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pubmed-search-mcp

by u9401066
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Remote

get_compound_literature

Read-onlyIdempotent

Fetch PubMed articles linked to a compound via NCBI's curated compound-to-publication links. Provide a PubChem CID to receive linked PubMed IDs.

Instructions

Get PubMed articles linked to a compound.

Uses NCBI's curated compound-to-publication links.

Args: cid: PubChem Compound ID limit: Maximum PubMed IDs to return (1-100)

Returns: JSON with linked PubMed IDs

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
cidYes
limitNo

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]*$",
+    "type": "string"
+  }
+]
    • removedInput schema / properties / limit / maximum
      Removed value: -100
    • removedInput schema / properties / limit / minimum
      Removed value: -1
    • removedInput schema / properties / limit / type
      Removed value: -"integer"
  2. Changed11 schema fields changedv0.7.2
    • addedInput schema / additionalProperties
      Added value: +false
    • removedInput schema / properties / cid / anyOf
      Removed value: -[
-  {
-    "type": "string"
-  },
-  {
-    "type": "integer"
-  }
-]
    • addedInput schema / properties / cid / maxLength
      Added value: +20
    • addedInput schema / properties / cid / minLength
      Added value: +1
    • addedInput schema / properties / cid / pattern
      Added value: +"^[1-9][0-9]{0,19}$"
    • addedInput schema / properties / cid / 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_compound_literatureOutput",
-  "type": "object"
-}New value: +null
  3. First observedv0.5.16

TDQS

A3.7/5.0
Behavior3/5

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

Annotations already declare readOnlyHint, idempotentHint, openWorldHint and destructiveHint=false, so the safety and idempotence profile is covered. The description adds useful provenance (data comes from NCBI curated links, not free-text mining) but says nothing about pagination, behavior on zero results, or rate limits, so it is a modest addition rather than rich behavioral context.

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-loads the purpose in one sentence, then adds a provenance line and Args/Returns sections that each carry information not present in the 0%-coverage schema. Structure is clear, though the Args/Returns block is formulaic rather than tightly integrated.

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, explaining the return value ('JSON with linked PubMed IDs') is genuinely necessary and present, as is the data source and both parameter meanings. For a simple two-parameter lookup this is close to complete; only edge-case behavior (no links found, ordering) is absent.

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 it does: it identifies 'cid' as a PubChem Compound ID (the schema only gives a string pattern) and gives the 'limit' range of 1-100. It omits the default of 20 and any format/ordering semantics for the returned IDs, keeping it short of a 5.

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 and resource ('Get PubMed articles linked to a compound') plus the mechanism ('NCBI's curated compound-to-publication links'). An agent can distinguish this from the analogous get_gene_literature and from general search tools like unified_search without opening a schema.

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

Usage Guidelines2/5

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

There is no explicit when-to-use, when-not-to-use, or alternative tool guidance. It never clarifies the relationship to siblings like find_related_articles, get_compound_details, or search_compound, leaving the agent to infer the boundary from purpose alone.

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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