alterlab-fda

name: alterlab-fda description: Query the openFDA API for drugs, medical devices, adverse event reports, recalls, regulatory submissions (510k, PMA), and substance identification (UNII). Use when searching FDA safety data, pharmacovigilance and adverse-event signals, device clearances, drug labels, or recall records for regulatory data analysis and safety research. Part of the AlterLab Academic Skills suite. license: MIT allowed-tools: Read WebFetch Bash(curl:) Bash(python:) compatibility: Keyless openFDA REST API; optional API key raises rate limits metadata: skill-author: AlterLab version: "1.0.0"

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: open-fda@fda.hhs.gov