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OpenFDA Example Prompts for AI Agents

This document provides example prompts that demonstrate effective use of BioMCP's OpenFDA integration for various precision oncology use cases.

Drug Safety Assessment

Basic Safety Profile

What are the most common adverse events reported for pembrolizumab?
Include both serious and non-serious events.

Expected BioMCP Usage:

  1. think - Plan safety assessment approach
  2. openfda_adverse_searcher(drug="pembrolizumab", limit=50)
  3. Analyze and summarize top reactions

Comparative Safety Analysis

Compare the adverse event profiles of imatinib and dasatinib for CML treatment.
Focus on serious events and their frequencies.

Expected BioMCP Usage:

  1. think - Plan comparative analysis
  2. openfda_adverse_searcher(drug="imatinib", serious=True)
  3. openfda_adverse_searcher(drug="dasatinib", serious=True)
  4. Compare and contrast findings

Drug Interaction Investigation

A patient on warfarin needs to start erlotinib for NSCLC. What drug interactions
and adverse events should we monitor based on FDA data?

Expected BioMCP Usage:

  1. think - Consider interaction risks
  2. openfda_label_searcher(name="erlotinib") - Check drug interactions section
  3. openfda_adverse_searcher(drug="erlotinib", reaction="bleeding")
  4. openfda_adverse_searcher(drug="erlotinib", reaction="INR")

Treatment Planning

Indication Verification

Is trastuzumab deruxtecan FDA-approved for HER2-low breast cancer?
What are the specific approved indications?

Expected BioMCP Usage:

  1. think - Plan indication search
  2. openfda_label_searcher(name="trastuzumab deruxtecan")
  3. openfda_label_getter(set_id="...") - Get full indications section
  4. Extract and summarize approved uses

Contraindication Screening

Patient has severe hepatic impairment. Which targeted therapy drugs for
melanoma have contraindications or warnings for liver dysfunction?

Expected BioMCP Usage:

  1. think - Identify melanoma drugs to check
  2. openfda_label_searcher(indication="melanoma")
  3. For each drug: openfda_label_getter(set_id="...", sections=["contraindications", "warnings_and_precautions"])
  4. Summarize liver-related contraindications

Dosing Guidelines

What is the FDA-recommended dosing for osimertinib in EGFR-mutated NSCLC,
including dose modifications for adverse events?

Expected BioMCP Usage:

  1. think - Plan dosing information retrieval
  2. openfda_label_searcher(name="osimertinib")
  3. openfda_label_getter(set_id="...", sections=["dosage_and_administration", "dose_modifications"])
  4. Extract dosing guidelines

Device Reliability Assessment

Genomic Test Reliability

What adverse events have been reported for NGS-based cancer diagnostic devices?
Show me any false positive or accuracy issues.

Expected BioMCP Usage:

  1. think - Consider test reliability factors
  2. openfda_device_searcher(genomics_only=True, limit=25) - Get all genomic device events
  3. openfda_device_searcher(problem="false positive", genomics_only=True)
  4. openfda_device_searcher(problem="accuracy", genomics_only=True)
  5. For significant events: openfda_device_getter(mdr_report_key="...")

Note: The FDA database uses abbreviated names (e.g., "F1CDX" instead of "FoundationOne CDx"). For specific devices, try: openfda_device_searcher(device="F1CDX") or search by key terms.

Laboratory Equipment Issues

Our lab uses Illumina sequencers. What device malfunctions have been
reported that could impact our genomic testing workflow?

Expected BioMCP Usage:

  1. think - Assess potential workflow impacts
  2. openfda_device_searcher(manufacturer="Illumina", genomics_only=True)
  3. Analyze problem patterns
  4. openfda_device_getter(mdr_report_key="...") for critical issues

Comprehensive Drug Evaluation

New Drug Assessment

Provide a comprehensive safety and efficacy profile for sotorasib (Lumakras)
including FDA approval, indications, major warnings, and post-market adverse events.

Expected BioMCP Usage:

  1. think - Plan comprehensive assessment
  2. drug_getter("sotorasib") - Basic drug info
  3. openfda_label_searcher(name="sotorasib")
  4. openfda_label_getter(set_id="...") - Full label
  5. openfda_adverse_searcher(drug="sotorasib", serious=True)
  6. trial_searcher(interventions=["sotorasib"]) - Ongoing trials

Risk-Benefit Analysis

For a 75-year-old patient with metastatic melanoma, analyze the risk-benefit
profile of nivolumab plus ipilimumab combination therapy based on FDA data.

Expected BioMCP Usage:

  1. think - Structure risk-benefit analysis
  2. openfda_label_searcher(name="nivolumab")
  3. openfda_label_searcher(name="ipilimumab")
  4. openfda_label_getter(set_id="...", sections=["geriatric_use", "warnings_and_precautions"])
  5. openfda_adverse_searcher(drug="nivolumab", serious=True)
  6. openfda_adverse_searcher(drug="ipilimumab", serious=True)

Special Populations

Pregnancy Considerations

Which FDA-approved lung cancer treatments have pregnancy category data
or specific warnings for pregnant patients?

Expected BioMCP Usage:

  1. think - Plan pregnancy safety search
  2. openfda_label_searcher(indication="lung cancer")
  3. For each drug: openfda_label_getter(set_id="...", sections=["pregnancy", "use_in_specific_populations"])
  4. Compile pregnancy categories and warnings

Pediatric Oncology

What FDA-approved indications and safety data exist for using
checkpoint inhibitors in pediatric cancer patients?

Expected BioMCP Usage:

  1. think - Identify checkpoint inhibitors
  2. openfda_label_searcher(name="pembrolizumab")
  3. openfda_label_getter(set_id="...", sections=["pediatric_use"])
  4. openfda_adverse_searcher(drug="pembrolizumab") - Filter for pediatric if possible
  5. Repeat for other checkpoint inhibitors

Complex Queries

Multi-Drug Regimen Safety

Analyze potential safety concerns for the FOLFOX chemotherapy regimen
(5-FU, leucovorin, oxaliplatin) based on FDA adverse event data.

Expected BioMCP Usage:

  1. think - Plan multi-drug analysis
  2. openfda_adverse_searcher(drug="fluorouracil")
  3. openfda_adverse_searcher(drug="leucovorin")
  4. openfda_adverse_searcher(drug="oxaliplatin")
  5. Identify overlapping toxicities
  6. openfda_label_searcher(name="oxaliplatin") - Check for combination warnings

Biomarker-Driven Treatment Selection

For a patient with BRAF V600E mutant melanoma with brain metastases,
what FDA-approved treatments are available and what are their CNS-specific
efficacy and safety considerations?

Expected BioMCP Usage:

  1. think - Structure biomarker-driven search
  2. article_searcher(genes=["BRAF"], variants=["V600E"], diseases=["melanoma"])
  3. openfda_label_searcher(indication="melanoma")
  4. For BRAF inhibitors: openfda_label_getter(set_id="...", sections=["clinical_studies", "warnings_and_precautions"])
  5. openfda_adverse_searcher(drug="dabrafenib", reaction="seizure")
  6. openfda_adverse_searcher(drug="vemurafenib", reaction="brain")

Treatment Failure Analysis

A patient's lung adenocarcinoma progressed on osimertinib. Based on FDA data,
what are the documented resistance mechanisms and alternative approved treatments?

Expected BioMCP Usage:

  1. think - Analyze resistance and alternatives
  2. openfda_label_getter(set_id="...", sections=["clinical_studies"]) for osimertinib
  3. article_searcher(genes=["EGFR"], keywords=["resistance", "osimertinib"])
  4. openfda_label_searcher(indication="non-small cell lung cancer")
  5. trial_searcher(conditions=["NSCLC"], keywords=["osimertinib resistant"])

Safety Monitoring

Post-Market Surveillance

Have there been any new safety signals for CDK4/6 inhibitors
(palbociclib, ribociclib, abemaciclib) in the past year?

Expected BioMCP Usage:

  1. think - Plan safety signal detection
  2. openfda_adverse_searcher(drug="palbociclib", limit=100)
  3. openfda_adverse_searcher(drug="ribociclib", limit=100)
  4. openfda_adverse_searcher(drug="abemaciclib", limit=100)
  5. Analyze for unusual patterns or frequencies

Rare Adverse Event Investigation

Investigate reports of pneumonitis associated with immune checkpoint inhibitors.
Which drugs have the highest frequency and what are the typical outcomes?

Expected BioMCP Usage:

  1. think - Structure pneumonitis investigation
  2. openfda_adverse_searcher(drug="pembrolizumab", reaction="pneumonitis")
  3. openfda_adverse_searcher(drug="nivolumab", reaction="pneumonitis")
  4. openfda_adverse_searcher(drug="atezolizumab", reaction="pneumonitis")
  5. Compare frequencies and outcomes
  6. openfda_adverse_getter(report_id="...") for severe cases

Quality Assurance

Diagnostic Test Validation

What quality issues have been reported for liquid biopsy ctDNA tests
that could affect treatment decisions?

Expected BioMCP Usage:

  1. think - Identify quality factors
  2. openfda_device_searcher(device="liquid biopsy", genomics_only=True)
  3. openfda_device_searcher(device="ctDNA", genomics_only=True)
  4. openfda_device_searcher(device="circulating tumor", genomics_only=True)
  5. Analyze failure modes

Tips for Effective Prompts

  1. Be specific about the data needed: Specify if you want adverse events, labels, or device data
  2. Include relevant filters: Mention if focusing on serious events, specific populations, or genomic devices
  3. Request appropriate analysis: Ask for comparisons, trends, or specific data points
  4. Consider multiple data sources: Combine OpenFDA with literature and trial data for comprehensive answers
  5. Include time frames when relevant: Though OpenFDA doesn't support date filtering in queries, you can ask for analysis of recent reports

Integration Examples

Find FDA adverse events for venetoclax in CLL, then search for published
case reports that provide more clinical context for the most serious events.

Combining with Clinical Trials

What adverse events are reported for FDA-approved CAR-T therapies, and how
do these compare to adverse events being monitored in current clinical trials?

Combining with Variant Data

For patients with RET fusion-positive cancers, what FDA-approved targeted
therapies are available and what are their mutation-specific response rates?

Using Your OpenFDA API Key

The OpenFDA API has rate limits: 40 requests/minute without a key, or 240 requests/minute with a key. You can get a free API key at https://open.fda.gov/apis/authentication/

Method 1: Include API Key in Your Prompt

You can provide your API key directly in your conversation with the AI:

My OpenFDA API key is: YOUR_API_KEY_HERE

Search for all serious adverse events reported for pembrolizumab in the last year.
Include both death and hospitalization events.

Using my OpenFDA API key YOUR_API_KEY_HERE, compare the safety profiles of
all FDA-approved BRAF inhibitors for melanoma treatment.

I have an OpenFDA API key: YOUR_API_KEY_HERE

Analyze device malfunction reports for all NGS-based cancer diagnostic tests.
Focus on false positive and false negative results that could impact treatment decisions.

If you're using BioMCP regularly, set the environment variable once:

export OPENFDA_API_KEY="YOUR_API_KEY_HERE"

Then your prompts don't need to include the key:

Retrieve the complete FDA label for trastuzumab deruxtecan, including all
warnings and contraindications for HER2-low breast cancer patients.

Method 3: CLI Usage with API Key

When using the BioMCP CLI directly:

# Pass API key as parameter
biomcp openfda adverse search --drug pembrolizumab --serious --api-key YOUR_API_KEY_HERE

# Or set environment variable first
export OPENFDA_API_KEY="YOUR_API_KEY_HERE"
biomcp openfda device search --manufacturer Illumina --genomics-only

Example Prompts with API Key

Comprehensive Drug Safety Analysis

My OpenFDA API key is: YOUR_API_KEY_HERE

Perform a comprehensive safety analysis of sotorasib (Lumakras) including:
1. All serious adverse events from post-market surveillance
2. Complete FDA label with all sections
3. Any device issues if it's a companion diagnostic drug
4. Compare its safety profile to other KRAS G12C inhibitors if available

This is for a clinical review, so I need detailed data from all available FDA sources.

Large-Scale Adverse Event Analysis

Using my OpenFDA API key YOUR_API_KEY_HERE, analyze adverse events for all
FDA-approved checkpoint inhibitors (pembrolizumab, nivolumab, atezolizumab,
durvalumab, avelumab, cemiplimab).

For each drug:
- Get the top 20 most frequent adverse events
- Identify immune-related adverse events
- Check for any black box warnings in their labels
- Note any fatal events

This requires many API calls, so please use my API key for higher rate limits.

Multi-Device Comparison

I have an OpenFDA API key: YOUR_API_KEY_HERE

Compare all FDA adverse event reports for NGS-based companion diagnostic devices
from major manufacturers (Foundation Medicine, Guardant Health, Tempus, etc.).
Focus on:
- Test failure rates
- Sample quality issues
- False positive/negative reports
- Software-related problems

This analysis requires querying multiple device records, so the API key will help
avoid rate limiting.

Batch Label Retrieval

My OpenFDA API key is YOUR_API_KEY_HERE.

Retrieve the complete FDA labels for all CDK4/6 inhibitors (palbociclib,
ribociclib, abemaciclib) and extract:
- Approved indications
- Dose modifications for adverse events
- Drug-drug interactions
- Special population considerations

Then create a comparison table of their safety profiles and dosing guidelines.

When to Provide an API Key

You should provide your API key when:

  1. Performing large-scale analyses requiring many API calls
  2. Conducting comprehensive safety reviews across multiple drugs/devices
  3. Running batch operations like comparing multiple products
  4. Doing rapid iterative searches that might hit rate limits
  5. Performing systematic reviews requiring extensive data retrieval

API Key Security Notes

  • Never share your actual API key in public forums or repositories
  • The AI will use your key only for the current session
  • Keys passed as parameters override environment variables
  • The FDA API key is free and can be regenerated if compromised

Important Notes

  • Always expect the AI to use the think tool first for complex queries
  • The AI should include appropriate disclaimers about adverse events not proving causation
  • Results are limited by FDA's data availability and reporting patterns
  • The AI should suggest when additional data sources might provide complementary information
  • With an API key, you can make 240 requests/minute vs 40 without

Known Limitations

Drug Shortage Data

Important: The FDA does not currently provide a machine-readable API for drug shortage data. The shortage search tools will return an informative message directing users to the FDA's web-based shortage database. This is a limitation of FDA's current data infrastructure, not a bug in BioMCP.

Alternative resources for drug shortage information:

  • FDA Drug Shortages Database: https://www.accessdata.fda.gov/scripts/drugshortages/
  • ASHP Drug Shortages: https://www.ashp.org/drug-shortages/current-shortages

Other Limitations

  • Device adverse event reports use abbreviated device names (e.g., "F1CDX" instead of "FoundationOne CDx")
  • Adverse event reports represent voluntary submissions and may not reflect true incidence rates
  • Recall information may have a delay of 24-48 hours from initial FDA announcement