ImmunoGraph MCP

fetch_compound

Read-onlyIdempotent

Retrieve compound identity and SMILES from PubChem or an exact fixture using a known reference before validation or ligand preparation.

Instructions

Retrieve compound identity and SMILES from configured PubChem access or replay an exact fixture. Use with a known compound reference before validation or ligand preparation; this does not calculate descriptors. LIVE_ONLY requires PubChem access and returns source provenance.

Input Schema

Name	Required	Description
`runId`	Yes	Caller-chosen identifier linking this call to one research run.
`source`	Yes	Selected remote provider or exact fixture source.
`compoundRef`	Yes	Provider compound reference or exact fixture key; PubChem uses its CID.
`fallbackPolicy`	Yes	Allowed source order; LIVE_ONLY forbids cache and fixture substitution, FIXTURE_ONLY forbids live calls.

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 / compoundRef / description

Added value: +"Provider compound reference or exact fixture key; PubChem uses its CID."

addedInput schema / properties / fallbackPolicy / description

Added value: +"Allowed source order; LIVE_ONLY forbids cache and fixture substitution, FIXTURE_ONLY forbids live calls."

addedInput schema / properties / runId / description

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

addedInput schema / properties / source / description

Added value: +"Selected remote provider or exact fixture source."

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

A4.1/5.0

Behavior4/5

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

Annotations already declare readOnlyHint and idempotentHint, so the safety profile is covered. The description adds useful behavioral context: it mentions source provenance, fallback policy implications (LIVE_ONLY requires access), and that it does not calculate descriptors. It stops short of detailing error or rate-limit behavior.

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?

Two tight sentences front-load the core action and end with a key constraint. No filler, though the second sentence could be slightly more structured.

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 annotations covering safety, a full input schema, and an output schema, the description need not explain return values. It provides enough context about sources and fallback to call the tool correctly, though it could more explicitly route to sibling tools.

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 all parameters. The description mentions compoundRef, source, and fallbackPolicy in passing but adds little syntax or format detail beyond what the schema provides. Baseline 3 is appropriate.

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?

The description states a specific verb (retrieve) and resource (compound identity and SMILES), names the two source modes (PubChem or fixture), and explicitly excludes descriptor calculation. This clearly distinguishes it from siblings like validate_compound, calculate_molecular_descriptors, and prepare_ligand.

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?

It says to use this 'with a known compound reference before validation or ligand preparation,' giving a clear context of use, and notes that LIVE_ONLY requires PubChem access. However, it does not explicitly name the alternative tools or state when-not to use it beyond the descriptor exclusion.

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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