FAQ

Does BioMCP require API keys?

No for most workflows.

Optional keys improve access for specific enrichments and source variants. See API keys.

Where are cached files stored?

BioMCP uses platform cache directories.

Typical locations:

• Linux: ~/.cache/biomcp/
• macOS: ~/Library/Caches/biomcp/

The cache generally contains:

• http-cacache/ for HTTP responses,
• downloads/ for retrieved text artifacts.

Why do invalid dates fail immediately?

Date validation is performed before network calls.

Examples of invalid inputs:

• 2024-13-01 (invalid month)
• 2024-02-30 (invalid day)
• 2023-02-29 (non-leap-year day)

This behavior provides immediate feedback and avoids unnecessary API requests.

How do I request full article text now?

Use positional sections:

biomcp get article 22663011 fulltext

The same model applies to other entities:

biomcp get trial NCT02576665 eligibility
biomcp get gene BRAF pathways
biomcp get variant "BRAF V600E" predict

How do I use BioMCP with Claude Desktop?

Configure an MCP server entry using biomcp serve. See Claude Desktop setup.

Why are some fields missing?

BioMCP returns concise defaults and depends on upstream source completeness.

When you need more detail:

1. request a section,
2. switch to JSON,
3. verify source availability with biomcp health --apis-only.

How do I inspect available commands quickly?

biomcp list
biomcp list trial
biomcp list variant

Is BioMCP suitable for final clinical decisions?

BioMCP is a retrieval and workflow tool. Clinical decisions require domain-expert review and institutional validation processes.

How do I report reproducible issues?

Include:

• exact command,
• expected vs actual behavior,
• biomcp --version,
• relevant environment details,
• whether the issue reproduces with --json.