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mgi-link

mgi-link

by berntpopp
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
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Get Marker Disease Models

get_marker_diseases
Read-onlyIdempotent

Get human-mouse disease model associations for a gene from MGI curated DO annotations. Accepts mouse or human gene identifiers, returning Disease Ontology and OMIM IDs.

Instructions

Return the human-mouse disease models associated with a marker (Disease Ontology id + name + OMIM ids), from MGI's curated DO annotations. Accepts a mouse symbol/MGI id or a human ortholog. Signature: get_marker_diseases(query).

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "query": "<query>"
    },
    "name": "get_marker_diseases"
  }
}

Input Schema

NameRequiredDescriptionDefault
queryYesA mouse marker symbol (current or synonym, case-insensitive), an MGI id (MGI:98968 or 98968), or a human gene symbol / HGNC id for the ortholog.

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed1 schema field changedv0.6.0
    • changedOutput schema / (root)
      Previous value: -{
-  "additionalProperties": true,
-  "properties": {
-    "_meta": {
-      "additionalProperties": true,
-      "type": "object"
-    },
-    "allowed_values": {
-      "type": "array"
-    },
-    "candidates": {
-      "type": "array"
-    },
-    "count": {
-      "type": "integer"
-    },
-    "diseases": {
-      "type": "array"
-    },
-    "error_code": {
-      "type": "string"
-    },
-    "field": {
-      "type": "string"
-    },
-    "hint": {
-      "type": "string"
-    },
-    "message": {
-      "type": "string"
-    },
-    "mgi_id": {
-      "type": "string"
-    },
-    "recovery_action": {
-      "type": "string"
-    },
-    "retryable": {
-      "type": "boolean"
-    },
-    "success": {
-      "type": "boolean"
-    },
-    "symbol": {
-      "type": "string"
-    }
-  },
-  "type": "object"
-}New value: +null
  2. First observedv0.1.0

TDQS

A3.5/5.0
Behavior3/5

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

Annotations already declare readOnlyHint=true, openWorldHint=true, idempotentHint=true, destructiveHint=false. The description adds context about output content (disease models, DO id, name, OMIM ids) and data source, but does not disclose additional behavioral traits beyond what annotations provide, meeting expectations without exceeding.

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?

Two sentences plus a concise signature. Front-loaded with purpose, no filler words. Every sentence adds value.

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 simplicity (1 parameter, no output schema), the description adequately explains input and output. It could optionally mention pagination or rate limits, but the openWorldHint reduces need. Generally complete for an agent's invocation.

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?

Schema covers 100% of parameters. Description adds valuable details beyond schema: clarifies case-insensitivity, synonym support, and alternative human identifier formats (HGNC id). This enhances parameter understanding beyond basic schema.

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 it returns disease models (Disease Ontology id + name + OMIM ids) from MGI annotations, with specific verb 'Return' and resource. However, it does not differentiate from sibling tools like get_marker_phenotypes, so it's not a 5.

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?

The description lists accepted input types (mouse symbol/MGI id or human ortholog) but provides no guidance on when to use this tool versus alternatives like get_marker_phenotypes or search_markers. No explicit when/not-to-use or alternative names.

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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