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Mygene Info

by io.github.pipeworx-io
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Query Many

query_many
Read-onlyIdempotent

Batch-resolve a list of gene symbols, Entrez IDs, or Ensembl IDs (up to 1000) via a single POST to mygene.info, searching across specified scopes (default: symbol) and returning annotations for each matched gene.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
idsYes
fieldsNo
scopesNoComma-sep fields to search in (default symbol).
speciesNo

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
countYesNumber of items returned.
itemsYesArray of batch lookup results

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed2 schema fields changed
    • addedInput schema / examples
      Added value: +[
+  {
+    "ids": [
+      "BRCA1",
+      "TP53",
+      "EGFR"
+    ]
+  },
+  {
+    "ids": [
+      "1017",
+      "7157"
+    ],
+    "scopes": "entrezgene",
+    "species": "9606"
+  }
+]
    • changedOutput schema / (root)
      Previous value: -nullNew value: +{
+  "properties": {
+    "count": {
+      "description": "Number of items returned.",
+      "type": "integer"
+    },
+    "items": {
+      "description": "Array of batch lookup results",
+      "items": {
+        "properties": {
+          "_id": {
+            "description": "Gene ID",
+            "type": "string"
+          },
+          "_score": {
+            "description": "Match score",
+            "type": "number"
+          },
+          "found": {
+            "description": "Whether a match was found",
+            "type": "boolean"
+          },
+          "name": {
+            "description": "Gene name",
+            "type": "string"
+          },
+          "query": {
+            "description": "Input query string",
+            "type": "string"
+          },
+          "symbol": {
+            "description": "Gene symbol",
+            "type": "string"
+          }
+        },
+        "type": "object"
+      },
+      "type": "array"
+    }
+  },
+  "required": [
+    "items",
+    "count"
+  ],
+  "type": "object"
+}
  2. First observed

TDQS

A3.8/5.0
Behavior4/5

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 safety. The description adds useful behavioral context beyond annotations, including the HTTP method (POST), the batch limit (1000), default scope, and that it returns annotations, without contradicting any annotation.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is a single dense sentence that efficiently conveys the core purpose, method, limits, default, and return value. It contains no fluff, though it could be split into two sentences for readability without losing information.

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

Completeness3/5

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

The description covers the core functionality and batch aspect, but it misses parameter semantics for fields and species, and offers minimal guidance on when to use the tool versus siblings. The presence of an output schema reduces the need to describe return values, but the gaps in parameter explanation and usage guidance make it only partially 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 description coverage is only 25% (only scopes has a description). The description clarifies that ids accepts gene symbols, Entrez IDs, or Ensembl IDs, and that scopes defaults to 'symbol', but it does not explain 'fields' or 'species', which are important for customizing queries. The schema examples partially fill this gap.

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 (Batch-resolve), the resource (list of gene symbols, Entrez IDs, or Ensembl IDs), the method (single POST to mygene.info), and the output (annotations). This distinguishes it from sibling tools like 'query' or 'gene' which likely handle single queries.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description implies usage for batch lookups with a limit of 1000, but it does not explicitly state when to choose this over alternatives such as 'query' or 'gene', nor does it mention exclusions or prerequisites. Usage context is implied rather than clearly defined.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

All Mygene Info toolsInspect
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