io.github.cyanheads/brapi-mcp-server

Open a connection to a BrAPI v2 server, authenticate, and return the full orientation envelope (server identity, capability profile, content summary). Required handshake before other BrAPI tools. Supp…

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 sum…

Return the full orientation envelope for a registered BrAPI connection — server identity, capabilities, content counts, and notes. Re-running refreshes the cached capability scan; pass an alias to rea…

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. …

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…

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.

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 …

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 observati…

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, l…

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-an…

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 adve…

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 w…

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 ex…

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 filesy…

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 c…

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…

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 trunc…

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…

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 (…

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.t…

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. …

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 `load…

Orientation envelope for the default BrAPI connection — identity, capabilities, content counts, notes. Same payload as the brapi_server_info tool.

Capability profile for the default BrAPI connection — supported services, their HTTP methods, declared versions, and crops list. Mirrors what /serverinfo + /calls returned at the last load.

Filter names accepted by /germplasm on a BrAPI v2.1 server.

Filter names accepted by /images on a BrAPI v2.1 server.

Filter names accepted by /locations on a BrAPI v2.1 server.

Filter names accepted by /observations on a BrAPI v2.1 server.

Filter names accepted by /studies on a BrAPI v2.1 server.

Filter names accepted by /variables on a BrAPI v2.1 server.

Filter names accepted by /variants on a BrAPI v2.1 server.

Run an exploratory-data-analysis pass over a single BrAPI study — structure, variables, coverage, outliers, missing data — using the curated brapi_* tools.

Run a cross-study meta-analysis on a germplasm × trait combination — resolve trait, find studies, pull observations, harmonize scales, summarize across studies.