How to Use the Ensembl MCP in CrewAI

Q: How do I give my CrewAI agents access to Ensembl MCP tools?

Add your Vinkius server URL to the mcps list when defining your agents. This MCP Server exposes all 27 genomic tools, allowing your agents to call getsequenceid or getlookupid as needed.

Q: Can a CrewAI agent lookup multiple Ensembl IDs at once?

Yes, you can assign a data-gatherer agent to run getlookupbulk for batch queries. This agent then shares the resulting gene metadata with the rest of the crew through their common memory pool.

Q: How do CrewAI agents handle Ensembl coordinate conversions?

Your agents can use getmap to convert coordinates between different assembly versions. A specialized coordinator agent handles the mapping before passing the updated coordinates to other agents for sequence extraction.

Q: Does CrewAI store the genomic variant data retrieved from Ensembl?

No, genomic coordinates and variant data retrieved via getvariation are only held in your local crew's short-term memory. Vinkius provides a secure, ephemeral MCP gateway that never stores your genomic payloads.

Run specialized agent crews to analyze Ensembl genomic data and map variant consequences autonomously.

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Connect Ensembl MCP to CrewAI

Create your Vinkius account to connect Ensembl to CrewAI and route execution through our secure gateway. The platform manages server hosting, runtime updates, and security layers. Configuration requires no manual server provisioning.

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Setup Ensembl with CrewAI

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Coordinate variant annotation across a CrewAI team

`get_vep_id` lets your variant annotator agent fetch consequence predictions for specific rsIDs. This agent then hands the raw consequence data to a clinical interpreter agent in the crew for downstream analysis. If the rsID is missing, the annotator falls back to `get_vep_hgvs` to analyze the variant using standard HGVS notation. The entire process runs autonomously, utilizing CrewAI's shared memory to track variant histories across the team.

Map genetic associations using this MCP Server

`get_ld` calculates linkage disequilibrium values between variants for your population genetics crew. One agent can query a specific genomic region while another calculates the correlation between alleles. The crew then uses `get_overlap_region` to find genes overlapping those high-LD regions. This collaborative loop allows your agents to narrow down candidate causal variants without human intervention.

Track evolutionary history across species with CrewAI

`get_homology` retrieves evolutionary relationships to help your comparative genomics crew map gene conservation. The researcher agent fetches orthology data and passes it to the sequence analyzer agent. That analyzer agent then runs `get_alignment` to pull the exact sequence alignments for those homologous regions. By dividing the work, your crew avoids API bottlenecks and processes comparative genomic data in parallel.

Setup guide

Set up Ensembl MCP in CrewAI

Prerequisites

Python 3.10+ installed
crewai package (pip install crewai)
Active Vinkius subscription with a valid endpoint token

1

Install CrewAI
Run pip install crewai to install the framework. MCP support is built-in via the mcps parameter.
2

Add the MCP URL to your agent
Pass your Vinkius endpoint directly to the mcps list. Replace [YOUR_TOKEN_HERE] with your token from cloud.vinkius.com. CrewAI handles tool discovery and caching automatically.
3

Kick off your crew
Create a Crew with your agent and tasks. Call crew.kickoff() — the agent will automatically invoke Ensembl tools as needed.

crew.py

from crewai import Agent, Task, Crew

agent = Agent(
    role="Ensembl Analyst",
    goal="Access and analyze Ensembl data via MCP.",
    backstory="Expert analyst with direct Ensembl access.",
    mcps=[
        "https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"
    ],
)

task = Task(
    description="List recent Ensembl transactions",
    agent=agent,
    expected_output="A summary of recent activity",
)

crew = Crew(agents=[agent], tasks=[task])
result = crew.kickoff()
print(result)

Get your connection token →

Prerequisites

Python 3.10+ installed
crewai + crewai-tools packages
Active Vinkius subscription with a valid endpoint token

1

Install dependencies
Run pip install crewai crewai-tools. The MCPServerAdapter handles lifecycle management and tool conversion.
2

Connect with MCPServerAdapter
Use MCPServerAdapter as a context manager with SseServerParameters pointing to your Vinkius endpoint. The adapter automatically manages connection lifecycle.
3

Assign tools and run
Pass the returned mcp_tools to your agent's tools parameter. The adapter converts MCP tools to native BaseTool objects compatible with all CrewAI agents.

crew.py

from crewai import Agent, Task, Crew
from crewai_tools import MCPServerAdapter
from mcp import SseServerParameters

server_params = SseServerParameters(
    url="https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"
)

with MCPServerAdapter(server_params) as mcp_tools:
    agent = Agent(
        role="Ensembl Analyst",
        goal="Access and analyze Ensembl data via MCP.",
        backstory="Expert analyst with direct Ensembl access.",
        tools=mcp_tools,
    )

    task = Task(
        description="List recent Ensembl transactions",
        agent=agent,
        expected_output="A summary of recent activity",
    )

    crew = Crew(agents=[agent], tasks=[task])
    result = crew.kickoff()
    print(result)

Get your connection token →

Independent Platform Disclaimer: Vinkius is an independent platform and is not affiliated with, endorsed by, sponsored by, verified by, or otherwise authorized by Ensembl. All third-party trademarks, logos, and brand names are the property of their respective owners. Their use on this website is strictly for informational purposes to identify service compatibility and interoperability.

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Common questions about Ensembl MCP in CrewAI

Add your Vinkius server URL to the `mcps` list when defining your agents. This MCP Server exposes all 27 genomic tools, allowing your agents to call `get_sequence_id` or `get_lookup_id` as needed.

Yes, you can assign a data-gatherer agent to run `get_lookup_bulk` for batch queries. This agent then shares the resulting gene metadata with the rest of the crew through their common memory pool.

Your agents can use `get_map` to convert coordinates between different assembly versions. A specialized coordinator agent handles the mapping before passing the updated coordinates to other agents for sequence extraction.

CrewAI's self-healing mechanisms allow agents to retry failed tool calls like `ping` or `get_info_rest`. If an endpoint is unresponsive, the agent can log the error and pivot to alternative lookup methods.

No, genomic coordinates and variant data retrieved via `get_variation` are only held in your local crew's short-term memory. Vinkius provides a secure, ephemeral MCP gateway that never stores your genomic payloads.

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