Pride Archive Search FAQs

Question 1

Which AI models are compatible with Pride Archive Search?

Accepted Answer

Any LLM that supports the Model Context Protocol (MCP) can be integrated, including Anthropic Claude, Google Gemini, open-source MCP clients, and custom RAG pipelines.

Question 2

What kind of datasets can I find using this tool?

Accepted Answer

You can find various proteomics datasets related to biomedical research, mass spectrometry experiments, and other proteomics projects stored in the PRIDE Archive. You can query datasets by keyword, submission date, popularity, and more.

Question 3

How do I install and use Pride Archive Search?

Accepted Answer

Clone the repository, install dependencies using Poetry or pip, and then start the MCP server using the command: `python -m mcp_pride_archive_search --connection_type http --port 9999`.

Question 4

What is MCP and how does Pride Archive Search use it?

Accepted Answer

MCP (Model Context Protocol) is a protocol that allows AI models to use functions or tools. Pride Archive Search implements an MCP-compliant API server powered by FastMCP, allowing LLMs to call the `search_archive_tool()` and search the archive.

Question 5

What is Pride Archive Search?

Accepted Answer

It's an API server that allows AI models to programmatically search the PRIDE Archive, a major repository for proteomics data, using structured function calling. It enables AI to find and interact with proteomics datasets.

Pride Archive Search

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