The Cure Protocol

compare_diseases

Read-only

FIND SHARED TARGETS across 2-3 disease domains among each one's top source associations, with per-domain scores and pairwise overlap counts. Alphabetical, hypothesis leads. NEXT: get_target_evidence per disease, get_target_profile for the gene.

Input Schema

Name	Required	Description	Default
`top`	No	Top targets per domain.
`diseases`	Yes	2 or 3 domain ids, comma-separated.

Output Schema

Name	Required	Description	Default
`data`	No	The answer. Shape depends on the tool; describe_tool documents it.
`_meta`	No	source, generatedAt, sources (per-source lastSyncedAt and ageHours), rateLimit, disclaimer.

Schema Changelog

Changes observed during successful MCP inspections.

Changed1 schema field changedOct 28, 2026

changedOutput schema / (root)

Previous value: -nullNew value: +{
+  "$schema": "http://json-schema.org/draft-07/schema#",
+  "additionalProperties": {},
+  "properties": {
+    "_meta": {
+      "additionalProperties": {},
+      "description": "source, generatedAt, sources (per-source lastSyncedAt and ageHours), rateLimit, disclaimer.",
+      "propertyNames": {
+        "type": "string"
+      },
+      "type": "object"
+    },
+    "data": {
+      "description": "The answer. Shape depends on the tool; describe_tool documents it."
+    }
+  },
+  "type": "object"
+}

Changed2 schema fields changedOct 24, 2026

addedInput schema / properties / diseases / anyOf

Added value: +[
+  {
+    "maxLength": 2000,
+    "type": "string"
+  },
+  {
+    "items": {
+      "maxLength": 200,
+      "type": "string"
+    },
+    "maxItems": 100,
+    "minItems": 1,
+    "type": "array"
+  }
+]

removedInput schema / properties / diseases / type
```
Removed value: -"string"
```

AddedOct 20, 2026

TDQS

A4.2/5.0

Behavior4/5

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

Annotations already establish readOnlyHint=true and openWorldHint=true. The description adds useful behavioral context by noting per-domain scores, pairwise overlap counts, and that results are hypothesis leads, which signals interpretation limits beyond the annotations and schema.

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?

The description is front-loaded with the core action, then briefly covers output characteristics and next steps. Every sentence contributes relevant information without wasted prose.

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 and an output schema present, the description only needs to orient the agent. It does so by naming the comparison scope, output score/overlap details, and downstream tools, though it could clarify what 'hypothesis leads' means for interpretation.

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 both parameters are already documented in the schema. The description reinforces the 2-3 domain constraint and top associations but adds no syntax or format details beyond what the schema provides.

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 and resource: find shared targets across 2-3 disease domains. The scope over multiple domains and pairwise overlap clearly distinguishes it from single-disease target retrieval siblings such as get_disease_targets.

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 gives a clear context for use: comparing 2-3 disease domains by shared targets, and it points to next tools for follow-up. It does not explicitly state when not to use it or name alternatives, so it falls short of full when/when-not/alternatives guidance.

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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