brapi_build_phenotype_matrix

MCP tool from Brapi MCP Server by cyanheads

Build a germplasm × trait matrix from one or more studies and materialize it as a canvas dataframe. Supports wide (pivot) or long shape with configurable per-cell aggregation.

How to use it

brapi_build_phenotype_matrix is exposed by the Brapi MCP Server MCP server. Add the server to your MCP client (Claude Desktop, Cursor, Windsurf and others), and the brapi_build_phenotype_matrix tool becomes available to the model automatically. See the full listing for setup details and every tool this server provides.

Install Brapi MCP Server

$docker run --rm -p 3010:3010 brapi-mcp-server

FULL BRAPI MCP SERVER LISTING

Other tools in Brapi MCP Server (24)

brapi_connect

Authenticate, register the connection under an alias, cache the capability profile, and return the orientation envelope inline. One call fully orients the agent.

brapi_dataframe_describe

Start here after a spillover. Lists dataframes (or describes one) with column schema, row counts, and originating-source provenance.

brapi_dataframe_drop

Opt-in via BRAPICANVASDROPENABLED=true. Drop a dataframe by name. Idempotent. Dataframes also expire via TTL when left unmanaged.

brapi_dataframe_export

Opt-in via BRAPIEXPORTDIR=<path>, stdio-only. Export a dataframe to disk (CSV / Parquet / JSON) under the configured directory and return the absolute path for the human to open. Optional columns projection or sql filter materializes a derived table for the export, dropped after.

brapi_dataframe_query

SELECT SQL across in-memory dataframes (DuckDB-backed). Spilled find rows auto-register as df<uuid>. Read-only — multi-statement, non-SELECT, file-reads, and exports rejected. Returns typed columns ({ name, type }[]).

brapi_describe_filters

Static BrAPI v2.1 filter catalog for any endpoint — powers extraFilters discovery on every find tool.

brapi_export_genotype_matrix

Export genotype calls for a variant set as a germplasm × variant canvas dataframe; also serializes to VCF-lite or PLINK .ped/.map text. Distinct-variant columns bounded by BRAPIGENOTYPEMATRIXMAXCOLUMNS (default 10k, max 500k).

brapi_find_genotype_calls

Pull genotype calls via async-search polling. Upstream pull bounded by BRAPIGENOTYPECALLSMAXPULL (default 100k, max 500k).

brapi_find_germplasm

Find germplasm by name, synonym, accession, PUI, crop, or free-text. Distributions + dataframe spillover.

brapi_find_images

Filter image metadata by unit / study / ontology / MIME type. Bytes via brapigetimage.

brapi_find_locations

Find research stations by country (ISO alpha-3 code, or English country name resolved client-side) / type / abbreviation, with optional client-side bbox filter.

brapi_find_observations

Pull observation records by study / germplasm / variable / season / unit / timestamp. Dataframe spillover.

brapi_find_studies

Find studies by crop / trial type / season / location / program. Distributions + dataframe spillover.

brapi_find_variables

Find observation variables by name / class / ontology / free-text; ranked client-side via OntologyResolver when text is supplied.

brapi_find_variants

Find variant records by variant set, reference, or genomic region (1-based inclusive / exclusive).

brapi_germplasm_performance

Per-variable performance aggregates (n, mean, median, sd, min, max, studyCount) for a single germplasm across all studies where it has observations.

brapi_get_germplasm

Fetch a germplasm with attributes, direct parents, and companion counts (studies, parents, descendants).

brapi_get_image

Fetch image bytes for up to 5 imageDbIds inline as type: image blocks. Prefers /imagecontent, falls back to imageURL.

brapi_get_study

Fetch a study with program / trial / location FKs resolved and companion counts (observations, units, variables).

brapi_raw_get

Passthrough to any BrAPI GET /{path} not covered by curated tools. Emits a routing nudge when one applies.

brapi_raw_search

Passthrough to any POST /search/{noun} with async polling handled transparently. Same nudge pattern.

brapi_server_info

Re-fetch the orientation envelope for a registered alias — identity, auth, capabilities, content counts, attribution, notes.

brapi_submit_observations

Two-phase observation write — mode: preview validates; mode: apply elicits confirmation, then fans POST + PUT in parallel. Additive only — no destructive deletion.

brapi_walk_pedigree

BFS-walk ancestry / descendancy as a deduplicated DAG with cycle detection, depth limits, and traversal stats.