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io.github.cyanheads/brapi-mcp-server

io.github.cyanheads/brapi-mcp-server · v0.10.1

Measured by MCP Station

Description written by the publisher, not verified

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

Connect

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

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

Tools as reported by the server

• 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). Other BrAPI tools connect an alias the server has a URL configured for (a built-in or operator-configured alias, or `default` o
• 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 it with brapi_dataframe_describe and brapi_dataframe_query) plus a summary of dimensions and aggregate method. Long-form output is suitable
• brapi_server_info
  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 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. results[] holds the leading matches up to loadLimit and a 24,000-byte budget; when it holds fewer rows than matched, the matched set is materialized as a datafram
• 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-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. results[] holds the leading matches up to loadLimit and a 24,000-byte budget; when it holds fewer rows than matched, the matched set is materialized as a dataframe — read it with bra
• 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 cycle detection and depth limits. leafCount counts graph terminals, confirmedLeafCount counts successfully verified leaves, and frontier records unresolved directions. Nodes and edges each fit loadLimit and a 24,000-byte preview budge
• brapi_germplasm_performance
  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 uses advertised germplasm-scoped observation units with embedded measurements, including zeros. Other s
• 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, synonym, and trait text; a candidate carries the ontology PUI of its row as termId when the row has one. results[] holds the leading rows
• brapi_find_observations
  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 count probe and skips the bulk pull (warnings says so) when the probe fails or reports more than 5,000 m
• 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. results[] holds the leading matches up to loadLimit and a 24,000-byte budget; when it holds fewer rows than matched, the match
• 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 or that request fails. 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, 0-based inclusive / exclusive per the BrAPI spec; servers may differ). results[] holds the leading matches up to loadLimit and a 24,000-byte budget; when it holds fewer rows than matched, the matched set is materi
• 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. results[] holds the leading calls up to `loadLimit` and a 24,000-byte budg
• 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 in `vcf`; `plink` adds .ped/.map text in `ped`/`map`. Text formats pull /variants metadata and convert zero-based BrAPI start to one-based
• 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 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 representation; an oversized first row returns no inline rows. Omitted fetched rows remain in a datafr
• 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. List previews fit loadLimit and a 24,000-byte budget on each serialized row representation; an oversized first row returns no inline rows. Eve

Tool changes

• 2026-10-20: brapi_connect, brapi_build_phenotype_matrix, brapi_server_info, brapi_describe_filters, brapi_find_studies, brapi_get_study, brapi_find_germplasm, brapi_get_germplasm, brapi_walk_pedigree, brapi_germplasm_performance, brapi_find_variables, brapi_find_observations
• 2026-10-19: brapi_connect, brapi_build_phenotype_matrix, brapi_server_info, brapi_describe_filters, brapi_find_studies, brapi_get_study, brapi_find_germplasm, brapi_get_germplasm, brapi_walk_pedigree, brapi_germplasm_performance, brapi_find_variables, brapi_find_observations
• 2026-10-18: brapi_connect, brapi_build_phenotype_matrix, brapi_server_info, brapi_describe_filters, brapi_find_studies, brapi_get_study, brapi_find_germplasm, brapi_get_germplasm, brapi_walk_pedigree, brapi_germplasm_performance, brapi_find_variables, brapi_find_observations
• 2026-10-16: brapi_connect, brapi_build_phenotype_matrix, brapi_server_info, brapi_describe_filters, brapi_find_studies, brapi_get_study, brapi_find_germplasm, brapi_get_germplasm, brapi_walk_pedigree, brapi_germplasm_performance, brapi_find_variables, brapi_find_observations

Repository · JSON · Text for agents · Registry updated 2026-10-19