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Monarch Initiative

by io.github.pipeworx-io

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Read-onlyIdempotent

Full-text search across the Monarch biomedical knowledge graph for diseases, genes, phenotypes, and other biolink entities by query string; filter by category (e.g. biolink:Disease) and paginate with limit/offset.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
limitNo1-500 (default 20)
queryYes
offsetNo
categoryNobiolink:Disease | biolink:Gene | biolink:PhenotypicFeature | …

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
limitNoResult limit applied
totalNoTotal matching results
offsetNoResult offset applied
resultsNoSearch result nodes

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: +[
+  {
+    "category": "biolink:Disease",
+    "limit": 20,
+    "query": "cystic fibrosis"
+  },
+  {
+    "category": "biolink:Gene",
+    "query": "BRCA1"
+  }
+]
    • changedOutput schema / (root)
      Previous value: -nullNew value: +{
+  "description": "Full-text search results from Monarch Initiative",
+  "properties": {
+    "limit": {
+      "description": "Result limit applied",
+      "type": "number"
+    },
+    "offset": {
+      "description": "Result offset applied",
+      "type": "number"
+    },
+    "results": {
+      "description": "Search result nodes",
+      "items": {
+        "properties": {
+          "category": {
+            "description": "Biolink category",
+            "type": "string"
+          },
+          "description": {
+            "description": "Node description",
+            "type": "string"
+          },
+          "id": {
+            "description": "Node curie identifier",
+            "type": "string"
+          },
+          "name": {
+            "description": "Node name",
+            "type": "string"
+          }
+        },
+        "type": "object"
+      },
+      "type": "array"
+    },
+    "total": {
+      "description": "Total matching results",
+      "type": "number"
+    }
+  },
+  "type": "object"
+}
  2. First observed

TDQS

A4.2/5.0
Behavior3/5

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

Annotations already declare readOnlyHint, openWorldHint, and idempotentHint, covering safety and idempotency. The description adds behavioral context about full-text search, category filtering, and pagination, but does not disclose additional traits like rate limits, auth requirements, or result format (which is handled by the output schema). This is consistent with the expected bar when annotations are present, providing some extra value but not deeply expanding beyond them.

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 that immediately states the action and resource. Every phrase adds useful information (entity types, filtering, pagination) without redundantly repeating schema details. It is concise and well-structured.

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?

Given the tool's moderate complexity (4 params, 1 required), existing annotations, and an output schema, the description covers all essential aspects: scope, filtering, and pagination. It does not explain explicit differences from sibling tools, which is a minor gap, but the description is otherwise complete enough for an agent to invoke the tool correctly.

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 schema has descriptions for only 'limit' and 'category' (50% coverage), leaving 'query' and 'offset' undocumented. The description compensates by explaining 'query string', 'filter by category', and 'paginate with limit/offset', thereby covering all four parameters conceptually. It adds value beyond the schema by explicitly tying the parameters to the search behavior.

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 specifies a clear verb ('search') and resource ('Monarch biomedical knowledge graph'), and details the scope ('diseases, genes, phenotypes, and other biolink entities'). It also mentions filtering and pagination, which distinguishes it from generic search tools. This is a specific, non-tautological statement of purpose.

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 clearly indicates when to use the tool: for full-text search across the knowledge graph by query string. It mentions filtering by category and pagination, giving a clear context of use. However, it does not explicitly compare against siblings like 'search_within' or 'deep_research' to exclude them, so it stops short of full when-not-to-use 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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TDQS

A3.7/5.0
Disambiguation4/5

Most tools have clear, distinct purposes, especially within the same domain (e.g., Polymarket betting tools each serve a specific function). However, the multiple data-querying tools (ask_pipeworx, ask_pipeworx_grounded, deep_research) could cause confusion despite detailed descriptions.

Naming Consistency3/5

Many tools follow a verb_noun snake_case pattern (e.g., bet_research, compare_entities), but there are exceptions like ai_visibility_check, forget, and suggest_questions. The mix of imperative verbs and descriptive phrases creates inconsistency.

Tool Count2/5

With 35 tools, the server feels overloaded. While each domain (biomedical, financial, betting) is covered extensively, the sheer number of tools likely overwhelms agents, and many tools could be merged or split into separate servers.

Completeness4/5

The tool set is comprehensive for its declared purpose, covering biomedical queries, company data, betting analysis, memory management, and more. Minor gaps exist (e.g., no tool to delete a bet, no write operations for biomedical data), but the breadth is impressive.

Resources