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knowledgebase-mcp

Verified Safe

by biocontext-ai

Overview

Provides a standardized connection layer between artificial intelligence systems (LLMs) and biomedical research resources for information retrieval and domain-specific tasks.

Installation

Run Command
export MCP_ENVIRONMENT=PRODUCTION && export PORT=8000 && uvx biocontext_kb

Environment Variables

  • MCP_ENVIRONMENT
  • PORT
  • MCP_INCLUDE_KEGG
  • MCP_INCLUDE_SCHOLARLY

Security Notes

The project uses standard Python libraries like 'requests' and 'gql' for external API calls, which are generally secure. Input validation is present for some tool parameters (e.g., DOI, NCT ID formats), mitigating direct injection risks into external API calls. No 'eval' or direct arbitrary code execution on user input was observed. Hardcoded secrets are not present in the provided code, with sensitive configurations like port and environment mode managed via environment variables. A potential indirect risk lies in the 'openapi/config.yaml' which allows users to configure additional OpenAPI servers; if this file is compromised or misconfigured with malicious external URLs, it could lead to SSRF-like issues, but this assumes prior file system access to the server. The README explicitly warns users about adherence to external API usage limits and licensing, demonstrating security awareness.

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Stats

Interest Score37
Security Score8
Cost ClassMedium
Avg Tokens1000
Stars16
Forks4
Last Update2025-11-20

Tags

BiomedicalKnowledgebaseAI IntegrationAPI GatewayResearch Tools