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pubmed-search-mcp

by u9401066
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Remote

get_gene_literature

Read-onlyIdempotent

Retrieve PubMed article IDs linked to an NCBI Gene ID via curated gene-to-publication links, avoiding imprecise keyword searches.

Instructions

Get PubMed articles linked to a gene.

This uses NCBI's curated gene-to-publication links, which are more precise than keyword searches.

Args: gene_id: NCBI Gene ID limit: Maximum PubMed IDs to return (1-100)

Returns: JSON with linked PubMed IDs

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
limitNo
gene_idYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed11 schema fields changedv0.7.2
    • addedInput schema / additionalProperties
      Added value: +false
    • removedInput schema / properties / gene_id / anyOf
      Removed value: -[
-  {
-    "type": "string"
-  },
-  {
-    "type": "integer"
-  }
-]
    • addedInput schema / properties / gene_id / maxLength
      Added value: +20
    • addedInput schema / properties / gene_id / minLength
      Added value: +1
    • addedInput schema / properties / gene_id / pattern
      Added value: +"^[1-9][0-9]{0,19}$"
    • addedInput schema / properties / gene_id / type
      Added value: +"string"
    • removedInput schema / properties / limit / anyOf
      Removed value: -[
-  {
-    "type": "integer"
-  },
-  {
-    "type": "string"
-  }
-]
    • addedInput schema / properties / limit / maximum
      Added value: +100
    • addedInput schema / properties / limit / minimum
      Added value: +1
    • addedInput schema / properties / limit / type
      Added value: +"integer"
    • changedOutput schema / (root)
      Previous value: -{
-  "properties": {
-    "result": {
-      "title": "Result",
-      "type": "string"
-    }
-  },
-  "required": [
-    "result"
-  ],
-  "title": "get_gene_literatureOutput",
-  "type": "object"
-}New value: +null
  2. First observedv0.5.16

TDQS

A4/5.0
Behavior3/5

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

Annotations already declare readOnlyHint, openWorldHint, idempotentHint, and destructiveHint=false, so the safety profile is covered. The description adds that it uses NCBI's curated links, which is useful behavioral context, but doesn't disclose rate limits, permissions, or return format details beyond a brief mention.

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?

The description is concise and front-loaded: a clear one-sentence purpose, then a rationale, then parameter and return sections. Every part earns its place without unnecessary detail.

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 read-only tool with two parameters and no output schema, the description covers purpose, parameters, and return type adequately. It could mention pagination or handling of large result sets, but given the limit parameter and annotations, it is largely complete.

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. It documents both parameters: gene_id as NCBI Gene ID and limit as maximum PubMed IDs to return (1-100), matching the schema's constraints. This fully compensates for the lack of schema descriptions, though it doesn't elaborate on format beyond 'NCBI Gene ID'.

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?

States a specific verb (Get) and resource (PubMed articles linked to a gene), and distinguishes itself from keyword-based search by explaining the source of the links. Sibling tools like search_gene and get_gene_details are clearly different, and get_gene_literature is explicitly about literature linked to a gene ID.

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 retrieving linked articles but does not explicitly state when to use this versus alternatives like unified_search or get_compound_literature. It notes the method is 'more precise than keyword searches', which subtly suggests preference, but lacks clear when-to-use/when-not-to-use 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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