Chembl

ChEMBL MCP — drug discovery database (EBI).

Open source Repository Open in the app JSON README (API)

About

ChEMBL MCP — drug discovery database (EBI).

Details

Kind: MCP servers
Topic: Databases
Publisher: pipeworx-io
Origin: official
Category: ferramentas
Transport: http
Version: 0.1.0
Last push: 2026-08-26T16:47:47Z
Repository state: ativo
Language: TypeScript
License: MIT
Added: 2026-08-29 04:01:03
Updated: 2026-08-29 04:01:03
Origin id: io.github.pipeworx-io/chembl

README

# @pipeworx/chembl

[ChEMBL](https://www.ebi.ac.uk/chembl/) MCP — drug-discovery database from EBI: bioactive molecules, drug targets, mechanism of action, clinical phases. Keyless.

Part of [Pipeworx](https://pipeworx.io) — an MCP gateway connecting AI agents to 1476+ live data sources.

## Tools

- `search(query, type?, limit?)` — search molecules / targets / assays / docs
- `molecule(chembl_id)` — full molecule record
- `target(chembl_id)` — target (protein) record
- `mechanism(chembl_id)` — raw mechanism rows for one exact molecule ID
- `chembl_mechanism(drug | molecule_chembl_id, candidates?, limit?)` — mechanism of action
  from a drug **name**. Searches every molecule form the name matched (base + salts) in one
  mechanism query, so drugs whose pharmacology is curated on the salt still resolve —
  e.g. metformin's two mechanisms live on `CHEMBL1703` (METFORMIN HYDROCHLORIDE), while the
  best name match `CHEMBL1431` (METFORMIN) has none. Returns action_type, mechanism text,
  named target + organism, the form each mechanism was recorded on, and PubMed refs.
- `activities(molecule_chembl_id?, target_chembl_id?, limit?)` — activity records
- `drug_indications(molecule_chembl_id?, mesh_id?, limit?)` — disease indications

## Data source

`https://www.ebi.ac.uk/chembl/api/data/`

## Quick Start

Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):

```json
{
  "mcpServers": {
    "chembl": {
      "url": "https://gateway.pipeworx.io/chembl/mcp"
    }
  }
}
```

### What this endpoint actually serves

`tools/list` at `https://gateway.pipeworx.io/chembl/mcp` returns the tools in the table
above **plus the shared Pipeworx meta-tools** — `ask_pipeworx`,
`discover_tools`, `search_within`, `remember`/`recall` and the rest of the
gateway-wide set. So the tool count you see is larger than this table: a
single-pack endpoint currently lists roughly 30 shared tools alongside the
pack's own. The connection's `initialize` response states its exact scope, and
is the authoritative answer for a given day.

This is deliberate, not multiplexing by accident. The meta-tools are what let a
scoped connection answer a question this pack does not cover — via
`ask_pipeworx`, which routes across the whole catalog — without you adding a
second MCP server. There is currently no way to mount a pack endpoint without
them; if the extra schemas cost you more context than the routing is worth,
connect to the full gateway once rather than to several pack endpoints.

Or connect to the full Pipeworx gateway to get every pack's tools listed
directly, instead of just this one's:

```json
{
  "mcpServers": {
    "pipeworx": {
      "url": "https://gateway.pipeworx.io/mcp"
    }
  }
}
```

Both URLs reach the same gateway and the same 1476+ data sources. The
only difference is which pack's tools are listed **directly**; `ask_pipeworx`
reaches all of them from either one.

## Using with ask_pipeworx

Instead of calling tools directly, you can ask questions in plain English —
this works on the pack endpoint above as well as on the full gateway:

```
ask_pipeworx({ question: "your question about Chembl data" })
```

The gateway picks the right tool and fills the arguments automatically.

## More

- [Docs and guides](https://pipeworx.io/docs)
- [pipeworx.io](https://pipeworx.io)

## License

MIT