"""
Drug Safety Analysis Pipeline
Comprehensive drug safety analysis combining adverse event data, literature review, and molecular information
"""
[docs]
def compose(arguments, tooluniverse, call_tool):
"""
Main composition function for DrugSafetyAnalyzer
Args:
arguments (dict): Input arguments containing drug_name, patient_sex, serious_events_only
tooluniverse: ToolUniverse instance
call_tool: Function to call other tools
Returns:
dict: Comprehensive drug safety analysis result
"""
drug_name = arguments["drug_name"]
patient_sex = arguments.get("patient_sex")
serious_only = arguments.get("serious_events_only", False)
print(f"Starting comprehensive safety analysis for: {drug_name}")
# Step 1: Get adverse event data from FDA FAERS
faers_result = None
try:
# Prepare FAERS query parameters - only include non-None values
faers_params = {"medicinalproduct": drug_name}
if patient_sex:
faers_params["patientsex"] = patient_sex
if serious_only:
faers_params["serious"] = "Yes"
faers_result = call_tool("FAERS_count_reactions_by_drug_event", faers_params)
except Exception as e:
print(f"FAERS query failed: {e}")
# Step 2: Get molecular information from PubChem
molecular_info = None
try:
pubchem_cid_result = call_tool(
"PubChem_get_CID_by_compound_name", {"name": drug_name}
)
if (
isinstance(pubchem_cid_result, dict)
and "IdentifierList" in pubchem_cid_result
):
cid_list = pubchem_cid_result["IdentifierList"].get("CID", [])
if cid_list:
first_cid = cid_list[0]
molecular_info = call_tool(
"PubChem_get_compound_properties_by_CID", {"cid": first_cid}
)
except Exception as e:
print(f"PubChem query failed: {e}")
# Step 3: Search for safety-related literature
literature_result = None
try:
literature_query = f"{drug_name} safety adverse effects"
literature_result = call_tool(
"EuropePMC_search_articles", {"query": literature_query, "limit": 10}
)
except Exception as e:
print(f"Literature search failed: {e}")
# Step 4: Compile comprehensive analysis result
result = {
"drug_name": drug_name,
"analysis_parameters": {
"patient_sex_filter": patient_sex,
"serious_events_only": serious_only,
},
"adverse_events": faers_result,
"molecular_properties": molecular_info,
"safety_literature": literature_result,
"analysis_summary": {
"has_adverse_events": bool(faers_result),
"has_molecular_data": bool(molecular_info),
"literature_papers_found": (
len(literature_result.get("resultList", {}).get("result", []))
if literature_result and isinstance(literature_result, dict)
else 0
),
},
}
print(f"Safety analysis complete for {drug_name}")
return result
