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pubchem-mcp-server

by cyanheads
OverviewSchemaSourceRelated ServersScoreDiscussionsAdmin
TypeScript
Remote

Get Entity Summary

pubchem_get_summary
Read-onlyIdempotent

Fetch concise descriptive summaries for PubChem entities—assays, genes, proteins, taxonomy—using their IDs. Handles up to 10 identifiers per call.

Instructions

Get descriptive summaries for PubChem entities by ID. Supports assays (AID), genes (Gene ID), proteins (UniProt accession), and taxonomy (Tax ID). Up to 10 per call.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
entityTypeYesEntity type. Determines ID format and returned fields.
identifiersYesEntity identifiers (1-10). Type depends on entityType: - assay: AID (number), e.g. [1000] - gene: Gene ID (number), e.g. [1956] - protein: UniProt accession (string), e.g. ["P00533"] - taxonomy: Tax ID (number), e.g. [9606]

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
errorNoPresent when the call failed. Absent on success.
noticeNoRecovery guidance when one or more identifiers were not found.
summariesNoSummary results.
entityTypeNoEntity type queried.
foundCountNoIdentifiers resolved to a summary.
requestedCountNoIdentifiers requested.

Schema Changelog

Changes observed during successful MCP inspections. Dates show when Glama detected each change.

  1. Changed6 schema fields changedv0.6.1
    • changedInput schema / $schema
      Previous value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"
    • addedInput schema / additionalProperties
      Added value: +false
    • changedOutput schema / $schema
      Previous value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"
    • addedOutput schema / anyOf
      Added value: +[
+  {
+    "not": {
+      "required": [
+        "error"
+      ]
+    },
+    "required": [
+      "entityType",
+      "summaries",
+      "requestedCount",
+      "foundCount"
+    ]
+  },
+  {
+    "required": [
+      "error"
+    ]
+  }
+]
    • addedOutput schema / properties / error
      Added value: +{
+  "additionalProperties": {},
+  "description": "Present when the call failed. Absent on success.",
+  "properties": {
+    "code": {
+      "description": "JSON-RPC error code for this failure.",
+      "maximum": 9007199254740991,
+      "minimum": -9007199254740991,
+      "type": "integer"
+    },
+    "data": {
+      "additionalProperties": {},
+      "properties": {
+        "reason": {
+          "description": "Machine-readable failure mode.",
+          "type": "string"
+        },
+        "recovery": {
+          "additionalProperties": {},
+          "description": "Actionable next step for the caller.",
+          "properties": {
+            "hint": {
+              "type": "string"
+            }
+          },
+          "required": [
+            "hint"
+          ],
+          "type": "object"
+        },
+        "retryable": {
+          "description": "Whether retrying may succeed.",
+          "type": "boolean"
+        }
+      },
+      "type": "object"
+    },
+    "message": {
+      "description": "Human-readable description of what went wrong.",
+      "type": "string"
+    }
+  },
+  "required": [
+    "code",
+    "message"
+  ],
+  "type": "object"
+}
    • removedOutput schema / required
      Removed value: -[
-  "entityType",
-  "summaries",
-  "requestedCount",
-  "foundCount"
-]
  2. Changed1 schema field changedv0.6.0
    • changedOutput schema / properties / summaries / items / properties / data / properties / lineage / description
      Previous value: -"Parent taxonomy lineage (taxonomy summaries)."New value: +"Taxonomic lineage ordered from the most inclusive rank to the most specific, e.g. [\"Eukaryota\", \"Metazoa\", \"Chordata\"] (taxonomy summaries). Ranks that do not apply to the entity are omitted."
  3. Changed4 schema fields changedv0.2.2
    • addedOutput schema / properties / foundCount
      Added value: +{
+  "description": "Identifiers resolved to a summary.",
+  "type": "number"
+}
    • addedOutput schema / properties / notice
      Added value: +{
+  "description": "Recovery guidance when one or more identifiers were not found.",
+  "type": "string"
+}
    • addedOutput schema / properties / requestedCount
      Added value: +{
+  "description": "Identifiers requested.",
+  "type": "number"
+}
    • changedOutput schema / required
      Previous value: -[
-  "entityType",
-  "summaries"
-]New value: +[
+  "entityType",
+  "summaries",
+  "requestedCount",
+  "foundCount"
+]
  4. Changed8 schema fields changedv0.1.22
    • changedInput schema / properties / identifiers / items / anyOf
      Previous value: -[
-  {
-    "type": "string"
-  },
-  {
-    "type": "number"
-  }
-]New value: +[
+  {
+    "description": "String identifier (e.g. UniProt accession).",
+    "type": "string"
+  },
+  {
+    "description": "Numeric identifier (e.g. AID, Gene ID, Tax ID).",
+    "type": "number"
+  }
+]
    • addedInput schema / properties / identifiers / items / description
      Added value: +"Entity identifier — string or number depending on entityType."
    • addedOutput schema / properties / summaries / items / description
      Added value: +"Per-identifier summary result."
    • changedOutput schema / properties / summaries / items / properties / data / additionalProperties
      Previous value: -{}New value: +false
    • changedOutput schema / properties / summaries / items / properties / data / description
      Previous value: -"Entity summary data (shape varies by type)."New value: +"Entity summary data. Populated fields depend on entityType."
    • addedOutput schema / properties / summaries / items / properties / data / properties
      Added value: +{
+  "aid": {
+    "description": "Assay ID — present on assay summaries.",
+    "type": "number"
+  },
+  "commonName": {
+    "description": "Common name (taxonomy summaries).",
+    "type": "string"
+  },
+  "description": {
+    "description": "Descriptive text when available.",
+    "type": "string"
+  },
+  "geneId": {
+    "description": "NCBI Gene ID (gene summaries).",
+    "type": "number"
+  },
+  "lineage": {
+    "description": "Parent taxonomy lineage (taxonomy summaries).",
+    "items": {
+      "type": "string"
+    },
+    "type": "array"
+  },
+  "name": {
+    "description": "Primary display name.",
+    "type": "string"
+  },
+  "numActive": {
+    "description": "Substances marked active (assay summaries).",
+    "type": "number"
+  },
+  "numSubstances": {
+    "description": "Substances tested (assay summaries).",
+    "type": "number"
+  },
+  "proteinAccession": {
+    "description": "Protein accession (protein summaries).",
+    "type": "string"
+  },
+  "rank": {
+    "description": "Taxonomic rank (taxonomy summaries).",
+    "type": "string"
+  },
+  "scientificName": {
+    "description": "Scientific name (taxonomy summaries).",
+    "type": "string"
+  },
+  "sourceName": {
+    "description": "Data source attribution (assay summaries).",
+    "type": "string"
+  },
+  "symbol": {
+    "description": "Gene symbol (gene summaries).",
+    "type": "string"
+  },
+  "synonyms": {
+    "description": "Known synonyms / other names.",
+    "items": {
+      "type": "string"
+    },
+    "type": "array"
+  },
+  "taxonomy": {
+    "description": "Taxonomy scientific name (gene/protein summaries).",
+    "type": "string"
+  },
+  "taxonomyId": {
+    "description": "NCBI Taxonomy ID (gene/protein/taxonomy summaries).",
+    "type": "number"
+  }
+}
    • removedOutput schema / properties / summaries / items / properties / data / propertyNames
      Removed value: -{
-  "type": "string"
-}
    • changedOutput schema / properties / summaries / items / properties / identifier / anyOf
      Previous value: -[
-  {
-    "type": "string"
-  },
-  {
-    "type": "number"
-  }
-]New value: +[
+  {
+    "description": "String identifier (e.g. UniProt accession).",
+    "type": "string"
+  },
+  {
+    "description": "Numeric identifier (e.g. AID, Gene ID, Tax ID).",
+    "type": "number"
+  }
+]
  5. First observedv0.1.11

TDQS

A3.6/5.0
Behavior3/5

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

Annotations already declare readOnlyHint, openWorldHint, and idempotentHint, covering the main safety and repeatability traits. The description adds 'Up to 10 per call,' but this repeats the schema maxItems and does not disclose new behavioral context beyond the structured data.

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?

Two sentences with no filler. The main purpose is front-loaded, and the supported entity types are listed compactly without redundancy.

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?

The description covers the four entity categories and the batch limit, while the schema and output schema supply parameter and return details. It is sufficient for a read-only lookup tool, though it omits alternative-tool guidance entirely.

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 100%, including detailed identifier formats for each entity type. The description's entity-type list is a useful high-level summary but does not add meaning beyond what the input schema already provides.

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?

The description states a clear verb and resource: 'Get descriptive summaries for PubChem entities by ID.' It also enumerates four supported entity types, which distinguishes it from compound-specific siblings like pubchem_get_compound_details.

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 guidance on when to use this tool versus sibling tools. It does not name alternatives or provide exclusions such as 'for detailed compound data, use pubchem_get_compound_details instead.'

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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