ImmunoGraph MCP

detect_overlapping_epitopes

Read-onlyIdempotent

Detect positional overlap competitors and connected components among candidate intervals before constraint review. Returns interval relationships without selecting winners or deduplicating identities.

Instructions

Find positional overlap competitors and connected components among candidate intervals. Use before apply_constraint_rules when overlaps need review; this tool does not choose a winner or deduplicate identities. Returns interval relationships from caller-supplied coordinates.

Input Schema

Name	Required	Description
`runId`	Yes	Caller-chosen identifier linking this call to one research run.
`threshold`	Yes	Numeric cutoff for the selected overlap or decision operation.
`candidates`	Yes	Caller-supplied candidate records; required nested fields depend on this operation.

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.

Changed7 schema fields changedv0.2.1Oct 31, 2026

addedInput schema / properties / candidates / description

Added value: +"Caller-supplied candidate records; required nested fields depend on this operation."

addedInput schema / properties / candidates / items / properties / candidateKey / description
```
Added value: +"Stable key identifying one epitope candidate across evidence stages."
```
addedInput schema / properties / candidates / items / properties / candidateType / description
```
Added value: +"MHC class or candidate category this operation applies to."
```

addedInput schema / properties / candidates / items / properties / proteinHash / description

Added value: +"SHA-256 identity of the protein sequence associated with these candidates."

addedInput schema / properties / runId / description

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

addedInput schema / properties / threshold / description

Added value: +"Numeric cutoff for the selected overlap or decision operation."

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

A4/5.0

Behavior4/5

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

Annotations already declare readOnlyHint and idempotentHint, so safety is covered; the description still adds real value by clarifying that the tool reports relationships rather than resolving them (no winner selection, no identity dedup) and that output derives from caller-supplied coordinates rather than external lookup. It does not explain how 'connected components' are formed or how threshold affects grouping, which keeps it from 5.

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: purpose first, then usage/sequencing, then output scope. No filler, no restatement of the tool name, and the key routing constraint appears before the caveats.

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

Completeness4/5

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

With an output schema present, the description needn't describe return values, and annotations plus full schema coverage handle safety and fields. What remains under-explained is the domain meaning of threshold in this specific operation and the shape of the 'connected components' notion, a modest but real gap for a 3-parameter analysis tool.

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 description coverage is 100%, so the schema already documents runId, threshold, and the candidate record fields, making 3 the baseline. The description adds no threshold semantics specific to overlap detection (e.g. what value means strict vs. permissive overlap) and says nothing about candidate ordering or the required nested fields.

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

Purpose4/5

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

States a concrete verb and resource: "Find positional overlap competitors and connected components among candidate intervals." It also rules out two confusable behaviors (choosing a winner, deduplicating identities), which separates it from remove_duplicate_candidates and rank_candidates, though it does not name those siblings explicitly.

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

Usage Guidelines4/5

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

"Use before apply_constraint_rules when overlaps need review" gives explicit ordering and a triggering condition, and "does not choose a winner or deduplicate identities" implicitly routes deduplication elsewhere. No explicit when-not-to-use case or named alternative tool, so not a 5.

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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