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pubmed-search-mcp

by u9401066
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Remote

search_compound

Read-onlyIdempotent

Query PubChem to find chemical compounds by name or description. Retrieve molecular formulas, structures, synonyms, and identifiers for drug research.

Instructions

Search PubChem for chemical compounds.

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

  • Look up drug/compound information

  • Find molecular formula and structure

  • Get compound synonyms and identifiers

  • Research chemical properties

Args: query: Compound name or description limit: Maximum results (1-50)

Returns: JSON with compound records including names, formulas, properties

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
limitNo
queryYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed8 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"
    • 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_compoundOutput",
-  "type": "object"
-}New value: +null
  2. First observedv0.5.16

TDQS

B3.3/5.0
Behavior3/5

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

Annotations already declare readOnlyHint, idempotentHint, and non-destructive, so the safety profile is covered. The description adds that results come back as 'JSON with compound records including names, formulas, properties' — useful since there is no output schema — but says nothing about rate limits or how PubChem misses are handled despite openWorldHint.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness3/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The opening sentence is correctly front-loaded and the content is short, but the boxed '═══' dividers and USE CASES/Args/Returns scaffolding consume lines without adding information — decoration rather than earned structure.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness3/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For a two-parameter read-only search with no output schema, the description is adequate: it names the source, the use cases, the args, and the rough return shape. It stops short of explaining pagination, ranking, or the distinction from compound-detail siblings, leaving gaps for a tool with several close relatives.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

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 load: it labels query as 'Compound name or description' and limit as 'Maximum results (1-50)'. That compensates for both parameters, but shallowly — no format hints, examples, or handling of ambiguous names.

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+resource+source: 'Search PubChem for chemical compounds.' An agent immediately knows this queries PubChem. However, it does not distinguish itself from siblings get_compound_details and get_compound_literature, which are the obvious adjacent tools for compound lookups.

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 USE CASES list implies when to reach for this tool (compound info, formulas, synonyms, properties), which is more than nothing. But it gives no when-NOT guidance and never mentions the alternatives (get_compound_details for a known compound, get_compound_literature for papers), so an agent must infer the routing itself.

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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