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Reactome

by io.github.pipeworx-io
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Pathway

pathway
Read-onlyIdempotent

Full pathway record by stable id (e.g. R-HSA-68886).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
idYes

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
countYesNumber of items returned.
itemsYesContained events in a pathway

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed2 schema fields changed
    • addedInput schema / examples
      Added value: +[
+  {
+    "id": "R-HSA-68886"
+  }
+]
    • changedOutput schema / (root)
      Previous value: -nullNew value: +{
+  "properties": {
+    "count": {
+      "description": "Number of items returned.",
+      "type": "integer"
+    },
+    "items": {
+      "description": "Contained events in a pathway",
+      "items": {
+        "properties": {
+          "className": {
+            "description": "Type of event",
+            "type": "string"
+          },
+          "dbId": {
+            "description": "Internal database ID",
+            "type": "number"
+          },
+          "displayName": {
+            "description": "Event name",
+            "type": "string"
+          },
+          "schemaClass": {
+            "description": "Schema class",
+            "type": "string"
+          },
+          "stableId": {
+            "description": "Stable identifier",
+            "type": "string"
+          }
+        },
+        "type": "object"
+      },
+      "type": "array"
+    }
+  },
+  "required": [
+    "items",
+    "count"
+  ],
+  "type": "object"
+}
  2. First observed

TDQS

A3.5/5.0
Behavior3/5

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

Annotations already declare the tool as read-only, idempotent, and non-destructive, so the safety profile is covered. The description adds context about the stable id requirement and the 'full' nature of the record, which is useful. However, it does not disclose rate limits, error behavior, or the structure of the returned data beyond what the output schema presumably provides.

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 a single, directly stated sentence that is front-loaded and free of any redundant information. Given the simplicity of the tool (one parameter), it is appropriately sized and every word earns its place.

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?

The tool has one parameter, an output schema, and comprehensive annotations. The description sufficiently explains the input and the nature of the response ('full pathway record') for a simple lookup. It could mention potential failure modes or the specific domain of the stable id (Reactome), but with the output schema and annotations present, the description is largely complete.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

The input schema provides only a parameter name and type with no description, and the schema description coverage is 0%. The description compensates by clarifying that the 'id' is a stable pathway identifier and gives a concrete example (R-HSA-68886). This significantly aids the agent in understanding what value to supply, even though it could offer more detail about the id format or source.

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?

The description clearly states that the tool retrieves a full pathway record using a stable identifier, with a concrete example. It distinguishes itself from sibling tools like 'pathways_for_entity' by emphasizing the full record for a single pathway. However, it lacks an explicit verb (e.g., 'Get' or 'Return'), which prevents a perfect score.

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

Usage Guidelines2/5

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

No explicit guidance is given on when to use this tool versus the many sibling tools such as 'pathways_for_entity' or 'entity_profile'. The phrase 'by stable id' implies usage when the agent has a stable identifier, but there is no mention of alternatives, exclusions, or specific scenarios. This is essentially no guidance beyond the basic description.

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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