brapi-mcp-server

Brapi Germplasm Performance

brapi_germplasm_performance

Read-only

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 servers discover up to 200 studies before pulling per study. Pass studyDbIds to skip discovery and restrict collection to known studies. Per-study observation limits, page limits, failures, and incomplete scans appear in coverage and warnings. For the underlying matrix, use brapi_build_phenotype_matrix.

Input Schema

Name	Required	Description
`alias`	No	Connection alias. Omit to use alias `default`. An alias registered via brapi_connect works, and so does one the server has a URL configured for (a built-in alias, an operator-configured alias, or `default` on a deployment with a default server), which connects on first use. Calls that used a non-default alias must pass that same alias here.
`variables`	No	Optional subset of observationVariableDbIds to aggregate. Omit to include every variable observed for the germplasm.
`studyDbIds`	No	Optional studyDbIds to restrict collection to known studies and skip automatic discovery. Omit to walk germplasm-scoped embedded units on SGN/Breedbase, or discover up to 200 studies on other servers. Find known study IDs with brapi_find_studies; some servers ignore its germplasm filter.
`germplasmDbId`	Yes	The germplasmDbId to summarize performance for.

Output Schema

Name	Required	Description
`alias`	No	Connection alias the call used.
`error`	No	Present when the call failed. Absent on success.
`coverage`	No	Collection coverage, independent of the number of contributing studies.
`warnings`	No	Advisory messages (study-discovery limits, dropped filters, fallback paths, per-study failures, partial study scans).
`studyCount`	No	Number of distinct studies that contributed any observation.
`studyDbIds`	No	Distinct studyDbIds that contributed observations.
`perVariable`	No	Per-variable aggregates, sorted by observationVariableDbId.
`germplasmDbId`	No	The germplasm that was analyzed.
`germplasmName`	No	Display name of the germplasm, when the server provides one.

Schema Changelog

Changes observed during successful MCP inspections.

Changed2 schema fields changedOct 19, 2026

changedOutput schema / properties / error / properties / data / properties / reason / description

Previous value: -"Machine-readable failure mode. Declared by this tool: `unknown_alias`: No connection is registered under the requested alias, and the server has no base URL configured for it to connect on first use. `auth_token_exchange_failed`: Connecting the alias on first use, the SGN or OAuth token exchange against the BrAPI /token endpoint failed. `auth_no_access_token`: Connecting the alias on first use, the token endpoint answered without returning an access token. `capability_discovery_unavailable`: Neither /serverinfo nor /calls listed any call, and at least one of them timed out, was unreachable, or answered 429 or a 5xx other than 501, so nothing was cached. `upstream_unauthorized`: The BrAPI server answered HTTP 401: it requires credentials, or rejected the ones sent. `upstream_forbidden`: The BrAPI server answered HTTP 403: the credentials sent, or their absence, lack access. `alias_base_url_invalid`: The base URL configured on the server for this alias is not an absolute http(s) URL, or carries credentials. `private_address_blocked`: The base URL configured for this alias, or its token URL, is on a private or reserved address this server may not reach. `germplasm_not_found`: Upstream returned no germplasm record for the requested germplasmDbId. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `upstream_not_found`: An uncaught BrAPI data request answered HTTP 404. `upstream_rate_limited`: An uncaught BrAPI data request exhausted retries after HTTP 429. `unknown_alias`: No connection is registered under the requested alias, and the server has no base URL configured for it to connect on first use. `auth_token_exchange_failed`: Connecting the alias on first use, the SGN or OAuth token exchange against the BrAPI /token endpoint failed. `auth_no_access_token`: Connecting the alias on first use, the token endpoint answered without returning an access token. `capability_discovery_unavailable`: Neither /serverinfo nor /calls listed any call, and at least one of them timed out, was unreachable, or answered 429 or a 5xx other than 501, so nothing was cached. `upstream_unauthorized`: The BrAPI server answered HTTP 401: it requires credentials, or rejected the ones sent. `upstream_forbidden`: The BrAPI server answered HTTP 403: the credentials sent, or their absence, lack access. `alias_base_url_invalid`: The base URL configured on the server for this alias is not an absolute http(s) URL, or carries credentials. `private_address_blocked`: The base URL configured for this alias, or its token URL, is on a private or reserved address this server may not reach. `germplasm_not_found`: Upstream returned no germplasm record for the requested germplasmDbId. Other values are possible when a failure originates below the handler."

changedOutput schema / properties / error / properties / data / properties / reason / examples

Previous value: -[
-  "unknown_alias",
-  "auth_token_exchange_failed",
-  "auth_no_access_token",
-  "capability_discovery_unavailable",
-  "upstream_unauthorized",
-  "upstream_forbidden",
-  "alias_base_url_invalid",
-  "private_address_blocked",
-  "germplasm_not_found"
-]New value: +[
+  "upstream_not_found",
+  "upstream_rate_limited",
+  "unknown_alias",
+  "auth_token_exchange_failed",
+  "auth_no_access_token",
+  "capability_discovery_unavailable",
+  "upstream_unauthorized",
+  "upstream_forbidden",
+  "alias_base_url_invalid",
+  "private_address_blocked",
+  "germplasm_not_found"
+]

Changed3 schema fields changedOct 18, 2026

changedInput schema / properties / studyDbIds / description

Previous value: -"Optional explicit set of studyDbIds to aggregate over. When supplied, skips automatic study discovery and its 200-study cap entirely — use it to process a specific slice of studies, e.g. the full germplasm-scoped study set retrieved via brapi_find_studies with extraFilters.germplasmDbIds. Omit to let the tool discover the germplasm’s studies automatically."New value: +"Optional studyDbIds to restrict collection to known studies and skip automatic discovery. Omit to walk germplasm-scoped embedded units on SGN/Breedbase, or discover up to 200 studies on other servers. Find known study IDs with brapi_find_studies; some servers ignore its germplasm filter."

changedOutput schema / anyOf

Previous value: -[
-  {
-    "not": {
-      "required": [
-        "error"
-      ]
-    },
-    "required": [
-      "alias",
-      "germplasmDbId",
-      "studyCount",
-      "studyDbIds",
-      "perVariable",
-      "warnings"
-    ]
-  },
-  {
-    "required": [
-      "error"
-    ]
-  }
-]New value: +[
+  {
+    "not": {
+      "required": [
+        "error"
+      ]
+    },
+    "required": [
+      "alias",
+      "germplasmDbId",
+      "studyCount",
+      "studyDbIds",
+      "coverage",
+      "perVariable",
+      "warnings"
+    ]
+  },
+  {
+    "required": [
+      "error"
+    ]
+  }
+]

addedOutput schema / properties / coverage

Added value: +{
+  "additionalProperties": false,
+  "description": "Collection coverage, independent of the number of contributing studies.",
+  "properties": {
+    "discoveryLimited": {
+      "description": "True when generic study discovery reached its bound; additional studies may exist.",
+      "type": "boolean"
+    },
+    "partial": {
+      "description": "True when failed, truncated, or unprocessed work leaves coverage incomplete.",
+      "type": "boolean"
+    },
+    "scan": {
+      "additionalProperties": false,
+      "description": "Scoped-unit scan coverage; unseen studies are unknown after an incomplete walk.",
+      "properties": {
+        "complete": {
+          "description": "Whether the scoped unit walk exhausted its authoritative total.",
+          "type": "boolean"
+        },
+        "pagesFetched": {
+          "description": "Unit pages returned before stopping.",
+          "maximum": 9007199254740991,
+          "minimum": 0,
+          "type": "integer"
+        },
+        "reason": {
+          "description": "Bound or failure that stopped the unit walk.",
+          "type": "string"
+        },
+        "scannedUnits": {
+          "description": "Raw upstream units examined, including repeated IDs.",
+          "maximum": 9007199254740991,
+          "minimum": 0,
+          "type": "integer"
+        },
+        "totalUnits": {
+          "description": "Upstream raw unit total, when reported.",
+          "maximum": 9007199254740991,
+          "minimum": 0,
+          "type": "integer"
+        }
+      },
+      "required": [
+        "complete",
+        "scannedUnits",
+        "pagesFetched"
+      ],
+      "type": "object"
+    },
+    "studies": {
+      "description": "Per-study outcomes in requested or encounter order.",
+      "items": {
+        "additionalProperties": false,
+        "description": "One study collection outcome.",
+        "properties": {
+          "observationCount": {
+            "description": "Matching observations collected for this study.",
+            "maximum": 9007199254740991,
+            "minimum": 0,
+            "type": "integer"
+          },
+          "reason": {
+            "description": "Why collection failed or remained incomplete.",
+            "type": "string"
+          },
+          "status": {
+            "description": "Outcome of collecting this study; partial may contain observations.",
+            "enum": [
+              "contributed",
+              "empty",
+              "failed",
+              "partial",
+              "unprocessed"
+            ],
+            "type": "string"
+          },
+          "studyDbId": {
+            "description": "Requested study, or a study encountered in scoped units.",
+            "type": "string"
+          }
+        },
+        "required": [
+          "studyDbId",
+          "status",
+          "observationCount"
+        ],
+        "type": "object"
+      },
+      "type": "array"
+    }
+  },
+  "required": [
+    "partial",
+    "studies"
+  ],
+  "type": "object"
+}

Changed10 schema fields changedOct 18, 2026

changedInput schema / properties / alias / description

Previous value: -"Connection alias registered via brapi_connect. Omit to read the connection registered under alias `default` — i.e. a prior brapi_connect call that did not specify an alias. Calls that used a non-default alias must pass that same alias here."New value: +"Connection alias. Omit to use alias `default`. An alias registered via brapi_connect works, and so does one the server has a URL configured for (a built-in alias, an operator-configured alias, or `default` on a deployment with a default server), which connects on first use. Calls that used a non-default alias must pass that same alias here."

removedInput schema / properties / germplasmDbId / minLength
```
Removed value: -1
```
addedInput schema / properties / germplasmDbId / pattern
```
Added value: +"\\S"
```
removedInput schema / properties / studyDbIds / items / minLength
```
Removed value: -1
```
addedInput schema / properties / studyDbIds / items / pattern
```
Added value: +"\\S"
```
addedInput schema / properties / variables / items / pattern
```
Added value: +"\\S"
```

changedOutput schema / properties / alias / description

Previous value: -"Alias of the registered BrAPI connection used."New value: +"Connection alias the call used."

changedOutput schema / properties / error / properties / data / properties / reason / description

Previous value: -"Machine-readable failure mode. Declared by this tool: `unknown_alias`: No connection has been registered under the requested alias. `germplasm_not_found`: Upstream returned no germplasm record for the requested germplasmDbId. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `unknown_alias`: No connection is registered under the requested alias, and the server has no base URL configured for it to connect on first use. `auth_token_exchange_failed`: Connecting the alias on first use, the SGN or OAuth token exchange against the BrAPI /token endpoint failed. `auth_no_access_token`: Connecting the alias on first use, the token endpoint answered without returning an access token. `capability_discovery_unavailable`: Neither /serverinfo nor /calls listed any call, and at least one of them timed out, was unreachable, or answered 429 or a 5xx other than 501, so nothing was cached. `upstream_unauthorized`: The BrAPI server answered HTTP 401: it requires credentials, or rejected the ones sent. `upstream_forbidden`: The BrAPI server answered HTTP 403: the credentials sent, or their absence, lack access. `alias_base_url_invalid`: The base URL configured on the server for this alias is not an absolute http(s) URL, or carries credentials. `private_address_blocked`: The base URL configured for this alias, or its token URL, is on a private or reserved address this server may not reach. `germplasm_not_found`: Upstream returned no germplasm record for the requested germplasmDbId. Other values are possible when a failure originates below the handler."

changedOutput schema / properties / error / properties / data / properties / reason / examples

Previous value: -[
-  "unknown_alias",
-  "germplasm_not_found"
-]New value: +[
+  "unknown_alias",
+  "auth_token_exchange_failed",
+  "auth_no_access_token",
+  "capability_discovery_unavailable",
+  "upstream_unauthorized",
+  "upstream_forbidden",
+  "alias_base_url_invalid",
+  "private_address_blocked",
+  "germplasm_not_found"
+]

changedOutput schema / properties / warnings / description

Previous value: -"Advisory messages (study-discovery limits, dropped filters, fallback paths, per-study failures)."New value: +"Advisory messages (study-discovery limits, dropped filters, fallback paths, per-study failures, partial study scans)."

First observedSep 19, 2026

TDQS

A4.8/5.0

Behavior5/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations only declare readOnlyHint and openWorldHint; the description goes well beyond by disclosing the discovery cap (200 studies), that per-study observation limits, page limits, failures, and incomplete scans surface in coverage and warnings, and that zeros are included in embedded measurements. This is exactly the kind of partial-result behavior an agent needs to interpret output correctly.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Five sentences, all front-loaded with purpose then routing then caveats; nothing is redundant boilerplate. Slightly dense, and the trailing 'For the underlying matrix' sentence could arguably sit earlier next to the sibling comparison, but it earns its place.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

With an output schema present, return values need not be explained, yet the description still characterizes coverage/warnings semantics that a schema alone would not convey. Discovery limits, partial-data behavior, and the alternative tool are all covered, leaving no material gap for correct invocation.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 100%, so the baseline is 3; the description still adds meaning by explaining that studyDbIds skips automatic discovery (not just 'restricts studies') and that omitting variables includes every observed variable. The alias parameter is documented thoroughly in the schema itself and needs no description help.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

Opens with a specific verb and resource ('Aggregate a single germplasm's observations across studies') and enumerates the exact return shape (n, mean, median, sd, min, max, contributing studies, seasons, coverage). It also explicitly names the sibling brapi_build_phenotype_matrix as the tool for the underlying matrix, so an agent can separate the two without inspecting schemas.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines5/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

States a concrete decision rule: pass studyDbIds to skip discovery and restrict collection, otherwise the server walks embedded units (SGN/Breedbase) or discovers up to 200 studies. It also routes the agent to brapi_build_phenotype_matrix for the raw matrix, and the schema covers finding study IDs via brapi_find_studies.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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