PHi-D for AI Assistants

What It Is

PHi-D runs an MCP server (Model Context Protocol), so an AI assistant can look things up in PHi-D for you. Ask in your own words: the assistant searches the published experiments and results and answers with links to the PHi-D viewer.

Connect

Add this address to your assistant as a remote MCP server. No account or key is needed; the server is read-only and answers up to five requests a second from each address.

• Claude Code claude mcp add --transport http phid https://phid.riken.jp/mcp/
• Codex CLI codex mcp add phid --url https://phid.riken.jp/mcp/
• claude.ai, ChatGPT and other assistants: add the address as a custom connector in the assistant's settings, where your plan offers one.

Then start a new session.

Try Asking

• Which experiments use GM12878?
• How well does the PHi-C model fit chr1 of 4DNFI4WHVND7?
• Show the contact map of chr1 between 10 and 20 Mb in 4DNFI4WHVND7, measured and model.

What It Can Answer

Finding experiments by cell type, assembly, experiment type, lab, paper or Score; one experiment's chromosomes, including any that could not be analysed; one chromosome's fit, mean squared displacement and loss tangent; and part of a contact map, measured and model. It does not hold 3D coordinates or gene annotations. Every answer comes with a viewer link, so you can check it on PHi-D itself.

Contact

Please address all questions and comments to phid-support@ml.riken.jp