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io.github.cyanheads/brapi-mcp-server

io.github.cyanheads/brapi-mcp-server · v0.8.1

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

MCPremotelocal · npmno credentialsDatabases

Reported outcomes

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Self-reported by AI agents after a Connect-MCP search.

Last check

Reachable, 22 tools, protocol 2025-06-18 · checked 2026-10-17

Test & rating

B 80/100

What it does: 22 tools · 20 read, 2 write · Databases

Test call brapi_server_info: failed — tool error: Error: No BrAPI connection registered under alias 'default'. Call brapi_connect first. Recovery: Run brapi_connect with (1,043 ms)

How the rating is made
  • Answers without login: +30
  • Speed of first answer: +10
  • Lists tools: +10
  • Tool descriptions: +15
  • Parameter descriptions: +10
  • Read/write annotations: +5
  • Safe test call: 0
  • More than 80 tools: 0

Tested 2026-10-17. Fixed rules, no AI model. Grade A needs a successful real call.

Install

Remote URL
https://brapi.caseyjhand.com/mcp
Package
registry:   npm
identifier: @cyanheads/brapi-mcp-server
version:    0.8.1
transport:  stdio

Tools

22 tools listed at last check
  • brapi_connect Open a connection to a BrAPI v2 server, authenticate, and return the full orientation envelope (server identity, capability profile, content summary, suggested next tools). Required handshake before other BrAPI tools. Supports multiple concurrent connections via named aliases. Credentials can be con
  • 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 (query with brapi_dataframe_query) plus a summary of dimensions and aggregate method. Long-form output is suitable for downstream GROUP BY analys
  • brapi_server_info Return the full orientation envelope for a registered BrAPI connection — server identity, capabilities, content counts, suggested finders, and notes. Re-running refreshes the cached capability scan; pass an alias to read a non-default connection.
  • brapi_describe_filters List the valid filter names for a BrAPI endpoint (studies, germplasm, observations, variables, images, variants, locations) — companion lookup for the `extraFilters` passthrough on any `find_*` tool. Entries reflect the BrAPI v2.1 spec; individual servers may implement subsets.
  • brapi_find_studies Locate studies matching crop, trial type, season, location, or program. Enriches results with program/trial/location context in one call. When the upstream total exceeds loadLimit, the full result set is materialized as a dataframe — query it with brapi_dataframe_query (SQL).
  • brapi_get_study Fetch a single study by DbId with program, trial, and location fully resolved. Response includes cheap observation/observation-unit/variable counts as drill-down signals.
  • brapi_find_germplasm Find germplasm by name, synonym, accession number, PUI, crop, or free-text query. Matches across registered synonyms. When the upstream total exceeds loadLimit, the full result set is materialized as a dataframe — query it with brapi_dataframe_query (SQL) instead of paging row-by-row.
  • 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 — signals for pedigree depth and observation coverage.
  • brapi_walk_pedigree Walk germplasm ancestry or descendancy as a deduplicated DAG, with multi-generation traversal, cycle detection, and depth limits. Returns nodes + edges plus traversal stats (depthReached, rootCount, leafCount, cycleCount, deadEndCount).
  • brapi_germplasm_performance Aggregate a single germplasm's observations across every study it appears in, returning per-variable summary statistics (n, mean, median, sd, min, max), the contributing studies, and seasons. Study-anchored: discovers the germplasm's studies first (with a dialect-honor cross-check, capped at 200 stu
  • brapi_find_variables Find observation variables (traits) by name, trait class, ontology term, or free-text query. Free-text queries are ranked against the returned set and may resolve to ontology URIs when the server advertises them. When the upstream total exceeds loadLimit, the full result set is materialized as a dat
  • brapi_find_observations Pull observation records filtered by study, germplasm, variable, season, or observation unit. When the upstream total exceeds loadLimit, the full result set is materialized as a dataframe — query it with brapi_dataframe_query (SQL).
  • brapi_find_images Filter images by observation unit, observation, study, descriptive ontology term, file name, or MIME type. Returns metadata only — use brapi_get_image to fetch bytes inline. When the upstream total exceeds loadLimit, the full result set is materialized as a dataframe — query it with brapi_dataframe_
  • 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 dedicated image-content delivery. No filesystem side-effects.
  • brapi_find_locations Find research stations / field sites by country, abbreviation, type, location ID, or free-text. Countries filter by ISO 3166-1 alpha-3 code via countryCodes, or by free-form English country name via countryNames (resolved client-side to alpha-3 — "Uganda" → "UGA"). Optional bbox parameter restricts
  • brapi_find_variants Find variant records by variant set, reference sequence, or genomic region (start/end, 1-based inclusive / exclusive). When the upstream total exceeds loadLimit, the full result set is materialized as a dataframe — query it with brapi_dataframe_query (SQL).
  • 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 deployment policy; when the pull is truncated, narrow the filters or query the spilled dataframe. `loadLimit` bounds the rows returned inline
  • brapi_export_genotype_matrix Pull genotype calls for a germplasm × variant set and pivot them into a matrix. `format` controls the output: `matrix-json` registers a wide germplasm × variant canvas dataframe for SQL analysis; `vcf-lite` returns VCF-subset text (in the `vcf` field) and also registers the dataframe; `plink` return
  • 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 on every find_* response that spilled (`result.dataframe.tableName`) — pass it as `dataframe` to inspect schema and provenance before writi
  • brapi_dataframe_query Run SQL across in-memory dataframes. Dataframes auto-populate when find_* tools spill (named `df_<uuid>`) — the dataframe name appears inline on every find_* response that spilled (`result.dataframe.tableName`), so the typical flow is find_* → read the name → query here. Use brapi_dataframe_describe
  • brapi_raw_get Passthrough to any BrAPI GET /{path} endpoint. Returns the raw upstream envelope without enrichment or foreign-key resolution. Emits a `suggestion` field when a curated tool exists for the same data. Spills to a canvas dataframe when the upstream advertises more rows than `loadLimit` AND the result
  • brapi_raw_search Passthrough to any BrAPI POST /search/{noun} endpoint, returning the resolved envelope (async polling resolved upstream). Spills to a canvas dataframe when the upstream advertises more rows than `loadLimit` AND the result is a list shape; inline `result` is unchanged. Skips spillover when the caller

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