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FAQ - Quick Answers

Getting Started

Q: What is BioMCP? A: A unified interface to biomedical databases (PubMed, ClinicalTrials.gov, MyVariant, etc.) for researchers and AI assistants.

Q: Do I need API keys? A: No for basic use. Yes for: NCI trials (cancer-specific), AlphaGenome (variant predictions), enhanced cBioPortal features.

Q: How do I install it? A: uv tool install biomcp (recommended) or pip install biomcp-python

Common Issues

Q: "Command not found" after installation A: Restart terminal, or use full path: ~/.local/bin/biomcp

Q: No results for gene search A: Use official symbols (ERBB2 not HER2). Check at genenames.org

Q: Location search not working A: Must provide coordinates: --latitude 42.3601 --longitude -71.0589

Q: Why does the AI use 'think' first? A: Required for systematic analysis. Improves search quality and prevents missed connections.

Search Tips

Q: How to search variant notations? A: Use OR syntax: --keyword "V600E|p.V600E|c.1799T>A"

Q: Include/exclude preprints? A: Included by default. Use --no-preprints to exclude.

Q: Search multiple databases? A: Use unified search: search(query="gene:BRAF AND disease:melanoma")

Data Questions

Q: How current is the data? A: Daily updates for PubMed/trials, weekly for BioThings, varies for cBioPortal.

Q: ClinicalTrials.gov vs NCI? A: CT.gov = comprehensive, NCI = cancer-focused with biomarker filters (needs API key).

Q: What's MSI/TMB/VAF? A: MSI = Microsatellite Instability, TMB = Tumor Mutational Burden, VAF = Variant Allele Frequency

Technical

Q: Rate limits? A: ~3 req/sec without keys, higher with keys. NCI = 1000/day with key.

Q: Cache issues? A: Clear with: rm -rf ~/.biomcp/cache

Q: Which Python version? A: 3.10+ required

Quick References

Common Gene Aliases:

  • HER2 → ERBB2
  • PD-L1 → CD274
  • c-MET → MET

City Coordinates:

  • NYC: 40.7128, -74.0060
  • Boston: 42.3601, -71.0589
  • LA: 34.0522, -118.2437

Trial Status:

  • RECRUITING = Currently enrolling
  • ACTIVE_NOT_RECRUITING = Ongoing
  • COMPLETED = Finished

Getting Help

  1. Check this FAQ
  2. Read Troubleshooting
  3. Search GitHub Issues
  4. Ask with version info: biomcp --version