io.github.cyanheads/brapi-mcp-server

up checked 2026-11-11T06:38:07.345Z

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Publisher-provided description

Collaborative BrAPI v2.1 MCP workspace: studies, germplasm, genotypes across Breedbase, T3, more.

Summary by lookupd

Lets agents query BrAPI v2.1 servers for studies, germplasm, observations, genotypes and pedigrees, returning results as dataframes.

Install

Claude Code, remote (streamable-http)

claude mcp add --transport http brapi-mcp-server https://brapi.caseyjhand.com/mcp

Claude Code, npm package (stdio)

claude mcp add brapi-mcp-server -- npx -y @cyanheads/brapi-mcp-server

Claude Code, npm package (stdio)

claude mcp add brapi-mcp-server -- npx -y @cyanheads/brapi-mcp-server

Codex, remote (streamable-http)

codex mcp add brapi-mcp-server --url https://brapi.caseyjhand.com/mcp

Codex, npm package (stdio)

codex mcp add brapi-mcp-server -- npx -y @cyanheads/brapi-mcp-server

Codex, npm package (stdio)

codex mcp add brapi-mcp-server -- npx -y @cyanheads/brapi-mcp-server

Cursor, remote (streamable-http) → .cursor/mcp.json

{
  "mcpServers": {
    "brapi-mcp-server": {
      "url": "https://brapi.caseyjhand.com/mcp"
    }
  }
}

Cursor, npm package (stdio) → .cursor/mcp.json

{
  "mcpServers": {
    "brapi-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/brapi-mcp-server"
      ]
    }
  }
}

Cursor, npm package (stdio) → .cursor/mcp.json

{
  "mcpServers": {
    "brapi-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/brapi-mcp-server"
      ]
    }
  }
}

Other clients: docs. Or tell your agent: Set up lookupd for me: read https://lookupd.com/agent.md and follow it.

Tools (22 tools)

Publisher-provided text

brapi_connect Open a connection to a BrAPI v2 server, authenticate, and return the full orientation envelope (server identity, capability profile, content summary, suggested
brapi_build_phenotype_matrix Pull observations across one or more studies and pivot them into a germplasm × trait matrix materialized as a canvas dataframe. Returns a dataframe handle (read
brapi_server_info Return the full orientation envelope for a BrAPI connection — server identity, capabilities, content counts, suggested finders, and notes. Pass forceRefresh to
brapi_describe_filters List the valid filter names for a BrAPI endpoint (studies, germplasm, observations, variables, images, variants, locations) — companion lookup for the `extraFil
brapi_find_studies Locate studies matching crop, trial type, season, location, or program. Enriches results with program/trial/location context in one call. results[] holds the le
brapi_get_study Fetch a single study by DbId with its program, trial, and location records resolved where those lookups succeed. Response includes cheap observation/observation
brapi_find_germplasm Find germplasm by name, synonym, accession number, PUI, crop, or free-text query. Matches across registered synonyms. results[] holds the leading matches up to
brapi_get_germplasm Fetch a single germplasm by DbId with attributes and direct parents. Response companions report study count, direct parent count, and direct descendant count —
brapi_walk_pedigree Walk germplasm ancestry or descendancy as a deduplicated DAG with cycle detection and depth limits. leafCount counts graph terminals, confirmedLeafCount counts
brapi_germplasm_performance Aggregate a single germplasm's observations across studies, returning per-variable statistics (n, mean, median, sd, min, max), contributing studies, seasons, an
brapi_find_variables Find observation variables (traits) by name, trait class, ontology term, or free-text query. Free-text queries are ranked against every fetched row by PUI, name
brapi_find_observations Pull observation records filtered by study, germplasm, variable, season, or observation unit. SGN/Breedbase uses advertised embedded units for study or germplas
brapi_find_images Filter images by observation unit, observation, study, descriptive ontology term, file name, or MIME type. Named mimeTypes are verified case-insensitively on ea
brapi_get_image Fetch image bytes for up to 5 imageDbIds and return them inline as `type: image` content blocks. Falls back to the metadata `imageURL` when the server lacks ded
brapi_find_locations Find research stations / field sites by country, abbreviation, type, location ID, or free-text. Pass countryCodes directly or use English countryNames to resolv
brapi_find_variants Find variant records by variant set, reference sequence, or genomic region. Named reference and region filters are verified on each scanned row using exact refe
brapi_find_genotype_calls Pull genotype calls for a germplasm × variant set. Filter to bound cost — at minimum, set `variantSetDbId` or `germplasmDbIds`. The upstream pull is capped by d
brapi_export_genotype_matrix Pull genotype calls for a germplasm × variant set and pivot them into a matrix. `matrix-json` registers a wide canvas dataframe; `vcf-lite` adds VCF-subset text
brapi_dataframe_describe Start here after a spillover. Lists dataframes (or describes one) with columns, row counts, and originating-source provenance. The dataframe name appears inline
brapi_dataframe_query Run read-only SQL across in-memory dataframes. Dataframes auto-populate when find_* tools spill (named `df_<uuid>`) — the dataframe name appears inline on every
brapi_raw_get Passthrough to BrAPI GET /{path} without foreign-key resolution. List results (result array or result.data) return a leading preview within loadLimit and a 24,0
brapi_raw_search Passthrough to BrAPI POST /search/{noun}, polling async search IDs. Sends loadLimit as the initial pageSize unless body.page/pageSize drives explicit paging. Li

Changes

Newest first, as lookupd saw them

2026-11-11: version 0.10.1 → 0.11.0

Details

Version: 0.11.0
Transports: streamable-http, stdio
Uptime (7 days): 100%
Median latency: 988 ms
First indexed: 2026-11-01T09:25:46.357Z
Last seen in registry: 2026-11-11T06:17:19.711Z
Repository: https://github.com/cyanheads/brapi-mcp-server

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