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mcp-geo-database

Verified Safe

by yixianfan

Overview

Accessing NCBI Gene Expression Omnibus (GEO) database for searching, downloading, parsing, and analyzing gene expression and genomics data.

Installation

Run Command
python geo_database_server.py

Security Notes

The server primarily interacts with external NCBI services (Entrez E-utilities, FTP) for data. File system operations for downloading are constrained to a user-defined or default directory ('./data') using `os.makedirs(destdir, exist_ok=True)` and `os.path.join` to prevent path traversal. The `parse_soft_file` function reads the content of a specified file, which could potentially expose local files if the `filepath` argument is maliciously crafted to point outside the intended data directory. However, it only reads and prints content, not executes it. There is no usage of `eval`, `exec`, or direct shell command execution. The `Entrez.email` is hardcoded, which is a minor configuration concern but not a direct security vulnerability.

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Stats

Interest Score0
Security Score8
Cost ClassHigh
Avg Tokens5000
Stars0
Forks0
Last Update2026-01-17

Tags

GEOgene expressiongenomicsbioinformaticsNCBI