The Cure Protocol

get_pathways

Read-only

LIST REACTOME PATHWAYS for a gene (symbol or UniProt), with disease-pathway flags and stable ids. Use for mechanism context before modelling. NEXT: twin_experiment_guide to encode a mechanism, search_literature for sources.

Input Schema

Name	Required	Description
`gene`	No	HGNC symbol. gene or uniprot is required.
`limit`	No	Pathways to return.
`uniprot`	No	UniProt accession.
`diseaseOnly`	No	Disease pathways only.

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 / gene / maxLength
```
Added value: +20000
```
- addedInput schema / properties / uniprot / maxLength
```
Added value: +20000
```
AddedOct 20, 2026

TDQS

A4/5.0

Behavior3/5

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

Annotations already declare readOnlyHint=true and openWorldHint=true, so the safety and openness profile is covered. The description adds that results include disease-pathway flags and stable ids, which is useful, but says nothing about limits, pagination, or empty-result behavior beyond what the schema's limit parameter already implies.

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 clauses: what it does, when to use it, where to go next. Front-loaded with the core action and no filler; every sentence carries routing or scoping information.

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 a full output schema and 100% parameter coverage, the description only needs to carry purpose and routing, which it does. Minor gap: it doesn't mention the limit cap or what happens when a gene has no pathways, but nothing essential to correct invocation is missing.

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%, with each of the four parameters documented inline, so the baseline is 3. The description only echoes the gene-symbol/UniProt duality already captured in the schema and adds no extra semantics for diseaseOnly or limit.

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 ('LIST REACTOME PATHWAYS') plus the accepted identifier types (symbol or UniProt) and what the output carries (disease-pathway flags, stable ids). An agent can distinguish this from sibling lookups like get_gene or search_literature without opening the schema.

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 an explicit usage context ('mechanism context before modelling') and names two concrete next-step alternatives (twin_experiment_guide for encoding a mechanism, search_literature for sources). It lacks an explicit 'do not use when' exclusion, but the routing guidance is actionable.

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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