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Glama

Monarch Initiative

by io.github.pipeworx-io

Associations

associations
Read-onlyIdempotent

Fetch biolink associations (edges) involving a Monarch entity by its CURIE ID (e.g. MONDO:0007947); filter by association category (e.g. biolink:DiseaseToPhenotypicFeatureAssociation), predicate, or direction (subject/object/both).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
limitNo
categoryNoe.g. "biolink:DiseaseToPhenotypicFeatureAssociation"
directionNosubject (default) | object | both
entity_idYes
predicateNoe.g. "biolink:has_phenotype"

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
limitNoResult limit applied
totalNoTotal matching associations
associationsNoList of associations

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:DiseaseToPhenotypicFeatureAssociation",
+    "entity_id": "MONDO:0007947"
+  },
+  {
+    "direction": "subject",
+    "entity_id": "NCBIGene:207",
+    "limit": 50,
+    "predicate": "biolink:associated_with_increased_likelihood_of"
+  }
+]
    • changedOutput schema / (root)
      Previous value: -nullNew value: +{
+  "description": "Associations involving an entity",
+  "properties": {
+    "associations": {
+      "description": "List of associations",
+      "items": {
+        "properties": {
+          "category": {
+            "description": "Association category",
+            "type": "string"
+          },
+          "id": {
+            "description": "Association identifier",
+            "type": "string"
+          },
+          "object": {
+            "description": "Object node curie",
+            "type": "string"
+          },
+          "predicate": {
+            "description": "Association predicate",
+            "type": "string"
+          },
+          "subject": {
+            "description": "Subject node curie",
+            "type": "string"
+          }
+        },
+        "type": "object"
+      },
+      "type": "array"
+    },
+    "limit": {
+      "description": "Result limit applied",
+      "type": "number"
+    },
+    "total": {
+      "description": "Total matching associations",
+      "type": "number"
+    }
+  },
+  "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, covering the safety profile. The description adds that it fetches edges and supports filtering by category/predicate/direction, but does not disclose additional behavioral details like pagination, limits, or error cases beyond what annotations provide.

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?

A single, front-loaded sentence that efficiently presents the core action and filtering capabilities with an example. No wasted words.

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 output schema exists, return values need not be described. The description covers the main purpose, required parameter, and filters. However, the 'limit' parameter behavior is not mentioned, and the default direction is only in the schema, not the description. Minor gaps but still fairly complete.

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 coverage is 60% with descriptions for category, direction, and predicate, but not for entity_id or limit. The description clarifies that entity_id is a CURIE ID, adding meaning, but limit remains unexplained. Overall, the description partially compensates for schema gaps but not fully.

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 action ('Fetch'), the resource ('biolink associations (edges)'), and the input ('Monarch entity by its CURIE ID'). It also lists filtering options, distinguishing it from sibling tools like 'entity' or 'gene_to_disease'.

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?

Provides clear context: use when you need associations involving a Monarch entity, with optional filters. However, no explicit when-not-to-use or comparison to alternatives is given, so it does not fully meet the 'explicit alternatives' bar.

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