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pubmed-search-mcp

by u9401066
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Remote

search_compound

Read-onlyIdempotent

Search PubChem for chemical compounds to find molecular formulas, structures, synonyms, and identifiers. Use for drug lookup and property 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. Changed4 schema fields changedv0.7.7
    • addedInput schema / properties / limit / anyOf
      Added value: +[
+  {
+    "default": 10,
+    "maximum": 50,
+    "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: -50
    • removedInput schema / properties / limit / minimum
      Removed value: -1
    • removedInput schema / properties / limit / type
      Removed value: -"integer"
  2. 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
  3. 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, openWorldHint, and destructiveHint=false, so the safety profile is covered by structured data. The description adds only the return shape (JSON records with names, formulas, properties) and the 1-50 limit; nothing about upstream rate limits, match behavior (fuzzy vs. exact), or empty-result handling.

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 purpose and use cases are front-loaded correctly, but the heavy box-drawing separator banners add visual noise without information, and the Args/Returns restatement pads the entry beyond what a two-parameter tool needs.

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?

With no output schema, the description does supply a brief Returns line, and both parameters are named, so nothing critical is missing. It stops short of describing result ordering, result count behavior when limit is hit, or how queries are matched, which matters for an external open-world search.

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 burden. It documents both parameters — query as 'compound name or description' and limit as 'maximum results (1-50)' — but the query hint is thin (no format/synonym guidance) and the limit note merely restates the schema bounds, leaving the default of 10 unmentioned.

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?

The first line states a specific verb and resource: search PubChem for chemical compounds, which is unambiguous on its own. It does not, however, distinguish itself from nearby siblings such as get_compound_details or get_compound_literature, so an agent must infer the boundary.

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 block enumerates good reasons to call it (drug lookups, molecular formula, synonyms, properties), which implies usage. But there is no when-not guidance and no explicit routing to get_compound_details (fetch details for a known compound) or get_compound_literature, which are the obvious alternatives.

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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