How to Use the EBI Proteins API MCP in OpenAI Agents SDK

Q: How do I configure the EBI Proteins API MCP Server in the OpenAI Agents SDK?

Instantiate the server using MCPServerStreamableHttp with your Vinkius endpoint. Pass this instance in the mcpservers list when initializing your Agent, and set cacheToolsList=True to speed up tool discovery.

Q: Can my OpenAI Agents SDK system handle variant annotation using the EBI Proteins API?

Yes, your agent calls getvariation to fetch clinical significance and consequence types for specific proteins. The SDK lets you trace these tool calls in real time to verify that the agent parses the variant annotations correctly.

Q: How does the agent handle coordinate mapping between proteins and genomes?

The agent calls getcoordinates to retrieve Ensembl gene, transcript, and translation IDs. It then maps these chromosome positions to your OpenAI Agents SDK execution environment for downstream processing.

Connect your OpenAI Agents SDK pipeline directly to the EBI Proteins API MCP Server to fetch UniProt sequences without managing flatfiles.

See Vinkius in Action

Works with every AI agent you already use

…and any MCP-compatible client

MCP Servers - Free for Subscribers

Connect EBI Proteins API MCP to OpenAI Agents SDK

Create your Vinkius account to connect EBI Proteins API 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.

GDPR Free for Subscribers

Setup EBI Proteins API with OpenAI Agents SDK

Ask AI about this MCP

ChatGPT

Claude

Perplexity

Resolve UniProt accessions using OpenAI Agents SDK

`get_protein` retrieves raw sequence data and annotations directly inside your Python execution loop. Your agent uses this tool to resolve accession numbers like P12345 without manual parsing code or external database maintenance. When building multi-agent systems, one agent can fetch the sequence while another uses `get_variation` to check clinical significance. This handoff runs natively over the MCP Server connection, letting you trace every step on your OpenAI dashboard.

Map active sites and PTM locations dynamically

`get_protein_features` extracts domain boundaries, active sites, and signal peptides directly into the agent's context window. The agent reads this JSON payload to isolate functional regions without processing heavy XML files. For deep mass-spectrometry analysis, the agent calls `get_proteomics_ptm` to pinpoint exact residue-level modifications. You define guardrails in your SDK setup to validate these payloads before they pass to downstream analysis agents.

Filter protein data by species with this MCP Server

`search_taxonomy` resolves taxon IDs for target organisms before your agent queries specific proteomes or proteins. The agent maps common names to NCBI taxon IDs like 9606 to prevent cross-species data contamination. Once the correct ID is verified, `get_proteome` pulls complete reference proteomes for your pipeline. The OpenAI Agents SDK handles the streaming connection to the MCP server, keeping your local memory footprint low.

Setup guide

Set up EBI Proteins API 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 EBI Proteins API tools at runtime.
3

Create your Agent

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

Run the agent

Call Runner.run(agent, prompt) to execute. The agent invokes the appropriate EBI Proteins API 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="EBI Proteins API Agent",
            instructions="You have access to EBI Proteins API tools.",
            mcp_servers=[server],
        )
        result = await Runner.run(agent, "List recent transactions")
        print(result.final_output)

asyncio.run(main())

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 EMBL-EBI Proteins API. 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.

Why Choose Vinkius

Vinkius connects your tools to AI with real-time monitoring and automatic cost savings — all from one dashboard.

Connect EBI Proteins API now

Real-time monitoring

Live

visibility into every interaction

Connect your favorite tools to your AI and see exactly what's happening — every request, every response, in real time.

Built-in savings

60%

lower AI costs

Vinkius compresses data between your apps and your AI automatically. Lower bills every month — no configuration required.

Single dashboard

One

place for every integration

Every tool your AI connects to, managed from a single screen. One account, complete control.

Common questions about EBI Proteins API MCP in OpenAI Agents SDK

Instantiate the server using `MCPServerStreamableHttp` with your Vinkius endpoint. Pass this instance in the `mcp_servers` list when initializing your Agent, and set `cacheToolsList=True` to speed up tool discovery.

Yes, your agent calls `get_variation` to fetch clinical significance and consequence types for specific proteins. The SDK lets you trace these tool calls in real time to verify that the agent parses the variant annotations correctly.

The SDK automatically queries the MCP Server to discover all 16 tools, including `get_mutagenesis` and `get_antigen`. This means you do not need to write custom JSON schemas or manual tool definitions in Python.

The agent calls `get_coordinates` to retrieve Ensembl gene, transcript, and translation IDs. It then maps these chromosome positions to your OpenAI Agents SDK execution environment for downstream processing.

Your queries for protein sequences and NCBI taxon IDs go through a secure V8 isolate sandbox managed by Vinkius. No local genetic datasets or private protein sequences are stored or leaked during these API calls.

Use it with your favorite AI tools

Connect this server to Cursor, Claude, VS Code, and more.

OpenAI Agents SDK sdk-python

Google ADK sdk-python

Pydantic AI sdk-python

Vercel AI SDK sdk-typescript