io.github.pipeworx-io/ensembl

Ensembl REST — vertebrate genomes, sequences, comparative genomics, variation

7 tools GitHub

No known CVEs

MIT license

Actively maintained

Last commit 19d ago

Works with most clients

Transport:

7 tools · ~278 tok

Grade A · 0.1% of 200K ctx

MCPpedia last refreshed this data 15h ago

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io.github.pipeworx-io/ensembl is an MCP server that ensembl REST — vertebrate genomes, sequences, comparative genomics, variation. Its tool list has not been published yet, requires no API key, and scores 68/100 on MCPpedia's security, maintenance and efficiency rubric.

Health

Step 1

Install in your client

Config is the same across clients — only the file and path differ.

Supported in Claude Desktopstdio · Node 18+

Paste into ~/Library/Application Support/Claude/claude_desktop_config.json

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

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[![MCPpedia Score](https://mcppedia.org/api/badge/io-github-pipeworx-io-ensembl)](https://mcppedia.org/s/io-github-pipeworx-io-ensembl)

Read me

What io.github.pipeworx-io/ensembl does

Part of Pipeworx — an MCP gateway connecting AI agents to 673+ live data sources.

Test This Server

No automated test available for this server. Check the GitHub README for setup instructions.

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Scored, not listed

Why this score

Five weighted categories — click any category to see the underlying evidence.

Score breakdown

68/100across 5 weighted dimensions

How we score →

0255075100

−32

Security

Maintenance

Efficiency

Documentation

Compatibility

Categoriesclick a row to see evidence

Security

OSV.dev

No known CVEs.

No package registry to scan.

Inventory

Tools (7)

Click any tool to inspect its schema.

~278 tokens total

Community

Reviews

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How easy was setup?Did it work reliably?How was the documentation?

Frequently Asked Questions

Is io.github.pipeworx-io/ensembl safe to use?: io.github.pipeworx-io/ensembl has no known CVEs as of the latest MCPpedia security scan. It does not require authentication, so any local process can connect — keep this in mind in shared environments. Licensed under MIT.
How do I install io.github.pipeworx-io/ensembl?: io.github.pipeworx-io/ensembl supports copy-paste install configs on its MCPpedia page for Claude Desktop, Cursor, and Claude Code. Scroll to the Quick Install section and select your client.
What can io.github.pipeworx-io/ensembl do?: io.github.pipeworx-io/ensembl provides 7 tools: lookup, lookup_symbol, xrefs, sequence, homology and 2 more. See the full tools list on the server page for descriptions and parameters.
What AI clients work with io.github.pipeworx-io/ensembl?: io.github.pipeworx-io/ensembl is compatible with claude-desktop, cursor, claude-code. It uses stdio transport.
Is io.github.pipeworx-io/ensembl actively maintained?: io.github.pipeworx-io/ensembl is actively maintained — last commit was 19 days ago.

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Community

Discussion

Start a conversation

Ask a question, share a tip, or report an issue.

Has anyone used this with Cursor?How do you handle auth?Any alternatives?

Tools

lookup(id, expand?) — by stable id (gene/transcript/exon/translation)

lookup_symbol(species, symbol) — gene by symbol within a species

xrefs(species, symbol) — external cross-references for a gene symbol

sequence(id, type?) — DNA / cDNA / CDS / protein sequence

homology(species, symbol_or_id, target_species?) — homology mappings

variation(species, variant_id) — variation by name (e.g. "rs56116432")

vep(species, region, allele) — Variant Effect Predictor (region: "9:22125504-22125504:1")

xref_symbol(species, symbol) — symbol lookup (alias for /xrefs/symbol)

Quick Start

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

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

Or connect to the full Pipeworx gateway for access to all 1394+ data sources:

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

Frequently Asked Questions

Is io.github.pipeworx-io/ensembl safe to use?

io.github.pipeworx-io/ensembl has no known CVEs as of the latest MCPpedia security scan. It does not require authentication, so any local process can connect — keep this in mind in shared environments. Licensed under MIT.

How do I install io.github.pipeworx-io/ensembl?

io.github.pipeworx-io/ensembl supports copy-paste install configs on its MCPpedia page for Claude Desktop, Cursor, and Claude Code. Scroll to the Quick Install section and select your client.

What can io.github.pipeworx-io/ensembl do?

io.github.pipeworx-io/ensembl provides 7 tools: lookup, lookup_symbol, xrefs, sequence, homology and 2 more. See the full tools list on the server page for descriptions and parameters.

What AI clients work with io.github.pipeworx-io/ensembl?

io.github.pipeworx-io/ensembl is compatible with claude-desktop, cursor, claude-code. It uses stdio transport.

Is io.github.pipeworx-io/ensembl actively maintained?

io.github.pipeworx-io/ensembl is actively maintained — last commit was 19 days ago.

@pipeworx/ensembl

Ensembl REST API MCP — vertebrate genomes, gene annotations, sequences, comparative genomics, variation. Keyless.

Part of Pipeworx — an MCP gateway connecting AI agents to 1394+ live data sources.

Tools

lookup(id, expand?) — by stable id (gene/transcript/exon/translation)
lookup_symbol(species, symbol) — gene by symbol within a species
xrefs(species, symbol) — external cross-references for a gene symbol
sequence(id, type?) — DNA / cDNA / CDS / protein sequence
homology(species, symbol_or_id, target_species?) — homology mappings
variation(species, variant_id) — variation by name (e.g. "rs56116432")
vep(species, region, allele) — Variant Effect Predictor (region: "9:22125504-22125504:1")
xref_symbol(species, symbol) — symbol lookup (alias for /xrefs/symbol)

Data source

https://rest.ensembl.org

Quick Start

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

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

Or connect to the full Pipeworx gateway for access to all 1394+ data sources:

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

Using with ask_pipeworx

Instead of calling tools directly, you can ask questions in plain English:

ask_pipeworx({ question: "your question about Ensembl data" })

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

License

MIT

io.github.pipeworx-io/ensembl

Install in your client

What io.github.pipeworx-io/ensembl does

Test This Server

Why this score

68/100across 5 weighted dimensions

Security

Tools (7)

Reviews

Frequently Asked Questions

Similar servers

Discussion

io.github.pipeworx-io/ensembl

Install in your client

What io.github.pipeworx-io/ensembl does

Test This Server

@pipeworx/ensembl

Tools

Data source

Quick Start

Using with ask_pipeworx

More

License

Why this score

68/100across 5 weighted dimensions

Security

Tools (7)

Reviews

Frequently Asked Questions

Similar servers

Discussion

@pipeworx/ensembl

Tools

Data source

Quick Start

Using with ask_pipeworx

More

License