How to Use the EBI Proteins API MCP in Mastra AI

Build automated bioinformatics workflows in Mastra AI with direct access to UniProt sequence data and variant annotations.

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Connect EBI Proteins API MCP to Mastra AI

Create your Vinkius account to connect EBI Proteins API to Mastra AI 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 EBI Proteins API with Mastra AI

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Claude

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Automate variant analysis pipelines

Chain `get_variation` and `get_mutagenesis` to identify functional impacts in your automated workflows. Mastra AI handles the logic flow while the server provides the clinical evidence. Your agents can now automatically flag variants based on real-time UniProt data. If a specific mutation check fails, the framework triggers your custom retry logic.

Coordinate multi-step protein research

Use `get_genecentric` to map proteomes before performing deep dives with `get_proteomics`. This allows your agents to follow a logical path from gene to peptide. Your workflow engine manages the state of these calls. If an API call hits a limit, the agent handles the backoff and retries without manual intervention.

Integrate taxonomy lookups into agents

Search for specific organisms using `search_taxonomy` to verify species IDs before running protein queries. This prevents data mismatch errors in your automation. Your agents maintain context across steps by storing the taxon IDs. This ensures every `get_proteome` call targets the correct organism for your research.

Setup guide

Set up EBI Proteins API MCP in Mastra AI

Prerequisites

Node.js 18+ and a TypeScript project
@mastra/mcp + @mastra/core packages
Active Vinkius subscription with a valid endpoint token

1

Install dependencies
Run npm install @mastra/mcp @mastra/core plus your preferred model provider (e.g. @ai-sdk/openai).
2

Configure the MCPClient
Create an MCPClient with your Vinkius endpoint as a URL object. Replace [YOUR_TOKEN_HERE] with your token from cloud.vinkius.com.
3

Discover and inject tools
Call mcpClient.listTools() and spread the result into your agent's tools object. All EBI Proteins API tools become native Mastra tools.
4

Run with any model
Swap openai("gpt-4o") for any AI SDK-compatible provider. Call agent.generate() and the agent routes tool calls through MCP automatically.

agent.ts

import { MCPClient } from "@mastra/mcp";
import { Agent } from "@mastra/core/agent";
import { openai } from "@ai-sdk/openai";

const mcpClient = new MCPClient({
  id: "ebi-proteins-api-mcp-client",
  servers: {
    "ebi-proteins-api-mcp": {
      url: new URL(
        "https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"
      ),
    },
  },
});

const agent = new Agent({
  name: "EBI Proteins API Agent",
  model: openai("gpt-4o"),
  instructions: "You have access to EBI Proteins API tools.",
  tools: {
    ...(await mcpClient.listTools()),
  },
});

const result = await agent.generate(
  "List recent EBI Proteins API transactions"
);
console.log(result.text);

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Common questions about EBI Proteins API MCP in Mastra AI

Add the server URL to your MCP client configuration in the agent definition. Once added, the tools become available for your agent to execute.

Mastra AI supports automatic retries with exponential backoff. You can configure this in your workflow to ensure the server handles transient network issues.

Enable the requireToolApproval setting in your agent config. This forces the agent to pause for your input before it queries the protein database.

Yes, you can use the output of any tool to determine the next step. If a protein lookup returns no data, your agent can branch to a different search strategy.

The server processes only public UniProt accession strings and returns open-access biological data. Your internal pipeline logic and proprietary research remain isolated.

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