brapi-mcp-server

Open a connection to a BrAPI v2 server, authenticate, and return the full orientation envelope (server identity, capability profile, content summary, suggested next tools). Other BrAPI tools connect a…

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 it with brapi_dataframe_describe and br…

Return the full orientation envelope for a BrAPI connection — server identity, capabilities, content counts, suggested finders, and notes. Pass forceRefresh to refetch the cached capability scan; pass…

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. results[] holds the leading matches up to loadLimit and a 24,0…

Fetch a single study by DbId with its program, trial, and location records resolved where those lookups succeed. Response includes cheap observation/observation-unit/variable counts as drill-down sign…

Find germplasm by name, synonym, accession number, PUI, crop, or free-text query. Matches across registered synonyms. results[] holds the leading matches up to loadLimit and a 24,000-byte budget; when…

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 cycle detection and depth limits. leafCount counts graph terminals, confirmedLeafCount counts successfully verified leaves, and fronti…

Aggregate a single germplasm's observations across studies, returning per-variable statistics (n, mean, median, sd, min, max), contributing studies, seasons, and collection coverage. SGN/Breedbase use…

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, synonym, and trait text; a candidate c…

Pull observation records filtered by study, germplasm, variable, season, or observation unit. Without a studies, trials, observationUnits, or observations anchor, a GET query first runs a one-row coun…

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. results[] holds the leadin…

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 or that re…

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, 0-based inclusive / exclusive per the BrAPI spec; servers may differ). results[] holds the leading matches up to …

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. `matrix-json` registers a wide canvas dataframe; `vcf-lite` adds VCF-subset text in `vcf`; `plink` adds .ped/.map text i…

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 BrAPI GET /{path} without foreign-key resolution. List results (result array or result.data) return a leading preview within loadLimit and a 24,000-byte budget on each serialized row re…

Passthrough to BrAPI POST /search/{noun}, polling async search IDs. Sends loadLimit as the initial pageSize unless body.page/pageSize drives explicit paging. List previews fit loadLimit and a 24,000-b…

Orientation envelope for the default BrAPI connection — identity, capabilities, content counts, suggested finders, 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.