fda-database

# 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

```python
from scripts.fda_query import FDAQuery

# Initialize (API key optional but recommended)
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:
```bash
export FDA_API_KEY="your_key_here"
```

### 3. Running Examples

```bash
# 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:**
```python
# 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
shortages = fda.query("drug", "drugshortages",
                     search="status:Currently+in+Shortage")
```

**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:**
```python
# 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:**
```python
# 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:**
```python
# 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:**
```python
# 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

## Common Query Patterns

### Pattern 1: Safety Profile Analysis

Create comprehensive safety profiles combining multiple data sources:

```python
def drug_safety_profile(fda, drug_name):
    """Generate complete safety profile."""

    # 1. Total adverse events
    events = fda.query_drug_events(drug_name, limit=1)
    total = events["meta"]["results"]["total"]

    # 2. Most common reactions
    reactions = fda.count_by_field(
        "drug", "event",
        search=f"patient.drug.medicinalproduct:*{drug_name}*",
        field="patient.reaction.reactionmeddrapt",
        exact=True
    )

    # 3. Serious events
    serious = fda.query("drug", "event",
        search=f"patient.drug.medicinalproduct:*{drug_name}*+AND+serious:1",
        limit=1)

    # 4. Recent recalls
    recalls = fda.query_drug_recalls(drug_name=drug_name)

    return {
        "total_events": total,
        "top_reactions": reactions["results"][:10],
        "serious_events": serious["meta"]["results"]["total"],
        "recalls": recalls["results"]
    }
```

### Pattern 2: Temporal Trend Analysis

Analyze trends over time using date ranges:

```python
from datetime import datetime, timedelta

def get_monthly_trends(fda, drug_name, months=12):
    """Get monthly adverse event trends."""
    trends = []

    for i in range(months):
        end = datetime.now() - timedelta(days=30*i)
        start = end - timedelta(days=30)

        date_range = f"[{start.strftime('%Y%m%d')}+TO+{end.strftime('%Y%m%d')}]"
        search = f"patient.drug.medicinalproduct:*{drug_name}*+AND+receivedate:{date_range}"

        result = fda.query("drug", "event", search=search, limit=1)
        count = result["meta"]["results"]["total"] if "meta" in result else 0

        trends.append({
            "month": start.strftime("%Y-%m"),
            "events": count
        })

    return trends
```

### Pattern 3: Comparative Analysis

Compare multiple products side-by-side:

```python
def compare_drugs(fda, drug_list):
    """Compare safety profiles of multiple drugs."""
    comparison = {}

    for drug in drug_list:
        # Total events
        events = fda.query_drug_events(drug, limit=1)
        total = events["meta"]["results"]["total"] if "meta" in events else 0

        # Serious events
        serious = fda.query("drug", "event",
            search=f"patient.drug.medicinalproduct:*{drug}*+AND+serious:1",
            limit=1)
        serious_count = serious["meta"]["results"]["total"] if "meta" in serious else 0

        comparison[drug] = {
            "total_events": total,
            "serious_events": serious_count,
            "serious_rate": (serious_count/total*100) if total > 0 else 0
        }

    return comparison
```

### Pattern 4: Cross-Database Lookup

Link data across multiple endpoints:

```python
def comprehensive_device_lookup(fda, device_name):
    """Look up device across all relevant databases."""

    return {
        "adverse_events": fda.query_device_events(device_name, limit=10),
        "510k_clearances": fda.query_device_510k(device_name=device_name),
        "recalls": fda.query("device", "enforcement",
                           search=f"product_description:*{device_name}*"),
        "udi_info": fda.query("device", "udi",
                            search=f"brand_name:*{device_name}*")
    }
```

## Working with Results

### Response Structure

All API responses follow this structure:

```python
{
    "meta": {
        "disclaimer": "...",
        "results": {
            "skip": 0,
            "limit": 100,
            "total": 15234
        }
    },
    "results": [
        # Array of result objects
    ]
}
```

### Error Handling

Always handle potential errors:

```python
result = fda.query_drug_events("aspirin", limit=10)

if "error" in result:
    print(f"Error: {result['error']}")
elif "results" not in result or len(result["results"]) == 0:
    print("No results found")
else:
    # Process results
    for event in result["results"]:
        # Handle event data
        pass
```

### Pagination

For large result sets, use pagination:

```python
# Automatic pagination
all_results = fda.query_all(
    "drug", "event",
    search="patient.drug.medicinalproduct:aspirin",
    max_results=5000
)

# Manual pagination
for skip in range(0, 1000, 100):
    batch = fda.query("drug", "event",
                     search="...",
                     limit=100,
                     skip=skip)
    # Process batch
```

## Best Practices

### 1. Use Specific Searches

**DO:**
```python
# Specific field search
search="patient.drug.medicinalproduct:aspirin"
```

**DON'T:**
```python
# Overly broad wildcard
search="*aspirin*"
```

### 2. Implement Rate Limiting

The `FDAQuery` class handles rate limiting automatically, but be aware of limits:
- 240 requests per minute
- 120,000 requests per day (with API key)

### 3. Cache Frequently Accessed Data

The `FDAQuery` class includes built-in caching (enabled by default):

```python
# Caching is automatic
fda = FDAQuery(api_key=api_key, use_cache=True, cache_ttl=3600)
```

### 4. Use Exact Matching for Counting

When counting/aggregating, use `.exact` suffix:

```python
# Count exact phrases
fda.count_by_field("drug", "event",
                  search="...",
                  field="patient.reaction.reactionmeddrapt",
                  exact=True)  # Adds .exact automatically
```

### 5. Validate Input Data

Clean and validate search terms:

```python
def clean_drug_name(name):
    """Clean drug name for query."""
    return name.strip().replace('"', '\\"')

drug_name = clean_drug_name(user_input)
```

## API Reference

For detailed information about:
- **Authentication and rate limits** → See `references/api_basics.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:
```bash
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