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specs-mcp-server

Verified Safe

by pharmbio

Overview

The server provides a suite of tools for similarity search and analytics on a compound dataset, focusing on compound-to-compound and MOA-to-MOA relationships, gene co-occurrence, and disease rollups for drug discovery and bioinformatics.

Installation

Run Command
docker build -t specs-mcp . && docker run --rm -p 8000:8000 specs-mcp

Environment Variables

  • MCP_TRANSPORT
  • HOST
  • PORT

Security Notes

The code appears to be well-structured and minimizes obvious security risks. It primarily uses pandas for data manipulation and scikit-learn for similarity calculations. User inputs are generally sanitized (e.g., lowercased, stripped, regex=False) before being used in DataFrame queries or fuzzy matching. There are no apparent uses of `eval`, `exec`, or direct shell command injections. The dataset path is hardcoded, preventing arbitrary file access. Environment variables are used for server configuration (host, port, transport), which is a good practice. The main risk, if any, would stem from vulnerabilities in the underlying `FastMCP`, `pandas`, or `numpy` libraries, or if the `compound_aggregate_with_annotations.csv` file itself is untrusted and can be modified by an attacker in a deployment scenario, though the application itself does not facilitate arbitrary modifications to this file.

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Stats

Interest Score0
Security Score9
Cost ClassMedium
Stars0
Forks0
Last Update2025-12-16

Tags

drug discoverybioinformaticssimilarity searchdata analyticschemical compounds