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pubmed-search-mcp

by u9401066
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Remote

get_gene_literature

Read-onlyIdempotent

Retrieve PubMed articles linked to a gene using NCBI curated gene-to-publication links, giving precise results over 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. Changed4 schema fields changedv0.7.7
    • addedInput schema / properties / limit / anyOf
      Added value: +[
+  {
+    "default": 20,
+    "maximum": 100,
+    "minimum": 1,
+    "title": "Limit",
+    "type": "integer"
+  },
+  {
+    "description": "ASCII decimal integer; the integer branch's bounds apply after conversion.",
+    "maxLength": 32,
+    "pattern": "^[ \\t\\r\\n]*-?(?:0|[1-9][0-9]*)[ \\t\\r\\n]*$",
+    "type": "string"
+  }
+]
    • removedInput schema / properties / limit / maximum
      Removed value: -100
    • removedInput schema / properties / limit / minimum
      Removed value: -1
    • removedInput schema / properties / limit / type
      Removed value: -"integer"
  2. Changed11 schema fields changedv0.7.2
    • addedInput schema / additionalProperties
      Added value: +false
    • removedInput schema / properties / gene_id / anyOf
      Removed value: -[
-  {
-    "type": "string"
-  },
-  {
-    "type": "integer"
-  }
-]
    • addedInput schema / properties / gene_id / maxLength
      Added value: +20
    • addedInput schema / properties / gene_id / minLength
      Added value: +1
    • addedInput schema / properties / gene_id / pattern
      Added value: +"^[1-9][0-9]{0,19}$"
    • 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
  3. First observedv0.5.16

TDQS

A3.9/5.0
Behavior3/5

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

Annotations already cover the safety profile (readOnly, idempotent, non-destructive, openWorld). The description adds the data provenance (NCBI curated links over keyword search), which is useful for interpreting result trust, but says nothing about auth, rate limits, or truncation behavior. With annotations doing the heavy lifting, a 3 is appropriate.

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?

Front-loaded one-line purpose, then concise provenance note, then Args/Returns blocks. Every line earns its place and nothing is padded.

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?

With no output schema, the description correctly states the return shape ('JSON with linked PubMed IDs'), and annotations cover safety. Both parameters are documented, so an agent has what it needs; only edge-case behaviors remain unspecified.

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 carries the burden and mostly does: it clarifies gene_id is an NCBI Gene ID (not a symbol) and gives limit's meaning and 1-100 bound. It still doesn't explain the format constraint on gene_id beyond the schema pattern, so not a 5.

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 ('Get PubMed articles linked to a gene') and explicitly contrasts itself with keyword-based retrieval, so an agent can separate it from unified_search. It does not name or distinguish itself from other article-linking siblings like find_related_articles, so it falls just short of 5.

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?

Gives clear context for when this tool is the right choice: when you want curated gene-to-publication links rather than keyword matches. No explicit when-not conditions or prerequisites are stated, which keeps it from a 5.

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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