Alterlab fda

FDA Database Access

Overview

Access comprehensive FDA regulatory data through openFDA, the FDA's initiative to provide open APIs for public datasets. Query information about drugs, medical devices, foods, animal/veterinary products, and substances using Python with standardized interfaces.

Key capabilities:

• Query adverse events for drugs, devices, foods, and veterinary products
• Access product labeling, approvals, and regulatory submissions
• Monitor recalls and enforcement actions
• Look up National Drug Codes (NDC) and substance identifiers (UNII)
• Analyze device classifications and clearances (510k, PMA)
• Track drug shortages and supply issues
• Research chemical structures and substance relationships

When to Use This Skill

This skill should be used when working with:

• Drug research: Safety profiles, adverse events, labeling, approvals, shortages
• Medical device surveillance: Adverse events, recalls, 510(k) clearances, PMA approvals
• Food safety: Recalls, allergen tracking, adverse events, dietary supplements
• Veterinary medicine: Animal drug adverse events by species and breed
• Chemical/substance data: UNII lookup, CAS number mapping, molecular structures
• Regulatory analysis: Approval pathways, enforcement actions, compliance tracking
• Pharmacovigilance: Post-market surveillance, safety signal detection
• Scientific research: Drug interactions, comparative safety, epidemiological studies

Quick Start

1. Basic Setup

# Run from the skill's scripts/ dir, or add it to sys.path first.
from fda_query import FDAQuery

# API key is optional (works keyless); pass it or set FDA_API_KEY.
fda = FDAQuery(api_key="YOUR_API_KEY")

# Query drug adverse events
events = fda.query_drug_events("aspirin", limit=100)

# Get drug labeling
label = fda.query_drug_label("Lipitor", brand=True)

# Search device recalls
recalls = fda.query("device", "enforcement",
                   search="classification:Class+I",
                   limit=50)

2. API Key Setup

While the API works without a key, registering provides higher rate limits:

• Without key: 240 requests/min, 1,000/day
• With key: 240 requests/min, 120,000/day

Register at: https://open.fda.gov/apis/authentication/

Set as environment variable:

export FDA_API_KEY="your_key_here"

3. Running Examples

# Run comprehensive examples
python scripts/fda_examples.py

# This demonstrates:
# - Drug safety profiles
# - Device surveillance
# - Food recall monitoring
# - Substance lookup
# - Comparative drug analysis
# - Veterinary drug analysis

FDA Database Categories

Drugs

Access 6 drug-related endpoints covering the full drug lifecycle from approval to post-market surveillance.

Endpoints:

1. Adverse Events - Reports of side effects, errors, and therapeutic failures
2. Product Labeling - Prescribing information, warnings, indications
3. NDC Directory - National Drug Code product information
4. Enforcement Reports - Drug recalls and safety actions
5. Drugs@FDA - Historical approval data since 1939
6. Drug Shortages - Current and resolved supply issues

Common use cases:

# Safety signal detection
fda.count_by_field("drug", "event",
                  search="patient.drug.medicinalproduct:metformin",
                  field="patient.reaction.reactionmeddrapt")

# Get prescribing information
label = fda.query_drug_label("Keytruda", brand=True)

# Check for recalls
recalls = fda.query_drug_recalls(drug_name="metformin")

# Monitor shortages (endpoint is drug/shortages; status values:
# "Current", "To Be Discontinued", "Resolved")
shortages = fda.query("drug", "shortages",
                     search="status:Current")

Reference: See references/drugs.md for detailed documentation

Devices

Access 9 device-related endpoints covering medical device safety, approvals, and registrations.

Endpoints:

1. Adverse Events - Device malfunctions, injuries, deaths
2. 510(k) Clearances - Premarket notifications
3. Classification - Device categories and risk classes
4. Enforcement Reports - Device recalls
5. Recalls - Detailed recall information
6. PMA - Premarket approval data for Class III devices
7. Registrations & Listings - Manufacturing facility data
8. UDI - Unique Device Identification database
9. COVID-19 Serology - Antibody test performance data

Common use cases:

# Monitor device safety
events = fda.query_device_events("pacemaker", limit=100)

# Look up device classification
classification = fda.query_device_classification("DQY")

# Find 510(k) clearances
clearances = fda.query_device_510k(applicant="Medtronic")

# Search by UDI
device_info = fda.query("device", "udi",
                       search="identifiers.id:00884838003019")

Reference: See references/devices.md for detailed documentation

Foods

Access 2 food-related endpoints for safety monitoring and recalls.

Endpoints:

1. Adverse Events - Food, dietary supplement, and cosmetic events
2. Enforcement Reports - Food product recalls

Common use cases:

# Monitor allergen recalls
recalls = fda.query_food_recalls(reason="undeclared peanut")

# Track dietary supplement events
events = fda.query_food_events(
    industry="Dietary Supplements")

# Find contamination recalls
listeria = fda.query_food_recalls(
    reason="listeria",
    classification="I")

Reference: See references/foods.md for detailed documentation

Animal & Veterinary

Access veterinary drug adverse event data with species-specific information.

Endpoint:

1. Adverse Events - Animal drug side effects by species, breed, and product

Common use cases:

# Species-specific events
dog_events = fda.query_animal_events(
    species="Dog",
    drug_name="flea collar")

# Breed predisposition analysis
breed_query = fda.query("animalandveterinary", "event",
    search="reaction.veddra_term_name:*seizure*+AND+"
           "animal.breed.breed_component:*Labrador*")

Reference: See references/animal_veterinary.md for detailed documentation

Substances & Other

Access molecular-level substance data with UNII codes, chemical structures, and relationships.

Endpoints:

1. Substance Data - UNII, CAS, chemical structures, relationships
2. NSDE - Historical substance data (legacy)

Common use cases:

# UNII to CAS mapping
substance = fda.query_substance_by_unii("R16CO5Y76E")

# Search by name
results = fda.query_substance_by_name("acetaminophen")

# Get chemical structure
structure = fda.query("other", "substance",
    search="names.name:ibuprofen+AND+substanceClass:chemical")

Reference: See references/other.md for detailed documentation

Query Patterns & Result Handling

Reusable FDAQuery patterns (safety profiles, temporal trends, comparative and cross-database lookups), the response structure, error handling, pagination, and best practices live in references/query_patterns.md.

Essentials to keep in mind:

• Use specific field searches (patient.drug.medicinalproduct:aspirin), not bare wildcards.
• FDAQuery handles rate limiting (240/min, 120,000/day with key) and caching automatically.
• Use exact=True on count_by_field to count exact phrases (adds .exact).
• All responses share the {meta: {results: {total, ...}}, results: [...]} shape; always check for error and empty results.

API Reference

For detailed information about:

• Authentication and rate limits → See references/api_basics.md
• Query patterns & result handling → See references/query_patterns.md
• Drug databases → See references/drugs.md
• Device databases → See references/devices.md
• Food databases → See references/foods.md
• Animal/veterinary databases → See references/animal_veterinary.md
• Substance databases → See references/other.md

Scripts

scripts/fda_query.py

Main query module with FDAQuery class providing:

• Unified interface to all FDA endpoints
• Automatic rate limiting and caching
• Error handling and retry logic
• Common query patterns

scripts/fda_examples.py

Comprehensive examples demonstrating:

• Drug safety profile analysis
• Device surveillance monitoring
• Food recall tracking
• Substance lookup
• Comparative drug analysis
• Veterinary drug analysis

Run examples:

python scripts/fda_examples.py

Additional Resources

• openFDA Homepage: https://open.fda.gov/
• API Documentation: https://open.fda.gov/apis/
• Interactive API Explorer: https://open.fda.gov/apis/try-the-api/
• GitHub Repository: https://github.com/FDA/openfda
• Terms of Service: https://open.fda.gov/terms/

Support and Troubleshooting

Common Issues

Issue: Rate limit exceeded

• Solution: Use API key, implement delays, or reduce request frequency

Issue: No results found

• Solution: Try broader search terms, check spelling, use wildcards

Issue: Invalid query syntax

• Solution: Review query syntax in references/api_basics.md

Issue: Missing fields in results

• Solution: Not all records contain all fields; always check field existence

Getting Help

• GitHub Issues: https://github.com/FDA/openfda/issues
• Email: [email protected]