EBI Proteins API MCP Server for OpenAI Agents SDKGive OpenAI Agents SDK instant access to 16 tools to Get Antigen, Get Coordinates, Get Genecentric, and more

Name: EBI Proteins API
Price: 29 USD
Availability: InStock
Rating: 4.9 (1 reviews)
Author: Vinkius

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The OpenAI Agents SDK enables production-grade agent workflows in Python. Connect EBI Proteins API through Vinkius and your agents gain typed, auto-discovered tools with built-in guardrails. no manual schema definitions required.

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The EBI Proteins API MCP Server for OpenAI Agents SDK is a standout in the The Unthinkable category — giving your AI agent 16 tools to work with, ready to go from day one.

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python

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

async def main():
    # Your Vinkius token. get it at cloud.vinkius.com
    async with MCPServerStreamableHttp(
        url="https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"
    ) as mcp_server:

        agent = Agent(
            name="EBI Proteins API Assistant",
            instructions=(
                "You help users interact with EBI Proteins API. "
                "You have access to 16 tools."
            ),
            mcp_servers=[mcp_server],
        )

        result = await Runner.run(
            agent, "List all available tools from EBI Proteins API"
        )
        print(result.final_output)

asyncio.run(main())

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About EBI Proteins API MCP Server

Connect to the EMBL-EBI Proteins API and access comprehensive protein biology data from one of the world's leading bioinformatics institutes.

The OpenAI Agents SDK auto-discovers all 16 tools from EBI Proteins API through native MCP integration. Build agents with built-in guardrails, tracing, and handoff patterns. chain multiple agents where one queries EBI Proteins API, another analyzes results, and a third generates reports, all orchestrated through Vinkius.

What you can do

Protein Retrieval — Fetch complete protein entries by UniProt accession with names, organisms, gene information, sequences, and cross-references
Sequence Features — Retrieve annotated domains, binding sites, active sites, signal peptides, transmembrane regions, and disulfide bonds for any protein
Genetic Variants — Access curated variants from UniProtKB aggregated with large-scale studies including ClinVar, gnomAD, 1000 Genomes, COSMIC, and TOPMed
Proteomics & PTMs — Query mass-spectrometry peptide evidence and post-translational modifications from PeptideAtlas, MaxQB, EPD, and ProteomicsDB
Mutagenesis — Explore curated mutagenesis experiments with detailed phenotypic effect descriptions
Proteomes & Taxonomy — Search reference proteomes and navigate the taxonomy tree by ID or organism name
Genome Coordinates — Map proteins to genome positions on GRCh38/GRCh37 with Ensembl gene, transcript, and translation IDs

The EBI Proteins API MCP Server exposes 16 tools through the Vinkius. Connect it to OpenAI Agents SDK in under two minutes — credentials fully managed, no infrastructure to provision, no vendor lock-in. Your configuration, your data, your control.

All 16 EBI Proteins API tools available for OpenAI Agents SDK

When OpenAI Agents SDK connects to EBI Proteins API through Vinkius, your AI agent gets direct access to every tool listed below — spanning proteins, uniprot, bioinformatics, and more. Every call runs in a secure, isolated environment with full audit visibility. Beyond a simple connection, you get real-time monitoring of agent activity, enterprise governance, and optimized token usage.

get

Get antigen on EBI Proteins API

These are peptide regions used for antibody generation, indicating experimentally validated protein expression targets. Useful for immunology and antibody-based research. Get antigen sequences from Human Protein Atlas

get

Get coordinates on EBI Proteins API

Returns Ensembl gene, transcript, and translation IDs along with chromosome, start/end positions, and strand information. Essential for bridging protein annotations with genomic data. Get genome coordinate mappings for a protein

get

Get genecentric on EBI Proteins API

Shows canonical protein and related protein count for each gene. Use with a UniProt Proteome ID (e.g. UP000005640). Get the gene-centric view of a proteome

get

Get mutagenesis on EBI Proteins API

Each entry includes the wild-type and mutant residues, position, and a description of the functional impact. Critical for understanding structure-function relationships. Get mutagenesis experiments and phenotypic effects

get

Get protein on EBI Proteins API

Use a UniProt accession such as P12345, Q9Y6K9, or P53_HUMAN. Retrieve a full protein entry by UniProt accession

get

Get protein features on EBI Proteins API

Features include domains, binding sites, active sites, signal peptides, transmembrane regions, disulfide bonds, glycosylation sites, and more. Each feature has start/end positions and evidence counts. Get sequence feature annotations for a protein

get

Get proteome on EBI Proteins API

Returns taxonomy, protein count, gene count, reference status, and component information. Use IDs like UP000005640 for human proteome or UP000000589 for mouse. Get a specific proteome by UniProt Proteome ID

get

Get proteomics on EBI Proteins API

Shows which peptides have been experimentally detected and whether they are unique to this protein. Essential for validating protein expression. Get mass-spectrometry proteomics data for a protein

get

Get proteomics ptm on EBI Proteins API

Provides residue-level PTM positions with evidence counts. Get post-translational modifications from mass-spec data

get

Get taxonomy on EBI Proteins API

Returns scientific name, common name, rank, lineage, parent, and children nodes. Use IDs like 9606 for human, 10090 for mouse, 562 for E. coli. Get taxonomy node details by NCBI taxon ID

get

Get variation on EBI Proteins API

Each variant includes wild-type and mutant residues, clinical significance, consequence type (e.g. missense, nonsense), and cross-references. Critical for clinical genomics and variant interpretation. Get genetic variants for a protein from multiple sources

Search features by type on EBI Proteins API

Valid types include: DOMAIN, BINDING, ACTIVE_SITE, SIGNAL, TRANSMEM, DISULFID, CARBOHYD, MOD_RES, VARIANT, MUTAGEN, REGION, MOTIF, SITE, REPEAT, COILED, COMPBIAS, HELIX, STRAND, TURN. Search features by type across proteins

Search proteins on EBI Proteins API

You can combine gene name (e.g. TP53), organism (e.g. human, 9606), keyword (e.g. kinase), or accession. Returns a summarized list of matching proteins with names, organisms, and sequence lengths. Search proteins by gene name, organism, or keyword

Search proteomes on EBI Proteins API

Returns proteome IDs, taxonomy, protein counts, gene counts, and reference proteome status. Use queries like "homo sapiens", "escherichia coli", "arabidopsis". Search proteomes by organism name

Search taxonomy on EBI Proteins API

Returns matching taxonomy entries with scientific names, common names, taxon IDs, and ranks. Useful for finding the correct taxon ID before querying proteins or proteomes for a specific organism. Search taxonomy by organism name

Search variation on EBI Proteins API

g. large_scale_study, uniprot, mixed), consequence type (e.g. missense, stop gained), and wild-type residue. Use this to find clinically relevant variants across the proteome. Search variants by consequence type, source, or residue

Connect EBI Proteins API to OpenAI Agents SDK via MCP

Follow these steps to wire EBI Proteins API into OpenAI Agents SDK. The entire setup takes under two minutes — your credentials stay safe behind Vinkius.

Install the SDK

Run pip install openai-agents in your Python environment

Replace the token

Replace [YOUR_TOKEN_HERE] with your Vinkius token from cloud.vinkius.com

Run the script

Save the code above and run it: python agent.py

Explore tools

The agent will automatically discover 16 tools from EBI Proteins API

Why Use OpenAI Agents SDK with the EBI Proteins API MCP Server

OpenAI Agents SDK provides unique advantages when paired with EBI Proteins API through the Model Context Protocol.

Native MCP integration via `MCPServerSse`, pass the URL and the SDK auto-discovers all tools with full type safety

Built-in guardrails, tracing, and handoff patterns let you build production-grade agents without reinventing safety infrastructure

Lightweight and composable: chain multiple agents and MCP servers in a single pipeline with minimal boilerplate

First-party OpenAI support ensures optimal compatibility with GPT models for tool calling and structured output

EBI Proteins API + OpenAI Agents SDK Use Cases

Practical scenarios where OpenAI Agents SDK combined with the EBI Proteins API MCP Server delivers measurable value.

Automated workflows: build agents that query EBI Proteins API, process the data, and trigger follow-up actions autonomously

Multi-agent orchestration: create specialist agents. one queries EBI Proteins API, another analyzes results, a third generates reports

Data enrichment pipelines: stream data through EBI Proteins API tools and transform it with OpenAI models in a single async loop

Customer support bots: agents query EBI Proteins API to resolve tickets, look up records, and update statuses without human intervention

Example Prompts for EBI Proteins API in OpenAI Agents SDK

Ready-to-use prompts you can give your OpenAI Agents SDK agent to start working with EBI Proteins API immediately.

"Get all known genetic variants for the TP53 tumor suppressor protein."

"Show me the domain architecture and binding sites of the EGFR protein."

"Map the BRCA1 protein to its genome coordinates on GRCh38."

Troubleshooting EBI Proteins API MCP Server with OpenAI Agents SDK

Common issues when connecting EBI Proteins API to OpenAI Agents SDK through Vinkius, and how to resolve them.

MCPServerStreamableHttp not found

Ensure you have the latest version: pip install --upgrade openai-agents

Agent not calling tools

Make sure your prompt explicitly references the task the tools can help with.

EBI Proteins API + OpenAI Agents SDK FAQ

Common questions about integrating EBI Proteins API MCP Server with OpenAI Agents SDK.

How does the OpenAI Agents SDK connect to MCP?

Use MCPServerSse(url=...) to create a server connection. The SDK auto-discovers all tools and makes them available to your agent with full type information.