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

Does NOT Trigger

Scenario	Use Instead
Clinical trial registry records (NCT IDs, recruitment, eligibility)	`alterlab-clinicaltrials`
Curated drug–target / DDI knowledge from DrugBank	`alterlab-drugbank`
Compound bioactivity and mechanism data	`alterlab-chembl`
Pharmacogenomic dosing guidance (CPIC/DPWG)	`alterlab-clinpgx`

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

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:

Adverse Events - Reports of side effects, errors, and therapeutic failures
Product Labeling - Prescribing information, warnings, indications
NDC Directory - National Drug Code product information
Enforcement Reports - Drug recalls and safety actions
Drugs@FDA - Historical approval data since 1939
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:

Adverse Events - Device malfunctions, injuries, deaths
510(k) Clearances - Premarket notifications
Classification - Device categories and risk classes
Enforcement Reports - Device recalls
Recalls - Detailed recall information
PMA - Premarket approval data for Class III devices
Registrations & Listings - Manufacturing facility data
UDI - Unique Device Identification database
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:

Adverse Events - Food and dietary-supplement events (CAERS; food/event)
Enforcement Reports - Food product recalls

Cosmetic adverse events now have their own endpoint, cosmetic/event.

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:

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:

Substance Data (other/substance) - UNII, CAS, chemical structures, relationships
UNII (other/unii) - UNII code ↔ substance name lookup
NSDE (other/nsde) - Comprehensive NDC SPL Data Elements file
Historical documents (other/historicaldocument) - archival FDA documents

Also live (verified 2026-09): transparency/crl (published complete response letters) and tobacco/problem (tobacco product problem reports).

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.
skip is capped at 25,000 (query_all stops there); page deeper via the search_after cursor in the Link response header, narrower date-range searches, or the bulk downloads. meta.last_updated tells you how fresh each endpoint is — FAERS (drug/event) lags by a quarter.
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

About this skill

Overview

When to Use This Skill

Does NOT Trigger

Quick Start

1. Basic Setup

2. API Key Setup

3. Running Examples

FDA Database Categories

Drugs

Devices

Foods

Animal & Veterinary

Substances & Other

Query Patterns & Result Handling

API Reference

Scripts

scripts/fda_query.py

scripts/fda_examples.py

Additional Resources

Support and Troubleshooting

Common Issues

Getting Help

`scripts/fda_query.py`

`scripts/fda_examples.py`