How to Use the Ensembl MCP in OpenAI Agents SDK

Q: How do I integrate Ensembl with OpenAI Agents SDK?

You use the MCPServerStreamableHttp class to point your agent at the Ensembl server endpoint. The SDK automatically discovers all 27 tools, allowing your agent to invoke them immediately.

Q: Does Ensembl support bulk operations in OpenAI Agents SDK?

Yes. You can trigger getvepbulk or getlookupbulk to handle multiple IDs in a single request. This is the preferred way to maintain performance for large datasets.

Connect Ensembl genomic data directly to your OpenAI Agents SDK production workflows without manual API handling.

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Connect Ensembl MCP to OpenAI Agents SDK

Create your Vinkius account to connect Ensembl to OpenAI Agents SDK 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 OpenAI Agents SDK

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Claude

Perplexity

Automated variant and gene analysis

Stop hardcoding API requests. Your agent uses `get_vep_id` and `get_vep_bulk` to pull variant consequences directly into your memory state. It handles the heavy lifting of parsing Ensembl responses so your agent can focus on interpreting genomic data rather than wrestling with HTTP payloads.

Real-time genomic reference lookups

Your agent queries live assembly data using `get_info_assembly` to ensure it always operates on the correct coordinate space. By calling `get_lookup_id` within your agentic loop, you maintain perfect alignment between external identifiers and internal research records.

Efficient cross-reference resolution

Map symbols to Ensembl IDs in one step with `get_xrefs_symbol`. It eliminates the need for intermediate databases or manual mapping tables. When your agent needs to correlate data, it simply calls the tool and receives the linked objects, keeping your production pipeline clean and fast.

Setup guide

Set up Ensembl MCP in OpenAI Agents SDK

Prerequisites

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

1

Install the SDK

Run pip install openai-agents to install the OpenAI Agents SDK. The MCP integration is built-in — no extra dependencies needed.
2

Connect via SSE transport

Use MCPServerSse with your Vinkius endpoint URL. Replace [YOUR_TOKEN_HERE] with your token from cloud.vinkius.com. The SDK auto-discovers all Ensembl tools at runtime.
3

Create your Agent

Pass the MCP to Agent(mcp_servers=[server]). The agent receives Ensembl tools as native definitions — JSON schemas resolve automatically.
4

Run the agent

Call Runner.run(agent, prompt) to execute. The agent invokes the appropriate Ensembl tools and returns structured results. Copy the full example on the right to get started.

agent.py

import asyncio
from agents import Agent, Runner
from agents.mcp import MCPServerSse

async def main():
    async with MCPServerSse(
        url="https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"
    ) as server:
        agent = Agent(
            name="Ensembl Agent",
            instructions="You have access to Ensembl tools.",
            mcp_servers=[server],
        )
        result = await Runner.run(agent, "List recent transactions")
        print(result.final_output)

asyncio.run(main())

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Common questions about Ensembl MCP in OpenAI Agents SDK

You use the `MCPServerStreamableHttp` class to point your agent at the Ensembl server endpoint. The SDK automatically discovers all 27 tools, allowing your agent to invoke them immediately.

Yes. You can trigger `get_vep_bulk` or `get_lookup_bulk` to handle multiple IDs in a single request. This is the preferred way to maintain performance for large datasets.

The server doesn't enforce client-side throttling natively, so you should implement retry logic in your agent. Keep an eye on your request frequency to respect the 15 requests per second limit.

The agent receives a standard error response from the tool execution. You can wrap these calls in your own error-handling blocks to manage retries or log failures.

Ensembl provides public biological data, but your agent only touches the specific identifiers you request. No persistent data is stored on the server—it's strictly a pass-through for your queries.

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