update expert eval with ui changes and using new data

app.py

@@ -1,13 +1,61 @@
 import gradio as gr
 from gradio_modal import Modal
+from gradio_pdf import PDF
 from huggingface_hub import hf_hub_download, list_repo_files
 import os, csv, datetime, sys
 import json
 from utils import format_chat, append_to_sheet, read_sheet_to_df
 import random
 import base64
+import io
+from PIL import Image
 import re
 
+#Required file paths
+REPO_ID  = "agenticx/TxAgentEvalData"
+EVALUATOR_MAP_DICT = "evaluator_map_dict.json"
+TXAGENT_RESULTS_SHEET_BASE_NAME = "TxAgent_Human_Eval_Results_CROWDSOURCED"
+
+#Load tool lists from 'tool_lists' subdirectory---make sure to update this with the latest from ToolUniverse if necessary!
+tools_dir = os.path.join(os.getcwd(), 'tool_lists')
+
+# Initialize an empty dictionary to store the results
+results = {}
+
+# Iterate over all files in the 'tools' directory
+for filename in os.listdir(tools_dir):
+    # Process only files that end with '.json'
+    if filename.endswith('.json'):
+        filepath = os.path.join(tools_dir, filename)
+        key = os.path.splitext(filename)[0]  # Remove '.json' extension
+        try:
+            with open(filepath, 'r', encoding='utf-8') as f:
+                data = json.load(f)
+                # Extract 'name' fields if present
+                names = [item['name'] for item in data if isinstance(item, dict) and 'name' in item]
+                results[key] = names
+        except Exception as e:
+            print(f"Error processing {filename}: {e}")
+            results[key] = [f"Error loading {filename}"]
+
+#for labeling the different tool calls in format_chat
+tool_database_labels_raw = {
+    "chembl_tools": "**from the ChEMBL database**",
+    "efo_tools": "**from the Experimental Factor Ontology**",
+    "europe_pmc_tools": "**from the Europe PMC database**",
+    "fda_drug_adverse_event_tools": "**from the FDA Adverse Event Reporting System**",
+    "fda_drug_labeling_tools": "**from approved FDA drug labels**",
+    "monarch_tools": "**from the Monarch Initiative databases**",
+    "opentarget_tools": "**from the Open Targets database**",
+    "pubtator_tools": "**from PubTator-accessible PubMed and PMC biomedical literature**",
+    "semantic_scholar_tools": "**from Semantic-Scholar-accessible literature**"
+}
+tool_database_labels = {
+    tool_database_labels_raw[key]: results[key]
+    for key in results
+    if key in tool_database_labels_raw
+}
+
 def encode_image_to_base64(image_path):
     """Encodes an image file to a base64 string."""
     try:
@@ -43,42 +91,6 @@ except Exception as e:
     print(f"Error reading HTML file: {e}")
     TxAgent_Project_Page_HTML = "<p>Error: Project page content could not be loaded.</p>"
 
-# 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 = [
     {
@@ -158,14 +170,16 @@ mapping = {   #for pairwise mapping between model comparison selections
     "👎 Neither model did well": "neither"
 }
 
-#Prepare data
-REPO_ID  = "RichardZhu52/TxAgent_human_eval"
-CROWDSOURCING_DATA_DIRECTORY = "crowdsourcing_eval_data_0430"
-TXAGENT_RESULTS_SHEET_BASE_NAME = "TxAgent_Human_Eval_Results"
-DISEASE_SPECIALTY_MAP_FILENAME = "disease_specialty_map.json"
-QUESTION_MAP_FILENAME = "question_map.json"
+def preprocess_question_id(question_id):
+    if isinstance(question_id, str):
+        return question_id
+    elif isinstance(question_id, list) and len(question_id) == 1:
+        return question_id[0]
+    else:
+        print("Error: Invalid question ID format. Expected a string or a single-element list.")
+        return None
 
-def get_evaluator_questions(evaluator_id, all_files, evaluator_directory, question_map):
+def get_evaluator_questions(evaluator_id, all_files, evaluator_directory):
 
     # Filter to only the files in that directory
     evaluator_files = [f for f in all_files if f.startswith(f"{evaluator_directory}/")]
@@ -177,14 +191,25 @@ def get_evaluator_questions(evaluator_id, all_files, evaluator_directory, questi
             revision="main", #fetches the most recent version of the dataset each time this command is called
             filename=remote_path,
             # force_download=True,
+            token = os.getenv("HF_TOKEN")
         )
         with open(local_path, "r") as f:
             model_name_key = os.path.basename(remote_path).replace('.json', '')
             data_by_filename[model_name_key] = json.load(f)
 
+    
+    evaluator_question_ids = []
+    # Assuming 'TxAgent-T1-Llama-3.1-8B' data is representative for question IDs and associated diseases
+    if 'TxAgent-T1-Llama-3.1-8B' in data_by_filename:
+        for entry in data_by_filename['TxAgent-T1-Llama-3.1-8B']:
+            question_id = preprocess_question_id(entry.get("id"))
+            evaluator_question_ids.append(question_id)
+    # Handle case where no relevant questions are found based on specialty
+    if not evaluator_question_ids:
+        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']
-    evaluator_question_ids = question_map.get(evaluator_id).get('question_ids')
+    model_names = [key for key in data_by_filename.keys() if key != 'TxAgent-T1-Llama-3.1-8B']
     full_question_ids_list = []
     for other_model_name in model_names:
         for q_id in evaluator_question_ids:
@@ -196,11 +221,11 @@ def get_evaluator_questions(evaluator_id, all_files, evaluator_directory, questi
         matched_pairs = set()
         for _, row in results_df.iterrows():
             q = row["Question ID"]
-            # pick whichever response isn’t 'txagent'
+            # pick whichever response isn’t 'TxAgent-T1-Llama-3.1-8B'
             a, b = row["ResponseA_Model"], row["ResponseB_Model"]
-            if a == "txagent" and b != "txagent":
+            if a == 'TxAgent-T1-Llama-3.1-8B' and b != 'TxAgent-T1-Llama-3.1-8B':
                 matched_pairs.add((q, b))
-            elif b == "txagent" and a != "txagent":
+            elif b == 'TxAgent-T1-Llama-3.1-8B' and a != 'TxAgent-T1-Llama-3.1-8B':
                 matched_pairs.add((q, a))
 
         # filter out any tuple whose (q_id, other_model) was already matched
@@ -221,14 +246,15 @@ def go_to_eval_progress_modal(name, email, evaluator_id, specialty_dd, subspecia
 
     # ADDED: Validate that name and email are non-empty before proceeding
     if not name or not email or not evaluator_id 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, evaluator ID, 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), ""
+        return gr.update(visible=True), gr.update(visible=False), None, "Please fill out all the required fields (name, email, evaluator ID, 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.Markdown(),gr.State(),gr.update(visible=False), ""
 
     question_map_path = hf_hub_download(
         repo_id=REPO_ID,
-        filename=QUESTION_MAP_FILENAME,
+        filename=EVALUATOR_MAP_DICT,
         repo_type="dataset",       # or omit if it's a Model/Space
         # force_download=True,       # ← always fetch new copy
-        revision="main"            # branch/tag/commit, fetches the most recent version of the dataset each time this command is called
+        revision="main",            # branch/tag/commit, fetches the most recent version of the dataset each time this command is called
+        token = os.getenv("HF_TOKEN")
     )
 
     # Load the question map from the downloaded file
@@ -236,19 +262,20 @@ def go_to_eval_progress_modal(name, email, evaluator_id, specialty_dd, subspecia
         question_map = json.load(f)
 
     #retrieve data from HF
-    evaluator_directory = question_map.get(evaluator_id, {}).get('evaluator_name', None)
+    evaluator_directory = question_map.get(evaluator_id, None)
     if evaluator_directory is None:
         return gr.update(visible=True), gr.update(visible=False), None, "Invalid Evaluator ID, please try again.", gr.Chatbot(), gr.Chatbot(), gr.HTML(),gr.State(),gr.update(visible=False),"" 
     all_files = list_repo_files(
         repo_id=REPO_ID,
         repo_type="dataset",
         revision="main",
+        token = os.getenv("HF_TOKEN")
     )
 
-    full_question_ids_list, data_by_filename = get_evaluator_questions(evaluator_id, all_files, evaluator_directory, question_map)
+    full_question_ids_list, data_by_filename = get_evaluator_questions(evaluator_id, all_files, evaluator_directory)
 
     if len(full_question_ids_list) == 0:
-        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),""
+        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.Markdown(),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
@@ -256,17 +283,17 @@ def go_to_eval_progress_modal(name, email, evaluator_id, specialty_dd, subspecia
 
     #Constructing question_for_eval, the question to evaluate this round
     txagent_matched_entry = next(
-        (entry for entry in data_by_filename['txagent'] if entry.get("question_ID") == q_id),
+        (entry for entry in data_by_filename['TxAgent-T1-Llama-3.1-8B'] if preprocess_question_id(entry.get("id")) == q_id),
         None
     )
     other_model_matched_entry = next(
-        (entry for entry in data_by_filename[other_model_name] if entry.get("question_ID") == q_id),
+        (entry for entry in data_by_filename[other_model_name] if preprocess_question_id(entry.get("id")) == q_id),
         None
     )
 
     models_list = [
         {
-            "model": "txagent",
+            "model": 'TxAgent-T1-Llama-3.1-8B',
             "reasoning_trace": txagent_matched_entry.get("solution")
         },
         {
@@ -278,7 +305,8 @@ def go_to_eval_progress_modal(name, email, evaluator_id, specialty_dd, subspecia
 
     question_for_eval = {
         "question": txagent_matched_entry.get("question"),
-        "question_ID": q_id,
+        "correct_answer": txagent_matched_entry.get("correct_answer"),
+        "id": q_id,
         "models": models_list,
     }
 
@@ -290,6 +318,7 @@ def go_to_eval_progress_modal(name, email, evaluator_id, specialty_dd, subspecia
 
     # Construct the question-specific elements of the pairwise rating page (page 1)
     page1_prompt = gr.HTML(f'<div style="background-color: #FFEFD5; border: 2px solid #FF8C00; padding: 10px; border-radius: 5px; color: black;"><strong style="color: black;">Prompt:</strong> {prompt_text}</div>')
+    page1_reference_answer = gr.Markdown(txagent_matched_entry.get("correct_answer"))
     chat_a = gr.Chatbot(
                     value=chat_A_value,
                     type="messages",
@@ -312,7 +341,7 @@ def go_to_eval_progress_modal(name, email, evaluator_id, specialty_dd, subspecia
                     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 are about to evaluate the next question. 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, page1_reference_answer, question_for_eval, gr.update(visible=True), f"You are about to evaluate the next question. 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():
@@ -340,7 +369,7 @@ def go_to_page2(data_subset_state,*pairwise_values):
     pairwise_results_for_display = [gr.Markdown(f"***As a reminder, your pairwise comparison answer for this criterion was: {pairwise_list[i]}. Your answer choices will be restricted based on your comparison answer, but you may go back and change the comparison answer if you wish.***") for i in range(len(criteria))]
 
     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
+        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(), gr.Markdown(),*pairwise_results_for_display
 
     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)
@@ -366,8 +395,9 @@ def go_to_page2(data_subset_state,*pairwise_values):
                 )
 
     page2_prompt = gr.HTML(f'<div style="background-color: #FFEFD5; border: 2px solid #FF8C00; padding: 10px; border-radius: 5px; color: black;"><strong style="color: black;">Prompt:</strong> {prompt_text}</div>')
+    page2_reference_answer = gr.Markdown(data_subset_state['correct_answer'])
     
-    return gr.update(visible=False), gr.update(visible=True), pairwise_list, comparison_reasons_list, "", chat_A_rating, chat_B_rating, page2_prompt, *pairwise_results_for_display
+    return gr.update(visible=False), gr.update(visible=True), pairwise_list, comparison_reasons_list, "", chat_A_rating, chat_B_rating, page2_prompt, page2_reference_answer, *pairwise_results_for_display
 
 
 # Callback to store scores for Response A.
@@ -417,6 +447,21 @@ def toggle_slider(is_unqualified):
     # When the checkbox is checked (True), set interactive to False to disable the slider.
     return gr.update(interactive=not is_unqualified)
 
+#show reference answer
+def toggle_reference(selection):
+    if selection == "Show Reference Answer":
+        return gr.update(visible=True)
+    else:
+        return gr.update(visible=False)
+
+#nonsense button helper
+def mark_invalid_question(btn_clicked_status):
+    new_status = not btn_clicked_status
+    if new_status == True:
+        return new_status, gr.update(value="Undo; this question makes biomedical sense", variant="primary")
+    else:
+        return new_status, gr.update(value="This question does not make sense or is not biomedically-relevant",variant="stop")
+
 centered_col_css = """
 #centered-column {
     margin-left: auto;
@@ -434,6 +479,13 @@ centered_col_css = """
     color: white !important;
     border-color: #F08080 !important;
 }
+#reference-box {
+    background-color: #9191FF !important;
+    color: white !important;
+    border: 1px solid #ccc;
+    padding: 10px;
+    border-radius: 5px;
+}
 """
 with gr.Blocks(css=centered_col_css) as demo:
     # States to save information between pages.
@@ -441,6 +493,7 @@ with gr.Blocks(css=centered_col_css) as demo:
     pairwise_state = gr.State()
     scores_A_state = gr.State()
     comparison_reasons = gr.State()
+    nonsense_btn_clicked = gr.State(False)
     unqualified_A_state = gr.State()
     data_subset_state = gr.State()
 
@@ -489,12 +542,32 @@ with gr.Blocks(css=centered_col_css) as demo:
         - Each session requires a minimum commitment of 5-10 minutes to complete one question.
         - If you wish to evaluate multiple questions, you may do so; you will never be asked to re-evaluate questions you have already seen.
         - When evaluating a question, you will be asked to compare the responses of two different models to the question and then rate each model's response on a scale of 1-5.
+        - If you feel that a question does not make sense or is not biomedically relevant, there is a RED BUTTON at the top of the first model comparison page to indicate this
         - You may use the Back and Next buttons at the bottom of each page to edit any of your responses before submitting.
-        - You may use the Instruction Page and Home Page buttons at the bottom of each page to return to this page or the home page. Your progress will be saved but not submitted.
+        - You may use the Home Page button at the bottom of each page to the home page. Your progress will be saved but not submitted.
         - You must submit your answers to the current question before moving on to evaluate the next question.
         - You may stop in between questions and return at a later time; however, you must submit your answers to the current question if you would like them saved.
+        - Please review the example question and LLM model response below:
 
-        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!
+        """)
+        # Assume 'your_image.png' is in the same directory
+        with open("anatomyofAgentResponse.jpg", "rb") as image_file:
+            img = Image.open(image_file)
+            new_size = (int(img.width * 0.5), int(img.height * 0.5))
+            img = img.resize(new_size, Image.LANCZOS)
+            buffer = io.BytesIO()
+            img.save(buffer, format="PNG")
+            encoded_string = base64.b64encode(buffer.getvalue()).decode("utf-8")
+            #encoded_string = base64.b64encode(image_file.read()).decode("utf-8")
+
+        image_html = f'<div style="text-align:center;"><img src="data:image/png;base64,{encoded_string}" alt="Your Image"></div>'
+        ReasoningTraceExampleHTML = f"""
+        <div>
+            {image_html}
+        </div>
+        """
+        gr.HTML(ReasoningTraceExampleHTML)
+        gr.Markdown("""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 (required)")
@@ -524,6 +597,30 @@ with gr.Blocks(css=centered_col_css) as demo:
     with gr.Column(visible=False) as page1:
         gr.Markdown("## Part 1/2: Pairwise Comparison") #Make the number controlled by question indexing!
         page1_prompt = gr.HTML()
+
+        # Add small red button under the prompt
+        nonsense_btn = gr.Button(
+            "This question does not make sense or is not biomedically-relevant",
+            size="sm",
+            variant="stop",  # red variant
+            elem_id="invalid-question-btn"
+        )
+
+        nonsense_btn.click(
+            fn=mark_invalid_question,
+            inputs=[nonsense_btn_clicked],
+            outputs=[nonsense_btn_clicked, nonsense_btn],
+            queue=False,
+        )
+
+        with gr.Accordion("Show reference answer (this is ONE correct answer, but there may be multiple)", open=False, elem_id="reference-box"):
+            page1_reference_answer = gr.Markdown(
+                """
+                **Reference Answer:**
+
+                This is the reference answer content.
+                """
+            )
         with gr.Row():
             # ADDED: Use gr.Chatbot to display the scrollable chat window for Response A.
             with gr.Column():
@@ -587,6 +684,14 @@ with gr.Blocks(css=centered_col_css) as demo:
         gr.Markdown("## Part 2/2: Rate Model Responses")
         # ### EDIT: Show a highlighted prompt as on previous pages.
         page2_prompt = gr.HTML()
+        with gr.Accordion("Show reference answer (this is ONE correct answer, but there may be multiple)", open=False, elem_id="reference-box"):
+            page2_reference_answer = gr.Markdown(
+                """
+                **Reference Answer:**
+
+                This is the reference answer content.
+                """
+            )
         # ### EDIT: Display both responses side-by-side using Chatbot windows.
         with gr.Row():
             with gr.Column():
@@ -717,7 +822,7 @@ 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", size="sm",elem_id="clear_btn")
+                clear_btn = gr.Button("Clear Selection", size="sm", elem_id="clear_btn")
                 clear_btn.click(fn=clear_selection, outputs=[rating_a,rating_b])
 
                 # wire each to re‐restrict the other on change
@@ -761,7 +866,7 @@ with gr.Blocks(css=centered_col_css) as demo:
             cancel_btn = gr.Button("Cancel")
     
     # --- Define Callback Functions for Confirmation Flow ---
-    def build_row_dict(data_subset_state, user_info, pairwise, comparisons_reasons, *args):
+    def build_row_dict(data_subset_state, user_info, pairwise, comparisons_reasons, nonsense_btn_clicked, *args):
         num_criteria = len(criteria)
         ratings_A_vals = list(args[:num_criteria])
         ratings_B_vals = list(args[num_criteria:])
@@ -785,6 +890,7 @@ with gr.Blocks(css=centered_col_css) as demo:
             "Prompt": prompt_text,
             "ResponseA_Model": response_A_model,
             "ResponseB_Model": response_B_model,
+            "Question Makes No Sense or Biomedically Irrelevant": nonsense_btn_clicked,
         }
 
         pairwise = [mapping.get(val, val) for val in pairwise]
@@ -797,16 +903,9 @@ with gr.Blocks(css=centered_col_css) as demo:
 
         return row
 
-    # def final_submit(data_subset_state, user_info, pairwise, comparisons_reasons, *args):
-
-    #     row_dict = build_row_dict(data_subset_state, user_info, pairwise, comparisons_reasons, *args)
-    #     append_to_sheet(user_data=None, custom_row_dict=row_dict, custom_sheet_name=str(TXAGENT_RESULTS_SHEET_BASE_NAME), add_header_when_create_sheet=True)
-
-    #     return gr.update(visible=False), gr.update(visible=True), gr.update(visible=False)
-
-    def final_submit(data_subset_state, user_info, pairwise, comparisons_reasons, *args):
+    def final_submit(data_subset_state, user_info, pairwise, comparisons_reasons, nonsense_btn_clicked, *args):
         # --- Part 1: Submit the current results (Existing Logic) ---
-        row_dict = build_row_dict(data_subset_state, user_info, pairwise, comparisons_reasons, *args)
+        row_dict = build_row_dict(data_subset_state, user_info, pairwise, comparisons_reasons, nonsense_btn_clicked, *args)
         _, _, _, _, _, _, _, _, evaluator_id = user_info
         append_to_sheet(user_data=None, custom_row_dict=row_dict, custom_sheet_name=str(TXAGENT_RESULTS_SHEET_BASE_NAME + f"_{evaluator_id}"), add_header_when_create_sheet=True)
 
@@ -816,23 +915,25 @@ with gr.Blocks(css=centered_col_css) as demo:
         # --- Re-fetch data and filter questions (Same logic as before) ---
         question_map_path = hf_hub_download(
             repo_id=REPO_ID,
-            filename=QUESTION_MAP_FILENAME,
+            filename=EVALUATOR_MAP_DICT,
             repo_type="dataset",       # or omit if it's a Model/Space
             # force_download=True,       # ← always fetch new copy
-            revision="main"            # branch/tag/commit, fetches the most recent version of the dataset each time this command is called
+            revision="main",            # branch/tag/commit, fetches the most recent version of the dataset each time this command is called
+            token = os.getenv("HF_TOKEN")
         )
 
         with open(question_map_path, 'r') as f:
             question_map = json.load(f)
 
-        evaluator_directory = question_map.get(evaluator_id, {}).get('evaluator_name', None)
+        evaluator_directory = question_map.get(evaluator_id, None)
         all_files = list_repo_files(
             repo_id=REPO_ID,
             repo_type="dataset",
             revision="main",
+            token = os.getenv("HF_TOKEN")
         )
 
-        full_question_ids_list, data_by_filename = get_evaluator_questions(evaluator_id, all_files, evaluator_directory, question_map)
+        full_question_ids_list, data_by_filename = get_evaluator_questions(evaluator_id, all_files, evaluator_directory)
         remaining_count = len(full_question_ids_list)
 
         # --- Part 3: Determine UI updates based on remaining count ---
@@ -849,6 +950,7 @@ with gr.Blocks(css=centered_col_css) as demo:
                 None,
                 None,
                 None,
+                None,
                 None
             )
         
@@ -858,17 +960,17 @@ with gr.Blocks(css=centered_col_css) as demo:
 
         #Constructing question_for_eval, the question to evaluate this round
         txagent_matched_entry = next(
-            (entry for entry in data_by_filename['txagent'] if entry.get("question_ID") == q_id),
+            (entry for entry in data_by_filename['TxAgent-T1-Llama-3.1-8B'] if preprocess_question_id(entry.get("id")) == q_id),
             None
         )
         other_model_matched_entry = next(
-            (entry for entry in data_by_filename[other_model_name] if entry.get("question_ID") == q_id),
+            (entry for entry in data_by_filename[other_model_name] if preprocess_question_id(entry.get("id")) == q_id),
             None
         )
 
         models_list = [
             {
-                "model": "txagent",
+                "model": 'TxAgent-T1-Llama-3.1-8B',
                 "reasoning_trace": txagent_matched_entry.get("solution")
             },
             {
@@ -880,7 +982,7 @@ with gr.Blocks(css=centered_col_css) as demo:
 
         question_for_eval = {
             "question": txagent_matched_entry.get("question"),
-            "question_ID": q_id,
+            "id": q_id,
             "models": models_list,
         }
 
@@ -890,6 +992,7 @@ with gr.Blocks(css=centered_col_css) as demo:
 
         # Construct the question-specific elements of the pairwise rating page (page 1)
         page1_prompt = gr.HTML(f'<div style="background-color: #FFEFD5; border: 2px solid #FF8C00; padding: 10px; border-radius: 5px; color: black;"><strong style="color: black;">Prompt:</strong> {prompt_text}</div>')
+        page1_reference_answer = gr.Markdown(txagent_matched_entry.get("correct_answer"))
         chat_a = gr.Chatbot(
                 value=chat_A_value,
                 type="messages",
@@ -925,21 +1028,8 @@ with gr.Blocks(css=centered_col_css) as demo:
             chat_a,
             chat_b,
             page1_prompt,
+            page1_reference_answer,
             question_for_eval)
-
-        # except Exception as e:
-        #     error_message = f"Your submission was saved, but an error occurred while checking for remaining questions: {e}. Please try starting the process again by entering your details. If the problem persists, contact the administrator."
-        #     print(f"Error during recalculation in final_submit: {e}") # Keep logging for debugging
-        #     # *** MODIFIED RETURN ***: Error during recalculation
-        #     return (
-        #         gr.update(visible=True),   # page0 (Show) - Send user back to start
-        #         gr.update(visible=False),  # page2 (Hide)
-        #         gr.update(visible=False),  # confirm_modal (Hide)
-        #         gr.update(visible=False),  # eval_progress_modal (Hide)
-        #         "",                        # eval_progress_text (Clear)
-        #         gr.update(visible=False),  # final_page (Hide)
-        #         error_message              # page0_error_box (Update with error)
-        #     )
     
     def cancel_submission():
         # Cancel final submission: just hide the confirmation modal.
@@ -976,6 +1066,7 @@ with gr.Blocks(css=centered_col_css) as demo:
 
             # page2 elements that need to be reset
             gr.update(value=""),  #page2_prompt
+            gr.update(value=""),  #page2_reference_answer
             gr.update(value=[]),  #chat_a_rating
             gr.update(value=[]),  #chat_b_rating
             gr.update(value=""),  #result_text
@@ -1002,7 +1093,7 @@ with gr.Blocks(css=centered_col_css) as demo:
     next_btn_0.click(
         fn=go_to_eval_progress_modal,
         inputs=[name, email, evaluator_id, 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],
+        outputs=[page0, page1, user_info_state, page0_error_box, chat_a, chat_b, page1_prompt, page1_reference_answer, data_subset_state,eval_progress_modal,eval_progress_text],
         scroll_to_output=True
     )
 
@@ -1029,7 +1120,7 @@ with gr.Blocks(css=centered_col_css) as demo:
     next_btn_1.click(
         fn=go_to_page2,  # ### EDIT: Rename or update the function to simply pass the pairwise inputs if needed.
         inputs=[data_subset_state,*pairwise_inputs,*comparison_reasons_inputs],
-        outputs=[page1, page2, pairwise_state, comparison_reasons, page1_error_box, chat_a_rating, chat_b_rating, page2_prompt, *pairwise_results_for_display],
+        outputs=[page1, page2, pairwise_state, comparison_reasons, page1_error_box, chat_a_rating, chat_b_rating, page2_prompt, page2_reference_answer,*pairwise_results_for_display],
         scroll_to_output=True
     )
     
@@ -1082,7 +1173,7 @@ with gr.Blocks(css=centered_col_css) as demo:
     # )
     question_submission_event = yes_btn.click(
         fn=final_submit,
-        inputs=[data_subset_state, user_info_state, pairwise_state, comparison_reasons, *ratings_A, *ratings_B],
+        inputs=[data_subset_state, user_info_state, pairwise_state, comparison_reasons, nonsense_btn_clicked, *ratings_A, *ratings_B],
         outputs=[
             page0,                 # Controlled by final_submit return value 1
             page2,                 # Controlled by final_submit return value 2
@@ -1094,6 +1185,7 @@ with gr.Blocks(css=centered_col_css) as demo:
             chat_a,
             chat_b,
             page1_prompt,
+            page1_reference_answer,
             data_subset_state
         ],
         scroll_to_output=True
@@ -1131,6 +1223,7 @@ with gr.Blocks(css=centered_col_css) as demo:
 
             # page2 elements that need to be reset
             page2_prompt,
+            page2_reference_answer,
             chat_a_rating,
             chat_b_rating,
             result_text,

tool_lists/chembl_tools.json

@@ -0,0 +1,16 @@
+[
+    {
+        "type": "ChEMBLTool",
+        "name": "ChEMBL_search_similar_molecules",
+        "description": "Search for molecules similar to a given SMILES, chembl_id, or compound or drug name, using the ChEMBL Web Services.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "query": { "type": "string", "description": "SMILES string, chembl_id, or compound or drug name." },
+                "similarity_threshold": { "type": "integer", "description": "Similarity threshold (0–100).", "default": 80 },
+                "max_results": { "type": "integer", "description": "Maximum number of results to return.", "default": 20 }
+            },
+            "required": ["query"]
+        }
+    }
+]

tool_lists/efo_tools.json

@@ -0,0 +1,17 @@
+[
+    {
+        "type": "EFOTool",
+        "name": "OSL_get_efo_id_by_disease_name",
+        "description": "Tool to lookup Experimental Factor Ontology (EFO) IDs for diseases via the EMBL-EBI OLS API.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "disease": { 
+                    "type": "string", 
+                    "description": "Search query for diseases. Provide the disease name to lookup the corresponding EFO ID." 
+                }
+            },
+            "required": ["disease"]
+        }
+    }
+]

tool_lists/europe_pmc_tools.json

@@ -0,0 +1,22 @@
+[
+    {
+        "type": "EuropePMCTool",
+        "name": "EuropePMC_search_articles",
+        "description": "Search for articles on Europe PMC including abstracts. The tool queries the Europe PMC web service using provided keywords and returns articles with details such as title, abstract, journal, publication year, and a URL to the full article.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "query": { 
+                    "type": "string", 
+                    "description": "Search query for Europe PMC. Use keywords separated by spaces to refine your search." 
+                },
+                "limit": { 
+                    "type": "integer", 
+                    "description": "Number of articles to return. This sets the maximum number of articles retrieved from Europe PMC.", 
+                    "default": 5 
+                }
+            },
+            "required": ["query"]
+        }
+    }
+]

tool_lists/fda_drug_adverse_event_tools.json

@@ -0,0 +1,491 @@
+[
+    {
+      "type": "FDADrugAdverseEventTool",
+      "name": "FAERS_count_reactions_by_drug_event",
+      "description": "Count the number of adverse reactions reported for a given drug, filtered by patient details, event seriousness, and reaction outcomes. Data source: FDA Adverse Event Reporting System (FAERS).",
+      "parameter": {
+        "type": "object",
+        "properties": {
+          "medicinalproduct": { "type": "string", "description": "Drug name." },
+          "patient.patientsex": { "type": "string", "enum": ["Male", "Female"], "description": "Patient sex, leave it blank if you don't want to apply a filter." },
+          "patient.patientagegroup": { "type": "string", "enum": ["Neonate", "Infant", "Child", "Adolescent", "Adult", "Elderly"], "description": "Patient age group." },
+          "occurcountry": { "type": "string", "pattern": "^[A-Z]{2}$", "description": "Country where event occurred." },
+          "serious": { "type": "string", "enum": ["Yes","No"], "description": "Whether the event was serious." },
+          "seriousnessdeath": { "type": "string", "enum": ["Yes", "No"], "description": "Was death reported?" }
+        },
+        "required": ["medicinalproduct"]
+      },
+      "fields": {
+        "search_fields": {
+          "medicinalproduct": ["patient.drug.medicinalproduct"],
+          "patient.patientsex": ["patient.patientsex"],
+          "patient.patientagegroup": ["patient.patientagegroup"],
+          "occurcountry": ["occurcountry"],
+          "serious": ["serious"],
+          "seriousnessdeath": ["seriousnessdeath"]
+        },
+        "return_fields": ["patient.reaction.reactionmeddrapt.exact"]
+      }
+    },
+    {
+      "type": "FDADrugAdverseEventTool",
+      "name": "FAERS_count_drugs_by_drug_event",
+      "description": "Count the number of different drugs involved in FDA adverse event reports, filtered by patient details, country, and seriousness. Data source: FDA Adverse Event Reporting System (FAERS).",
+      "parameter": {
+        "type": "object",
+        "properties": {
+          "patient.patientsex": { "type": "string", "enum": ["Male", "Female"], "description": "Patient sex, leave it blank if you don't want to apply a filter." },
+          "patient.patientagegroup": { "type": "string", "enum": ["Neonate", "Infant", "Child", "Adolescent", "Adult", "Elderly"], "description": "Patient age group." },
+          "occurcountry": { "type": "string", "pattern": "^[A-Z]{2}$", "description": "Country where event occurred." },
+          "serious": { "type": "string", "enum": ["Yes","No"], "description": "Whether the event was serious." }
+        },
+        "required": []
+      },
+      "fields": {
+        "search_fields": {
+          "patient.patientsex": ["patient.patientsex"],
+          "patient.patientagegroup": ["patient.patientagegroup"],
+          "occurcountry": ["occurcountry"],
+          "serious": ["serious"]
+        },
+        "return_fields": ["patient.drug.medicinalproduct.exact"]
+      }
+    },
+    {
+      "type": "FDADrugAdverseEventTool",
+      "name": "FAERS_count_country_by_drug_event",
+      "description": "Count the number of adverse event reports per country of occurrence, filtered by drug, patient demographics, and seriousness. Data source: FDA Adverse Event Reporting System (FAERS).",
+      "parameter": {
+        "type": "object",
+        "properties": {
+          "medicinalproduct": { "type": "string", "description": "Drug name." },
+          "patient.patientsex": { "type": "string", "enum": ["Male", "Female"], "description": "Patient sex, leave it blank if you don't want to apply a filter." },
+          "patient.patientagegroup": { "type": "string", "enum": ["Neonate", "Infant", "Child", "Adolescent", "Adult", "Elderly"], "description": "Patient age group." },
+          "serious": { "type": "string", "enum": ["Yes","No"], "description": "Whether the event was serious." }
+        },
+        "required": []
+      },
+      "fields": {
+        "search_fields": {
+          "medicinalproduct": ["patient.drug.medicinalproduct"],
+          "patient.patientsex": ["patient.patientsex"],
+          "patient.patientagegroup": ["patient.patientagegroup"],
+          "serious": ["serious"]
+        },
+        "return_fields": ["occurcountry.exact"]
+      }
+    },
+    {
+      "type": "FDADrugAdverseEventTool",
+      "name": "FAERS_count_reportercountry_by_drug_event",
+      "description": "Count the number of FDA adverse event reports grouped by the country of the primary reporter. Data source: FDA Adverse Event Reporting System (FAERS).",
+      "parameter": {
+        "type": "object",
+        "properties": {
+          "medicinalproduct": { "type": "string", "description": "Drug name." },
+          "patient.patientsex": { "type": "string", "enum": ["Male", "Female"], "description": "Patient sex, leave it blank if you don't want to apply a filter." },
+          "patient.patientagegroup": { "type": "string", "enum": ["Neonate", "Infant", "Child", "Adolescent", "Adult", "Elderly"], "description": "Patient age group." },
+          "serious": { "type": "string", "enum": ["Yes","No"], "description": "Whether the event was serious." }
+        },
+        "required": []
+      },
+      "fields": {
+        "search_fields": {
+          "medicinalproduct": ["patient.drug.medicinalproduct"],
+          "patient.patientsex": ["patient.patientsex"],
+          "patient.patientagegroup": ["patient.patientagegroup"],
+          "serious": ["serious"]
+        },
+        "return_fields": ["primarysource.reportercountry.exact"]
+      }
+    },
+    {
+      "type": "FDADrugAdverseEventTool",
+      "name": "FAERS_count_seriousness_by_drug_event",
+      "description": "Count the number of adverse event reports classified as serious or non-serious, filtered by drug and patient demographics. In results, term Serious means: 'The adverse event resulted in death, a life threatening condition, hospitalization, disability, congenital anomaly, or other serious condition', term Non-serious means 'The adverse event did not result in any of the above' Data source: FDA Adverse Event Reporting System (FAERS).",
+      "parameter": {
+        "type": "object",
+        "properties": {
+          "medicinalproduct": { "type": "string", "description": "Drug name." },
+          "patient.patientsex": { "type": "string", "enum": ["Male", "Female"], "description": "Patient sex, leave it blank if you don't want to apply a filter." },
+          "patient.patientagegroup": { "type": "string", "enum": ["Neonate", "Infant", "Child", "Adolescent", "Adult", "Elderly"], "description": "Patient age group." },
+          "occurcountry": { "type": "string", "pattern": "^[A-Z]{2}$", "description": "Country where event occurred." }
+        },
+        "required": []
+      },
+      "fields": {
+        "search_fields": {
+          "medicinalproduct": ["patient.drug.medicinalproduct"],
+          "patient.patientsex": ["patient.patientsex"],
+          "patient.patientagegroup": ["patient.patientagegroup"],
+          "occurcountry": ["occurcountry"]
+        },
+        "return_fields": ["serious"],
+        "return_fields_mapping": {
+          "serious": {
+            "1": "Serious",
+            "2": "Non-serious"
+          }
+        }
+      }
+    },
+    {
+      "type": "FDADrugAdverseEventTool",
+      "name": "FAERS_count_outcomes_by_drug_event",
+      "description": "Count the outcome of adverse reactions (recovered, recovering, fatal, unresolved) filtered by drug, seriousness, and demographics. Data source: FDA Adverse Event Reporting System (FAERS).",
+      "parameter": {
+        "type": "object",
+        "properties": {
+          "medicinalproduct": { "type": "string", "description": "Drug name." },
+          "patient.patientsex": { "type": "string", "enum": [ "Male", "Female"] },
+          "patient.patientagegroup": { "type": "string", "enum": ["Neonate", "Infant", "Child", "Adolescent", "Adult", "Elderly"] },
+          "occurcountry": { "type": "string", "pattern": "^[A-Z]{2}$" }
+        },
+        "required": ["medicinalproduct"]
+      },
+      "fields": {
+        "search_fields": {
+          "medicinalproduct": ["patient.drug.medicinalproduct"],
+          "patient.patientsex": ["patient.patientsex"],
+          "patient.patientagegroup": ["patient.patientagegroup"],
+          "occurcountry": ["occurcountry"]
+        },
+        "return_fields": ["patient.reaction.reactionoutcome"],
+        "return_fields_mapping": {
+           "patient.reaction.reactionoutcome": {
+            "1": "Recovered/resolved",
+            "2": "Recovering/resolving",
+            "3": "Not recovered/not resolved",
+            "4": "Recovered/resolved with sequelae (consequent health issues)",
+            "5": "Fatal",
+            "6": "Unknown"
+          }
+        }
+      }
+    },
+    {
+      "type": "FDADrugAdverseEventTool",
+      "name": "FAERS_count_drug_routes_by_event",
+      "description": "Count the most common routes of administration for drugs involved in adverse event reports. Data source: FDA Adverse Event Reporting System (FAERS).",
+      "parameter": {
+        "type": "object",
+        "properties": {
+          "medicinalproduct": { "type": "string", "description": "Drug name." },
+          "serious": { "type": "string", "enum": ["Yes","No"], "description": "Seriousness of event." }
+        },
+        "required": ["medicinalproduct"]
+      },
+      "fields": {
+        "search_fields": {
+          "medicinalproduct": ["patient.drug.medicinalproduct"],
+          "serious": ["serious"]
+        },
+        "return_fields": ["patient.drug.drugadministrationroute.exact"],
+        "return_fields_mapping": {
+          "patient.drug.drugadministrationroute.exact": {
+            "001": "Auricular (otic)",
+            "002": "Buccal",
+            "003": "Cutaneous",
+            "004": "Dental",
+            "005": "Endocervical",
+            "006": "Endosinusial",
+            "007": "Endotracheal",
+            "008": "Epidural",
+            "009": "Extra-amniotic",
+            "010": "Hemodialysis",
+            "011": "Intra corpus cavernosum",
+            "012": "Intra-amniotic",
+            "013": "Intra-arterial",
+            "014": "Intra-articular",
+            "015": "Intra-uterine",
+            "016": "Intracardiac",
+            "017": "Intracavernous",
+            "018": "Intracerebral",
+            "019": "Intracervical",
+            "020": "Intracisternal",
+            "021": "Intracorneal",
+            "022": "Intracoronary",
+            "023": "Intradermal",
+            "024": "Intradiscal (intraspinal)",
+            "025": "Intrahepatic",
+            "026": "Intralesional",
+            "027": "Intralymphatic",
+            "028": "Intramedullar (bone marrow)",
+            "029": "Intrameningeal",
+            "030": "Intramuscular",
+            "031": "Intraocular",
+            "032": "Intrapericardial",
+            "033": "Intraperitoneal",
+            "034": "Intrapleural",
+            "035": "Intrasynovial",
+            "036": "Intratumor",
+            "037": "Intrathecal",
+            "038": "Intrathoracic",
+            "039": "Intratracheal",
+            "040": "Intravenous bolus",
+            "041": "Intravenous drip",
+            "042": "Intravenous (not otherwise specified)",
+            "043": "Intravesical",
+            "044": "Iontophoresis",
+            "045": "Nasal",
+            "046": "Occlusive dressing technique",
+            "047": "Ophthalmic",
+            "048": "Oral",
+            "049": "Oropharingeal",
+            "050": "Other",
+            "051": "Parenteral",
+            "052": "Periarticular",
+            "053": "Perineural",
+            "054": "Rectal",
+            "055": "Respiratory (inhalation)",
+            "056": "Retrobulbar",
+            "057": "Sunconjunctival",
+            "058": "Subcutaneous",
+            "059": "Subdermal",
+            "060": "Sublingual",
+            "061": "Topical",
+            "062": "Transdermal",
+            "063": "Transmammary",
+            "064": "Transplacental",
+            "065": "Unknown",
+            "066": "Urethral",
+            "067": "Vaginal"
+          }
+        }
+      }
+    },
+    {
+      "type": "FDADrugAdverseEventTool",
+      "name": "FAERS_count_patient_age_distribution",
+      "description": "Analyze the age distribution of patients experiencing adverse events for a specific drug. The age groups are: Neonate (0-28 days), Infant (29 days - 23 months), Child (2-11 years), Adolescent (12-17 years), Adult (18-64 years), Elderly (65+ years). Data source: FDA Adverse Event Reporting System (FAERS).",
+      "parameter": {
+        "type": "object",
+        "properties": {
+          "medicinalproduct": { "type": "string", "description": "Drug name." }
+        },
+        "required": ["medicinalproduct"]
+      },
+      "fields": {
+        "search_fields": {
+          "medicinalproduct": ["patient.drug.medicinalproduct"]
+        },
+        "return_fields": ["patient.patientagegroup"],
+        "return_fields_mapping": {
+          "patient.patientagegroup": {
+            "1": "Neonate",
+            "2": "Infant",
+            "3": "Child",
+            "4": "Adolescent",
+            "5": "Adult",
+            "6": "Elderly"
+          }
+        }
+      }
+    },
+    {
+      "type": "FDADrugAdverseEventTool",
+      "name": "FAERS_count_death_related_by_drug",
+      "description": "Count adverse events associated with patient death for a given drug. Data source: FDA Adverse Event Reporting System (FAERS).",
+      "parameter": {
+        "type": "object",
+        "properties": {
+          "medicinalproduct": { "type": "string", "description": "Drug name." }
+        },
+        "required": ["medicinalproduct"]
+      },
+      "fields": {
+        "search_fields": {
+          "medicinalproduct": ["patient.drug.medicinalproduct"],
+          "seriousnessdeath": ["seriousnessdeath"]
+        },
+        "return_fields": ["seriousnessdeath"],
+        "return_fields_mapping": {
+          "seriousnessdeath": {
+            "1": "death",
+            "2": "alive"
+          }
+        }
+      }
+    },
+    {
+      "type": "FDACountAdditiveReactionsTool",
+      "name": "FAERS_count_additive_adverse_reactions",
+      "description": "Additive multi-drug data: Aggregate adverse reaction counts across specified medicinal products, stratified by demographics, seriousness, and outcomes. Data source: FDA Adverse Event Reporting System (FAERS).",
+      "parameter": {
+        "type": "object",
+        "properties": {
+          "medicinalproducts": { "type": "array", "items": { "type": "string" }, "description": "Array of medicinal product names." },
+          "patient.patientsex": { "type": "string", "enum": ["Male","Female"], "description": "Filter by patient sex." },
+          "patient.patientagegroup": { "type": "string", "enum": ["Neonate","Infant","Child","Adolescent","Adult","Elderly"], "description": "Filter by patient age group." },
+          "occurcountry": { "type": "string", "pattern": "^[A-Z]{2}$", "description": "Filter by ISO2 country code of occurrence." },
+          "serious": { "type": "string", "enum": ["Yes","No"], "description": "Filter by seriousness classification." },
+          "seriousnessdeath": { "type": "string", "enum": ["Yes","No"], "description": "Filter for fatal outcomes." }
+        },
+        "required": ["medicinalproducts"]
+      },
+      "fields": {
+        "search_fields": {
+          "medicinalproducts": ["patient.drug.medicinalproduct"],
+          "patient.patientsex": ["patient.patientsex"],
+          "patient.patientagegroup": ["patient.patientagegroup"],
+          "occurcountry": ["occurcountry"],
+          "serious": ["serious"],
+          "seriousnessdeath": ["seriousnessdeath"]
+        },
+        "return_fields": ["patient.reaction.reactionmeddrapt.exact"]
+      }
+    },
+    {
+      "type": "FDACountAdditiveReactionsTool",
+      "name": "FAERS_count_additive_event_reports_by_country",
+      "description": "Additive multi-drug data: Aggregate report counts by country of occurrence across specified medicinal products. Data source: FDA Adverse Event Reporting System (FAERS).",
+      "parameter": {
+        "type": "object",
+        "properties": {
+          "medicinalproducts": { "type": "array", "items": { "type": "string" }, "description": "Array of medicinal product names." },
+          "patient.patientsex": { "type": "string", "enum": ["Male","Female"], "description": "Filter by sex." },
+          "patient.patientagegroup": { "type": "string", "enum": ["Neonate","Infant","Child","Adolescent","Adult","Elderly"], "description": "Filter by age group." },
+          "serious": { "type": "string", "enum": ["Yes","No"], "description": "Filter by seriousness." }
+        },
+        "required": ["medicinalproducts"]
+      },
+      "fields": {
+        "search_fields": {
+          "medicinalproducts": ["patient.drug.medicinalproduct"],
+          "patient.patientsex": ["patient.patientsex"],
+          "patient.patientagegroup": ["patient.patientagegroup"],
+          "serious": ["serious"]
+        },
+        "return_fields": ["occurcountry.exact"]
+      }
+    },
+    {
+      "type": "FDACountAdditiveReactionsTool",
+      "name": "FAERS_count_additive_reports_by_reporter_country",
+      "description": "Additive multi-drug data: Aggregate adverse event reports by primary reporter country across medicinal products. Data source: FDA Adverse Event Reporting System (FAERS).",
+      "parameter": {
+        "type": "object",
+        "properties": {
+          "medicinalproducts": { "type": "array", "items": { "type": "string" }, "description": "Array of medicinal product names." },
+          "patient.patientsex": { "type": "string", "enum": ["Male","Female"], "description": "Filter by sex." },
+          "patient.patientagegroup": { "type": "string", "enum": ["Neonate","Infant","Child","Adolescent","Adult","Elderly"], "description": "Filter by age group." },
+          "serious": { "type": "string", "enum": ["Yes","No"], "description": "Filter by seriousness." }
+        },
+        "required": ["medicinalproducts"]
+      },
+      "fields": {
+        "search_fields": {
+          "medicinalproducts": ["patient.drug.medicinalproduct"],
+          "patient.patientsex": ["patient.patientsex"],
+          "patient.patientagegroup": ["patient.patientagegroup"],
+          "serious": ["serious"]
+        },
+        "return_fields": ["primarysource.reportercountry.exact"]
+      }
+    },
+    {
+      "type": "FDACountAdditiveReactionsTool",
+      "name": "FAERS_count_additive_seriousness_classification",
+      "description": "Additive multi-drug data: Quantify serious vs non-serious classifications across medicinal products, annotated per regulatory definitions. Data source: FDA Adverse Event Reporting System (FAERS).",
+      "parameter": {
+        "type": "object",
+        "properties": {
+          "medicinalproducts": { "type": "array", "items": { "type": "string" }, "description": "Array of medicinal product names." },
+          "patient.patientsex": { "type": "string", "enum": ["Male","Female"], "description": "Filter by sex." },
+          "patient.patientagegroup": { "type": "string", "enum": ["Neonate","Infant","Child","Adolescent","Adult","Elderly"], "description": "Filter by age group." },
+          "occurcountry": { "type": "string", "pattern": "^[A-Z]{2}$", "description": "ISO2 country code filter." }
+        },
+        "required": ["medicinalproducts"]
+      },
+      "fields": {
+        "search_fields": {
+          "medicinalproducts": ["patient.drug.medicinalproduct"],
+          "patient.patientsex": ["patient.patientsex"],
+          "patient.patientagegroup": ["patient.patientagegroup"],
+          "occurcountry": ["occurcountry"]
+        },
+        "return_fields": ["serious"],
+        "return_fields_mapping": { "serious": { "1": "Serious", "2": "Non-serious" } }
+      }
+    },
+    {
+      "type": "FDACountAdditiveReactionsTool",
+      "name": "FAERS_count_additive_reaction_outcomes",
+      "description": "Additive multi-drug data: Determine reaction outcome counts (e.g., recovered, resolving, fatal) across medicinal products using standardized outcome mappings. Data source: FDA Adverse Event Reporting System (FAERS).",
+      "parameter": {
+        "type": "object",
+        "properties": {
+          "medicinalproducts": { "type": "array", "items": { "type": "string" }, "description": "Array of medicinal product names." },
+          "patient.patientsex": { "type": "string", "enum": ["Male","Female"] },
+          "patient.patientagegroup": { "type": "string", "enum": ["Neonate","Infant","Child","Adolescent","Adult","Elderly"] },
+          "occurcountry": { "type": "string", "pattern": "^[A-Z]{2}$" }
+        },
+        "required": ["medicinalproducts"]
+      },
+      "fields": {
+        "search_fields": {
+          "medicinalproducts": ["patient.drug.medicinalproduct"],
+          "patient.patientsex": ["patient.patientsex"],
+          "patient.patientagegroup": ["patient.patientagegroup"],
+          "occurcountry": ["occurcountry"]
+        },
+        "return_fields": ["patient.reaction.reactionoutcome"],
+        "return_fields_mapping": {
+          "patient.reaction.reactionoutcome": {
+            "1": "Recovered/resolved",
+            "2": "Recovering/resolving",
+            "3": "Not recovered/not resolved",
+            "4": "Recovered/resolved with sequelae",
+            "5": "Fatal",
+            "6": "Unknown"
+          }
+        }
+      }
+    },
+    {
+      "type": "FDACountAdditiveReactionsTool",
+      "name": "FAERS_count_additive_administration_routes",
+      "description": "Additive multi-drug data: Enumerate and count administration routes for adverse events across specified medicinal products, using standardized route codes. Data source: FDA Adverse Event Reporting System (FAERS).",
+      "parameter": {
+        "type": "object",
+        "properties": {
+          "medicinalproducts": { "type": "array", "items": { "type": "string" }, "description": "Array of medicinal product names." },
+          "serious": { "type": "string", "enum": ["Yes","No"], "description": "Filter by seriousness." }
+        },
+        "required": ["medicinalproducts"]
+      },
+      "fields": {
+        "search_fields": {
+          "medicinalproducts": ["patient.drug.medicinalproduct"],
+          "serious": ["serious"]
+        },
+        "return_fields": ["patient.drug.drugadministrationroute.exact"],
+        "return_fields_mapping": {
+          "patient.drug.drugadministrationroute.exact": {
+            "001": "Auricular (otic)", "002": "Buccal", "003": "Cutaneous", "004": "Dental",
+            "005": "Endocervical", "006": "Endosinusial", "007": "Endotracheal", "008": "Epidural",
+            "009": "Extra-amniotic", "010": "Hemodialysis", "011": "Intra corpus cavernosum",
+            "012": "Intra-amniotic", "013": "Intra-arterial", "014": "Intra-articular",
+            "015": "Intra-uterine", "016": "Intracardiac", "017": "Intracavernous",
+            "018": "Intracerebral", "019": "Intracervical", "020": "Intracisternal",
+            "021": "Intracorneal", "022": "Intracoronary", "023": "Intradermal",
+            "024": "Intradiscal (intraspinal)", "025": "Intrahepatic", "026": "Intralesional",
+            "027": "Intralymphatic", "028": "Intramedullar (bone marrow)", "029": "Intrameningeal",
+            "030": "Intramuscular", "031": "Intraocular", "032": "Intrapericardial",
+            "033": "Intraperitoneal", "034": "Intrapleural", "035": "Intrasynovial",
+            "036": "Intratumor", "037": "Intrathecal", "038": "Intrathoracic",
+            "039": "Intratracheal", "040": "Intravenous bolus", "041": "Intravenous drip",
+            "042": "Intravenous (not otherwise specified)", "043": "Intravesical",
+            "044": "Iontophoresis", "045": "Nasal", "046": "Occlusive dressing technique",
+            "047": "Ophthalmic", "048": "Oral", "049": "Oropharingeal", "050": "Other",
+            "051": "Parenteral", "052": "Periarticular", "053": "Perineural",
+            "054": "Rectal", "055": "Respiratory (inhalation)", "056": "Retrobulbar",
+            "057": "Sunconjunctival", "058": "Subcutaneous", "059": "Subdermal",
+            "060": "Sublingual", "061": "Topical", "062": "Transdermal",
+            "063": "Transmammary", "064": "Transplacental", "065": "Unknown",
+            "066": "Urethral", "067": "Vaginal"
+          }
+        }
+      }
+    }
+  ]

tool_lists/monarch_tools.json

@@ -0,0 +1,118 @@
+[
+    {
+        "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"
+    }
+]

tool_lists/opentarget_tools.json

@@ -0,0 +1,1439 @@
+[
+    {
+        "name": "OpenTargets_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: $efoId) {\n    id\n    name\n    associatedTargets {\n      count\n      rows {\n        target {\n          id\n          approvedSymbol\n        }\n        score\n      }\n    }\n  }\n}\n",
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_associated_diseases_phenotypes_by_target_ensemblID",
+        "description": "Find diseases or phenotypes associated with a specific target using ensemblId.",
+        "label": [
+            "Target",
+            "Disease",
+            "Phenotype",
+            "Association",
+            "OpenTarget",
+            "GraphQL"
+        ],
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "ensemblId": {
+                    "type": "string",
+                    "description": "The ensemblId of a target.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\nquery associatedDiseases($ensemblId: String!) {\n  target(ensemblId: $ensemblId) {\n    id\n    approvedSymbol\n    associatedDiseases {\n      count\n      rows {\n        disease {\n          id\n          name\n        }\n        datasourceScores {\n          id\n          score\n        }\n      }\n    }\n  }\n}\n",
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_target_disease_evidence",
+        "description": "Explore evidence that supports a specific target-disease association. Input is disease efoId and target ensemblID.",
+        "label": [
+            "Target",
+            "Disease",
+            "Evidence",
+            "Association",
+            "OpenTarget",
+            "GraphQL"
+        ],
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "efoId": {
+                    "type": "string",
+                    "description": "The efoId of a disease or phenotype.",
+                    "required": true
+                },
+                "ensemblId": {
+                    "type": "string",
+                    "description": "The ensemblId of a target.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\nquery targetDiseaseEvidence($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": "OpenTargets_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: $chemblId) {\n      id\n      name\n      drugWarnings {\n        warningType\n        description\n        country\n        year\n        toxicityClass\n        chemblIds\n     efoIdForWarningClass\n      references {\n          id\n          source\n          url\n        }\n      }\n    }\n  }\n  ",
+        "label": [
+            "Drug",
+            "AdverseEvents",
+            "SafetyLiability",
+            "OpenTarget",
+            "GraphQL",
+            "Warnings",
+            "Safety",
+            "Withdrawal",
+            "Toxicity"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_drug_mechanisms_of_action_by_chemblId",
+        "description": "Retrieve the mechanisms of action associated with a specific drug using chemblId.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "chemblId": {
+                    "type": "string",
+                    "description": "The ChEMBL ID of the drug.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n  query drugMechanismsOfAction($chemblId: String!) {\n    drug(chemblId: $chemblId) {\n      id\n      name\n      mechanismsOfAction {\n        rows {\n          mechanismOfAction\n          actionType\n         targetName\n          targets {\n            id\n            approvedSymbol\n          }\n        }\n      }\n    }\n  }\n  ",
+        "label": [
+            "Drug",
+            "MechanismsOfAction",
+            "Target",
+            "Pharmacology",
+            "ChemblId",
+            "OpenTarget",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_associated_drugs_by_disease_efoId",
+        "description": "Retrieve known drugs associated with a specific disease by disease efoId.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "efoId": {
+                    "type": "string",
+                    "description": "The EFO ID of the disease.",
+                    "required": true
+                },
+                "size": {
+                    "type": "integer",
+                    "description": "Number of entries to fetch, recomanding a large number to avoid missing drugs.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n  query diseaseKnownDrugs($efoId: String!, $size: Int!, $freeTextQuery: String) {\n    disease(efoId: $efoId) {\n      id\n      name\n      knownDrugs(size: $size, freeTextQuery: $freeTextQuery) {\n        count\n        rows {\n          drug {\n            id\n            name\n            tradeNames\n            maximumClinicalTrialPhase\n            isApproved\n            hasBeenWithdrawn\n          }\n          phase\n          status\n          mechanismOfAction\n          target {\n            id\n            approvedSymbol\n          }\n        }\n      }\n    }\n  }\n  ",
+        "label": [
+            "OpenTarget",
+            "Disease",
+            "Drug",
+            "Pagination",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_similar_entities_by_disease_efoId",
+        "description": "Retrieve similar entities for a given disease efoId using a model trained with PubMed.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "efoId": {
+                    "type": "string",
+                    "description": "The EFO ID of the disease.",
+                    "required": true
+                },
+                "threshold": {
+                    "type": "number",
+                    "description": "Threshold similarity between 0 and 1. Only results above threshold are returned.",
+                    "required": true
+                },
+                "size": {
+                    "type": "integer",
+                    "description": "Number of similar entities to fetch.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n  query diseaseSimilarEntities($efoId: String!, $threshold: Float!, $size: Int!) {\n    disease(efoId: $efoId) {\n      id\n      name\n      similarEntities(threshold: $threshold, size: $size) {\n        id\n        category\n        score\n        object {\n          ... on Disease {\n            id\n            name\n          }\n          ... on Target {\n            id\n            approvedSymbol\n          }\n          ... on Drug {\n            id\n            name\n          }\n        }\n      }\n    }\n  }\n  ",
+        "label": [
+            "Disease",
+            "Similarity",
+            "Model",
+            "Entities",
+            "OpenTarget",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_similar_entities_by_drug_chemblId",
+        "description": "Retrieve similar entities for a given drug chemblId using a model trained with PubMed.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "chemblId": {
+                    "type": "string",
+                    "description": "The chemblId of the disease.",
+                    "required": true
+                },
+                "threshold": {
+                    "type": "number",
+                    "description": "Threshold similarity between 0 and 1. Only results above threshold are returned.",
+                    "required": true
+                },
+                "size": {
+                    "type": "integer",
+                    "description": "Number of similar entities to fetch.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n  query diseaseSimilarEntities($chemblId: String!, $threshold: Float!, $size: Int!) {\n    drug(chemblId: $chemblId) {\n      id\n      name\n      similarEntities(threshold: $threshold, size: $size) {\n        id\n        category\n        score\n        object {\n          ... on Disease {\n            id\n            name\n          }\n          ... on Target {\n            id\n            approvedSymbol\n          }\n          ... on Drug {\n            id\n            name\n          }\n        }\n      }\n    }\n  }\n  ",
+        "label": [
+            "Drug",
+            "Similarity",
+            "Model",
+            "Entities",
+            "OpenTarget",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_similar_entities_by_target_ensemblID",
+        "description": "Retrieve similar entities for a given target ensemblID using a model trained with PubMed.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "ensemblId": {
+                    "type": "string",
+                    "description": "The ensemblID of the disease.",
+                    "required": true
+                },
+                "threshold": {
+                    "type": "number",
+                    "description": "Threshold similarity between 0 and 1. Only results above threshold are returned.",
+                    "required": true
+                },
+                "size": {
+                    "type": "integer",
+                    "description": "Number of similar entities to fetch.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n  query diseaseSimilarEntities($ensemblId: String!, $threshold: Float!, $size: Int!) {\n    target(ensemblId: $ensemblId) {\n      id\n      approvedSymbol\n      similarEntities(threshold: $threshold, size: $size) {\n        id\n        category\n        score\n        object {\n          ... on Disease {\n            id\n            name\n          }\n          ... on Target {\n            id\n            approvedSymbol\n          }\n          ... on Drug {\n            id\n            name\n          }\n        }\n      }\n    }\n  }\n  ",
+        "label": [
+            "Disease",
+            "Similarity",
+            "Model",
+            "Entities",
+            "OpenTarget",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_associated_phenotypes_by_disease_efoId",
+        "description": "Find HPO phenotypes asosciated with the specified disease efoId.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "efoId": {
+                    "type": "string",
+                    "description": "The efoId of a disease or phenotype.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "query diseaseAnnotation($efoId: String!) {\n  disease(efoId: $efoId) {\n    id\n    name\n    phenotypes {\n      rows {\n        phenotypeHPO {\n          id\n          name\n          description\n          namespace\n        }\n        phenotypeEFO {\n          id\n          name\n        }\n      }\n    }\n  }\n}",
+        "label": [
+            "Disease",
+            "OpenTarget",
+            "GraphQL",
+            "Phenotype",
+            "Symptoms",
+            "Clinical signs"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_drug_withdrawn_blackbox_status_by_chemblId",
+        "description": "Find withdrawn and black-box warning statuses for a specific drug by chemblId.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "chemblId": {
+                    "type": "array",
+                    "items": {
+                        "type": "string"
+                    },
+                    "description": "The chemblId of a drug.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n  query drugWithdrawnWarningData($chemblId: String!) {\n    drug(chemblId: $chemblId) {\n      name\n      id\n      hasBeenWithdrawn\n      blackBoxWarning\n    }\n  }\n  ",
+        "label": [
+            "Drug",
+            "SafetyWarnings",
+            "Withdrawal",
+            "OpenTarget",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_search_category_counts_by_query_string",
+        "description": "Get the count of entries in each entity category (disease, target, drug) based on a query string.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "queryString": {
+                    "type": "string",
+                    "description": "The search string for querying information.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n  query searchCategoryCounts($queryString: String!) {\n    search(queryString: $queryString) {\n      aggregations {\n        total\n        entities {\n          total\n          name\n        }\n      }\n    }\n  }\n  ",
+        "label": [
+            "OpenTarget",
+            "GraphQL",
+            "SearchResults",
+            "Search",
+            "Query",
+            "Counts",
+            "Categories"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_disease_id_description_by_name",
+        "description": "Retrieve the efoId and additional details of a disease based on its name.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "diseaseName": {
+                    "type": "string",
+                    "description": "The name of the disease to search for.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n    query getDiseaseIdByName($diseaseName: String!) {\n      search(queryString: $diseaseName, entityNames: [\"disease\"]) {\n        hits {\n          id\n          name\n          description\n        }\n      }\n    }\n    ",
+        "label": [
+            "Disease",
+            "Identification",
+            "Search",
+            "Name",
+            "Disease",
+            "OpenTarget",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_drug_id_description_by_name",
+        "description": "Fetch the drug chemblId and description based on the drug generic name.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "drugName": {
+                    "type": "string",
+                    "description": "The name of the drug for which the ID is required.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n  query getDrugIdByName($drugName: String!) {\n    search(queryString: $drugName, entityNames: [\"drug\"]) {\n      hits {\n        id\n        name\n       description\n      }\n    }\n  }\n  ",
+        "label": [
+            "Identification",
+            "Search",
+            "Name",
+            "Drug",
+            "OpenTarget",
+            "GraphQL"
+        ],
+        "type": "OpentargetToolDrugNameMatch"
+    },
+    {
+        "name": "OpenTargets_get_drug_chembId_by_generic_name",
+        "description": "Fetch the drug chemblId and description based on the drug generic name.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "drugName": {
+                    "type": "string",
+                    "description": "The generic name of the drug for which the ID is required.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n  query getDrugIdByName($drugName: String!) {\n    search(queryString: $drugName, entityNames: [\"drug\"]) {\n      hits {\n        id\n        name\n       description\n      }\n    }\n  }\n  ",
+        "label": [
+            "Identification",
+            "Search",
+            "Name",
+            "Drug",
+            "OpenTarget",
+            "GraphQL"
+        ],
+        "type": "OpentargetToolDrugNameMatch"
+    },
+    {
+        "name": "OpenTargets_get_drug_indications_by_chemblId",
+        "description": "Fetch indications (treatable phenotypes/diseases) for a given drug chemblId.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "chemblId": {
+                    "type": "string",
+                    "description": "The chemblId of the drug for which to retrieve treatable phenotypes information.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n    query drugIndications($chemblId: String!) {\n      drug(chemblId: $chemblId) {\n     id\n    name\n        indications {\n          rows {\n            disease {\n              id\n              name\n              }\n      maxPhaseForIndication\n     references {\n       source\n        }\n         }\n        }\n      }\n    }\n    ",
+        "label": [
+            "Drug",
+            "Indications",
+            "Disease",
+            "Treatment",
+            "OpenTarget",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_target_gene_ontology_by_ensemblID",
+        "description": "Retrieve Gene Ontology annotations for a specific target by Ensembl ID.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "ensemblId": {
+                    "type": "string",
+                    "description": "The Ensembl ID of the target for which to retrieve Gene Ontology annotations.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query targetGeneOntology($ensemblId: String!) {\n        target(ensemblId: $ensemblId) {\n          id\n          approvedSymbol\n          geneOntology {\n            aspect\n            evidence\n            geneProduct\n            source\n            term {\n              id\n              name\n            }\n          }\n        }\n      }\n    ",
+        "label": [
+            "Target",
+            "GeneOntology",
+            "OpenTarget",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_target_homologues_by_ensemblID",
+        "description": "Fetch homologues for a specific target by Ensembl ID.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "ensemblId": {
+                    "type": "string",
+                    "description": "The Ensembl ID of the target for which to retrieve homologues.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query targetHomologues($ensemblId: String!) {\n        target(ensemblId: $ensemblId) {\n          id\n          approvedSymbol\n          homologues {\n            homologyType\n            queryPercentageIdentity\n            speciesId\n            speciesName\n            targetGeneId\n            targetGeneSymbol\n            targetPercentageIdentity\n            isHighConfidence\n          }\n        }\n      }\n    ",
+        "label": [
+            "OpenTarget",
+            "Target Information",
+            "GraphQL",
+            "Homologue"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_target_safety_profile_by_ensemblID",
+        "description": "Retrieve known target safety liabilities for a specific target Ensembl ID.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "ensemblId": {
+                    "type": "string",
+                    "description": "The Ensembl ID of the target for which to retrieve safety liabilities.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query targetSafetyLiabilities($ensemblId: String!) {\n        target(ensemblId: $ensemblId) {\n          id\n          approvedSymbol\n          safetyLiabilities {\n            event\n            eventId\n            biosamples {\n              cellFormat\n              cellLabel\n              tissueLabel\n              tissueId\n            }\n            effects {\n              dosing\n              direction\n            }\n            studies {\n              name\n              type\n              description\n            }\n            datasource\n            literature\n          }\n        }\n      }\n    ",
+        "label": [
+            "Target",
+            "SafetyLiability",
+            "OpenTarget",
+            "GraphQL",
+            "Safety",
+            "Liabilities"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_biological_mouse_models_by_ensemblID",
+        "description": "Retrieve biological mouse models, including allelic compositions and genetic backgrounds, for a specific target.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "ensemblId": {
+                    "type": "string",
+                    "description": "The Ensembl ID of the target.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query fetchBiologicalModels($ensemblId: String!) {\n        target(ensemblId: $ensemblId) {\n          id\n          approvedSymbol\n          mousePhenotypes {\n            biologicalModels {\n              allelicComposition\n              geneticBackground\n              id\n              literature\n            }\n          }\n        }\n      }\n    ",
+        "label": [
+            "OpenTarget",
+            "Target Information",
+            "BiologicalModels",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_target_genomic_location_by_ensemblID",
+        "description": "Retrieve genomic location data for a specific target, including chromosome, start, end, and strand.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "ensemblId": {
+                    "type": "string",
+                    "description": "The Ensembl ID of the target for which to retrieve genomic location information.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query targetGenomicLocation($ensemblId: String!) {\n        target(ensemblId: $ensemblId) {\n          id\n          approvedSymbol\n          genomicLocation {\n            chromosome\n            start\n            end\n            strand\n          }\n        }\n      }\n    ",
+        "label": [
+            "Target",
+            "GenomicLocation",
+            "OpenTarget",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_target_subcellular_locations_by_ensemblID",
+        "description": "Retrieve information about subcellular locations for a specific target ensemblID.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "ensemblId": {
+                    "type": "string",
+                    "description": "The ensemblId of a target.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query targetSubcellularLocations($ensemblId: String!) {\n        target(ensemblId: $ensemblId) {\n          id\n          approvedSymbol\n          subcellularLocations {\n            location\n            source\n            termSL\n            labelSL\n          }\n        }\n      }\n    ",
+        "label": [
+            "Target",
+            "Subcellular Locations",
+            "GraphQL",
+            "OpenTarget"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_target_synonyms_by_ensemblID",
+        "description": "Retrieve synonyms for specified target, including alternative names and symbols, using given ensemblID.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "ensemblId": {
+                    "type": "string",
+                    "description": "The Ensembl ID of the target.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query retrieveTargetSynonyms($ensemblId: String!) {\n        target(ensemblId: $ensemblId) {\n          id\n          approvedSymbol\n          synonyms {\n            label\n            source\n          }\n          symbolSynonyms {\n            label\n            source\n          }\n          nameSynonyms {\n            label\n            source\n          }\n        }\n      }\n    ",
+        "label": [
+            "OpenTarget",
+            "Target Information",
+            "GraphQL",
+            "Target"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_target_tractability_by_ensemblID",
+        "description": "Retrieve tractability assessments, including modality and values, for a specific target ensembl ID.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "ensemblId": {
+                    "type": "string",
+                    "description": "The Ensembl ID of the target.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query targetTractabilityAssessment($ensemblId: String!) {\n        target(ensemblId: $ensemblId) {\n          id\n          approvedSymbol\n          tractability {\n            label\n            modality\n            value\n          }\n        }\n      }\n    ",
+        "label": [
+            "Target",
+            "Tractability",
+            "OpenTarget",
+            "Target Information",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_target_classes_by_ensemblID",
+        "description": "Retrieve the target classes associated with a specific target ensemblID.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "ensemblId": {
+                    "type": "string",
+                    "description": "The Ensembl ID of the target.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query fetchTargetClasses($ensemblId: String!) {\n        target(ensemblId: $ensemblId) {\n          id\n          approvedSymbol\n          targetClass {\n            id\n            label\n            level\n          }\n        }\n      }\n    ",
+        "label": [
+            "OpenTarget",
+            "Target Information",
+            "GraphQL",
+            "Target"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_target_enabling_packages_by_ensemblID",
+        "description": "Retrieve the Target Enabling Packages (TEP) associated with a specific target ensemblID.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "ensemblId": {
+                    "type": "string",
+                    "description": "The Ensembl ID of the target.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query fetchTargetEnablingPackages($ensemblId: String!) {\n        target(ensemblId: $ensemblId) {\n          id\n          approvedSymbol\n          tep {\n            name\n            uri\n            therapeuticArea\n            description\n          }\n        }\n      }\n    ",
+        "label": [
+            "OpenTarget",
+            "Target Information",
+            "GraphQL",
+            "Target"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_target_interactions_by_ensemblID",
+        "description": "Retrieve interaction data for a specific target ensemblID, including interaction partners and evidence.",
+        "label": [
+            "Target",
+            "Interaction",
+            "Evidence",
+            "GraphQL",
+            "Pagination",
+            "OpenTarget"
+        ],
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "ensemblId": {
+                    "type": "string",
+                    "description": "The Ensembl ID of the target.",
+                    "required": true
+                },
+                "page": {
+                    "type": "object",
+                    "properties": {
+                        "index": {
+                            "type": "integer",
+                            "description": "The index of the page to retrieve.",
+                            "required": true
+                        },
+                        "size": {
+                            "type": "integer",
+                            "description": "The number of items per page.",
+                            "required": true
+                        }
+                    },
+                    "description": "Pagination parameters.",
+                    "required": false
+                }
+            }
+        },
+        "query_schema": "\n      query targetInteractions($ensemblId: String!, $page: Pagination) {\n        target(ensemblId: $ensemblId) {\n          id\n          approvedSymbol\n          interactions(page: $page) {\n            count\n            rows {\n              intA\n              targetA {\n              id\n          approvedSymbol\n        }\n        intB\n        targetB {\n          id\n          approvedSymbol\n        }\n              score\n              sourceDatabase\n              evidences {\n                evidenceScore\n                pubmedId\n                interactionDetectionMethodShortName\n              }\n            }\n          }\n        }\n      }\n    ",
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_disease_ancestors_parents_by_efoId",
+        "description": "Retrieve the disease ancestors and parents in the ontology using the disease EFO ID.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "efoId": {
+                    "type": "string",
+                    "description": "The EFO ID of the disease.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query getDiseaseDetailsByEfoId($efoId: String!) {\n        disease(efoId: $efoId) {\n          id\n          name\n          ancestors\n          parents {\n            id\n            name\n          }\n          }\n      }\n ",
+        "label": [
+            "OpenTarget",
+            "Disease",
+            "Disease Information",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_disease_descendants_children_by_efoId",
+        "description": "Retrieve the disease descendants and children in the ontology using the disease EFO ID.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "efoId": {
+                    "type": "string",
+                    "description": "The EFO ID of the disease.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query getDiseaseDetailsByEfoId($efoId: String!) {\n        disease(efoId: $efoId) {\n          id\n          name\n          descendants\n          children {\n            id\n            name\n          }\n          }\n       }\n",
+        "label": [
+            "OpenTarget",
+            "Disease",
+            "Disease Information",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_disease_locations_by_efoId",
+        "description": "Retrieve the disease's direct location and indirect location disease terms and IDs using the disease EFO ID.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "efoId": {
+                    "type": "string",
+                    "description": "The EFO ID of the disease.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query getDiseaseDetailsByEfoId($efoId: String!) {\n        disease(efoId: $efoId) {\n          id\n          name\n          directLocationIds\n          indirectLocationIds\n          directLocations {\n            id\n            name\n          }\n          indirectLocations {\n            id\n            name\n          }\n        }\n      }\n    ",
+        "label": [
+            "OpenTarget",
+            "Disease",
+            "Disease Information",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_disease_synonyms_by_efoId",
+        "description": "Retrieve disease synonyms by its EFO ID.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "efoId": {
+                    "type": "string",
+                    "description": "The EFO ID of the disease.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query getDiseaseDetailsByEfoId($efoId: String!) {\n        disease(efoId: $efoId) {\n          id\n          name\n        synonyms {\n            relation\n            terms\n          }\n      }\n     }\n",
+        "label": [
+            "OpenTarget",
+            "Disease",
+            "Disease Information",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_disease_description_by_efoId",
+        "description": "Retrieve disease description, name, database cros references, obsolete terms, and whether it's a therapeutic area, all using the specified efoId.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "efoId": {
+                    "type": "string",
+                    "description": "The EFO ID of the disease.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query getDiseaseDetailsByEfoId($efoId: String!) {\n        disease(efoId: $efoId) {\n          id\n          name\n          description\n          dbXRefs\n          obsoleteTerms\n          isTherapeuticArea\n        }\n      }\n    ",
+        "label": [
+            "OpenTarget",
+            "Disease",
+            "Disease Information",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_disease_therapeutic_areas_by_efoId",
+        "description": "Retrieve the therapeutic areas associated with a specific disease efoId.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "efoId": {
+                    "type": "string",
+                    "description": "The EFO ID of the disease.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query diseaseTherapeuticAreas($efoId: String!) {\n        disease(efoId: $efoId) {\n          id\n          name\n          therapeuticAreas {\n            id\n            name\n          }\n        }\n      }\n    ",
+        "label": [
+            "OpenTarget",
+            "Disease",
+            "TherapeuticArea",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_drug_adverse_events_by_chemblId",
+        "description": "Retrieve significant adverse events reported for a specific drug chemblId.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "chemblId": {
+                    "type": "string",
+                    "description": "The ChEMBL ID of the drug.",
+                    "required": true
+                },
+                "page": {
+                    "type": "object",
+                    "properties": {
+                        "index": {
+                            "type": "integer",
+                            "description": "Index of the page to fetch, starting from 0.",
+                            "required": true
+                        },
+                        "size": {
+                            "type": "integer",
+                            "description": "Number of entries per page.",
+                            "required": true
+                        }
+                    },
+                    "description": "Pagination settings.",
+                    "required": false
+                }
+            }
+        },
+        "query_schema": "\n  query drugAdverseEvents($chemblId: String!, $page: Pagination) {\n    drug(chemblId: $chemblId) {\n      id\n      name\n      adverseEvents(page: $page) {\n        count\n        criticalValue\n       rows {\n          name\n          meddraCode\n          count\n          logLR\n        }\n      }\n    }\n  }\n  ",
+        "label": [
+            "Drug",
+            "AdverseEvents",
+            "Safety",
+            "Reporting",
+            "Pagination",
+            "OpenTarget",
+            "GraphQL",
+            "AdverseEvents"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_known_drugs_by_drug_chemblId",
+        "description": "Get a list of known drugs and associated information using the specified chemblId.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "chemblId": {
+                    "type": "string",
+                    "description": "The ChEMBL ID of the drug.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query retrieveMultipleDrugsInfo($chemblId: String!) {\n        drug(chemblId: $chemblId) {\n          id\n          name\n        knownDrugs {\n            uniqueDrugs\n            uniqueDiseases\n            uniqueTargets\n            count\n            cursor\n            rows {\n              approvedSymbol\n              approvedName\n              label\n              prefName\n              drugType\n              targetId\n              diseaseId\n              drugId\n              phase\n              mechanismOfAction\n              status\n              targetClass\n              references {\n                source\n                ids\n                urls\n              }\n              ctIds\n              urls {\n                url\n                name\n              }\n              disease {\n                id\n                name\n              }\n              target {\n                id\n                approvedSymbol\n              }\n              drug {\n                id\n                name\n              }\n            }\n          }\n        }\n      }\n    ",
+        "label": [
+            "OpenTarget",
+            "Drug",
+            "Drug Information",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_parent_child_molecules_by_drug_chembl_ID",
+        "description": "Get parent and child molecules of specified drug chemblId.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "chemblId": {
+                    "type": "string",
+                    "description": "The ChEMBL ID of the drug.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query retrieveMultipleDrugsInfo($chemblId: String!) {\n        drug(chemblId: $chemblId) {\n          id\n          name\n          parentMolecule {\n            id\n            name\n          }\n          childMolecules {\n            id\n            name\n          }\n          }\n      }\n    ",
+        "label": [
+            "OpenTarget",
+            "Drug",
+            "Drug Information",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_approved_indications_by_drug_chemblId",
+        "description": "Retrieve detailed information about multiple drugs using a list of ChEMBL IDs.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "chemblId": {
+                    "type": "string",
+                    "description": "The ChEMBL ID of the drug.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query retrieveMultipleDrugsInfo($chemblId: String!) {\n        drug(chemblId: $chemblId) {\n          id\n          name\n          approvedIndications\n          }\n      }\n    ",
+        "label": [
+            "OpenTarget",
+            "Drug",
+            "Drug Information",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_drug_description_by_chemblId",
+        "description": "Get drug name, year of first approval, type, cross references, and max clinical trial phase based on specified chemblId.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "chemblId": {
+                    "type": "string",
+                    "description": "The ChEMBL ID of the drug.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query retrieveMultipleDrugsInfo($chemblId: String!) {\n        drug(chemblId: $chemblId) {\n          id\n          name\n          yearOfFirstApproval\n          drugType\n          crossReferences {\n            source\n            reference\n          }\n          maximumClinicalTrialPhase\n        }\n      }\n    ",
+        "label": [
+            "OpenTarget",
+            "Drug",
+            "Drug Information",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_drug_synonyms_by_chemblId",
+        "description": "Retrieve the synonyms associated with a specific drug chemblId.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "chemblId": {
+                    "type": "string",
+                    "description": "The ChEMBL ID of the drug.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query drugSynonyms($chemblId: String!) {\n        drug(chemblId: $chemblId) {\n          id\n          name\n          synonyms\n        }\n      }\n    ",
+        "label": [
+            "OpenTarget",
+            "Drug Information",
+            "Drug",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_drug_trade_names_by_chemblId",
+        "description": "Retrieve the trade names associated with a specific drug chemblId.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "chemblId": {
+                    "type": "string",
+                    "description": "The ChEMBL ID of the drug.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query drugTradeNames($chemblId: String!) {\n        drug(chemblId: $chemblId) {\n          id\n          name\n          tradeNames\n        }\n      }\n    ",
+        "label": [
+            "Drug",
+            "OpenTarget",
+            "Drug Information",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_drug_approval_status_by_chemblId",
+        "description": "Retrieve the approval status of a specific drug chemblId.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "chemblId": {
+                    "type": "string",
+                    "description": "The ChEMBL ID of the drug.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query drugApprovalStatus($chemblId: String!) {\n        drug(chemblId: $chemblId) {\n          id\n          name\n          isApproved\n        }\n      }\n    ",
+        "label": [
+            "Drug",
+            "Drug Information",
+            "GraphQL",
+            "OpenTarget"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_chemical_probes_by_target_ensemblID",
+        "description": "Retrieve chemical probes associated with a specific target using its ensemblID.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "ensemblId": {
+                    "type": "string",
+                    "description": "The Ensembl ID of the target for which to retrieve chemical probes.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query getTargetChemicalProbes($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    ",
+        "label": [
+            "OpenTarget",
+            "Drug Information",
+            "ChemicalProbe",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_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: $page) {\n            datasourceId\n            datatypeId\n            genotype\n            evidenceLevel\n            genotypeAnnotationText\n            genotypeId\n            haplotypeFromSourceId\n            haplotypeId\n            literature\n            pgxCategory\n            phenotypeFromSourceId\n            phenotypeText\n            studyId\n            targetFromSourceId\n            variantFunctionalConsequenceId\n            variantRsId\n            isDirectTarget\n            variantFunctionalConsequence {\n              id\n              label\n            }\n            drugs {\n              drugId\n              drug {\n        name\n      }\n            }\n            target {\n              id\n              approvedSymbol\n            }\n          }\n        }\n      }\n    ",
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_associated_drugs_by_target_ensemblID",
+        "description": "Get known drugs and information (e.g. id, name, MoA) associated with a specific target ensemblID, including clinical trial phase and mechanism of action of the drugs.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "ensemblId": {
+                    "type": "string",
+                    "description": "The Ensembl ID of the target.",
+                    "required": true
+                },
+                "size": {
+                    "type": "integer",
+                    "description": "Number of entries to fetch.",
+                    "required": true
+                },
+                "cursor": {
+                    "type": "string",
+                    "description": "Cursor for pagination.",
+                    "required": false
+                }
+            }
+        },
+        "query_schema": "\n      query targetKnownDrugs($ensemblId: String!, $size: Int!, $cursor: String) {\n        target(ensemblId: $ensemblId) {\n          id\n          approvedSymbol\n          knownDrugs(size: $size, cursor: $cursor) {\n            count\n            rows {\n              drug {\n                id\n                name\n                tradeNames\n                maximumClinicalTrialPhase\n                isApproved\n                hasBeenWithdrawn\n              }\n              phase\n              status\n              mechanismOfAction\n              disease {\n                id\n                name\n              }\n            }\n          }\n        }\n      }\n    ",
+        "label": [
+            "Target",
+            "Drug",
+            "MechanismsOfAction",
+            "Pagination",
+            "OpenTarget",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_associated_diseases_by_drug_chemblId",
+        "description": "Retrieve the list of diseases associated with a specific drug chemblId based on clinical trial data or post-marketed drugs.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "chemblId": {
+                    "type": "string",
+                    "description": "The ChEMBL ID of the drug.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query fetchLinkedDiseasesForDrug($chemblId: String!) {\n        drug(chemblId: $chemblId) {\n          id\n          name\n          linkedDiseases {\n            count\n            rows {\n              id\n              name\n              description\n            }\n          }\n        }\n      }\n    ",
+        "label": [
+            "Drug",
+            "Disease",
+            "OpenTarget",
+            "Drug Information",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_associated_targets_by_drug_chemblId",
+        "description": "Retrieve the list of targets linked to a specific drug chemblId based on its mechanism of action.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "chemblId": {
+                    "type": "string",
+                    "description": "The ChEMBL ID of the drug.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query fetchLinkedTargetsForDrug($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    ",
+        "label": [
+            "Drug",
+            "Target",
+            "MechanismsOfAction",
+            "OpenTarget",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_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: $page) {\n          total\n          hits {\n            id\n            entity\n            description\n            name\n            score\n          }\n        }\n      }\n    ",
+        "label": [
+            "Search and Mapping Functions",
+            "MultiEntitySearch",
+            "Pagination",
+            "OpenTarget",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_gene_ontology_terms_by_goID",
+        "description": "Retrieve Gene Ontology terms based on a list of GO IDs.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "goIds": {
+                    "type": "array",
+                    "items": {
+                        "type": "string"
+                    },
+                    "description": "A list of Gene Ontology (GO) IDs to fetch the corresponding terms.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query fetchGeneOntologyTerms($goIds: [String!]!) {\n        geneOntologyTerms(goIds: $goIds) {\n          id\n          name\n        }\n      }\n    ",
+        "label": [
+            "GeneOntology",
+            "Data Retrieval and Aggregation",
+            "OpenTarget",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_target_constraint_info_by_ensemblID",
+        "description": "Retrieve genetic constraint information for a specific target ensemblID, including expected and observed values, and scores.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "ensemblId": {
+                    "type": "string",
+                    "description": "The Ensembl ID of the target.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n      query targetConstraintInfo($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    ",
+        "label": [
+            "Target",
+            "Constraint",
+            "Data Retrieval and Aggregation",
+            "OpenTarget",
+            "GraphQL"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_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    ",
+        "label": [
+            "Publications",
+            "Data Retrieval and Aggregation",
+            "GraphQL",
+            "OpenTarget"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_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": "OpenTargets_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: $endMonth) {\n            count\n            filteredCount\n            earliestPubYear\n            rows {\n              pmid\n              pmcid\n              publicationDate\n              sentences {\n                section\n                matches {\n                  mappedId\n                  matchedLabel\n                  sectionStart\n                  sectionEnd\n                  startInSentence\n                  endInSentence\n                  matchedType\n                }\n              }\n            }\n          }\n        }\n      }\n    ",
+        "label": [
+            "Publications",
+            "Data Retrieval and Aggregation",
+            "GraphQL",
+            "OpenTarget"
+        ],
+        "type": "OpenTarget"
+    },
+    {
+        "name": "OpenTargets_get_target_id_description_by_name",
+        "description": "Get the ensemblId and description based on the target name.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "targetName": {
+                    "type": "string",
+                    "description": "The name of the target for which the ID is required.",
+                    "required": true
+                }
+            }
+        },
+        "query_schema": "\n        query getTargetIdByName($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"
+    }
+]

tool_lists/pubtator_tools.json

@@ -0,0 +1,68 @@
+[
+    {
+      "type": "PubTatorTool",
+      "name": "PubTator3_EntityAutocomplete",
+      "description": "Provides suggestions for the best‐matching standardized PubTator IDs for a partial biomedical term (gene, disease, chemical, or variant). Use this tool first to convert free‐text names into the stable @IDs required by the other PubTator APIs.",
+      "endpoint_path": "/entity/autocomplete/",
+      "method": "GET",
+      "param_map": {
+        "text": "query",
+        "entity_type": "concept",
+        "max_results": "limit"
+      },
+      "parameter": {
+        "type": "object",
+        "properties": {
+          "text": {
+            "type": "string",
+            "description": "A few characters or the full name of the biomedical concept you are trying to look up (e.g. “BRAF V6”)."
+          },
+          "entity_type": {
+            "type": "string",
+            "description": "Optional filter to restrict suggestions to a single category such as GENE, DISEASE, CHEMICAL, or VARIANT."
+          },
+          "max_results": {
+            "type": "integer",
+            "description": "Maximum number of suggestions to return (1 - 50, default = 10)."
+          }
+        },
+        "required": ["text"]
+      },
+      "fields": {
+        "tool_subtype": "PubTatorEntity"
+      }
+    },
+    {
+      "type": "PubTatorTool",
+      "name": "PubTator3_LiteratureSearch",
+      "description": "Find PubMed articles that match a keyword, a PubTator entity ID (e.g. “@GENE_BRAF”), or an entity-to-entity relation expression (e.g. “relations:treat|@CHEMICAL_Doxorubicin|@DISEASE_Neoplasms”).",
+      "endpoint_path": "/search/",
+      "method": "GET",
+      "param_map": {
+        "query": "text",
+        "page": "page",
+        "page_size": "page_size"
+      },
+      "parameter": {
+        "type": "object",
+        "properties": {
+          "query": {
+            "type": "string",
+            "description": "What you want to search for. This can be plain keywords, a single PubTator ID, or the special relation syntax shown above."
+          },
+          "page": {
+            "type": "integer",
+            "description": "Zero-based results page (optional; default = 0)."
+          },
+          "page_size": {
+            "type": "integer",
+            "description": "How many PMIDs to return per page (optional; default = 20, maximum = 200)."
+          }
+        },
+        "required": ["query"]
+      },
+      "fields": {
+        "tool_subtype": "PubTatorSearch"
+      }
+    }
+]

tool_lists/semantic_scholar_tools.json

@@ -0,0 +1,26 @@
+[
+    {
+        "type": "SemanticScholarTool",
+        "name": "SemanticScholar_search_papers",
+        "description": "Search for papers on Semantic Scholar including abstracts. This tool queries the Semantic Scholar API using natural language keywords and returns papers with details such as title, abstract, publication year, journal (venue), and URL.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "query": { 
+                    "type": "string", 
+                    "description": "Search query for Semantic Scholar. Use keywords separated by spaces to refine the search." 
+                },
+                "limit": { 
+                    "type": "integer", 
+                    "description": "Maximum number of papers to return from Semantic Scholar.", 
+                    "default": 5 
+                },
+                "api_key": { 
+                    "type": "string", 
+                    "description": "Optional API key for Semantic Scholar to obtain a higher quota." 
+                }
+            },
+            "required": ["query"]
+        }
+    }
+]

tool_lists/special_tools.json

@@ -0,0 +1,48 @@
+[
+  {
+    "name": "Finish",
+    "description": "Indicate the end of multi-step reasoning.",
+    "parameter": {
+      "type": "object",
+      "properties": null
+    }
+  },
+  {
+    "name": "Tool_RAG",
+    "description": "Retrieve related tools from the toolbox based on the provided description",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "description": {
+          "type": "string",
+          "description": "The description of the tool capability required.",
+          "required": true
+        },
+        "limit": {
+          "type": "integer",
+          "description": "The number of tools to retrieve",
+          "required": true
+        }
+      }
+    },
+    "required": [
+      "description",
+      "limit"
+    ]
+  },
+  {
+    "name": "CallAgent",
+    "description": "Give a solution plan to the agent and let it solve the problem. Solution plan should reflect a distinct method, approach, or viewpoint to solve the given question. Call these function multiple times, and each solution plan should start with different aspects of the question, for example, genes, phenotypes, diseases, or drugs, etc. The CallAgent will achieve the task based on the plan, so only give the plan instead of unverified information.",
+    "parameter": {
+      "type": "object",
+      "properties": 
+      {
+        "solution": {
+          "type": "string",
+          "description": "A feasible and concise solution plan that address the question.",
+          "required": true
+        }
+      }
+    }
+  }
+]