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Glama

Reactome

by io.github.pipeworx-io

Pathways For Entity

pathways_for_entity
Read-onlyIdempotent

Pathways containing an entity, looked up by external resource id (e.g. UniProt accession).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
speciesNoNCBI taxonomy id as a string (default "9606" — human).
resourceNoUniProt | ChEBI | Ensembl | NCBI | GeneCards | … (default UniProt)
entity_idYesIdentifier within the resource, e.g. "P04637" for TP53.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
countYesNumber of items returned.
itemsYesPathways containing the specified entity

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: +[
+  {
+    "entity_id": "P04637"
+  },
+  {
+    "entity_id": "CHEBI:15377",
+    "resource": "ChEBI",
+    "species": "9606"
+  }
+]
    • changedOutput schema / (root)
      Previous value: -nullNew value: +{
+  "properties": {
+    "count": {
+      "description": "Number of items returned.",
+      "type": "integer"
+    },
+    "items": {
+      "description": "Pathways containing the specified entity",
+      "items": {
+        "properties": {
+          "className": {
+            "description": "Type (usually Pathway)",
+            "type": "string"
+          },
+          "dbId": {
+            "description": "Internal database ID",
+            "type": "number"
+          },
+          "displayName": {
+            "description": "Pathway name",
+            "type": "string"
+          },
+          "schemaClass": {
+            "description": "Schema class",
+            "type": "string"
+          },
+          "species": {
+            "properties": {
+              "dbId": {
+                "type": "number"
+              },
+              "displayName": {
+                "type": "string"
+              }
+            },
+            "type": "object"
+          },
+          "stableId": {
+            "description": "Stable identifier",
+            "type": "string"
+          }
+        },
+        "type": "object"
+      },
+      "type": "array"
+    }
+  },
+  "required": [
+    "items",
+    "count"
+  ],
+  "type": "object"
+}
  2. First observed

TDQS

A4/5.0
Behavior3/5

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

Annotations already declare readOnlyHint=true, openWorldHint=true, idempotentHint=true, and destructiveHint=false. The description adds no extra behavioral context beyond what the schema provides (e.g., citing external resource id). With annotations covering the safety profile, the description meets the baseline but does not enrich transparency with details like return variability or pagination.

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, front-loaded sentence: 'Pathways containing an entity, looked up by external resource id (e.g. UniProt accession).' Every word earns its place, no redundancy or filler.

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 is a simple read-only lookup. It has a rich input schema, annotations for safety, and an output schema. The description, while brief, tells the agent what it does and the input style. It is sufficiently complete for this complexity level, though it could mention that multiple pathways may be returned, but the openWorldHint and output schema mitigate this.

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?

Input schema has 100% coverage: all three parameters (species, resource, entity_id) are described with defaults and examples. The description only reinforces the entity_id example (UniProt accession), adding no extra semantic meaning beyond the schema, so baseline 3 is appropriate.

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 the tool finds pathways containing an entity via external resource id, with a concrete example (UniProt accession). This clearly differentiates it from siblings like 'pathway' (which likely fetches a specific pathway) and 'participants' (which lists entities in a pathway). The verb 'containing' and resource scope are specific.

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 implies usage context: use this when you have an external resource identifier and need to find associated pathways. It does not explicitly state when not to use or mention alternatives, but the context is clear enough for a simple lookup tool.

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