# UDI setup (for people and AI agents)

UDI, the Universal Data Index from CellType, is a free search index of public biomedical data: datasets
(GEO, SRA, ArrayExpress, PRIDE, CELLxGENE and more) and measured results inside them, PubMed papers, clinical
trials, FDA and EU approvals, labels, safety reports, patents and genetic evidence, each with its source.
Your AI agent uses it through MCP.

- MCP server (Streamable HTTP): https://udi.celltype.com/mcp
- Sign-in: OAuth with your own free CellType Cloud account (Google, GitHub, or an email code); read-only scope `udi.read`.
  There is no shared key to copy. Until you sign in, the client shows UDI as "needs authentication" with no tools.
- In a browser, without an agent: https://cloud.celltype.com/udi
- Help: udi@celltype.com

Beta testers: if your invite gives a different address, use that address instead.

## If you are an AI agent setting this up for your user

1. Find which client you are running in below and run or show its connect step.
2. Sign-in needs your user: they open the sign-in link in a browser once. You cannot do it for them.
3. Most clients load MCP servers only when a chat starts: after connecting, the user starts a new chat.
4. Check it works with: "Use UDI to tell me what it has on PCSK9." (UDI's `udi_coverage` tool answers.)

## Claude Code

```bash
claude mcp add --transport http --scope user celltype-udi https://udi.celltype.com/mcp
```

`--scope user` makes UDI available in every project. Then start a new chat (or restart Claude Code), type `/mcp`,
pick `celltype-udi`, choose **Authenticate**, and sign in in the browser window. `claude mcp login` does not work
from an agent's non-interactive shell; use `/mcp` inside a chat.

## Claude desktop app and claude.ai

1. Settings → Connectors → **Add custom connector**.
2. Name `UDI`, URL `https://udi.celltype.com/mcp`, **Add**.
3. Click **Connect** next to UDI and sign in. In a chat, open the tools menu (sliders icon) and switch UDI on.

On Team and Enterprise plans an owner may need to add the connector first.

## ChatGPT

Needs a plan that allows custom apps (Plus, Pro, Business, Enterprise, Edu).

1. Settings → Apps & Connectors → Advanced settings: turn on **Developer mode**.
2. Apps & Connectors → **Create**. Name `UDI`, MCP server URL `https://udi.celltype.com/mcp`, Authentication **OAuth**.
3. Confirm and **Create**; sign in on the UDI page that opens.
4. In each new chat: **+** → Developer mode (or More → UDI) → select UDI.

## Codex (CLI and IDE extension)

```bash
codex mcp add udi --url https://udi.celltype.com/mcp
codex mcp login udi
```

Or in `~/.codex/config.toml`:

```toml
[mcp_servers.udi]
url = "https://udi.celltype.com/mcp"
```

Check with `codex mcp list`, then `/mcp` inside Codex.

## Cursor

`~/.cursor/mcp.json` (all projects) or `.cursor/mcp.json` (one project):

```json
{
  "mcpServers": {
    "udi": { "url": "https://udi.celltype.com/mcp" }
  }
}
```

Then Cursor Settings → MCP → click **Needs login** next to `udi` and sign in.

## Any other MCP client

Connect to `https://udi.celltype.com/mcp` (Streamable HTTP) and sign in with OAuth. The server publishes its sign-in
details at https://udi.celltype.com/.well-known/oauth-protected-resource/mcp (dynamic client registration and PKCE).

## Headless agents and scripts (no browser)

A headless agent uses a read-only service token issued by CellType (ask udi@celltype.com) as
`Authorization: Bearer <token>`, on MCP or the REST API:

```bash
curl https://udi.celltype.com/udi/tools/call -H "Authorization: Bearer $UDI_TOKEN" \
  -H 'Content-Type: application/json' -d '{"name": "udi_coverage", "arguments": {"entity": "PCSK9"}}'
```

- Search: `POST https://udi.celltype.com/udi/search` with `{"query": "...", "species": "human", "limit": 10}`
- List tools: `GET https://udi.celltype.com/udi/tools`
- Python: `pip install celltype-udi`, then `from celltype_udi import search, call` (reads `UDI_TOKEN`).
- CellType team with a CellData checkout: `udi login` (prints a sign-in URL; works from any shell), then
  `udi --hosted <command>`; `udi doctor` shows what is set up.

## First questions to try

1. Use UDI: who else is developing TL1A drugs, and how far along are they?
2. Use UDI: is there genetic evidence that PCSK9 matters in coronary artery disease, and what did evolocumab show?
3. Use UDI to find human single-cell RNA-seq of idiopathic pulmonary fibrosis lung, check the top three studies
   for at least 10 donors, and tell me which one to download first.

Say "use UDI" the first time in a chat. Every answer lists ready next calls; ask your agent to follow them.

## Feedback

Something wrong, missing or confusing? Tell your agent "tell UDI that …" with what you asked and what was wrong. If
your agent has no UDI feedback tool, it should email udi@celltype.com with your question and UDI's answer.

More: https://www.celltype.com/udi