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pubmed-search-mcp

by u9401066
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Remote

get_compound_literature

Read-onlyIdempotent

Retrieve PubMed articles linked to a compound via its PubChem Compound ID. Returns JSON with linked PubMed IDs for literature research.

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. 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
  2. First observedv0.5.16

TDQS

B3.4/5.0
Behavior3/5

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

Annotations already declare readOnly, idempotent, openWorld and non-destructive, so safety behavior needs no repetition. The description adds genuine value by disclosing provenance ('NCBI's curated compound-to-publication links') and a return summary, though with no output schema this remains thin on pagination or failure behavior.

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?

Short and front-loaded, with the core purpose in the first sentence and Args/Returns scaffolding after. The Args/Returns headers are slightly mechanical but cost little and aid scannability.

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 two-parameter read tool with no output schema, the description covers purpose, both parameters, the data source, and the return shape (JSON with linked PubMed IDs). Nothing essential for a correct invocation is missing.

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 carry parameter meaning, and it does: 'cid: PubChem Compound ID' and 'limit: Maximum PubMed IDs to return (1-100)'. This maps directly to both parameters and clarifies the cid format beyond the bare 'string' pattern, though it adds nothing about what happens when no links exist.

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 compound') and names the underlying data source, which cleanly separates it from sibling literature tools like get_gene_literature by resource type. It stops short of explicitly naming or contrasting alternatives, so it is clear but not sibling-differentiating at the highest level.

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?

The description gives no when-to-use, when-not-to-use, or alternative-tool guidance; an agent must infer from the resource name that this is the right call for compound-linked literature. The mention of NCBI's curated links hints at the data source but not at usage conditions.

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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