Brapi MCP Server

@cyanheads/brapi-mcp-server A collaborative BrAPI v2.1 workspace for multi-agent research via MCP. Search studies, germplasm, genotypes, and more across Breedbase, T3, Sweetpotatobase, and any BrAPI v2-compliant server. 25 Tools • 6 Resources • 2 Prompts

Public Hosted Server: https://brapi.caseyjhand.com/mcp

Overview

Plant-breeding data from any BrAPI (Breeding API) v2 server — Breedbase instances like Cassavabase and Sweetpotatobase, the Triticeae Toolbox (T3), and more, several at once. Search studies, germplasm, observations, and genotypes, walk pedigrees, and build phenotype and genotype matrices, with large results queryable in SQL.

Tools

Resources

Every resource reads the default connection and mirrors a tool; tool-only clients and multi-server workflows use the tools.

Prompts

Capability reference

Identifier filters also accept their BrAPI *DbId / *DbIds spellings where equivalent: for example, imageDbId for imageDbIds, studyDbIds for studies, and observationVariableDbIds for variables. Array filters accept a lone string or multiple IDs. Supply one spelling per filter; conflicting spellings are rejected.

brapi_connect tool

• baseUrl and auth are optional: omitted values come from BRAPI_ _* env vars, the built-in aliases, then BRAPI_DEFAULT_* (see Per-alias credentials); alias (default default, pattern ^[a-zA-Z0-9_-]+$) keeps several servers registered at once; auth.mode is none, bearer, api_key, sgn (Breedbase /token exchange), or oauth2 (client credentials)
• Returns the orientation envelope: server identity, auth summary, capabilities (supported, notableGaps), active dialect, content counts, attribution for built-in servers, and nextToolSuggestions naming the entry-point finders this server can serve
• Typed errors: auth_session_required, auth_base_url_mismatch, alias_base_url_unset, alias_base_url_invalid, private_address_blocked, auth_token_exchange_failed, auth_no_access_token, upstream_unauthorized, upstream_forbidden, capability_discovery_unavailable (retryable); a failed connect leaves any earlier registration under the alias intact
• Optional for an alias the server has a URL for (default when BRAPI_DEFAULT_BASE_URL is set, a built-in, or a BRAPI_ _BASE_URL alias): any other tool or resource connects it on first use, as brapi_connect with no baseUrl or auth would, and concurrent first calls share one connect. An alias with no URL of its own still fails unknown_alias, even with BRAPI_DEFAULT_* set, so a mistyped alias never reaches the default server. Those tools and resources declare the connect failures they can hit (the token, discovery, auth-wall, alias_base_url_invalid, and private_address_blocked errors above), each with a recovery hint

brapi_server_info tool

• alias optional; forceRefresh (default false) refetches the capability profile instead of reading the cache
• Returns the same orientation envelope as brapi_connect

brapi_describe_filters tool

• endpoint is one of studies, germplasm, observations, variables, images, variants, locations; unknown_endpoint carries availableEndpoints
• Each filter has name, type, description, and example; the catalog follows the v2.1 spec, and individual servers may honor a subset

brapi_find_studies tool

• Filters: crop, trialTypes, seasons, locations, programs, trials, studyNames, active; on SGN servers (CassavaBase, Breedbase, Sweetpotatobase), which ignore the location filter on /studies, locations is applied client-side over the scanned studies, and totalCount is the matched count
• distributions over programName, studyType, seasons, locationName, commonCropName
• SGN/Breedbase studies lift missing program IDs and names from additionalInfo, preserving the raw metadata.

brapi_get_study tool

• studyDbId required; resolves program, trial, and location inline; study_not_found when the upstream has no such study
• On SGN/Breedbase servers, missing program fields come from additionalInfo; when the study has no program ID, the fetched parent trial can supply it for program resolution.
• Companion counts observationCount, observationUnitCount, variableCount; a count the server can't scope to the study is omitted with a warning, never reported as the server-wide total

brapi_find_germplasm tool

• Filters: names, germplasmDbIds, germplasmPUIs, accessionNumbers, crops, synonyms, collections, genus, species; text is a client-side substring match on name, PUI, accession, display name, and synonyms that drops non-matching rows. Its first request uses BRAPI_PAGE_SIZE independently of inline loadLimit; it scans every upstream row when the set fits one dataframe walk (50,000 rows at the default page size). Above that, a first-page miss stops after one request and reports the actual rows scanned; it does not establish absence from the catalog, so pair it with a server-side filter.
• distributions over commonCropName, genus, species, collection, countryOfOriginCode

brapi_get_germplasm tool

• germplasmDbId required; returns attributes and direct parents; germplasm_not_found when the upstream has no such germplasm
• Companion counts studyCount, directParentCount, directDescendantCount

brapi_walk_pedigree tool

• 1–20 root germplasmDbIds (germplasmDbId also accepted); direction is ancestors (default), descendants, or both; maxDepth 1–10 (default 3); the walk stops at 1,000 nodes or 10,000 edges and sets truncated
• both is the union of the two walks: ancestors expand only through /pedigree and descendants only through /progeny, so a descendant's other parent is not pulled in
• One edge per parent–child pair; cycleCount counts the edges marked isCycle, where a germplasm becomes its own ancestor — shared ancestors and siblings are not cycles
• leafCount counts graph terminals, including depth-boundary nodes; confirmedLeafCount counts non-root nodes whose relevant lookups successfully returned no relatives. frontier / frontierCount distinguish depth-limited, safet