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u9401066

pubmed-search-mcp

by u9401066
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Remote

search_gene

Read-onlyIdempotent

Search NCBI Gene database to look up gene function, aliases, chromosome location, and official symbols. Filter by organism and limit results.

Instructions

Search NCBI Gene database for gene information.

═══════════════════════════════════════════════════════════════ USE CASES: ═══════════════════════════════════════════════════════════════

  • Look up gene function and description

  • Find gene aliases and official symbols

  • Get chromosome location

  • Find genes by name or function

Args: query: Gene name, symbol, or function keyword organism: Filter by organism (e.g., "human", "Homo sapiens", "mouse") limit: Maximum results (1-50)

Returns: JSON with gene records including symbols, names, locations

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
limitNo
queryYes
organismNo

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed9 schema fields changedv0.7.2
    • addedInput schema / additionalProperties
      Added value: +false
    • removedInput schema / properties / limit / anyOf
      Removed value: -[
-  {
-    "type": "integer"
-  },
-  {
-    "type": "string"
-  }
-]
    • addedInput schema / properties / limit / maximum
      Added value: +50
    • addedInput schema / properties / limit / minimum
      Added value: +1
    • addedInput schema / properties / limit / type
      Added value: +"integer"
    • changedInput schema / properties / organism / anyOf
      Previous value: -[
-  {
-    "type": "string"
-  },
-  {
-    "type": "null"
-  }
-]New value: +[
+  {
+    "maxLength": 200,
+    "minLength": 1,
+    "type": "string"
+  },
+  {
+    "type": "null"
+  }
+]
    • addedInput schema / properties / query / maxLength
      Added value: +500
    • addedInput schema / properties / query / minLength
      Added value: +1
    • changedOutput schema / (root)
      Previous value: -{
-  "properties": {
-    "result": {
-      "title": "Result",
-      "type": "string"
-    }
-  },
-  "required": [
-    "result"
-  ],
-  "title": "search_geneOutput",
-  "type": "object"
-}New value: +null
  2. First observedv0.5.16

TDQS

A3.8/5.0
Behavior3/5

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

Annotations already declare readOnlyHint, idempotentHint, openWorldHint and non-destructive, so the safety profile is covered. Beyond that the description only adds the return shape; it says nothing about rate limits, result ordering, or relevance ranking for what is an open-world search.

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?

Front-loaded with a one-line purpose, then scannable sections. The decorative separator lines and USE CASES header add formatting overhead but the content is tight and each bullet earns its place.

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?

No output schema exists, so the description appropriately summarizes the return (JSON with symbols, names, locations). All three parameters are covered and the use cases frame intent — a complete-enough definition for a simple three-param search.

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 description coverage is 0%, so the description must compensate, and it does: it labels all three parameters and adds concrete value — organism examples ('human', 'Homo sapiens', 'mouse') and the limit range (1-50). Minor gap: it doesn't explain query matching mode (symbol vs. free-text function).

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?

States a specific verb and resource: search the NCBI Gene database for gene information. Sibling tools like get_gene_details and get_gene_literature exist, but the description never differentiates this lookup from them, so the agent must infer the split (search vs. fetch-details).

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 USE CASES block gives clear situational context (look up function, aliases, chromosome location, find by name/function), which tells an agent when this tool applies. It stops short of naming an alternative or exclusion, so it's solid context without routing 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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