientific Consensus<br>2️⃣ Partially Aligned but Contains Significant Inaccuracies or Misinterpretations<br>3️⃣ Generally Aligned but Lacks Strong Scientific Rigor or Clarity<br>4️⃣ Mostly Aligned with Scientific Consensus, with Minor Omissions or Uncertainties<br>5️⃣ Fully Aligned with Established Scientific and Clinical Consensus"
+            "Clinical Consensus: Does the answer align with established scientific and clinical consensus?",
+            "1️⃣ Completely Misaligned with Clinical Consensus. 2️⃣ Partially Aligned but Contains Significant Inaccuracies or Misinterpretations. 3️⃣ Generally Aligned but Lacks Rigor or Clarity. 4️⃣ Mostly Aligned with Clinical Consensus, with Minor Omissions or Uncertainties. 5️⃣ Fully Aligned with Established Clinical Consensus."
         )
     },
     {
         "label": "Accuracy",
         "text": (
             "Accuracy of Content: Is there any incorrect or irrelevant content in the answer and the reasoning content?",
-            "1️⃣ Completely Inaccurate or Irrelevant<br>2️⃣ Mostly Inaccurate, with Some Relevant Elements<br>3️⃣ Partially Accurate, but Includes Some Errors or Omissions<br>4️⃣ Mostly Accurate, with Minor Issues or Unverified Claims<br>5️⃣ Completely Accurate and Relevant"
+            "1️⃣ Completely Inaccurate or Irrelevant. 2️⃣ Mostly Inaccurate, with Some Relevant Elements. 3️⃣ Partially Accurate, but Includes Some Errors or Omissions. 4️⃣ Mostly Accurate, with Minor Issues or Unverified Claims. 5️⃣ Completely Accurate and Relevant."
         )
     },
     {
         "label": "Completeness",
         "text": (
             "Completeness: Did the answer omit any essential content necessary for a comprehensive response?",
-            "1️⃣ Severely Incomplete – Major Content Omissions<br>2️⃣ Largely Incomplete – Missing Key Elements<br>3️⃣ Somewhat Complete – Covers Basics but Lacks Depth<br>4️⃣ Mostly Complete – Minor Omissions or Gaps<br>5️⃣ Fully Complete – No Important Omissions"
+            "1️⃣ Severely Incomplete – Major Content Omissions. 2️⃣ Largely Incomplete – Missing Key Elements. 3️⃣ Somewhat Complete – Covers Basics but Lacks Depth. 4️⃣ Mostly Complete – Minor Omissions or Gaps. 5️⃣ Fully Complete – No Important Omissions."
         )
     },
 ]
@@ -133,7 +169,7 @@ def get_evaluator_questions(email, disease_map_data, user_all_specs, all_files,
 
     # Handle case where no relevant questions are found based on specialty
     if not evaluator_question_ids:
-        return gr.update(visible=True), gr.update(visible=False), None, "No questions found matching your selected specialties. Please adjust your selections or contact the study administrator.", gr.Chatbot(), gr.Chatbot(), gr.HTML(),gr.State(),gr.update(visible=False),""
+        return [], data_by_filename
 
     #FINALLY, MAKE SURE THEY DIDNT ALREADY FILL IT OUT. Must go through every tuple of (question_ID, TxAgent, other model) where other model could be any of the other files in data_by_filename
     model_names = [key for key in data_by_filename.keys() if key != 'txagent']
@@ -148,8 +184,6 @@ def get_evaluator_questions(email, disease_map_data, user_all_specs, all_files,
         # collect all (question_ID, other_model) pairs already seen
         matched_pairs = set()
         for _, row in results_df.iterrows():
-            # Only consider rows submitted by the current evaluator
-            print(f"Evaluator ID: {row['Email']}")
             if row["Email"] == email:
                 q = row["Question ID"]
                 # pick whichever response isn’t 'txagent'
@@ -174,11 +208,11 @@ def get_evaluator_questions(email, disease_map_data, user_all_specs, all_files,
 def go_to_page0_from_minus1():
     return gr.update(visible=False), gr.update(visible=True)
 
-def go_to_eval_progress_modal(name, email, specialty_dd, subspecialty_dd, years_exp_radio, exp_explanation_tb):
+def go_to_eval_progress_modal(name, email, specialty_dd, subspecialty_dd, years_exp_radio, exp_explanation_tb, npi_id):
 
     # ADDED: Validate that name and email are non-empty before proceeding
-    if not name or not email:
-        return gr.update(visible=True), gr.update(visible=False), None, "Please fill out all the fields.", gr.Chatbot(), gr.Chatbot(), gr.HTML(),gr.State(),gr.update(visible=False), ""
+    if not name or not email or not specialty_dd or not years_exp_radio:
+        return gr.update(visible=True), gr.update(visible=False), None, "Please fill out all the required fields (name, email, specialty, years of experience). If you are not a licensed physician with a specific specialty, please choose the specialty that most closely aligns with your biomedical expertise.", gr.Chatbot(), gr.Chatbot(), gr.HTML(),gr.State(),gr.update(visible=False), ""
 
     # Combine user's selected specialties and subspecialties into a set for efficient lookup
     # Ensure inputs are lists, even if None or single strings are passed (though Dropdown with multiselect=True should return lists)
@@ -209,7 +243,7 @@ def go_to_eval_progress_modal(name, email, specialty_dd, subspecialty_dd, years_
     full_question_ids_list, data_by_filename = get_evaluator_questions(email, disease_map_data, user_all_specs, all_files, evaluator_directory)
 
     if len(full_question_ids_list) == 0:
-        return gr.update(visible=True), gr.update(visible=False), None, "Based on your Evaluator ID, you have evaluated all questions assigned to you. You may exit the page; we will follow-up if we require anything else from you. Thank you!", gr.Chatbot(), gr.Chatbot(), gr.HTML(),gr.State(),gr.update(visible=False),""
+        return gr.update(visible=True), gr.update(visible=False), None, "Based on your submitted data, you have no more questions to evaluate. You may exit the page; we will follow-up if we require anything else from you. Thank you!", gr.Chatbot(), gr.Chatbot(), gr.HTML(),gr.State(),gr.update(visible=False),""
 
     full_question_ids_list = sorted(full_question_ids_list, key=lambda x: str(x[0])+str(x[1]))
     #selected question is the first element
@@ -244,9 +278,9 @@ def go_to_eval_progress_modal(name, email, specialty_dd, subspecialty_dd, years_
     }
 
     #update user_info
-    user_info = (name, email, specialty_dd, subspecialty_dd, years_exp_radio, exp_explanation_tb, q_id)
-    chat_A_value = format_chat(question_for_eval['models'][0]['reasoning_trace'])
-    chat_B_value = format_chat(question_for_eval['models'][1]['reasoning_trace'])
+    user_info = (name, email, specialty_dd, subspecialty_dd, years_exp_radio, exp_explanation_tb, npi_id, q_id)
+    chat_A_value = format_chat(question_for_eval['models'][0]['reasoning_trace'], tool_database_labels)
+    chat_B_value = format_chat(question_for_eval['models'][1]['reasoning_trace'], tool_database_labels)
     prompt_text = question_for_eval['question']
 
     # Construct the question-specific elements of the pairwise rating page (page 1)
@@ -273,7 +307,7 @@ def go_to_eval_progress_modal(name, email, specialty_dd, subspecialty_dd, years_
                     avatar_images=None,    # Optional: omit user/assistant icons
                     rtl=False
                 )
-    return gr.update(visible=True), gr.update(visible=False), user_info,"", chat_a, chat_b, page1_prompt, question_for_eval, gr.update(visible=True), f"You have {len(full_question_ids_list)} question(s) remaining to evaluate."
+    return gr.update(visible=True), gr.update(visible=False), user_info,"", chat_a, chat_b, page1_prompt, question_for_eval, gr.update(visible=True), f"You are about to evaluate the next question."#f"You have {len(full_question_ids_list)} question(s) remaining to evaluate."
 
 #goes to page 1 from confirmation modal that tells users how many questions they have left to evaluate
 def go_to_page1():
@@ -303,8 +337,8 @@ def go_to_page2(data_subset_state,*pairwise_values):
     if any(answer is None for answer in pairwise_list):
         return gr.update(visible=True), gr.update(visible=False), None, None, "Error: Please select an option for every pairwise comparison.", gr.Chatbot(), gr.Chatbot(), gr.HTML(), *pairwise_results_for_display
 
-    chat_A_value = format_chat(data_subset_state['models'][0]['reasoning_trace'])
-    chat_B_value = format_chat(data_subset_state['models'][1]['reasoning_trace'])
+    chat_A_value = format_chat(data_subset_state['models'][0]['reasoning_trace'], tool_database_labels)
+    chat_B_value = format_chat(data_subset_state['models'][1]['reasoning_trace'], tool_database_labels)
     prompt_text = data_subset_state['question']
 
     # Construct the question-specific elements of the rating page (page 2)
@@ -382,7 +416,7 @@ centered_col_css = """
 #centered-column {
     margin-left: auto;
     margin-right: auto;
-    max-width: 650px; /* Adjust this width as desired */
+    max-width: 800px; /* Adjust this width as desired */
     width: 100%;
 }
 """
@@ -413,13 +447,20 @@ with gr.Blocks(css=centered_col_css) as demo:
         print(f"Error: Could not parse JSON from specialty files.")
         specialties_list = ["Error parsing specialties"]
         subspecialties_list = ["Error parsing subspecialties"]
-
+    
     # Page -1: Page to link them to question submission form or evaluation portal
     with gr.Column(visible=True, elem_id="page-1") as page_minus1:
         gr.HTML("""
         <div>
             <h1>TxAgent Evaluation Portal</h1>
             <p>Welcome to the TxAgent Evaluation Portal.</p>
+        </div>
+        """)
+        with gr.Row():
+            submit_questions_btn = gr.Button("Submit Questions for TxAgent Evaluation")
+            participate_eval_btn = gr.Button("Participate in TxAgent Evaluation")
+        gr.HTML("""
+        <div>
             <p><strong>About TxAgent:</strong> TxAgent is a first-of-its-kind AI model developed in the Zitnik Lab at Harvard Medical School. It leverages multi-step reasoning and real-time biomedical knowledge retrieval from a toolbox of 211 tools to analyze drug interactions, contraindications, and patient-specific treatment strategies. It is designed to provide personalized treatment recommendations across a wide range of diseases, including rare diseases.</p>
             <p>TxAgent evaluates how drugs interact at molecular, pharmacokinetic, and clinical levels, identifies contraindications based on patient comorbidities and concurrent medications, and tailors treatment strategies to individual patient characteristics, including age, genetic factors, and disease progression. It achieves 92.1% accuracy in open-ended drug reasoning tasks, surpassing GPT-4o by up to 25.8% and outperforming DeepSeek-R1 (671B) in structured multi-step reasoning.</p>
             <p>TxAgent's toolbox, ToolUniverse, consolidates 211 tools from trusted sources, including all US FDA-approved drugs since 1939 and validated clinical insights from Open Targets. By integrating multi-step inference, real-time knowledge grounding, and tool-assisted decision-making, TxAgent ensures that treatment recommendations align with established clinical guidelines and real-world evidence, reducing the risk of adverse events and improving therapeutic decision-making.</p>
@@ -432,9 +473,6 @@ with gr.Blocks(css=centered_col_css) as demo:
             <p>Your contribution is invaluable to us. Thank you for your time and expertise!</p>
         </div>
         """)
-        with gr.Row():
-            submit_questions_btn = gr.Button("Submit Questions for TxAgent Evaluation")
-            participate_eval_btn = gr.Button("Participate in TxAgent Evaluation")
 
         # Define actions for the new buttons
         # For the Google Form button, we'll use JavaScript to open a new tab.
@@ -464,13 +502,14 @@ with gr.Blocks(css=centered_col_css) as demo:
         By clicking 'Next' below, you will start the study, with your progress saved after submitting each question. If you have any other questions or concerns, please contact us directly. Thank you for your participation!
         """)
         gr.Markdown("## Please enter your information to get a question to evaluate. Please use the same email every time you log onto this evaluation portal, as we use your email to prevent showing repeat questions.")
-        name = gr.Textbox(label="Name")
-        email = gr.Textbox(label="Email. Please use the same email every time you log onto this evaluation portal, as we use your email to prevent showing repeat questions.")
-        specialty_dd = gr.Dropdown(choices=specialties_list, label="Primary Medical Specialty (if applicable, select one). Go to https://www.abms.org/member-boards/specialty-subspecialty-certificates/ for categorization)", multiselect=True)
-        subspecialty_dd = gr.Dropdown(choices=subspecialties_list, label="Subspecialty (if applicable, select one). Go to https://www.abms.org/member-boards/specialty-subspecialty-certificates/ for categorization)", multiselect=True)
+        name = gr.Textbox(label="Name (required)")
+        email = gr.Textbox(label="Email (required). Please use the same email every time you log onto this evaluation portal, as we use your email to prevent showing repeat questions.")
+        specialty_dd = gr.Dropdown(choices=specialties_list, label="Primary Medical Specialty (required). Go to https://www.abms.org/member-boards/specialty-subspecialty-certificates/ for categorization)", multiselect=True)
+        subspecialty_dd = gr.Dropdown(choices=subspecialties_list, label="Subspecialty (if applicable). Go to https://www.abms.org/member-boards/specialty-subspecialty-certificates/ for categorization)", multiselect=True)
+        npi_id = gr.Textbox(label="National Provider Identifier ID (optional). Got to https://npiregistry.cms.hhs.gov/search to search for your NPI ID. If you do not have an NPI ID, please leave this blank.")
         years_exp_radio = gr.Radio(
             choices=["0-2 years", "3-5 years", "6-10 years", "11-20 years", "20+ years", "Not Applicable"],
-            label="How many years have you been involved in clinical and/or research activities related to your biomedical area of expertise?"
+            label="How many years have you been involved in clinical and/or research activities related to your biomedical area of expertise? (required)"
         )
         exp_explanation_tb = gr.Textbox(label="Please briefly explain your expertise/experience relevant to evaluating AI for clinical decision support (optional)")
 
@@ -545,8 +584,7 @@ with gr.Blocks(css=centered_col_css) as demo:
             next_btn_1 = gr.Button("Next: Rate Responses")
         
         with gr.Row():
-            home_btn_1 = gr.Button("Home Page (your progress on this question will be saved but not submitted)")  # ADDED: Home button on page1
-            instructions_btn_1 = gr.Button("Instructions Page (your progress on this question will be saved but not submitted)")  # ADDED: FAQ button on page1
+            home_btn_1 = gr.Button("Home Page (your progress on this question will be saved but not submitted)")  # ADDED: Home button on page11
     
     # Page 2: Combined Rating Page for both responses.
     with gr.Column(visible=False) as page2:
@@ -683,7 +721,7 @@ with gr.Blocks(css=centered_col_css) as demo:
                                             label=f"Score for Response B - {crit['label']}",
                                             interactive=True)
             with gr.Row():
-                clear_btn = gr.Button("Clear Selection")
+                clear_btn = gr.Button("Clear Selection", size="sm")
                 clear_btn.click(fn=clear_selection, outputs=[rating_a,rating_b])
 
                 # wire each to re‐restrict the other on change
@@ -701,12 +739,10 @@ with gr.Blocks(css=centered_col_css) as demo:
                 ratings_B.append(rating_b)
         with gr.Row():
             back_btn_2 = gr.Button("Back")
-            instructions_btn_2 = gr.Button("Instructions Page (your progress on this question will be saved but not submitted)")  # ADDED: FAQ button on page1
             submit_btn = gr.Button("Submit (Note: Once submitted, you cannot edit your responses)", elem_id="submit_btn")
 
         with gr.Row():
             home_btn_2 = gr.Button("Home Page (your progress on this question will be saved but not submitted)")
-            instructions_btn_2 = gr.Button("Instructions Page (your progress on this question will be saved but not submitted)")  # ADDED: FAQ button on page1
 
         result_text = gr.Textbox(label="Validation Result")
     
@@ -748,7 +784,8 @@ with gr.Blocks(css=centered_col_css) as demo:
             "Subspecialty": str(user_info[3]),
             "Years of Experience": user_info[4],
             "Experience Explanation": user_info[5],
-            "Question ID": user_info[6],
+            "NPI ID": user_info[6],
+            "Question ID": user_info[7],
             "Prompt": prompt_text,
             "ResponseA_Model": response_A_model,
             "ResponseB_Model": response_B_model,
@@ -785,7 +822,7 @@ with gr.Blocks(css=centered_col_css) as demo:
         disease_specialty_map = hf_hub_download(repo_id=REPO_ID, filename=DISEASE_SPECIALTY_MAP_FILENAME, repo_type="dataset", revision="main")
         with open(disease_specialty_map, 'r') as f: disease_map_data = json.load(f)
 
-        _, email, specialty, subspecialty, _, _, _ = user_info
+        _, email, specialty, subspecialty, _, _, _, _ = user_info
         user_specialties = set(specialty if isinstance(specialty, list) else ([specialty] if specialty else []))
         user_subspecialties = set(subspecialty if isinstance(subspecialty, list) else ([subspecialty] if subspecialty else []))
         user_all_specs = user_specialties.union(user_subspecialties)
@@ -842,8 +879,8 @@ with gr.Blocks(css=centered_col_css) as demo:
             "models": models_list,
         }
 
-        chat_A_value = format_chat(question_for_eval['models'][0]['reasoning_trace'])
-        chat_B_value = format_chat(question_for_eval['models'][1]['reasoning_trace'])
+        chat_A_value = format_chat(question_for_eval['models'][0]['reasoning_trace'], tool_database_labels)
+        chat_B_value = format_chat(question_for_eval['models'][1]['reasoning_trace'], tool_database_labels)
         prompt_text = question_for_eval['question']
 
         # Construct the question-specific elements of the pairwise rating page (page 1)
@@ -877,7 +914,7 @@ with gr.Blocks(css=centered_col_css) as demo:
             gr.update(visible=False),  # page2 (Hide)
             gr.update(visible=False),  # confirm_modal (Hide)
             gr.update(visible=True),   # eval_progress_modal (Show)
-            f"Submission successful! You have {remaining_count} question(s) remaining to evaluate. You may exit the page and return later if you wish.", # eval_progress_text
+            f"Submission successful! There are more questions to evaluate. You may exit the page and return later if you wish.",#f"Submission successful! You have {remaining_count} question(s) remaining to evaluate. You may exit the page and return later if you wish.", # eval_progress_text
             gr.update(visible=False),  # final_page (Hide)
             "",         
             chat_a,
@@ -962,7 +999,7 @@ with gr.Blocks(css=centered_col_css) as demo:
     # Transition from Page 0 (Welcome) to Page 1.
     next_btn_0.click(
         fn=go_to_eval_progress_modal,
-        inputs=[name, email, specialty_dd, subspecialty_dd, years_exp_radio, exp_explanation_tb],
+        inputs=[name, email, specialty_dd, subspecialty_dd, years_exp_radio, exp_explanation_tb, npi_id],
         outputs=[page0, page1, user_info_state, page0_error_box, chat_a, chat_b, page1_prompt, data_subset_state,eval_progress_modal,eval_progress_text],
         scroll_to_output=True
     )
@@ -978,10 +1015,6 @@ with gr.Blocks(css=centered_col_css) as demo:
     home_btn_0.click(lambda: (gr.update(visible=True), gr.update(visible=False)), None, [page_minus1, page0])
     home_btn_1.click(lambda: (gr.update(visible=True), gr.update(visible=False)), None, [page_minus1, page1])
     home_btn_2.click(lambda: (gr.update(visible=True), gr.update(visible=False)), None, [page_minus1, page2])
-
-    # FAQ buttons simply bring back to page0
-    instructions_btn_1.click(lambda: (gr.update(visible=True), gr.update(visible=False)), None, [page0, page1])
-    instructions_btn_2.click(lambda: (gr.update(visible=True), gr.update(visible=False)), None, [page0, page2])
     
     # Transition from Page 1 to Page 0 (Back button).
     back_btn_0.click(
@@ -1035,7 +1068,8 @@ with gr.Blocks(css=centered_col_css) as demo:
     ).then(
         fn=process_result,
         inputs=error_message_box,
-        outputs=[page2, final_page, confirm_modal, error_modal, error_message_box]
+        outputs=[page2, final_page, confirm_modal, error_modal, error_message_box],
+        scroll_to_output=True
     )
     
     # Finalize submission if user confirms.

monarch_tools.json

@@ -0,0 +1,112 @@
+[
+    {
+        "name": "get_joint_associated_diseases_by_HPO_ID_list",
+        "description": "Retrieve diseases associated with a list of phenotypes or symptoms by a list of HPO IDs.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "HPO_ID_list": {
+                    "type": "array",
+                    "description": "List of phenotypes or symptoms",
+                    "items": {
+                        "type": "string",
+                        "description": "The HPO ID of the phenotype or symptom.",
+                        "required": true
+                    },
+                    "required": true
+                },
+                "limit": {
+                    "type": "integer",
+                    "description": "Number of entries to fetch.",
+                    "required": false
+                },
+                "offset": {
+                    "type": "integer",
+                    "description": "Number of initial entries to skip.",
+                    "required": false
+                }
+            }
+        },
+        "query_schema": {
+            "category": ["biolink:DiseaseToPhenotypicFeatureAssociation"],
+            "object": null,
+            "compact": true,
+            "object_category": ["biolink:PhenotypicFeature"],
+            "limit": 500,
+            "offset": 0
+        },
+        "label": [
+            "Monarch",
+            "Phenotype",
+            "Symptom",
+            "Disease",
+            "HPO_ID"
+        ],
+        "type": "MonarchDiseasesForMultiplePheno",
+        "tool_url": "/association"
+    },
+    {
+        "name": "get_phenotype_by_HPO_ID",
+        "description": "Retrieve a phenotype or symptom by its HPO ID.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "id": {
+                    "type": "string",
+                    "description": "The HPO ID of the phenotype or symptom.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": {
+            "id": null,
+            "url_key": "id"
+        },
+        "label": [
+            "Monarch",
+            "Phenotype",
+            "Symptom",
+            "HPO_ID"
+        ],
+        "type": "Monarch",
+        "tool_url": "/entity/{url_key}"
+    },
+    {
+        "name": "get_HPO_ID_by_phenotype",
+        "description": "Retrieve the HPO ID of a phenotype or symptom.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "query": {
+                    "type": "string",
+                    "description": "One query phenotype or symptom.",
+                    "required": true
+                },
+                "limit": {
+                    "type": "integer",
+                    "description": "Number of entries to fetch.",
+                    "required": false
+                },
+                "offset": {
+                    "type": "integer",
+                    "description": "Number of initial entries to skip.",
+                    "required": false
+                }
+            }
+        },
+        "query_schema": {
+            "query": null,
+            "category": ["biolink:PhenotypicFeature"],
+            "limit": 20,
+            "offset": 0
+        },
+        "label": [
+            "Monarch",
+            "Phenotype",
+            "Symptom",
+            "HPO_ID"
+        ],
+        "type": "Monarch",
+        "tool_url": "/search"
+    }
+]

opentarget_tools.json

@@ -0,0 +1,2166 @@
+[
+    {
+        "name": "get_associated_targets_by_disease_efoId",
+        "description": "Find targets associated with a specific disease or phenotype based on efoId.",
+        "label": [
+            "Disease",
+            "Phenotype",
+            "Target",
+            "Association",
+            "OpenTarget",
+            "GraphQL"
+        ],
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "efoId": {
+                    "type": "string",
+                    "description": "The efoId of a disease or phenotype.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\nquery associatedTargets($efoId: String!) {\n  disease(efoId: $efoId) {\n    id\n    name\n    associatedTargets {\n      count\n      rows {\n        target {\n          id\n          approvedSymbol\n        }\n        score\n      }\n    }\n  }\n}\n",
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_associated_diseases_phenotypes_by_target_ensemblID",
+        "description": "Find diseases or phenotypes associated with a specific target using ensemblId.",
+        "label": [
+            "Target",
+            "Disease",
+            "Phenotype",
+            "Association",
+            "OpenTarget",
+            "GraphQL"
+        ],
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "ensemblId": {
+                    "type": "string",
+                    "description": "The ensemblId of a target.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\nquery associatedDiseases($ensemblId: String!) {\n  target(ensemblId: $ensemblId) {\n    id\n    approvedSymbol\n    associatedDiseases {\n      count\n      rows {\n        disease {\n          id\n          name\n        }\n        datasourceScores {\n          id\n          score\n        }\n      }\n    }\n  }\n}\n",
+        "type": "OpenTarget"
+    },
+    {
+        "name": "target_disease_evidence",
+        "description": "Explore evidence that supports a specific target-disease association. Input is disease efoId and target ensemblID.",
+        "label": [
+            "Target",
+            "Disease",
+            "Evidence",
+            "Association",
+            "OpenTarget",
+            "GraphQL"
+        ],
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "efoId": {
+                    "type": "string",
+                    "description": "The efoId of a disease or phenotype.",
+                    "required": true
+                },
+                "ensemblId": {
+                    "type": "string",
+                    "description": "The ensemblId of a target.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\nquery targetDiseaseEvidence($efoId: String!, $ensemblId: String!) {\n  disease(efoId: $efoId) {\n    id\n    name\n    evidences(datasourceIds: [\"intogen\"], ensemblIds: [$ensemblId]) {\n      count\n      rows {\n        disease {\n          id\n          name\n        }\n        diseaseFromSource\n        target {\n          id\n          approvedSymbol\n        }\n        mutatedSamples {\n          functionalConsequence {\n            id\n            label\n          }\n          numberSamplesTested\n          numberMutatedSamples\n        }\n        resourceScore\n        significantDriverMethods\n        cohortId\n        cohortShortName\n        cohortDescription\n      }\n    }\n  }\n}\n",
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_drug_warnings_by_chemblId",
+        "description": "Retrieve warnings for a specific drug using ChEMBL ID.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "chemblId": {
+                    "type": "string",
+                    "description": "The ChEMBL ID of the drug.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n  query drugWarnings($chemblId: String!) {\n    drug(chemblId: $chemblId) {\n      id\n      name\n      drugWarnings {\n        warningType\n        description\n        country\n        year\n        toxicityClass\n        chemblIds\n     efoIdForWarningClass\n      references {\n          id\n          source\n          url\n        }\n      }\n    }\n  }\n  ",
+        "label": [
+            "Drug",
+            "AdverseEvents",
+            "SafetyLiability",
+            "OpenTarget",
+            "GraphQL",
+            "Warnings",
+            "Safety",
+            "Withdrawal",
+            "Toxicity"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_drug_mechanisms_of_action_by_chemblId",
+        "description": "Retrieve the mechanisms of action associated with a specific drug using chemblId.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "chemblId": {
+                    "type": "string",
+                    "description": "The ChEMBL ID of the drug.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n  query drugMechanismsOfAction($chemblId: String!) {\n    drug(chemblId: $chemblId) {\n      id\n      name\n      mechanismsOfAction {\n        rows {\n          mechanismOfAction\n          actionType\n         targetName\n          targets {\n            id\n            approvedSymbol\n          }\n        }\n      }\n    }\n  }\n  ",
+        "label": [
+            "Drug",
+            "MechanismsOfAction",
+            "Target",
+            "Pharmacology",
+            "ChemblId",
+            "OpenTarget",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_associated_drugs_by_disease_efoId",
+        "description": "Retrieve known drugs associated with a specific disease by disease efoId.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "efoId": {
+                    "type": "string",
+                    "description": "The EFO ID of the disease.",
+                    "required": true
+                },
+                "size": {
+                    "type": "integer",
+                    "description": "Number of entries to fetch, recomanding a large number to avoid missing drugs.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n  query diseaseKnownDrugs($efoId: String!, $size: Int!, $freeTextQuery: String) {\n    disease(efoId: $efoId) {\n      id\n      name\n      knownDrugs(size: $size, freeTextQuery: $freeTextQuery) {\n        count\n        rows {\n          drug {\n            id\n            name\n            tradeNames\n            maximumClinicalTrialPhase\n            isApproved\n            hasBeenWithdrawn\n          }\n          phase\n          status\n          mechanismOfAction\n          target {\n            id\n            approvedSymbol\n          }\n        }\n      }\n    }\n  }\n  ",
+        "examples": [
+            {
+                "question": "Please list the drugs associated with the disease with efoId 'EFO_0005548' and filter by 'dopamine'.",
+                "query": {
+                    "name": "get_associated_drugs_by_disease_efoId",
+                    "arguments": {
+                        "efoId": "EFO_0005548",
+                        "size": 10,
+                        "freeTextQuery": "dopamine"
+                    }
+                }
+            }
+        ],
+        "label": [
+            "OpenTarget",
+            "Disease",
+            "Drug",
+            "Pagination",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_similar_entities_by_disease_efoId",
+        "description": "Retrieve similar entities for a given disease efoId using a model trained with PubMed.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "efoId": {
+                    "type": "string",
+                    "description": "The EFO ID of the disease.",
+                    "required": true
+                },
+                "threshold": {
+                    "type": "number",
+                    "description": "Threshold similarity between 0 and 1. Only results above threshold are returned.",
+                    "required": true
+                },
+                "size": {
+                    "type": "integer",
+                    "description": "Number of similar entities to fetch.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n  query diseaseSimilarEntities($efoId: String!, $threshold: Float!, $size: Int!) {\n    disease(efoId: $efoId) {\n      id\n      name\n      similarEntities(threshold: $threshold, size: $size) {\n        id\n        category\n        score\n        object {\n          ... on Disease {\n            id\n            name\n          }\n          ... on Target {\n            id\n            approvedSymbol\n          }\n          ... on Drug {\n            id\n            name\n          }\n        }\n      }\n    }\n  }\n  ",
+        "label": [
+            "Disease",
+            "Similarity",
+            "Model",
+            "Entities",
+            "OpenTarget",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_similar_entities_by_drug_chemblId",
+        "description": "Retrieve similar entities for a given drug chemblId using a model trained with PubMed.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "chemblId": {
+                    "type": "string",
+                    "description": "The chemblId of the disease.",
+                    "required": true
+                },
+                "threshold": {
+                    "type": "number",
+                    "description": "Threshold similarity between 0 and 1. Only results above threshold are returned.",
+                    "required": true
+                },
+                "size": {
+                    "type": "integer",
+                    "description": "Number of similar entities to fetch.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n  query diseaseSimilarEntities($chemblId: String!, $threshold: Float!, $size: Int!) {\n    drug(chemblId: $chemblId) {\n      id\n      name\n      similarEntities(threshold: $threshold, size: $size) {\n        id\n        category\n        score\n        object {\n          ... on Disease {\n            id\n            name\n          }\n          ... on Target {\n            id\n            approvedSymbol\n          }\n          ... on Drug {\n            id\n            name\n          }\n        }\n      }\n    }\n  }\n  ",
+        "label": [
+            "Drug",
+            "Similarity",
+            "Model",
+            "Entities",
+            "OpenTarget",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_similar_entities_by_target_ensemblID",
+        "description": "Retrieve similar entities for a given target ensemblID using a model trained with PubMed.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "ensemblId": {
+                    "type": "string",
+                    "description": "The ensemblID of the disease.",
+                    "required": true
+                },
+                "threshold": {
+                    "type": "number",
+                    "description": "Threshold similarity between 0 and 1. Only results above threshold are returned.",
+                    "required": true
+                },
+                "size": {
+                    "type": "integer",
+                    "description": "Number of similar entities to fetch.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n  query diseaseSimilarEntities($ensemblId: String!, $threshold: Float!, $size: Int!) {\n    target(ensemblId: $ensemblId) {\n      id\n      approvedSymbol\n      similarEntities(threshold: $threshold, size: $size) {\n        id\n        category\n        score\n        object {\n          ... on Disease {\n            id\n            name\n          }\n          ... on Target {\n            id\n            approvedSymbol\n          }\n          ... on Drug {\n            id\n            name\n          }\n        }\n      }\n    }\n  }\n  ",
+        "label": [
+            "Disease",
+            "Similarity",
+            "Model",
+            "Entities",
+            "OpenTarget",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_associated_phenotypes_by_disease_efoId",
+        "description": "Find HPO phenotypes asosciated with the specified disease efoId.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "efoId": {
+                    "type": "string",
+                    "description": "The efoId of a disease or phenotype.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "query diseaseAnnotation($efoId: String!) {\n  disease(efoId: $efoId) {\n    id\n    name\n    phenotypes {\n      rows {\n        phenotypeHPO {\n          id\n          name\n          description\n          namespace\n        }\n        phenotypeEFO {\n          id\n          name\n        }\n      }\n    }\n  }\n}",
+        "label": [
+            "Disease",
+            "OpenTarget",
+            "GraphQL",
+            "Phenotype",
+            "Symptoms",
+            "Clinical signs"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_drug_withdrawn_blackbox_status_by_chemblId",
+        "description": "Find withdrawn and black-box warning statuses for a specific drug by chemblId.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "chemblId": {
+                    "type": "array",
+                    "items": {
+                        "type": "string"
+                    },
+                    "description": "The chemblId of a drug.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n  query drugWithdrawnWarningData($chemblId: String!) {\n    drug(chemblId: $chemblId) {\n      name\n      id\n      hasBeenWithdrawn\n      blackBoxWarning\n    }\n  }\n  ",
+        "label": [
+            "Drug",
+            "SafetyWarnings",
+            "Withdrawal",
+            "OpenTarget",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "search_category_counts_by_query_string",
+        "description": "Get the count of entries in each entity category (disease, target, drug) based on a query string.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "queryString": {
+                    "type": "string",
+                    "description": "The search string for querying information.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n  query searchCategoryCounts($queryString: String!) {\n    search(queryString: $queryString) {\n      aggregations {\n        total\n        entities {\n          total\n          name\n        }\n      }\n    }\n  }\n  ",
+        "label": [
+            "OpenTarget",
+            "GraphQL",
+            "SearchResults",
+            "Search",
+            "Query",
+            "Counts",
+            "Categories"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_disease_id_description_by_name",
+        "description": "Retrieve the efoId and additional details of a disease based on its name.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "diseaseName": {
+                    "type": "string",
+                    "description": "The name of the disease to search for.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n    query getDiseaseIdByName($diseaseName: String!) {\n      search(queryString: $diseaseName, entityNames: [\"disease\"]) {\n        hits {\n          id\n          name\n          description\n        }\n      }\n    }\n    ",
+        "label": [
+            "Disease",
+            "Identification",
+            "Search",
+            "Name",
+            "Disease",
+            "OpenTarget",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_drug_id_description_by_name",
+        "description": "Fetch the drug chemblId and description based on the drug name.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "drugName": {
+                    "type": "string",
+                    "description": "The name of the drug for which the ID is required.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n  query getDrugIdByName($drugName: String!) {\n    search(queryString: $drugName, entityNames: [\"drug\"]) {\n      hits {\n        id\n        name\n       description\n      }\n    }\n  }\n  ",
+        "label": [
+            "Identification",
+            "Search",
+            "Name",
+            "Drug",
+            "OpenTarget",
+            "GraphQL"
+        ],
+        "type": "OpentargetToolDrugNameMatch"
+    },
+    {
+        "name": "get_drug_indications_by_chemblId",
+        "description": "Fetch indications (treatable phenotypes/diseases) for a given drug chemblId.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "chemblId": {
+                    "type": "string",
+                    "description": "The chemblId of the drug for which to retrieve treatable phenotypes information.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n    query drugIndications($chemblId: String!) {\n      drug(chemblId: $chemblId) {\n     id\n    name\n        indications {\n          rows {\n            disease {\n              id\n              name\n              }\n      maxPhaseForIndication\n     references {\n       source\n        ids\n       }\n         }\n        }\n      }\n    }\n    ",
+        "label": [
+            "Drug",
+            "Indications",
+            "Disease",
+            "Treatment",
+            "OpenTarget",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_target_gene_ontology_by_ensemblID",
+        "description": "Retrieve Gene Ontology annotations for a specific target by Ensembl ID.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "ensemblId": {
+                    "type": "string",
+                    "description": "The Ensembl ID of the target for which to retrieve Gene Ontology annotations.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query targetGeneOntology($ensemblId: String!) {\n        target(ensemblId: $ensemblId) {\n          id\n          approvedSymbol\n          geneOntology {\n            aspect\n            evidence\n            geneProduct\n            source\n            term {\n              id\n              name\n            }\n          }\n        }\n      }\n    ",
+        "examples": [
+            {
+                "question": "Can you retrieve the Gene Ontology annotations for the target with Ensembl ID 'ENSG00000136492'?",
+                "query": {
+                    "name": "get_target_gene_ontology_by_ensemblID",
+                    "arguments": {
+                        "ensemblId": "ENSG00000136492"
+                    }
+                }
+            },
+            {
+                "question": "What are the Gene Ontology annotations for the target identified by Ensembl ID 'ENSG00000138653'?",
+                "query": {
+                    "name": "get_target_gene_ontology_by_ensemblID",
+                    "arguments": {
+                        "ensemblId": "ENSG00000138653"
+                    }
+                }
+            },
+            {
+                "question": "Please provide the Gene Ontology annotations for the target with Ensembl ID 'ENSG00000186162'.",
+                "query": {
+                    "name": "get_target_gene_ontology_by_ensemblID",
+                    "arguments": {
+                        "ensemblId": "ENSG00000186162"
+                    }
+                }
+            }
+        ],
+        "label": [
+            "Target",
+            "GeneOntology",
+            "OpenTarget",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_target_homologues_by_ensemblID",
+        "description": "Fetch homologues for a specific target by Ensembl ID.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "ensemblId": {
+                    "type": "string",
+                    "description": "The Ensembl ID of the target for which to retrieve homologues.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query targetHomologues($ensemblId: String!) {\n        target(ensemblId: $ensemblId) {\n          id\n          approvedSymbol\n          homologues {\n            homologyType\n            queryPercentageIdentity\n            speciesId\n            speciesName\n            targetGeneId\n            targetGeneSymbol\n            targetPercentageIdentity\n            isHighConfidence\n          }\n        }\n      }\n    ",
+        "examples": [
+            {
+                "question": "Can you fetch homologues for the target with Ensembl ID 'ENSG00000100033'?",
+                "query": {
+                    "name": "get_target_homologues_by_ensemblID",
+                    "arguments": {
+                        "ensemblId": "ENSG00000100033"
+                    }
+                }
+            },
+            {
+                "question": "What are the homologues for the target identified by Ensembl ID 'ENSG00000288534'?",
+                "query": {
+                    "name": "get_target_homologues_by_ensemblID",
+                    "arguments": {
+                        "ensemblId": "ENSG00000288534"
+                    }
+                }
+            },
+            {
+                "question": "Please provide the homologues for the target with Ensembl ID 'ENSG00000198937'.",
+                "query": {
+                    "name": "get_target_homologues_by_ensemblID",
+                    "arguments": {
+                        "ensemblId": "ENSG00000198937"
+                    }
+                }
+            }
+        ],
+        "label": [
+            "OpenTarget",
+            "Target Information",
+            "GraphQL",
+            "Homologue"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_target_safety_profile_by_ensemblID",
+        "description": "Retrieve known target safety liabilities for a specific target Ensembl ID.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "ensemblId": {
+                    "type": "string",
+                    "description": "The Ensembl ID of the target for which to retrieve safety liabilities.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query targetSafetyLiabilities($ensemblId: String!) {\n        target(ensemblId: $ensemblId) {\n          id\n          approvedSymbol\n          safetyLiabilities {\n            event\n            eventId\n            biosamples {\n              cellFormat\n              cellLabel\n              tissueLabel\n              tissueId\n            }\n            effects {\n              dosing\n              direction\n            }\n            studies {\n              name\n              type\n              description\n            }\n            datasource\n            literature\n          }\n        }\n      }\n    ",
+        "examples": [
+            {
+                "question": "Can you provide the safety liabilities for the target with Ensembl ID 'ENSG00000175274'?",
+                "query": {
+                    "name": "target_safety_liabilities",
+                    "arguments": {
+                        "ensemblId": "ENSG00000175274"
+                    }
+                }
+            },
+            {
+                "question": "What are the known safety effects for the target identified by Ensembl ID 'ENSG00000226446'?",
+                "query": {
+                    "name": "target_safety_liabilities",
+                    "arguments": {
+                        "ensemblId": "ENSG00000226446"
+                    }
+                }
+            },
+            {
+                "question": "Please retrieve the safety risk information for the target with Ensembl ID 'ENSG00000151929'.",
+                "query": {
+                    "name": "target_safety_liabilities",
+                    "arguments": {
+                        "ensemblId": "ENSG00000151929"
+                    }
+                }
+            }
+        ],
+        "label": [
+            "Target",
+            "SafetyLiability",
+            "OpenTarget",
+            "GraphQL",
+            "Safety",
+            "Liabilities"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_biological_mouse_models_by_ensemblID",
+        "description": "Retrieve biological mouse models, including allelic compositions and genetic backgrounds, for a specific target.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "ensemblId": {
+                    "type": "string",
+                    "description": "The Ensembl ID of the target.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query fetchBiologicalModels($ensemblId: String!) {\n        target(ensemblId: $ensemblId) {\n          id\n          approvedSymbol\n          mousePhenotypes {\n            biologicalModels {\n              allelicComposition\n              geneticBackground\n              id\n              literature\n            }\n          }\n        }\n      }\n    ",
+        "examples": [
+            {
+                "question": "What are the allelic compositions and genetic backgrounds for the target identified by Ensembl ID 'ENSG00000196639'?",
+                "query": {
+                    "name": "get_biological_mouse_models_by_ensemblID",
+                    "arguments": {
+                        "ensemblId": "ENSG00000196639"
+                    }
+                }
+            },
+            {
+                "question": "Please provide the biological models for the target with the Ensembl ID 'ENSG00000171862'.",
+                "query": {
+                    "name": "get_biological_mouse_models_by_ensemblID",
+                    "arguments": {
+                        "ensemblId": "ENSG00000171862"
+                    }
+                }
+            }
+        ],
+        "label": [
+            "OpenTarget",
+            "Target Information",
+            "BiologicalModels",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_target_genomic_location_by_ensemblID",
+        "description": "Retrieve genomic location data for a specific target, including chromosome, start, end, and strand.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "ensemblId": {
+                    "type": "string",
+                    "description": "The Ensembl ID of the target for which to retrieve genomic location information.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query targetGenomicLocation($ensemblId: String!) {\n        target(ensemblId: $ensemblId) {\n          id\n          approvedSymbol\n          genomicLocation {\n            chromosome\n            start\n            end\n            strand\n          }\n        }\n      }\n    ",
+        "examples": [
+            {
+                "question": "Can you provide the genomic location for the target with Ensembl ID 'ENSG00000114098'?",
+                "query": {
+                    "name": "get_target_genomic_location_by_ensemblID",
+                    "arguments": {
+                        "ensemblId": "ENSG00000114098"
+                    }
+                }
+            },
+            {
+                "question": "What is the genomic location data for the target identified by Ensembl ID 'ENSG00000231404'?",
+                "query": {
+                    "name": "get_target_genomic_location_by_ensemblID",
+                    "arguments": {
+                        "ensemblId": "ENSG00000231404"
+                    }
+                }
+            },
+            {
+                "question": "Please retrieve the genomic location information for the target with Ensembl ID 'ENSG00000167258'.",
+                "query": {
+                    "name": "get_target_genomic_location_by_ensemblID",
+                    "arguments": {
+                        "ensemblId": "ENSG00000167258"
+                    }
+                }
+            }
+        ],
+        "label": [
+            "Target",
+            "GenomicLocation",
+            "OpenTarget",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_target_subcellular_locations_by_ensemblID",
+        "description": "Retrieve information about subcellular locations for a specific target ensemblID.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "ensemblId": {
+                    "type": "string",
+                    "description": "The ensemblId of a target.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query targetSubcellularLocations($ensemblId: String!) {\n        target(ensemblId: $ensemblId) {\n          id\n          approvedSymbol\n          subcellularLocations {\n            location\n            source\n            termSL\n            labelSL\n          }\n        }\n      }\n    ",
+        "examples": [
+            {
+                "question": "Can you provide the subcellular locations for the target with Ensembl ID 'ENSG00000121898'?",
+                "query": {
+                    "name": "get_target_subcellular_locations_by_ensemblID",
+                    "arguments": {
+                        "ensemblId": "ENSG00000121898"
+                    }
+                }
+            },
+            {
+                "question": "What are the subcellular locations for the target identified by Ensembl ID 'ENSG00000274286'?",
+                "query": {
+                    "name": "get_target_subcellular_locations_by_ensemblID",
+                    "arguments": {
+                        "ensemblId": "ENSG00000274286"
+                    }
+                }
+            },
+            {
+                "question": "Please retrieve the subcellular location information for the target with Ensembl ID 'ENSG00000171843'.",
+                "query": {
+                    "name": "get_target_subcellular_locations_by_ensemblID",
+                    "arguments": {
+                        "ensemblId": "ENSG00000171843"
+                    }
+                }
+            }
+        ],
+        "label": [
+            "Target",
+            "Subcellular Locations",
+            "GraphQL",
+            "OpenTarget"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_target_synonyms_by_ensemblID",
+        "description": "Retrieve synonyms for specified target, including alternative names and symbols, using given ensemblID.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "ensemblId": {
+                    "type": "string",
+                    "description": "The Ensembl ID of the target.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query retrieveTargetSynonyms($ensemblId: String!) {\n        target(ensemblId: $ensemblId) {\n          id\n          approvedSymbol\n          synonyms {\n            label\n            source\n          }\n          symbolSynonyms {\n            label\n            source\n          }\n          nameSynonyms {\n            label\n            source\n          }\n        }\n      }\n    ",
+        "examples": [
+            {
+                "question": "Can you retrieve synonyms for the target with the Ensembl ID 'ENSG00000188986'?",
+                "query": {
+                    "name": "get_target_synonyms_by_ensemblID",
+                    "arguments": {
+                        "ensemblId": "ENSG00000188986"
+                    }
+                }
+            },
+            {
+                "question": "What are the alternative names and symbols for the target identified by Ensembl ID 'ENSG00000269335'?",
+                "query": {
+                    "name": "get_target_synonyms_by_ensemblID",
+                    "arguments": {
+                        "ensemblId": "ENSG00000269335"
+                    }
+                }
+            },
+            {
+                "question": "Please provide the synonyms for the target with Ensembl ID 'ENSG00000141052'.",
+                "query": {
+                    "name": "get_target_synonyms_by_ensemblID",
+                    "arguments": {
+                        "ensemblId": "ENSG00000141052"
+                    }
+                }
+            }
+        ],
+        "label": [
+            "OpenTarget",
+            "Target Information",
+            "GraphQL",
+            "Target"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_target_tractability_by_ensemblID",
+        "description": "Retrieve tractability assessments, including modality and values, for a specific target ensembl ID.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "ensemblId": {
+                    "type": "string",
+                    "description": "The Ensembl ID of the target.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query targetTractabilityAssessment($ensemblId: String!) {\n        target(ensemblId: $ensemblId) {\n          id\n          approvedSymbol\n          tractability {\n            label\n            modality\n            value\n          }\n        }\n      }\n    ",
+        "examples": [
+            {
+                "question": "Can you retrieve the tractability assessment for the target with Ensembl ID 'ENSG00000141736'?",
+                "query": {
+                    "name": "get_target_tractability_by_ensemblID",
+                    "arguments": {
+                        "ensemblId": "ENSG00000141736"
+                    }
+                }
+            },
+            {
+                "question": "What are the tractability assessments for the target identified by Ensembl ID 'ENSG00000169249'?",
+                "query": {
+                    "name": "get_target_tractability_by_ensemblID",
+                    "arguments": {
+                        "ensemblId": "ENSG00000169249"
+                    }
+                }
+            },
+            {
+                "question": "Please provide the tractability assessment details for the target with Ensembl ID 'ENSG00000122548'.",
+                "query": {
+                    "name": "get_target_tractability_by_ensemblID",
+                    "arguments": {
+                        "ensemblId": "ENSG00000122548"
+                    }
+                }
+            }
+        ],
+        "label": [
+            "Target",
+            "Tractability",
+            "OpenTarget",
+            "Target Information",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_target_classes_by_ensemblID",
+        "description": "Retrieve the target classes associated with a specific target ensemblID.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "ensemblId": {
+                    "type": "string",
+                    "description": "The Ensembl ID of the target.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query fetchTargetClasses($ensemblId: String!) {\n        target(ensemblId: $ensemblId) {\n          id\n          approvedSymbol\n          targetClass {\n            id\n            label\n            level\n          }\n        }\n      }\n    ",
+        "examples": [
+            {
+                "question": "Can you retrieve the target classes for the target with Ensembl ID 'ENSG00000185324'?",
+                "query": {
+                    "name": "get_target_classes_by_ensemblID",
+                    "arguments": {
+                        "ensemblId": "ENSG00000185324"
+                    }
+                }
+            },
+            {
+                "question": "What are the target classes associated with the Ensembl ID 'ENSG00000141646'?",
+                "query": {
+                    "name": "get_target_classes_by_ensemblID",
+                    "arguments": {
+                        "ensemblId": "ENSG00000141646"
+                    }
+                }
+            },
+            {
+                "question": "Please provide the target classes for the target identified by Ensembl ID 'ENSG00000141736'.",
+                "query": {
+                    "name": "get_target_classes_by_ensemblID",
+                    "arguments": {
+                        "ensemblId": "ENSG00000141736"
+                    }
+                }
+            }
+        ],
+        "label": [
+            "OpenTarget",
+            "Target Information",
+            "GraphQL",
+            "Target"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_target_enabling_packages_by_ensemblID",
+        "description": "Retrieve the Target Enabling Packages (TEP) associated with a specific target ensemblID.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "ensemblId": {
+                    "type": "string",
+                    "description": "The Ensembl ID of the target.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query fetchTargetEnablingPackages($ensemblId: String!) {\n        target(ensemblId: $ensemblId) {\n          id\n          approvedSymbol\n          tep {\n            name\n            uri\n            therapeuticArea\n            description\n          }\n        }\n      }\n    ",
+        "examples": [
+            {
+                "question": "Can you retrieve the Target Enabling Packages for the target with Ensembl ID 'ENSG00000167258'?",
+                "query": {
+                    "name": "get_target_enabling_packages_by_ensemblID",
+                    "arguments": {
+                        "ensemblId": "ENSG00000167258"
+                    }
+                }
+            }
+        ],
+        "label": [
+            "OpenTarget",
+            "Target Information",
+            "GraphQL",
+            "Target"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_target_interactions_by_ensemblID",
+        "description": "Retrieve interaction data for a specific target ensemblID, including interaction partners and evidence.",
+        "label": [
+            "Target",
+            "Interaction",
+            "Evidence",
+            "GraphQL",
+            "Pagination",
+            "OpenTarget"
+        ],
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "ensemblId": {
+                    "type": "string",
+                    "description": "The Ensembl ID of the target.",
+                    "required": true
+                },
+                "page": {
+                    "type": "object",
+                    "properties": {
+                        "index": {
+                            "type": "integer",
+                            "description": "The index of the page to retrieve.",
+                            "required": true
+                        },
+                        "size": {
+                            "type": "integer",
+                            "description": "The number of items per page.",
+                            "required": true
+                        }
+                    },
+                    "description": "Pagination parameters.",
+                    "required": false
+                }
+            }
+        },
+        "query_schema": "\n      query targetInteractions($ensemblId: String!, $page: Pagination!) {\n        target(ensemblId: $ensemblId) {\n          id\n          approvedSymbol\n          interactions(page: $page) {\n            count\n            rows {\n              intA\n              targetA {\n              id\n          approvedSymbol\n        }\n        intB\n        targetB {\n          id\n          approvedSymbol\n        }\n              score\n              sourceDatabase\n              evidences {\n                evidenceScore\n                pubmedId\n                interactionDetectionMethodShortName\n              }\n            }\n          }\n        }\n      }\n    ",
+        "examples": [
+            {
+                "question": "Can you retrieve interaction data for the target with Ensembl ID 'ENSG00000134508' from the source database 'BioGRID'?",
+                "query": {
+                    "name": "target_interactions",
+                    "arguments": {
+                        "ensemblId": "ENSG00000134508",
+                        "page": {
+                            "index": 1,
+                            "size": 10
+                        }
+                    }
+                }
+            },
+            {
+                "question": "What are the interaction partners and evidence for the target identified by Ensembl ID 'ENSG00000276601'?",
+                "query": {
+                    "name": "target_interactions",
+                    "arguments": {
+                        "ensemblId": "ENSG00000276601",
+                        "page": {
+                            "index": 2,
+                            "size": 5
+                        }
+                    }
+                }
+            },
+            {
+                "question": "Please provide the interaction data for the target with Ensembl ID 'ENSG00000287061' on the first page with 20 items per page.",
+                "query": {
+                    "name": "target_interactions",
+                    "arguments": {
+                        "ensemblId": "ENSG00000287061",
+                        "page": {
+                            "index": 1,
+                            "size": 20
+                        }
+                    }
+                }
+            }
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_disease_ancestors_parents_by_efoId",
+        "description": "Retrieve the disease ancestors and parents in the ontology using the disease EFO ID.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "efoId": {
+                    "type": "string",
+                    "description": "The EFO ID of the disease.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query getDiseaseDetailsByEfoId($efoId: String!) {\n        disease(efoId: $efoId) {\n          id\n          name\n          ancestors\n          parents {\n            id\n            name\n          }\n          }\n      }\n ",
+        "label": [
+            "OpenTarget",
+            "Disease",
+            "Disease Information",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_disease_descendants_children_by_efoId",
+        "description": "Retrieve the disease descendants and children in the ontology using the disease EFO ID.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "efoId": {
+                    "type": "string",
+                    "description": "The EFO ID of the disease.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query getDiseaseDetailsByEfoId($efoId: String!) {\n        disease(efoId: $efoId) {\n          id\n          name\n          descendants\n          children {\n            id\n            name\n          }\n          }\n       }\n",
+        "label": [
+            "OpenTarget",
+            "Disease",
+            "Disease Information",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_disease_locations_by_efoId",
+        "description": "Retrieve the disease's direct location and indirect location disease terms and IDs using the disease EFO ID.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "efoId": {
+                    "type": "string",
+                    "description": "The EFO ID of the disease.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query getDiseaseDetailsByEfoId($efoId: String!) {\n        disease(efoId: $efoId) {\n          id\n          name\n          directLocationIds\n          indirectLocationIds\n          directLocations {\n            id\n            name\n          }\n          indirectLocations {\n            id\n            name\n          }\n        }\n      }\n    ",
+        "label": [
+            "OpenTarget",
+            "Disease",
+            "Disease Information",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_disease_synonyms_by_efoId",
+        "description": "Retrieve disease synonyms by its EFO ID.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "efoId": {
+                    "type": "string",
+                    "description": "The EFO ID of the disease.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query getDiseaseDetailsByEfoId($efoId: String!) {\n        disease(efoId: $efoId) {\n          id\n          name\n        synonyms {\n            relation\n            terms\n          }\n      }\n     }\n",
+        "label": [
+            "OpenTarget",
+            "Disease",
+            "Disease Information",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_disease_description_by_efoId",
+        "description": "Retrieve disease description, name, database cros references, obsolete terms, and whether it's a therapeutic area, all using the specified efoId.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "efoId": {
+                    "type": "string",
+                    "description": "The EFO ID of the disease.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query getDiseaseDetailsByEfoId($efoId: String!) {\n        disease(efoId: $efoId) {\n          id\n          name\n          description\n          dbXRefs\n          obsoleteTerms\n          isTherapeuticArea\n        }\n      }\n    ",
+        "examples": [
+            {
+                "question": "Can you provide detailed information about the disease with the EFO ID 'MONDO_0000030'?",
+                "query": {
+                    "name": "get_disease_description_by_efoId",
+                    "arguments": {
+                        "efoId": "MONDO_0000030"
+                    }
+                }
+            },
+            {
+                "question": "What are the details of the disease identified by the EFO ID 'EFO_0007468'?",
+                "query": {
+                    "name": "get_disease_description_by_efoId",
+                    "arguments": {
+                        "efoId": "EFO_0007468"
+                    }
+                }
+            },
+            {
+                "question": "Please retrieve information about the disease with the EFO ID 'Orphanet_217563'.",
+                "query": {
+                    "name": "get_disease_description_by_efoId",
+                    "arguments": {
+                        "efoId": "Orphanet_217563"
+                    }
+                }
+            }
+        ],
+        "label": [
+            "OpenTarget",
+            "Disease",
+            "Disease Information",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_disease_therapeutic_areas_by_efoId",
+        "description": "Retrieve the therapeutic areas associated with a specific disease efoId.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "efoId": {
+                    "type": "string",
+                    "description": "The EFO ID of the disease.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query diseaseTherapeuticAreas($efoId: String!) {\n        disease(efoId: $efoId) {\n          id\n          name\n          therapeuticAreas {\n            id\n            name\n          }\n        }\n      }\n    ",
+        "examples": [
+            {
+                "question": "What therapeutic areas are linked to the disease with the efoId 'MONDO_0016474'?",
+                "query": {
+                    "name": "get_disease_therapeutic_areas_by_efoId",
+                    "arguments": {
+                        "efoId": "MONDO_0016474"
+                    }
+                }
+            },
+            {
+                "question": "Can you provide the therapeutic areas associated with the disease identified by efoId 'Orphanet_2579'?",
+                "query": {
+                    "name": "get_disease_therapeutic_areas_by_efoId",
+                    "arguments": {
+                        "efoId": "Orphanet_2579"
+                    }
+                }
+            },
+            {
+                "question": "Please list the therapeutic areas for the disease with the efoId 'MONDO_0000873'.",
+                "query": {
+                    "name": "get_disease_therapeutic_areas_by_efoId",
+                    "arguments": {
+                        "efoId": "MONDO_0000873"
+                    }
+                }
+            }
+        ],
+        "label": [
+            "OpenTarget",
+            "Disease",
+            "TherapeuticArea",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_drug_adverse_events_by_chemblId",
+        "description": "Retrieve significant adverse events reported for a specific drug chemblId.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "chemblId": {
+                    "type": "string",
+                    "description": "The ChEMBL ID of the drug.",
+                    "required": true
+                },
+                "page": {
+                    "type": "object",
+                    "properties": {
+                        "index": {
+                            "type": "integer",
+                            "description": "Index of the page to fetch, starting from 0.",
+                            "required": true
+                        },
+                        "size": {
+                            "type": "integer",
+                            "description": "Number of entries per page.",
+                            "required": true
+                        }
+                    },
+                    "description": "Pagination settings.",
+                    "required": false
+                }
+            }
+        },
+        "query_schema": "\n  query drugAdverseEvents($chemblId: String!, $page: Pagination!) {\n    drug(chemblId: $chemblId) {\n      id\n      name\n      adverseEvents(page: $page) {\n        count\n        criticalValue\n       rows {\n          name\n          meddraCode\n          count\n          logLR\n        }\n      }\n    }\n  }\n  ",
+        "label": [
+            "Drug",
+            "AdverseEvents",
+            "Safety",
+            "Reporting",
+            "Pagination",
+            "OpenTarget",
+            "GraphQL",
+            "AdverseEvents"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_known_drugs_by_drug_chemblId",
+        "description": "Get a list of known drugs and associated information using the specified chemblId.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "chemblId": {
+                    "type": "string",
+                    "description": "The ChEMBL ID of the drug.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query retrieveMultipleDrugsInfo($chemblId: String!) {\n        drug(chemblId: $chemblId) {\n          id\n          name\n        knownDrugs {\n            uniqueDrugs\n            uniqueDiseases\n            uniqueTargets\n            count\n            cursor\n            rows {\n              approvedSymbol\n              approvedName\n              label\n              prefName\n              drugType\n              targetId\n              diseaseId\n              drugId\n              phase\n              mechanismOfAction\n              status\n              targetClass\n              references {\n                source\n                ids\n                urls\n              }\n              ctIds\n              urls {\n                url\n                name\n              }\n              disease {\n                id\n                name\n              }\n              target {\n                id\n                approvedSymbol\n              }\n              drug {\n                id\n                name\n              }\n            }\n          }\n        }\n      }\n    ",
+        "label": [
+            "OpenTarget",
+            "Drug",
+            "Drug Information",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_parent_child_molecules_by_drug_chembl_ID",
+        "description": "Get parent and child molecules of specified drug chemblId.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "chemblId": {
+                    "type": "string",
+                    "description": "The ChEMBL ID of the drug.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query retrieveMultipleDrugsInfo($chemblId: String!) {\n        drug(chemblId: $chemblId) {\n          id\n          name\n          parentMolecule {\n            id\n            name\n          }\n          childMolecules {\n            id\n            name\n          }\n          }\n      }\n    ",
+        "label": [
+            "OpenTarget",
+            "Drug",
+            "Drug Information",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_approved_indications_by_drug_chemblId",
+        "description": "Retrieve detailed information about multiple drugs using a list of ChEMBL IDs.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "chemblId": {
+                    "type": "string",
+                    "description": "The ChEMBL ID of the drug.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query retrieveMultipleDrugsInfo($chemblId: String!) {\n        drug(chemblId: $chemblId) {\n          id\n          name\n          approvedIndications\n          }\n      }\n    ",
+        "label": [
+            "OpenTarget",
+            "Drug",
+            "Drug Information",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_drug_description_by_chemblId",
+        "description": "Get drug name, year of first approval, type, cross references, and max clinical trial phase based on specified chemblId.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "chemblId": {
+                    "type": "string",
+                    "description": "The ChEMBL ID of the drug.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query retrieveMultipleDrugsInfo($chemblId: String!) {\n        drug(chemblId: $chemblId) {\n          id\n          name\n          yearOfFirstApproval\n          drugType\n          crossReferences {\n            source\n            reference\n          }\n          maximumClinicalTrialPhase\n        }\n      }\n    ",
+        "label": [
+            "OpenTarget",
+            "Drug",
+            "Drug Information",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_drug_synonyms_by_chemblId",
+        "description": "Retrieve the synonyms associated with a specific drug chemblId.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "chemblId": {
+                    "type": "string",
+                    "description": "The ChEMBL ID of the drug.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query drugSynonyms($chemblId: String!) {\n        drug(chemblId: $chemblId) {\n          id\n          name\n          synonyms\n        }\n      }\n    ",
+        "examples": [
+            {
+                "question": "Can you provide the synonyms for the drug with ChEMBL ID 'CHEMBL2021430'?",
+                "query": {
+                    "name": "drug_synget_drug_synonyms_by_chemblIdonyms",
+                    "arguments": {
+                        "chemblId": "CHEMBL2021430"
+                    }
+                }
+            },
+            {
+                "question": "What are the synonyms associated with the drug identified by ChEMBL ID 'CHEMBL295698'?",
+                "query": {
+                    "name": "get_drug_synonyms_by_chemblId",
+                    "arguments": {
+                        "chemblId": "CHEMBL295698"
+                    }
+                }
+            },
+            {
+                "question": "Please list the synonyms for the drug that has the ChEMBL ID 'CHEMBL1084617'.",
+                "query": {
+                    "name": "get_drug_synonyms_by_chemblId",
+                    "arguments": {
+                        "chemblId": "CHEMBL1084617"
+                    }
+                }
+            }
+        ],
+        "label": [
+            "OpenTarget",
+            "Drug Information",
+            "Drug",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_drug_trade_names_by_chemblId",
+        "description": "Retrieve the trade names associated with a specific drug chemblId.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "chemblId": {
+                    "type": "string",
+                    "description": "The ChEMBL ID of the drug.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query drugTradeNames($chemblId: String!) {\n        drug(chemblId: $chemblId) {\n          id\n          name\n          tradeNames\n        }\n      }\n    ",
+        "examples": [
+            {
+                "question": "What are the trade names for the drug with ChEMBL ID 'CHEMBL25'?",
+                "query": {
+                    "name": "get_drug_trade_names_by_chemblId",
+                    "arguments": {
+                        "chemblId": "CHEMBL25"
+                    }
+                }
+            },
+            {
+                "question": "Can you provide the trade names associated with the drug identified by ChEMBL ID 'CHEMBL1201613'?",
+                "query": {
+                    "name": "get_drug_trade_names_by_chemblId",
+                    "arguments": {
+                        "chemblId": "CHEMBL1201613"
+                    }
+                }
+            },
+            {
+                "question": "Please list the trade names for the drug that has the ChEMBL ID 'CHEMBL3182621'.",
+                "query": {
+                    "name": "get_drug_trade_names_by_chemblId",
+                    "arguments": {
+                        "chemblId": "CHEMBL3182621"
+                    }
+                }
+            }
+        ],
+        "label": [
+            "Drug",
+            "OpenTarget",
+            "Drug Information",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_drug_approval_status_by_chemblId",
+        "description": "Retrieve the approval status of a specific drug chemblId.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "chemblId": {
+                    "type": "string",
+                    "description": "The ChEMBL ID of the drug.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query drugApprovalStatus($chemblId: String!) {\n        drug(chemblId: $chemblId) {\n          id\n          name\n          isApproved\n        }\n      }\n    ",
+        "examples": [
+            {
+                "question": "What is the approval status of the drug with ChEMBL ID 'CHEMBL2103799'?",
+                "query": {
+                    "name": "get_drug_approval_status_by_chemblId",
+                    "arguments": {
+                        "chemblId": "CHEMBL2103799"
+                    }
+                }
+            },
+            {
+                "question": "Can you tell me if the drug identified by ChEMBL ID 'CHEMBL1684' is approved?",
+                "query": {
+                    "name": "get_drug_approval_status_by_chemblId",
+                    "arguments": {
+                        "chemblId": "CHEMBL1684"
+                    }
+                }
+            },
+            {
+                "question": "Please provide the approval status for the drug with ChEMBL ID 'CHEMBL1086997'.",
+                "query": {
+                    "name": "get_drug_approval_status_by_chemblId",
+                    "arguments": {
+                        "chemblId": "CHEMBL1086997"
+                    }
+                }
+            }
+        ],
+        "label": [
+            "Drug",
+            "Drug Information",
+            "GraphQL",
+            "OpenTarget"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_chemical_probes_by_target_ensemblID",
+        "description": "Retrieve chemical probes associated with a specific target using its ensemblID.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "ensemblId": {
+                    "type": "string",
+                    "description": "The Ensembl ID of the target for which to retrieve chemical probes.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query getTargetChemicalProbes($ensemblId: String!) {\n        target(ensemblId: $ensemblId) {\n          chemicalProbes {\n            id\n            control\n            drugId\n            mechanismOfAction\n            isHighQuality\n            origin\n            probeMinerScore\n            probesDrugsScore\n            scoreInCells\n            scoreInOrganisms\n            targetFromSourceId\n            urls {\n              niceName\n              url\n            }\n          }\n        }\n      }\n    ",
+        "examples": [
+            {
+                "question": "Can you retrieve the chemical probes for the target with Ensembl ID 'ENSG00000163515'?",
+                "query": {
+                    "name": "get_chemical_probes_by_target_ensemblID",
+                    "arguments": {
+                        "ensemblId": "ENSG00000163515"
+                    }
+                }
+            },
+            {
+                "question": "What chemical probes are associated with the target identified by Ensembl ID 'ENSG00000157916'?",
+                "query": {
+                    "name": "get_chemical_probes_by_target_ensemblID",
+                    "arguments": {
+                        "ensemblId": "ENSG00000157916"
+                    }
+                }
+            },
+            {
+                "question": "Please list the chemical probes linked to the target with Ensembl ID 'ENSG00000253563'.",
+                "query": {
+                    "name": "get_chemical_probes_by_target_ensemblID",
+                    "arguments": {
+                        "ensemblId": "ENSG00000253563"
+                    }
+                }
+            }
+        ],
+        "label": [
+            "OpenTarget",
+            "Drug Information",
+            "ChemicalProbe",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "drug_pharmacogenomics_data",
+        "description": "Retrieve pharmacogenomics data for a specific drug, including evidence levels and genotype annotations.",
+        "label": [
+            "Drug",
+            "Pharmacogenomics",
+            "Evidence",
+            "Genotype",
+            "Pagination",
+            "OpenTarget",
+            "GraphQL"
+        ],
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "chemblId": {
+                    "type": "string",
+                    "description": "The ChEMBL ID of the drug.",
+                    "required": true
+                },
+                "page": {
+                    "type": "object",
+                    "description": "Pagination options.",
+                    "properties": {
+                        "index": {
+                            "type": "integer",
+                            "description": "Pagination index.",
+                            "required": true
+                        },
+                        "size": {
+                            "type": "integer",
+                            "description": "Number of records to fetch per page.",
+                            "required": true
+                        }
+                    },
+                    "required": false
+                }
+            }
+        },
+        "query_schema": "\n      query drugPharmacogenomicsData($chemblId: String!, $page: Pagination!) {\n        drug(chemblId: $chemblId) {\n          id\n          name\n          pharmacogenomics(page: $page) {\n            datasourceId\n            datatypeId\n            genotype\n            evidenceLevel\n            genotypeAnnotationText\n            genotypeId\n            haplotypeFromSourceId\n            haplotypeId\n            literature\n            pgxCategory\n            phenotypeFromSourceId\n            phenotypeText\n            studyId\n            targetFromSourceId\n            variantFunctionalConsequenceId\n            variantRsId\n            isDirectTarget\n            variantFunctionalConsequence {\n              id\n              label\n            }\n            drugs {\n              drugId\n              drug {\n        name\n      }\n            }\n            target {\n              id\n              approvedSymbol\n            }\n          }\n        }\n      }\n    ",
+        "examples": [
+            {
+                "question": "Can you provide the pharmacogenomics data for the drug with ChEMBL ID 'CHEMBL23261'?",
+                "query": {
+                    "name": "drug_pharmacogenomics_data",
+                    "arguments": {
+                        "chemblId": "CHEMBL23261",
+                        "page": {
+                            "index": 1,
+                            "size": 10
+                        }
+                    }
+                }
+            },
+            {
+                "question": "What are the genotype annotations and evidence levels for the drug identified by ChEMBL ID 'CHEMBL1497'?",
+                "query": {
+                    "name": "drug_pharmacogenomics_data",
+                    "arguments": {
+                        "chemblId": "CHEMBL1497",
+                        "page": {
+                            "index": 2,
+                            "size": 5
+                        }
+                    }
+                }
+            },
+            {
+                "question": "Retrieve the pharmacogenomics data for the drug with ChEMBL ID 'CHEMBL4455124', including evidence levels.",
+                "query": {
+                    "name": "drug_pharmacogenomics_data",
+                    "arguments": {
+                        "chemblId": "CHEMBL4455124",
+                        "page": {
+                            "index": 3,
+                            "size": 15
+                        }
+                    }
+                }
+            }
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_associated_drugs_by_target_ensemblID",
+        "description": "Get known drugs associated with a specific target ensemblID, including clinical trial phase and mechanism of action of the drugs.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "ensemblId": {
+                    "type": "string",
+                    "description": "The Ensembl ID of the target.",
+                    "required": true
+                },
+                "size": {
+                    "type": "integer",
+                    "description": "Number of entries to fetch.",
+                    "required": true
+                },
+                "cursor": {
+                    "type": "string",
+                    "description": "Cursor for pagination.",
+                    "required": false
+                }
+            }
+        },
+        "query_schema": "\n      query targetKnownDrugs($ensemblId: String!, $size: Int!, $cursor: String) {\n        target(ensemblId: $ensemblId) {\n          id\n          approvedSymbol\n          knownDrugs(size: $size, cursor: $cursor) {\n            count\n            rows {\n              drug {\n                id\n                name\n                tradeNames\n                maximumClinicalTrialPhase\n                isApproved\n                hasBeenWithdrawn\n              }\n              phase\n              status\n              mechanismOfAction\n              disease {\n                id\n                name\n              }\n            }\n          }\n        }\n      }\n    ",
+        "examples": [
+            {
+                "question": "Can you retrieve known drugs associated with the target having Ensembl ID 'ENSG00000141736' and fetch 10 entries?",
+                "query": {
+                    "name": "get_associated_drugs_by_target_ensemblID",
+                    "arguments": {
+                        "ensemblId": "ENSG00000141736",
+                        "size": 10
+                    }
+                }
+            },
+            {
+                "question": "What are the known drugs for the target with Ensembl ID 'ENSG00000184182', and can you provide 5 entries?",
+                "query": {
+                    "name": "get_associated_drugs_by_target_ensemblID",
+                    "arguments": {
+                        "ensemblId": "ENSG00000184182",
+                        "size": 5
+                    }
+                }
+            },
+            {
+                "question": "Please list the known drugs associated with the target identified by Ensembl ID 'ENSG00000104884', and fetch 15 entries. Use the cursor 'abc123' for pagination.",
+                "query": {
+                    "name": "get_associated_drugs_by_target_ensemblID",
+                    "arguments": {
+                        "ensemblId": "ENSG00000104884",
+                        "size": 15,
+                        "cursor": "abc123"
+                    }
+                }
+            }
+        ],
+        "label": [
+            "Target",
+            "Drug",
+            "MechanismsOfAction",
+            "Pagination",
+            "OpenTarget",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_associated_diseases_by_drug_chemblId",
+        "description": "Retrieve the list of diseases associated with a specific drug chemblId based on clinical trial data or post-marketed drugs.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "chemblId": {
+                    "type": "string",
+                    "description": "The ChEMBL ID of the drug.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query fetchLinkedDiseasesForDrug($chemblId: String!) {\n        drug(chemblId: $chemblId) {\n          id\n          name\n          linkedDiseases {\n            count\n            rows {\n              id\n              name\n              description\n            }\n          }\n        }\n      }\n    ",
+        "examples": [
+            {
+                "question": "Can you retrieve the list of diseases linked to the drug with ChEMBL ID 'CHEMBL3137349'?",
+                "query": {
+                    "name": "get_associated_diseases_by_drug_chemblId",
+                    "arguments": {
+                        "chemblId": "CHEMBL3137349"
+                    }
+                }
+            },
+            {
+                "question": "What diseases are associated with the drug identified by ChEMBL ID 'CHEMBL1389'?",
+                "query": {
+                    "name": "get_associated_diseases_by_drug_chemblId",
+                    "arguments": {
+                        "chemblId": "CHEMBL1389"
+                    }
+                }
+            },
+            {
+                "question": "Please provide the diseases linked to the drug that has the ChEMBL ID 'CHEMBL2109266'.",
+                "query": {
+                    "name": "get_associated_diseases_by_drug_chemblId",
+                    "arguments": {
+                        "chemblId": "CHEMBL2109266"
+                    }
+                }
+            }
+        ],
+        "label": [
+            "Drug",
+            "Disease",
+            "OpenTarget",
+            "Drug Information",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_associated_targets_by_drug_chemblId",
+        "description": "Retrieve the list of targets linked to a specific drug chemblId based on its mechanism of action.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "chemblId": {
+                    "type": "string",
+                    "description": "The ChEMBL ID of the drug.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query fetchLinkedTargetsForDrug($chemblId: String!) {\n        drug(chemblId: $chemblId) {\n          id\n          name\n          linkedTargets {\n            count\n            rows {\n              id\n              approvedSymbol\n              approvedName\n            }\n          }\n        }\n      }\n    ",
+        "examples": [
+            {
+                "question": "Can you retrieve the list of targets linked to the drug with ChEMBL ID 'CHEMBL459008'?",
+                "query": {
+                    "name": "get_associated_targets_by_drug_chemblId",
+                    "arguments": {
+                        "chemblId": "CHEMBL459008"
+                    }
+                }
+            },
+            {
+                "question": "What are the targets associated with the drug identified by ChEMBL ID 'CHEMBL1800955'?",
+                "query": {
+                    "name": "get_associated_targets_by_drug_chemblId",
+                    "arguments": {
+                        "chemblId": "CHEMBL1800955"
+                    }
+                }
+            },
+            {
+                "question": "Please provide the list of targets for the drug with ChEMBL ID 'CHEMBL32'.",
+                "query": {
+                    "name": "get_associated_targets_by_drug_chemblId",
+                    "arguments": {
+                        "chemblId": "CHEMBL32"
+                    }
+                }
+            }
+        ],
+        "label": [
+            "Drug",
+            "Target",
+            "MechanismsOfAction",
+            "OpenTarget",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "multi_entity_search_by_query_string",
+        "description": "Perform a multi-entity search based on a query string, filtering by entity names and pagination settings.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "queryString": {
+                    "type": "string",
+                    "description": "The search string for querying information.",
+                    "required": true
+                },
+                "entityNames": {
+                    "type": "array",
+                    "items": {
+                        "type": "string"
+                    },
+                    "description": "List of entity names to search for (e.g., target, disease, drug).",
+                    "required": false
+                },
+                "page": {
+                    "type": "object",
+                    "properties": {
+                        "index": {
+                            "type": "integer",
+                            "description": "Pagination index.",
+                            "required": "True"
+                        },
+                        "size": {
+                            "type": "integer",
+                            "description": "Pagination size.",
+                            "required": "True"
+                        }
+                    },
+                    "description": "Pagination settings with index and size.",
+                    "required": false
+                }
+            }
+        },
+        "query_schema": "\n      query multiEntitySearch($queryString: String!, $entityNames: [String!], $page: Pagination) {\n        search(queryString: $queryString, entityNames: $entityNames, page: $page) {\n          total\n          hits {\n            id\n            entity\n            description\n            name\n            score\n          }\n        }\n      }\n    ",
+        "examples": [
+            {
+                "question": "Can you search for information on the drug 'Aspirin' and the disease 'Hypertension'?",
+                "query": {
+                    "name": "multi_entity_search_by_query_string",
+                    "arguments": {
+                        "queryString": "Aspirin Hypertension",
+                        "entityNames": [
+                            "drug",
+                            "disease"
+                        ],
+                        "page": {
+                            "index": 1,
+                            "size": 10
+                        }
+                    }
+                }
+            },
+            {
+                "question": "Please find details about the target 'BRCA1' with pagination settings of index 2 and size 5.",
+                "query": {
+                    "name": "multi_entity_search_by_query_string",
+                    "arguments": {
+                        "queryString": "BRCA1",
+                        "entityNames": [
+                            "target"
+                        ],
+                        "page": {
+                            "index": 2,
+                            "size": 5
+                        }
+                    }
+                }
+            },
+            {
+                "question": "What information is available for the disease 'Diabetes'?",
+                "query": {
+                    "name": "multi_entity_search_by_query_string",
+                    "arguments": {
+                        "queryString": "Diabetes",
+                        "entityNames": [
+                            "disease"
+                        ]
+                    }
+                }
+            }
+        ],
+        "label": [
+            "Search and Mapping Functions",
+            "MultiEntitySearch",
+            "Pagination",
+            "OpenTarget",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_gene_ontology_terms_by_goID",
+        "description": "Retrieve Gene Ontology terms based on a list of GO IDs.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "goIds": {
+                    "type": "array",
+                    "items": {
+                        "type": "string"
+                    },
+                    "description": "A list of Gene Ontology (GO) IDs to fetch the corresponding terms.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query fetchGeneOntologyTerms($goIds: [String!]!) {\n        geneOntologyTerms(goIds: $goIds) {\n          id\n          name\n        }\n      }\n    ",
+        "examples": [
+            {
+                "question": "Can you retrieve the Gene Ontology terms for the GO IDs 'GO:0008150' and 'GO:0003674'?",
+                "query": {
+                    "name": "fetch_gene_ontology_terms",
+                    "arguments": {
+                        "goIds": [
+                            "GO:0008150",
+                            "GO:0003674"
+                        ]
+                    }
+                }
+            },
+            {
+                "question": "What are the Gene Ontology terms associated with the GO IDs 'GO:0005575', 'GO:0003674', and 'GO:0008150'?",
+                "query": {
+                    "name": "fetch_gene_ontology_terms",
+                    "arguments": {
+                        "goIds": [
+                            "GO:0005575",
+                            "GO:0003674",
+                            "GO:0008150"
+                        ]
+                    }
+                }
+            },
+            {
+                "question": "Please provide the Gene Ontology terms for the following GO IDs: 'GO:0008150', 'GO:0003674', 'GO:0005575', and 'GO:0003677'.",
+                "query": {
+                    "name": "fetch_gene_ontology_terms",
+                    "arguments": {
+                        "goIds": [
+                            "GO:0008150",
+                            "GO:0003674",
+                            "GO:0005575",
+                            "GO:0003677"
+                        ]
+                    }
+                }
+            }
+        ],
+        "label": [
+            "GeneOntology",
+            "Data Retrieval and Aggregation",
+            "OpenTarget",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_target_constraint_info_by_ensemblID",
+        "description": "Retrieve genetic constraint information for a specific target ensemblID, including expected and observed values, and scores.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "ensemblId": {
+                    "type": "string",
+                    "description": "The Ensembl ID of the target.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query targetConstraintInfo($ensemblId: String!) {\n        target(ensemblId: $ensemblId) {\n          id\n          approvedSymbol\n          geneticConstraint {\n            constraintType\n            exp\n            obs\n            oe\n            oeLower\n            oeUpper\n            score\n            upperBin\n            upperBin6\n            upperRank\n          }\n        }\n      }\n    ",
+        "examples": [
+            {
+                "question": "Can you provide the genetic constraint information for the target with Ensembl ID 'ENSG00000135476'?",
+                "query": {
+                    "name": "target_constraint_info",
+                    "arguments": {
+                        "ensemblId": "ENSG00000135476"
+                    }
+                }
+            },
+            {
+                "question": "What are the expected and observed values, and scores for the target identified by Ensembl ID 'ENSG00000290763'?",
+                "query": {
+                    "name": "target_constraint_info",
+                    "arguments": {
+                        "ensemblId": "ENSG00000290763"
+                    }
+                }
+            },
+            {
+                "question": "Please retrieve the genetic constraint details for the target with Ensembl ID 'ENSG00000109906'.",
+                "query": {
+                    "name": "target_constraint_info",
+                    "arguments": {
+                        "ensemblId": "ENSG00000109906"
+                    }
+                }
+            }
+        ],
+        "label": [
+            "Target",
+            "Constraint",
+            "Data Retrieval and Aggregation",
+            "OpenTarget",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_publications_by_disease_efoId",
+        "description": "Retrieve publications related to a disease efoId, including PubMed IDs and publication dates.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "entityId": {
+                    "type": "string",
+                    "description": "The ID of the entity (efoId).",
+                    "required": true
+                },
+                "additionalIds": {
+                    "type": "array",
+                    "items": {
+                        "type": "string"
+                    },
+                    "description": "List of additional IDs to include in the search.",
+                    "required": false
+                },
+                "startYear": {
+                    "type": "integer",
+                    "description": "Year at the lower end of the filter.",
+                    "required": false
+                },
+                "startMonth": {
+                    "type": "integer",
+                    "description": "Month at the lower end of the filter.",
+                    "required": false
+                },
+                "endYear": {
+                    "type": "integer",
+                    "description": "Year at the higher end of the filter.",
+                    "required": false
+                },
+                "endMonth": {
+                    "type": "integer",
+                    "description": "Month at the higher end of the filter.",
+                    "required": false
+                }
+            }
+        },
+        "query_schema": "\n      query entityPublications($entityId: String!, $additionalIds: [String!], $startYear: Int, $startMonth: Int, $endYear: Int, $endMonth: Int) {\n        disease(efoId: $entityId) {\n          id\n          name\n          literatureOcurrences(additionalIds: $additionalIds, startYear: $startYear, startMonth: $startMonth, endYear: $endYear, endMonth: $endMonth) {\n            count\n            filteredCount\n            earliestPubYear\n            rows {\n              pmid\n              pmcid\n              publicationDate\n              sentences {\n                section\n                matches {\n                  mappedId\n                  matchedLabel\n                  sectionStart\n                  sectionEnd\n                  startInSentence\n                  endInSentence\n                  matchedType\n                }\n              }\n            }\n          }\n        }\n      }\n    ",
+        "examples": [
+            {
+                "question": "Can you retrieve publications related to the entity with ID 'EFO_0000400'?",
+                "query": {
+                    "name": "get_publications_by_disease_efoId",
+                    "arguments": {
+                        "entityId": "EFO_0000400"
+                    }
+                }
+            }
+        ],
+        "label": [
+            "Publications",
+            "Data Retrieval and Aggregation",
+            "GraphQL",
+            "OpenTarget"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_publications_by_target_ensemblID",
+        "description": "Retrieve publications related to a target ensemblID, including PubMed IDs and publication dates.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "entityId": {
+                    "type": "string",
+                    "description": "The ID of the entity (ensemblID).",
+                    "required": true
+                },
+                "additionalIds": {
+                    "type": "array",
+                    "items": {
+                        "type": "string"
+                    },
+                    "description": "List of additional IDs to include in the search.",
+                    "required": false
+                },
+                "startYear": {
+                    "type": "integer",
+                    "description": "Year at the lower end of the filter.",
+                    "required": false
+                },
+                "startMonth": {
+                    "type": "integer",
+                    "description": "Month at the lower end of the filter.",
+                    "required": false
+                },
+                "endYear": {
+                    "type": "integer",
+                    "description": "Year at the higher end of the filter.",
+                    "required": false
+                },
+                "endMonth": {
+                    "type": "integer",
+                    "description": "Month at the higher end of the filter.",
+                    "required": false
+                }
+            }
+        },
+        "query_schema": "\n      query entityPublications($entityId: String!, $additionalIds: [String!], $startYear: Int, $startMonth: Int, $endYear: Int, $endMonth: Int) {\n        target(ensemblId: $entityId) {\n          id\n          approvedSymbol\n          literatureOcurrences(additionalIds: $additionalIds, startYear: $startYear, startMonth: $startMonth, endYear: $endYear, endMonth: $endMonth) {\n            count\n            filteredCount\n            earliestPubYear\n            rows {\n              pmid\n              pmcid\n              publicationDate\n              sentences {\n                section\n                matches {\n                  mappedId\n                  matchedLabel\n                  sectionStart\n                  sectionEnd\n                  startInSentence\n                  endInSentence\n                  matchedType\n                }\n              }\n            }\n          }\n        }\n      }\n    ",
+        "label": [
+            "Publications",
+            "Data Retrieval and Aggregation",
+            "GraphQL",
+            "OpenTarget"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_publications_by_drug_chemblId",
+        "description": "Retrieve publications related to a drug chemblId, including PubMed IDs and publication dates.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "entityId": {
+                    "type": "string",
+                    "description": "The ID of the entity (chemblId).",
+                    "required": true
+                },
+                "additionalIds": {
+                    "type": "array",
+                    "items": {
+                        "type": "string"
+                    },
+                    "description": "List of additional IDs to include in the search.",
+                    "required": false
+                },
+                "startYear": {
+                    "type": "integer",
+                    "description": "Year at the lower end of the filter.",
+                    "required": false
+                },
+                "startMonth": {
+                    "type": "integer",
+                    "description": "Month at the lower end of the filter.",
+                    "required": false
+                },
+                "endYear": {
+                    "type": "integer",
+                    "description": "Year at the higher end of the filter.",
+                    "required": false
+                },
+                "endMonth": {
+                    "type": "integer",
+                    "description": "Month at the higher end of the filter.",
+                    "required": false
+                }
+            }
+        },
+        "query_schema": "\n      query entityPublications($entityId: String!, $additionalIds: [String!], $startYear: Int, $startMonth: Int, $endYear: Int, $endMonth: Int) {\n        drug(chemblId: $entityId) {\n          id\n          name\n          literatureOcurrences(additionalIds: $additionalIds, startYear: $startYear, startMonth: $startMonth, endYear: $endYear, endMonth: $endMonth) {\n            count\n            filteredCount\n            earliestPubYear\n            rows {\n              pmid\n              pmcid\n              publicationDate\n              sentences {\n                section\n                matches {\n                  mappedId\n                  matchedLabel\n                  sectionStart\n                  sectionEnd\n                  startInSentence\n                  endInSentence\n                  matchedType\n                }\n              }\n            }\n          }\n        }\n      }\n    ",
+        "label": [
+            "Publications",
+            "Data Retrieval and Aggregation",
+            "GraphQL",
+            "OpenTarget"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "get_target_id_description_by_name",
+        "description": "Get the ensemblId and description based on the target name.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "targetName": {
+                    "type": "string",
+                    "description": "The name of the target for which the ID is required.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n        query getTargetIdByName($targetName: String!) {\n            search(queryString: $targetName, entityNames: [\"target\"]) {\n                hits {\n                    id\n          name\n     description\n                }\n            }\n        }\n    ",
+        "label": [
+            "Search",
+            "Name",
+            "Target",
+            "OpenTarget",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    } 
+]

utils.py

@@ -9,20 +9,9 @@ from oauth2client.service_account import ServiceAccountCredentials
 import pandas as pd
 import json
 import gradio as gr
+import os
 
-GSERVICE_ACCOUNT_INFO = {
-  "type": "service_account",
-  "project_id": "txagent",
-  "private_key_id": "cc1a12e427917244a93faf6f19e72b589a685e65",
-  "private_key": "-----BEGIN PRIVATE KEY-----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\nfpM1DKwTfLNCX6kQbLOoRR8j7w==\n-----END PRIVATE KEY-----\n",
-  "client_email": "[email protected]",
-  "client_id": "108950722202634464257",
-  "auth_uri": "https://accounts.google.com/o/oauth2/auth",
-  "token_uri": "https://oauth2.googleapis.com/token",
-  "auth_provider_x509_cert_url": "https://www.googleapis.com/oauth2/v1/certs",
-  "client_x509_cert_url": "https://www.googleapis.com/robot/v1/metadata/x509/shanghua%40txagent.iam.gserviceaccount.com",
-  "universe_domain": "googleapis.com"
-}
+GSERVICE_ACCOUNT_INFO = os.environ.get("GSERVICE_ACCOUNT_INFO")
 
 # Optionally, get the sheet name from environment (or use a default)
 # GSHEET_NAME = os.environ.get("GSHEET_NAME", "Your Google Sheet Name")
@@ -173,7 +162,7 @@ def append_to_sheet(user_data=None, custom_row_dict=None, custom_sheet_name=None
     # Append the custom or default row to the sheet
     sheet.append_row(custom_row)
 
-def format_chat(response):
+def format_chat(response, tool_database_labels):
     chat_history = []
     # Keep track of the last assistant message's tool_calls
     last_tool_calls = []
@@ -195,10 +184,16 @@ def format_chat(response):
                 args = tool_call.get("arguments", {})
 
                 # Determine icon + title
+                database_label = ""
                 if name == "Tool_RAG":
                     title = "🧰 Tool RAG"
                 else:
                     title = f"🛠️ {name}"
+                    for db_label, tool_list in tool_database_labels.items():
+                        if name in tool_list:
+                            title = f"🛠️ {name} (**retrieves** {db_label})"
+                            database_label = " (" + db_label + ")"
+                            break
 
                 # Parse and pretty-print the tool response content
                 raw = msg.get("content", "")
@@ -214,7 +209,7 @@ def format_chat(response):
                 chat_history.append(
                     gr.ChatMessage(
                         role="assistant",
-                        content=f"Input: {json.dumps(args)}\n\nResponse:\n{pretty}",
+                        content=f"Input: {json.dumps(args)}\n\nResponse{database_label}:\n{pretty}",
                         metadata={
                             "title": title
                         }