BioMCP

# 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 ### Combining with Literature Search ``` 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. ``` ### Method 2: Set Environment Variable (Recommended for Regular Use) If you're using BioMCP regularly, set the environment variable once: ```bash 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: ```bash # 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