ImmunoGraph MCP

calculate_synthetic_population_coverage

Read-onlyIdempotent

Calculate deterministic demonstration coverage from synthetic HLA-frequency inputs for teaching or testing the coverage pipeline; results are synthetic and not population estimates.

Instructions

Calculate deterministic demonstration coverage from synthetic HLA-frequency inputs. Use for teaching or testing the coverage pipeline, never as a population estimate; use calculate_population_coverage for a configured authoritative source. The output remains synthetic regardless of its numeric values.

Input Schema

Name	Required	Description	Default
`runId`	No	Caller-chosen identifier linking this call to one research run.	interactive-run
`classMode`	No	Whether coverage uses class-I, class-II, or combined associations.	COMBINED
`associations`	Yes	Peptide-to-HLA restrictions used for population coverage calculation.
`populationIds`	Yes	Population identifiers requested from the coverage source or synthetic dataset.

Output Schema

Name	Required	Description
`ok`	Yes	Whether execution completed successfully.
`data`	No	Tool-specific result fields on success.
`meta`	Yes	Run identifiers, timings, and input/output hashes.
`error`	No	Structured failure on unsuccessful execution.

Schema Changelog

Changes observed during successful MCP inspections.

Changed5 schema fields changedv0.2.1Oct 31, 2026

addedInput schema / properties / associations / description

Added value: +"Peptide-to-HLA restrictions used for population coverage calculation."

addedInput schema / properties / classMode / description

Added value: +"Whether coverage uses class-I, class-II, or combined associations."

addedInput schema / properties / populationIds / description

Added value: +"Population identifiers requested from the coverage source or synthetic dataset."

addedInput schema / properties / runId / description

Added value: +"Caller-chosen identifier linking this call to one research run."

changedOutput schema / (root)

Previous value: -nullNew value: +{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "additionalProperties": {},
+  "properties": {
+    "data": {
+      "additionalProperties": {},
+      "description": "Tool-specific result fields on success.",
+      "properties": {},
+      "type": "object"
+    },
+    "error": {
+      "additionalProperties": false,
+      "description": "Structured failure on unsuccessful execution.",
+      "properties": {
+        "category": {
+          "type": "string"
+        },
+        "code": {
+          "type": "string"
+        },
+        "details": {
+          "additionalProperties": {},
+          "properties": {},
+          "type": "object"
+        },
+        "message": {
+          "type": "string"
+        },
+        "retryable": {
+          "type": "boolean"
+        }
+      },
+      "required": [
+        "code",
+        "category",
+        "message",
+        "retryable"
+      ],
+      "type": "object"
+    },
+    "meta": {
+      "additionalProperties": {},
+      "description": "Run identifiers, timings, and input/output hashes.",
+      "properties": {
+        "completedAt": {
+          "type": "string"
+        },
+        "durationMs": {
+          "type": "number"
+        },
+        "inputHash": {
+          "type": "string"
+        },
+        "outputHash": {
+          "type": "string"
+        },
+        "requestId": {
+          "type": "string"
+        },
+        "runId": {
+          "type": "string"
+        },
+        "startedAt": {
+          "type": "string"
+        },
+        "toolName": {
+          "type": "string"
+        },
+        "toolVersion": {
+          "type": "string"
+        }
+      },
+      "required": [
+        "requestId",
+        "runId",
+        "toolName",
+        "toolVersion",
+        "startedAt",
+        "inputHash"
+      ],
+      "type": "object"
+    },
+    "ok": {
+      "description": "Whether execution completed successfully.",
+      "type": "boolean"
+    }
+  },
+  "required": [
+    "ok",
+    "meta"
+  ],
+  "type": "object"
+}

First observedv0.2.0Oct 31, 2026

TDQS

A4.5/5.0

Behavior4/5

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

Annotations already declare readOnlyHint and idempotentHint, and the description adds real behavioral context beyond them: the computation is deterministic ('demonstration'), and the result is synthetic regardless of how plausible the numbers look. That last caveat is exactly the kind of misinterpretation risk a mutation-free tool would otherwise leave open. It stops short of describing the numeric output itself, which the output schema covers.

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

Conciseness5/5

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

Three short sentences with zero redundancy: what it does, the use/avoid rule with an alternative, then the output caveat. The critical warning that the output is synthetic is front-loaded and reinforced at the end.

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?

Annotations cover the safety profile, the output schema covers return shape, and the description supplies the one thing structured fields cannot express: that these numbers must never be read as a population estimate. Complete for an agent to call it correctly and interpret it correctly.

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

Parameters3/5

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

Schema coverage is 100%, so associations, populationIds, runId and classMode are all documented in the schema. The description characterises the input domain ('synthetic HLA-frequency inputs') but adds no per-parameter semantics such as how populationIds resolve against the synthetic dataset versus the authoritative source. Baseline 3 is appropriate when the schema carries the detail.

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?

States a specific verb and resource ('Calculate deterministic demonstration coverage') plus the input domain (synthetic HLA-frequency inputs), and explicitly names the sibling it is not — calculate_population_coverage — so an agent can route without opening either schema.

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?

Covers when to use ('teaching or testing the coverage pipeline'), when not to use ('never as a population estimate'), and the concrete alternative ('use calculate_population_coverage for a configured authoritative source'). Nothing is left to inference.

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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