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Brapi MCP Server

Connects AI agents to BrAPI v2.1 breeding data for search, pedigree analysis, matrices, SQL, and controlled writes.

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Install Brapi MCP Server

Pick your client, then add it in one click or paste the config.

STDIONode.js
~/Library/Application Support/Claude/claude_desktop_config.json
claude_desktop_config.json
{
  "mcpServers": {
    "brapi-mcp-server": {
      "command": "bunx",
      "args": [
        "@cyanheads/brapi-mcp-server@latest"
      ]
    }
  }
}

Settings → Developer → Edit Config, merge this into mcpServers, then fully quit and reopen Claude Desktop.

We couldn’t confirm it starts correctly

We ran the install command but it didn't respond within our test window — this can mean a slow first-time install rather than a real problem.

bunx @cyanheads/brapi-mcp-server@latest

Process exited before answering initialize.

This is an experimental automated check and can have false negatives — missing environment variables, a slow cold install, etc. It doesn’t necessarily mean something’s wrong. Last checked 7d ago.

Overview

The brapi-mcp-server MCP server connects AI agents to BrAPI v2.1-compatible breeding databases, including multiple registered servers under named aliases. It provides tools for studies, germplasm, observations, variables, images, locations, variants, genotype calls, pedigrees, and dataframe analysis, with raw GET and search fallbacks. Use it when an agent needs to inspect plant-breeding data, combine results into phenotype or genotype matrices, query staged data with SQL, or submit observations through an explicit two-phase workflow.

Use cases

  • Search breeding studies by crop, season, program, or location
  • Trace germplasm ancestry and descendancy across pedigree records
  • Build phenotype and genotype matrices for downstream analysis
  • Query staged BrAPI results with read-only SQL
  • Validate and submit observation records in two phases

Key features

  • BrAPI v2.1 multi-server connections with aliases
  • Study, germplasm, observation, image, location, and variant search
  • Pedigree traversal with cycle detection
  • Phenotype and genotype matrix generation
  • DuckDB dataframe workspace with SQL queries
  • Opt-in observation writes and local exports

Tools25

What Brapi MCP Server lets your agent do. Expand a tool for its parameters.

Self-reported~575 tokens of context

Security & health

What it can reach and how reliably it runs — from our own checks, not the maintainer’s claims.

ActiveLast checked 1d ago

Recent health check succeeded.

7/7 checks healthy over the last 34d

Supply-chain signal

No high-severity advisories surfaced by our automated scan.

Critical 0High 0Medium 0Low 0

Scanned 11d ago via OSV.dev · @cyanheads/brapi-mcp-server@latest (npm)

Adoption & maintenance

Factual signals from GitHub, npm, and our automated checks — not a rating.

GitHub stars4Stargazers on the source repository.
npm downloads1.6kPackage downloads in the last 30 days.
Last commit16d agoMost recent push to the default branch.
Install checkInconclusiveDidn't respond in our test window — often a slow first install.
Tools exposed25Callable tools this server registers over MCP.

How Brapi MCP Server works

What brapi-mcp-server MCP server does

The brapi-mcp-server MCP server gives MCP clients access to plant-breeding data exposed through BrAPI v2.1. It can connect to one or more BrAPI servers, retain each connection under an alias, and report the server’s identity, authentication status, supported capabilities, notable gaps, and available content.

The covered data domains include studies, germplasm, observation variables, observations, images, research locations, variants, and genotype calls. Retrieved records can also be used for pedigree traversal, phenotype summaries, and matrix generation. The server is intended for BrAPI-compliant deployments, including Breedbase and other systems that implement the API.

How it works

An agent first uses brapi_connect to register a BrAPI endpoint. The connection can use no authentication, bearer tokens, API keys, Breedbase-style SGN token exchange, or OAuth2 client credentials. brapi_server_info can later refresh or return the registered server’s capability profile.

Finder tools provide domain-specific filtering, while brapi_describe_filters exposes the documented filter catalog for supported endpoints. Study and germplasm retrieval resolves related program, trial, location, attribute, or parent information where supported. Pedigree traversal returns a deduplicated graph and detects cycles.

Large or asynchronous retrievals are handled through the server’s search and polling behavior. Results that exceed the per-call pull limit can spill into a DuckDB dataframe workspace. Agents can inspect those dataframes, run read-only SQL, remove them when enabled, or export them from a stdio deployment. The two prompts listed by the project support study-level exploratory analysis and cross-study germplasm-by-trait meta-analysis.

Setup and configuration

The brapi-mcp-server MCP server can run as a stdio process, a local Streamable HTTP server, or through the project’s public hosted MCP endpoint at https://brapi.caseyjhand.com/mcp. The README provides installation paths for Claude Desktop, Cursor, and VS Code, including an npm-based command configuration.

Connections may receive their URL and authentication settings directly through brapi_connect. When omitted, settings are resolved from per-alias environment configuration, built-in aliases, and default configuration. Multiple aliases allow an agent to work with several BrAPI deployments in one session. The repository also publishes an npm package and a Docker image.

Tools and capabilities

Key operations include:

  • Searching studies, germplasm, variables, observations, images, locations, and variants with domain-specific filters.
  • Fetching detailed studies, germplasm, and images, including up to five images as inline image content.
  • Walking ancestry or descendancy graphs with duplicate suppression and cycle detection.
  • Pulling genotype calls asynchronously and exporting genotype matrices as VCF-lite or PLINK text.
  • Building phenotype matrices and calculating per-variable statistics for a germplasm across studies.
  • Querying dataframe results with read-only SQL and exporting dataframes as CSV, Parquet, or JSON when the relevant opt-in features are enabled.
  • Writing observations only through the opt-in preview-then-apply workflow.
  • Calling uncovered BrAPI GET paths or POST search endpoints through raw passthrough tools.

Limitations and notes

Support depends on the capabilities and filters implemented by the connected BrAPI deployment. The filter catalog follows BrAPI v2.1, but an individual server may support only part of it. Genotype retrieval is bounded by a deployment pull ceiling, and dataframe export is limited to stdio operation. Dataframe dropping and observation submission are opt-in. Resource reads use the default connection, so multi-server workflows should use tools and aliases instead.

The brapi-mcp-server MCP server is marked Beta in the project metadata. A failed connection does not replace an earlier registration under the same alias, and unavailable scoped counts are omitted rather than presented as server-wide totals.

Read the full README View source on GitHub

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Frequently Asked Questions about Brapi MCP Server

brapi-mcp-server is an MCP server that connects AI agents to BrAPI v2.1 breeding-data servers. Its main tools authenticate and register servers, search studies, germplasm, observations, variables, images, locations, variants, and genotype calls, and support pedigree walks, dataframe SQL, matrix generation, raw API access, and controlled observation submission.

Install it through the npm package or the README’s client-specific setup for Claude Desktop, Cursor, or VS Code. It can run as a stdio process, a local Streamable HTTP server, or use the hosted endpoint at https://brapi.caseyjhand.com/mcp.

Use `brapi_connect` with a BrAPI base URL and optional authentication settings, then assign an alias. The tool supports no authentication, bearer tokens, API keys, SGN token exchange, and OAuth2 client credentials. Omitted settings can come from alias or default environment configuration.

Yes, it can register several BrAPI servers under named aliases. Each alias maintains its own connection, while resources read from the `default` connection. Multi-server workflows should therefore use the tools and specify the relevant alias.

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