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Zhongwei Li
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skills/fda-database/scripts/fda_examples.py
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335
skills/fda-database/scripts/fda_examples.py
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#!/usr/bin/env python3
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"""
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FDA API Usage Examples
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Demonstrates common use cases for querying FDA databases.
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Usage:
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python fda_examples.py
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"""
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import os
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from fda_query import FDAQuery
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def example_drug_safety_profile(fda, drug_name):
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"""
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Create a comprehensive safety profile for a drug.
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Includes:
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- Total adverse events
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- Most common reactions
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- Serious events
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- Recent recalls
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"""
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print(f"\n{'='*60}")
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print(f"DRUG SAFETY PROFILE: {drug_name}")
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print(f"{'='*60}\n")
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# 1. Count total adverse events
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events = fda.query_drug_events(drug_name, limit=1)
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if "meta" in events and "results" in events["meta"]:
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total = events["meta"]["results"].get("total", 0)
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print(f"Total Adverse Event Reports: {total:,}")
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# 2. Most common reactions
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print(f"\nMost Common Adverse Reactions:")
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reactions = fda.count_by_field(
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"drug", "event",
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search=f"patient.drug.medicinalproduct:*{drug_name}*",
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field="patient.reaction.reactionmeddrapt",
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exact=True
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)
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if "results" in reactions:
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for i, item in enumerate(reactions["results"][:10], 1):
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print(f" {i}. {item['term']}: {item['count']:,} reports")
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# 3. Serious events
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serious_events = fda.query(
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"drug", "event",
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search=f"patient.drug.medicinalproduct:*{drug_name}*+AND+serious:1",
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limit=1
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)
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if "meta" in serious_events and "results" in serious_events["meta"]:
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serious_total = serious_events["meta"]["results"].get("total", 0)
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print(f"\nSerious Adverse Events: {serious_total:,}")
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# 4. Check for recent recalls
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recalls = fda.query_drug_recalls(drug_name=drug_name)
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if "results" in recalls and len(recalls["results"]) > 0:
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print(f"\nRecent Recalls: {len(recalls['results'])}")
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for recall in recalls["results"][:3]:
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print(f" - {recall.get('reason_for_recall', 'Unknown')} "
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f"(Class {recall.get('classification', 'Unknown')})")
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else:
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print(f"\nRecent Recalls: None found")
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def example_device_surveillance(fda, device_name):
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"""
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Monitor medical device safety.
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Includes:
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- Adverse events
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- Event types (death, injury, malfunction)
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- Recent recalls
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"""
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print(f"\n{'='*60}")
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print(f"DEVICE SURVEILLANCE: {device_name}")
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print(f"{'='*60}\n")
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# 1. Count adverse events
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events = fda.query_device_events(device_name, limit=1)
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if "meta" in events and "results" in events["meta"]:
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total = events["meta"]["results"].get("total", 0)
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print(f"Total Adverse Event Reports: {total:,}")
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# 2. Event types
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print(f"\nEvent Type Distribution:")
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event_types = fda.count_by_field(
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"device", "event",
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search=f"device.brand_name:*{device_name}*",
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field="event_type",
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exact=False
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)
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if "results" in event_types:
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for item in event_types["results"]:
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print(f" {item['term']}: {item['count']:,}")
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# 3. Recent events
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recent = fda.query_device_events(device_name, limit=5)
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if "results" in recent and len(recent["results"]) > 0:
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print(f"\nRecent Events (sample):")
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for i, event in enumerate(recent["results"][:3], 1):
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event_type = event.get("event_type", "Unknown")
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date = event.get("date_received", "Unknown")
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print(f" {i}. Type: {event_type}, Date: {date}")
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def example_food_recall_monitoring(fda, allergen):
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"""
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Monitor food recalls for specific allergen.
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Args:
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fda: FDAQuery instance
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allergen: Allergen to monitor (e.g., "peanut", "milk", "soy")
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"""
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print(f"\n{'='*60}")
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print(f"ALLERGEN RECALL MONITORING: {allergen}")
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print(f"{'='*60}\n")
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# Find recalls mentioning this allergen
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recalls = fda.query_food_recalls(reason=allergen)
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if "results" in recalls and len(recalls["results"]) > 0:
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print(f"Found {len(recalls['results'])} recalls mentioning '{allergen}':\n")
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for recall in recalls["results"][:10]:
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product = recall.get("product_description", "Unknown product")
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classification = recall.get("classification", "Unknown")
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reason = recall.get("reason_for_recall", "Unknown")
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date = recall.get("recall_initiation_date", "Unknown")
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status = recall.get("status", "Unknown")
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print(f"Product: {product}")
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print(f" Classification: {classification}")
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print(f" Reason: {reason}")
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print(f" Date: {date}")
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print(f" Status: {status}")
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print()
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else:
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print(f"No recent recalls found for allergen: {allergen}")
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def example_substance_lookup(fda, substance_name):
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"""
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Look up substance information.
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Includes:
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- UNII code
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- CAS numbers
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- Chemical structure
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- Related substances
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"""
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print(f"\n{'='*60}")
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print(f"SUBSTANCE INFORMATION: {substance_name}")
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print(f"{'='*60}\n")
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substances = fda.query_substance_by_name(substance_name)
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if "results" in substances and len(substances["results"]) > 0:
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for i, substance in enumerate(substances["results"][:3], 1):
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print(f"Match {i}:")
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# Names
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names = substance.get("names", [])
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if names:
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preferred = next((n["name"] for n in names if n.get("preferred")), names[0].get("name"))
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print(f" Name: {preferred}")
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# UNII
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unii = substance.get("approvalID")
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if unii:
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print(f" UNII: {unii}")
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# CAS numbers
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codes = substance.get("codes", [])
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cas_numbers = [c["code"] for c in codes if "CAS" in c.get("codeSystem", "")]
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if cas_numbers:
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print(f" CAS: {', '.join(cas_numbers)}")
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# Structure
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if "structure" in substance:
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structure = substance["structure"]
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formula = structure.get("formula")
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mol_weight = structure.get("molecularWeight")
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if formula:
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print(f" Formula: {formula}")
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if mol_weight:
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print(f" Molecular Weight: {mol_weight}")
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# Substance class
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substance_class = substance.get("substanceClass")
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if substance_class:
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print(f" Class: {substance_class}")
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print()
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else:
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print(f"No substances found matching: {substance_name}")
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def example_comparative_drug_analysis(fda, drug_list):
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"""
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Compare safety profiles of multiple drugs.
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Args:
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fda: FDAQuery instance
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drug_list: List of drug names to compare
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"""
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print(f"\n{'='*60}")
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print(f"COMPARATIVE DRUG ANALYSIS")
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print(f"{'='*60}\n")
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print(f"Comparing: {', '.join(drug_list)}\n")
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comparison = {}
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for drug in drug_list:
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# Get total events
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events = fda.query_drug_events(drug, limit=1)
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total = 0
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if "meta" in events and "results" in events["meta"]:
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total = events["meta"]["results"].get("total", 0)
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# Get serious events
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serious = fda.query(
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"drug", "event",
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search=f"patient.drug.medicinalproduct:*{drug}*+AND+serious:1",
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limit=1
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)
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serious_total = 0
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if "meta" in serious and "results" in serious["meta"]:
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serious_total = serious["meta"]["results"].get("total", 0)
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serious_rate = (serious_total / total * 100) if total > 0 else 0
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comparison[drug] = {
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"total_events": total,
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"serious_events": serious_total,
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"serious_rate": serious_rate
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}
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# Display comparison
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print(f"{'Drug':<20} {'Total Events':>15} {'Serious Events':>15} {'Serious %':>12}")
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print("-" * 65)
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for drug, data in comparison.items():
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print(f"{drug:<20} {data['total_events']:>15,} "
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f"{data['serious_events']:>15,} {data['serious_rate']:>11.2f}%")
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def example_veterinary_analysis(fda, species, drug_name):
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"""
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Analyze veterinary drug adverse events by species.
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Args:
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fda: FDAQuery instance
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species: Animal species (e.g., "Dog", "Cat", "Horse")
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drug_name: Veterinary drug name
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"""
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print(f"\n{'='*60}")
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print(f"VETERINARY DRUG ANALYSIS: {drug_name} in {species}")
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print(f"{'='*60}\n")
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events = fda.query_animal_events(species=species, drug_name=drug_name)
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if "results" in events and len(events["results"]) > 0:
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print(f"Found {len(events['results'])} adverse event reports\n")
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# Collect reactions
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reactions = []
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serious_count = 0
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for event in events["results"]:
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if event.get("serious_ae") == "true":
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serious_count += 1
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if "reaction" in event:
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for reaction in event["reaction"]:
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if "veddra_term_name" in reaction:
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reactions.append(reaction["veddra_term_name"])
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print(f"Serious Events: {serious_count} ({serious_count/len(events['results'])*100:.1f}%)")
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# Count reactions
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from collections import Counter
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reaction_counts = Counter(reactions)
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print(f"\nMost Common Reactions:")
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for reaction, count in reaction_counts.most_common(10):
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print(f" {reaction}: {count}")
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else:
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print(f"No adverse events found")
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def main():
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"""Run example analyses."""
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# Get API key from environment
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api_key = os.environ.get("FDA_API_KEY")
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if not api_key:
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print("Warning: No FDA_API_KEY found in environment.")
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print("You can still use the API but with lower rate limits.")
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print("Set FDA_API_KEY environment variable for better performance.\n")
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# Initialize FDA query client
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fda = FDAQuery(api_key=api_key)
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# Run examples
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try:
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# Example 1: Drug safety profile
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example_drug_safety_profile(fda, "aspirin")
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# Example 2: Device surveillance
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example_device_surveillance(fda, "pacemaker")
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# Example 3: Food recall monitoring
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example_food_recall_monitoring(fda, "undeclared peanut")
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# Example 4: Substance lookup
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example_substance_lookup(fda, "ibuprofen")
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# Example 5: Comparative analysis
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example_comparative_drug_analysis(fda, ["aspirin", "ibuprofen", "naproxen"])
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# Example 6: Veterinary analysis
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example_veterinary_analysis(fda, "Dog", "flea collar")
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except Exception as e:
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print(f"\nError running examples: {e}")
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print("This may be due to API rate limits or connectivity issues.")
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if __name__ == "__main__":
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main()
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