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Protein Atlas

by io.github.pipeworx-io
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Search Genes

search_genes
Read-onlyIdempotent

Search the Human Protein Atlas for human genes/proteins by gene symbol or keyword. Returns each gene with its Ensembl gene id (needed by get_protein and top_tissues), synonyms, and description. Keyless.

Example tool call

This call uses example arguments supplied in the tool’s input schema.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "query": "EGFR"
    },
    "name": "search_genes"
  }
}

Input Schema

NameRequiredDescriptionDefault
limitNoMax genes to return (default 15).
queryYesGene symbol (e.g. "EGFR") or keyword (e.g. "insulin receptor").

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed1 schema field changed
    • addedInput schema / examples
      Added value: +[
+  {
+    "query": "EGFR"
+  },
+  {
+    "limit": 10,
+    "query": "insulin receptor"
+  }
+]
  2. First observed

TDQS

A3.8/5.0
Behavior3/5

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

Annotations already indicate this is read-only, idempotent, and non-destructive. The description adds that it is 'Keyless' (no authentication needed) and lists the returned fields, providing some additional context but not significantly beyond annotations.

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 concise sentences: first states the purpose and data source, second lists key output and notes it's keyless. No unnecessary 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?

For a simple search tool with good annotations and full schema coverage, the description adequately covers the purpose, input, output, and access requirement. It could mention pagination or default limit, but the schema already handles that.

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 100% with descriptions for both parameters (query, limit). The description mentions 'by gene symbol or keyword' which aligns with the query parameter description, but adds no extra meaning beyond the schema.

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 it searches the Human Protein Atlas for human genes/proteins by gene symbol or keyword, and specifies it returns Ensembl gene id, synonyms, and description. This distinguishes it from sibling tools like get_protein and top_tissues that require the Ensembl id as input.

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 this tool is a prerequisite for get_protein and top_tissues by stating the returned Ensembl id is needed by those tools. However, it does not explicitly provide guidance on when to use vs. alternatives or when not to use it.

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

All Protein Atlas toolsInspect
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