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The Cure Protocol

by com.negativeresistance
OverviewDiscussionsAdmin

search_datasets

Read-only

FIND HUMAN OMICS DATASETS (GEO series) by text or disease domain: accession, study type, samples, platforms, linked PMIDs. Use to source calibration or replication data. NEXT: run_twin_benchmark or run_beta_cell with aggregate observations.

Input Schema

NameRequiredDescriptionDefault
qNoSearch text. q or disease is required.
limitNoDatasets to return.
cursorNoOpaque cursor. Pass _meta.pagination.nextCursor from the previous call unchanged to get the next page; omit it to start at the beginning.
offsetNoResults to skip.
diseaseNoDomain id.

Output Schema

NameRequiredDescriptionDefault
dataNoThe answer. Shape depends on the tool; describe_tool documents it.
_metaNosource, generatedAt, sources (per-source lastSyncedAt and ageHours), rateLimit, disclaimer.

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed1 schema field changed
    • addedInput schema / properties / cursor
      Added value: +{
+  "description": "Opaque cursor. Pass _meta.pagination.nextCursor from the previous call unchanged to get the next page; omit it to start at the beginning.",
+  "maxLength": 200,
+  "type": "string"
+}
  2. Changed1 schema field changed
    • 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"
+}
  3. Changed2 schema fields changed
    • addedInput schema / properties / disease / maxLength
      Added value: +20000
    • addedInput schema / properties / q / maxLength
      Added value: +500
  4. Added

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 openWorldHint, so the description's job is to add context — which it does by enumerating the result fields (accession, study type, samples, platforms, linked PMIDs). It doesn't disclose corpus size, rate limits, or result ordering, but the essential behavioral shape is conveyed without contradicting the annotations.

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?

Three short, front-loaded clauses: ident/target, use, next step. The telegraphic all-caps style ('FIND HUMAN OMICS DATASETS') is slightly shouty but efficient, and no sentence is wasted.

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?

An output schema exists and pagination is documented in the schema, so the description needn't repeat return-shape details. It covers purpose, data source, result contents, and follow-up tools — enough for an agent to call it correctly; only filtering precedence is left implicit.

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% and every parameter (q, limit, cursor, offset, disease) is described there, including the cursor contract. The description only restates the 'text or disease domain' duality and adds no format or precedence detail, so the schema does the heavy lifting.

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 ('FIND HUMAN OMICS DATASETS (GEO series)') plus the two axes of search (text or disease domain) and what a hit contains. This clearly separates it from sibling searches like search_literature and search_compounds, which target different corpora.

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?

Gives the intended purpose ('source calibration or replication data') and a concrete downstream step ('NEXT: run_twin_benchmark or run_beta_cell with aggregate observations'), which is real routing value. It doesn't say when to prefer q vs disease or when another search tool would be better, so it stops short of full when/when-not 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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