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Reactome

by io.github.pipeworx-io

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Read-onlyIdempotent

Search the Reactome biological pathway database by keyword across all object types (Pathway, Reaction, Protein, Complex, etc.); returns stable IDs and display names grouped by type.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
queryYes
typesNoComma-sep: Pathway,Reaction,Protein,Complex,…
clusterNoGroup results by type (default true).

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
entriesNoTotal number of results
resultsNoList of matching objects

Schema Changelog

Changes observed during successful MCP inspections. Dates show when Glama detected each change.

  1. Changed2 schema fields changed
    • addedInput schema / examples
      Added value: +[
+  {
+    "query": "apoptosis"
+  },
+  {
+    "cluster": true,
+    "query": "TP53",
+    "types": "Protein,Pathway"
+  }
+]
    • changedOutput schema / (root)
      Previous value: -nullNew value: +{
+  "description": "Search results from Reactome, optionally clustered by type",
+  "properties": {
+    "entries": {
+      "description": "Total number of results",
+      "type": "number"
+    },
+    "results": {
+      "description": "List of matching objects",
+      "items": {
+        "properties": {
+          "className": {
+            "description": "Type of object (Pathway, Reaction, Protein, etc.)",
+            "type": "string"
+          },
+          "dbId": {
+            "description": "Internal database ID",
+            "type": "number"
+          },
+          "displayName": {
+            "description": "Display name of the object",
+            "type": "string"
+          },
+          "species": {
+            "properties": {
+              "dbId": {
+                "type": "number"
+              },
+              "displayName": {
+                "type": "string"
+              }
+            },
+            "type": "object"
+          },
+          "stableId": {
+            "description": "Stable identifier for the object",
+            "type": "string"
+          }
+        },
+        "type": "object"
+      },
+      "type": "array"
+    }
+  },
+  "type": "object"
+}
  2. First observed

TDQS

A4.5/5.0
Behavior4/5

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

Annotations already declare readOnlyHint, openWorldHint, idempotentHint, and destructiveHint=false, so the safety profile is well covered. The description adds behavioral detail about the return format: 'returns stable IDs and display names grouped by type', and indicates the scope ('across all object types'). This goes beyond the annotations and gives the agent useful expectations about output structure.

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, tightly written sentence that front-loads the primary action and resource, then efficiently specifies scope and output. Every clause contributes, with no filler or redundancy.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

The tool is relatively simple (3 parameters, one required) and a structured output schema exists, so the description need not explain return values. The description covers the search scope, object types, and output grouping, which is sufficient for an agent to select and invoke the tool correctly. The available annotations further complete the picture.

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 covers the 'types' and 'cluster' parameters with descriptions, but 'query' is undocumented. The description compensates by identifying 'query' as a keyword, and the enum examples (Pathway, Reaction, Protein, Complex) clarify valid 'types' values. This adds meaning beyond the schema, though not exhaustive.

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 clearly states the tool's purpose: 'Search the Reactome biological pathway database by keyword across all object types'. It uses a specific verb ('Search') and resource ('Reactome biological pathway database'), lists example object types, and specifies the output ('returns stable IDs and display names grouped by type'). This unambiguously distinguishes it from a generic search tool.

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?

The description conveys clear usage context: it is a broad keyword search spanning all object types, making it appropriate as an initial discovery step. It does not explicitly mention alternatives or exclusions, but the phrase 'across all object types' implies a general-purpose search, and sibling tools like 'search_within' are implicitly different. This meets the 'clear context, no exclusions' level.

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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TDQS

B3.1/5.0
Disambiguation2/5

Many tools have overlapping research purposes (ask_pipeworx, deep_research, ask_pipeworx_grounded) and multiple bet-related tools (bet_research, polymarket_arbitrage, polymarket_edges). Reactome-specific tools are few but mixed in with unrelated tools, causing ambiguity.

Naming Consistency2/5

Tool names are inconsistent: some snake_case (ask_pipeworx, deep_research), some camelCase (generate_llms_txt, list_subscriptions), and some mixed (pipeworx_feedback, poly market_arbitrage). No uniform pattern.

Tool Count2/5

35 tools is excessive for a Reactome server, as only a handful are Reactome-specific. Many tools are unrelated (e.g., bet_research, compare_entities), making the tool count feel bloated and unfocused.

Completeness2/5

The Reactome-specific tools cover basic pathway lookups but miss key operations like reactions, complexes, or advanced queries. The server's completeness for the Reactome domain is poor, diluted by many non-Reactome tools.

Resources