# Ensembl (npm · @pipeworx/mcp-ensembl)

Ensembl REST MCP.

- Trust score: 81/100 (high trust)
- Change this week: +3
- Registry status: active
- Liveness: live
- Owner verified: no
- Last scored: 2026-11-05

## Components

- remote · `gateway.pipeworx.io`: 77/100, [markdown](https://verifymcp.io/servers/pipeworx-io-ensembl/ensembl-mcp.md), [page](https://verifymcp.io/servers/pipeworx-io-ensembl/ensembl-mcp)
- npm · `@pipeworx/mcp-ensembl`: 81/100 (this document), [markdown](https://verifymcp.io/servers/pipeworx-io-ensembl/pipeworx-mcp-ensembl.md), [page](https://verifymcp.io/servers/pipeworx-io-ensembl/pipeworx-mcp-ensembl)

## Channel facts

- Registry: `npm`
- Package: `@pipeworx/mcp-ensembl`
- Version: `0.2.1`
- Transport: `stdio`

## Trust breakdown

How this component scores in each security and reliability category. Every signal is checked automatically from public evidence about the published package, including repeated runs of it in an isolated sandbox, and we only credit what we can confirm. Scores are 0–100 per category. Scoring method: https://verifymcp.io/docs/scoring (what has changed: https://verifymcp.io/docs/scoring/changelog)

Scored 2026-11-05.

- **Supply Chain Security**: 100/100
  - No malware found by supply-chain analysis.
  - No known CVEs affecting this package version or its production dependencies.
  - No install/post-install scripts declared.
  - No production dependencies, so there is no dependency health to assess.
- **Provenance & Transparency**: 97/100
  - Source repository is publicly reachable at the declared URL.
  - Cryptographically verified build provenance (signed, bound to pipeworx-io/mcp-ensembl).
  - Clear OSI-approved license (MIT).
  - Actively maintained (last published 3 days ago).
  - Disclosure check failed: no security disclosure policy was found in the source repository.
- **Schema Quality & AI Usability**: 64/100
  - AI-judged instruction clarity (good).
  - Context-footprint check failed: tool/resource definitions use about 1227 tokens (~175/item across 7 items; 7 tools + 0 resources), over budget; trim descriptions and params.
  - Usage-examples check failed: none of the tools include examples.
- **Stability & Change Management**: 23/100
  - Stability observed for 7 of 30 days with no destabilising changes; credit accrues until the full window elapses.
- **Tool Coverage**: 85/100
  - 100% of tools have a non-trivial description (not blank, and not just the tool's name).
  - 55% of tool parameters carry a description.
- **Tool Safety**: 100/100
  - No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.
  - We read all 7 captured tool definition(s), and no name or description among them implies an irreversible operation.
  - An AI judge read all 8 captured unit(s) of tool text and found none that tries to manipulate the model reading it.
- **Capabilities**: 100/100
  - Implements a supported MCP spec version (2025-11-25); the latest is 2026-07-28.

## Install

### How do I install the Ensembl MCP server?

Ensembl runs locally as an npm package, launched with npx -y @pipeworx/mcp-ensembl. Ready-made configuration for Claude, Cursor, VS Code, Codex and 5 more is on this page, copied from each client's own documentation.

### Claude

```bash
claude mcp add pipeworx-io-ensembl -- npx -y @pipeworx/mcp-ensembl
```

### Cursor

```json
{
  "mcpServers": {
    "pipeworx-io-ensembl": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-ensembl"
      ]
    }
  }
}
```

### VS Code

```json
{
  "servers": {
    "pipeworx-io-ensembl": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-ensembl"
      ]
    }
  }
}
```

### Codex

```bash
codex mcp add pipeworx-io-ensembl -- npx -y @pipeworx/mcp-ensembl
```

### opencode

```json
{
  "$schema": "https://opencode.ai/config.json",
  "mcp": {
    "pipeworx-io-ensembl": {
      "type": "local",
      "command": [
        "npx",
        "-y",
        "@pipeworx/mcp-ensembl"
      ],
      "enabled": true
    }
  }
}
```

### OpenClaw

```bash
openclaw mcp add pipeworx-io-ensembl --command npx --arg -y --arg @pipeworx/mcp-ensembl
```

### Hermes

```yaml
mcp_servers:
  pipeworx-io-ensembl:
    command: "npx"
    args: ["-y", "@pipeworx/mcp-ensembl"]
```

### Netclaw

```json
{
  "McpServers": {
    "pipeworx-io-ensembl": {
      "Transport": "stdio",
      "Command": "npx",
      "Arguments": [
        "-y",
        "@pipeworx/mcp-ensembl"
      ]
    }
  }
}
```

### Vellum

```bash
assistant mcp add pipeworx-io-ensembl -t stdio -c npx -a -y @pipeworx/mcp-ensembl
```

### Other

```json
{
  "mcpServers": {
    "pipeworx-io-ensembl": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-ensembl"
      ]
    }
  }
}
```

## Changelog

Every change recorded for this component, newest first. Days that predate change tracking, or that we cannot explain, say so: "we were watching and nothing happened" and "we were not watching" are different claims.

### 2026-11-04 (score 81, +1)

No change was recorded against any check on this day. Stability & Change Management went from 17 to 20. That category is still filling its 30-day observation window: 5 days of observed history at the previous scan, 6 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-11-02 (score 80, +1)

No change was recorded against any check on this day. Stability & Change Management went from 10 to 13. That category is still filling its 30-day observation window: 3 days of observed history at the previous scan, 4 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-11-01 (score 79, 0)

- [security regression] Stability: 0.07 → unverified
- [security regression] Tool safety: pass → unverified
- [functional regression] Capabilities: pass → unverified
- [functional regression] Tool coverage: 100 → unverified
- [functional] First check of Schema quality: unverified
- [functional] Package version: 0.2.0 → 0.2.1

### 2026-10-31 (score 79, +1)

No change was recorded against any check on this day. Stability & Change Management went from 3 to 7. That category is still filling its 30-day observation window: 1 days of observed history at the previous scan, 2 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-10-29 (score 78)

First indexed and scored.

## MCP tools (7)

### `lookup` (~194 tokens)

"Ensembl gene info for [ENSG...]" / "look up [Ensembl ID]" / "fetch [ENST.../ENSE.../ENSP...]" — fetch metadata for an Ensembl stable ID (gene / transcript / exon / translation). Returns name, biotype, chromosomal position, strand, description. Pass expand=true to include child features (transcripts of a gene, exons of a transcript). Example: ENSG00000157764 (BRAF).

Input parameters:

- `assembly` (string): Human genome build: "GRCh38" (the default) or "GRCh37" (= hg19). Coordinates you pass and coordinates you get back are both in this build. Older variant lists, spreadsheets and published tables are u…
- `expand` (boolean): Include child features.
- `id` (string, required): e.g. "ENSG00000157764" (BRAF)

### `lookup_symbol` (~200 tokens)

"What's the Ensembl ID for [gene symbol]" / "look up [gene] in Ensembl" / "BRCA1 / TP53 / BRAF Ensembl info" / "find gene [symbol] in [species]" — look up a gene by symbol within a species (e.g. species="human" symbol="BRCA1"). Returns Ensembl gene ID, chromosomal position, biotype, description. Use to convert HGNC gene symbols to Ensembl IDs for genomics workflows.

Input parameters:

- `assembly` (string): Human genome build: "GRCh38" (the default) or "GRCh37" (= hg19). Coordinates you pass and coordinates you get back are both in this build. Older variant lists, spreadsheets and published tables are u…
- `expand` (boolean)
- `species` (string, required): e.g. "human", "mus_musculus"
- `symbol` (string, required)

### `xrefs` (~85 tokens)

"What's the UniProt / HGNC / RefSeq ID for [gene]" / "cross-references for [gene symbol]" — external database IDs (UniProt, RefSeq, HGNC, Entrez, OMIM, etc.) for a gene symbol. Use to map between bio-database identifier spaces.

Input parameters:

- `species` (string, required)
- `symbol` (string, required)

### `sequence` (~170 tokens)

"DNA / cDNA / CDS / protein sequence of [gene]" / "FASTA for [Ensembl ID]" / "get sequence of [transcript]" — sequence by Ensembl stable ID. Type defaults to "genomic"; pass "cdna", "cds", or "protein" for processed forms. Use for sequence retrieval in primer design, variant analysis, or downstream sequence tools.

Input parameters:

- `assembly` (string): Human genome build: "GRCh38" (the default) or "GRCh37" (= hg19). Coordinates you pass and coordinates you get back are both in this build. Older variant lists, spreadsheets and published tables are u…
- `id` (string, required)
- `type` (string): genomic (default) | cdna | cds | protein

### `homology` (~97 tokens)

"What's the mouse / rat / zebrafish ortholog of [human gene]" / "ortholog of [gene] in [species]" / "homologs of [gene]" — orthologs and paralogs for a gene across species. Use for cross-species comparison, model organism work, evolutionary analysis.

Input parameters:

- `species` (string, required)
- `symbol_or_id` (string, required)
- `target_species` (string)

### `variation` (~157 tokens)

"What is [rsID]" / "look up SNP [rs...]" / "variant info for [rsN]" — fetch a genetic variation record by ID (e.g. rs56116432). Returns alleles, genomic location, clinical significance, gene mappings. Use for SNP lookups, pharmacogenomics, GWAS follow-up.

Input parameters:

- `assembly` (string): Human genome build: "GRCh38" (the default) or "GRCh37" (= hg19). Coordinates you pass and coordinates you get back are both in this build. Older variant lists, spreadsheets and published tables are u…
- `species` (string, required)
- `variant_id` (string, required): e.g. "rs56116432"

### `vep` (~270 tokens)

"What's the effect of [variant]" / "predict consequences of [genomic change]" / "VEP for [chrom:pos]" — Variant Effect Predictor for a specified region + allele. Returns consequences (missense, synonymous, splice, etc.), affected genes, transcript impacts, SIFT/PolyPhen predictions. Use for variant interpretation in clinical or research genomics. THE REGION IS REQUIRED — there is no default. A GRCh37/hg19 position is also a valid GRCh38 position, so an unstated build cannot be detected, only guessed wrong, and a wrong guess returns confident annotations for a DIFFERENT gene rather than an error.

Input parameters:

- `allele` (string, required): e.g. "C"
- `assembly` (string, required): REQUIRED. The genome build your region is in: "GRCh38" (= hg38) or "GRCh37" (= hg19). There is no default on purpose — a genomic position is valid in BOTH builds, so an unstated build cannot be detec…
- `region` (string, required): e.g. "9:22125504-22125504:1" — in the build named by assembly.
- `species` (string, required)

## Diagnostics

Captured diagnostic sections: Provenance, Dependencies. The full working is on the page: https://verifymcp.io/servers/pipeworx-io-ensembl/pipeworx-mcp-ensembl#diagnostics

## Score history

- 2026-11-05: 81
- 2026-11-04: 81
- 2026-11-03: 80
- 2026-11-02: 80
- 2026-11-01: 79
- 2026-10-31: 79
- 2026-10-30: 78
- 2026-10-29: 78

## Common questions

### What is the Ensembl MCP server?

Ensembl is an MCP server listed in the public MCP registry as io.github.pipeworx-io/ensembl. Ensembl REST MCP. This page covers its npm package (@pipeworx/mcp-ensembl).

### Is the Ensembl MCP server safe to use?

Ensembl scores 81 out of 100 on VerifyMCP. We found no known CVEs affecting it as of 5 November 2026. It declares no install or post-install scripts. Its build provenance is signed and verified. That is a record of what we were able to check automatically, not an endorsement. The category breakdown on this page shows every signal behind the number, including the ones we could not confirm.

### What tools does the Ensembl MCP server expose?

Ensembl exposes 7 tools: lookup, lookup_symbol, xrefs, sequence, homology, and 2 more. Their descriptions and schemas cost roughly 1,173 tokens of context every time the server is loaded.

### Is the Ensembl MCP server still maintained?

Ensembl is still listed as active in the MCP registry. We last reached this channel on 5 November 2026. Those dates come from our own scans of the registry and the channel itself, not from anything the publisher announced.

### What licence is the Ensembl MCP server under?

Ensembl declares the MIT licence, which is OSI-approved. That covers the source only, and says nothing about the cost of any service it calls.

### What did VerifyMCP test on the Ensembl MCP server?

VerifyMCP ran 16 checks on Ensembl, covering Malware scan, Known CVEs, Install scripts, Dependency health and 12 more. Endpoint Security and Transport & Reachability do not apply to an npm package, so they were not tested. The score does not measure everything, and the scoring documentation lists what it leaves out.

## Links

- npm package: https://www.npmjs.com/package/@pipeworx/mcp-ensembl
- Socket report: https://socket.dev/npm/package/@pipeworx/mcp-ensembl
- Repository: https://github.com/pipeworx-io/mcp-ensembl
- Website: https://pipeworx.io/packs/ensembl
- Changelog RSS feed: https://verifymcp.io/servers/pipeworx-io-ensembl/pipeworx-mcp-ensembl.xml
- Changelog JSON feed: https://verifymcp.io/servers/pipeworx-io-ensembl/pipeworx-mcp-ensembl/changelog.json
- Trust report (JSON): https://verifymcp.io/servers/pipeworx-io-ensembl/pipeworx-mcp-ensembl.json
- HTML version of this page: https://verifymcp.io/servers/pipeworx-io-ensembl/pipeworx-mcp-ensembl