How does GEO access gene expression data?

GEO utilizes the NCBI E-Utils API to directly retrieve gene expression data from various GEO databases, including Profiles, DataSets, Series, Samples, and Platforms, ensuring real-time access.

What is the GEO tool?

GEO is a software tool providing a Model Context Protocol (MCP) server and HTTP API for real-time access to Gene Expression Omnibus (GEO) data through the NCBI E-Utils API.

What types of GEO data can I search using this tool?

The GEO tool enables searching across all major Gene Expression Omnibus databases: GEO Profiles, GEO DataSets, GEO Series, GEO Samples, and GEO Platforms, facilitating comprehensive data discovery.

Can I increase my data retrieval rate with GEO?

Yes, by configuring GEO with an optional NCBI API key, you can increase your request rate limit from 3 to 10 requests per second when interacting with the NCBI E-Utils API.

What are the primary use cases for the GEO tool?

GEO is designed for researchers, bioinformaticians, and developers to automate gene expression data acquisition, integrate GEO data into AI/ML workflows, and build applications requiring direct access to genomic data.

GEO

Name: GEO
Author: maflot

bymaflot

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API開発

データサイエンスとML

ウェブスクレイピングとデータ収集

Provides a Model Context Protocol (MCP) server interface for accessing Gene Expression Omnibus (GEO) data via the NCBI E-Utils API.

This tool functions as a Model Context Protocol (MCP) server, designed to give researchers, bioinformaticians, and developers streamlined access to the extensive Gene Expression Omnibus (GEO) data repository. It harnesses the NCBI E-Utils API to facilitate real-time searching and retrieval of high-throughput functional genomics data, including gene expression profiles, curated datasets, experimental series, individual samples, and microarray platform definitions. This direct integration enables seamless incorporation of GEO data into AI/ML workflows, custom applications, and automated data pipelines, significantly enhancing bioinformatics research and analysis.

主な機能

01Offers interfaces via both MCP stdio protocol and a dedicated HTTP API.

02Utilizes the NCBI E-Utils API for direct, real-time data retrieval.

03Configurable with an optional NCBI API key for higher request rate limits.

04Accesses multiple GEO databases: Profiles, DataSets, Series, Samples, and Platforms.

053 GitHub stars

06Enables automated data acquisition for bioinformatics projects.

ユースケース

01Integrate GEO data seamlessly into AI/ML workflows through the MCP.

02Automate the retrieval of gene expression data for diverse research projects.

03Build custom applications that require real-time access to functional genomics data.