pubchem-mcp-server

Search Assays

pubchem_search_assays

Read-onlyIdempotent

Find PubChem bioassays associated with a biological target. Search by gene symbol (e.g. "EGFR"), protein name, NCBI Gene ID, or UniProt accession. Returns a page of assay IDs (AIDs) — page past maxResults with offset — which can be explored further with pubchem_get_summary.

Input Schema

Name	Required	Description
`offset`	No	Zero-based index of the first AID to return. Pass the nextOffset from a previous call to read the following page. Default: 0.
`maxResults`	No	Max AIDs to return per page. The per-call cap is 200: a larger value (up to 1000) returns a page of 200 and is reported in cappedInputs. Popular targets may have thousands of assays; use offset to reach the ones past this page. Default: 50.
`targetType`	Yes	Target identifier type. "genesymbol" and "proteinname" accept text names. "geneid" accepts NCBI Gene IDs. "proteinaccession" accepts UniProt accessions.
`targetQuery`	Yes	Target identifier. Examples: "EGFR" (genesymbol), "Epidermal growth factor receptor" (proteinname), "1956" (geneid), "P00533" (proteinaccession; uppercased before lookup, except a PDB chain ID such as the "A" in "1ZHH_A", which is kept as given).

Output Schema

Name	Required	Description
`cap`	No	The page size applied: maxResults, or the per-call cap when maxResults exceeds it.
`aids`	No	PubChem Assay IDs.
`error`	No	Present when the call failed. Absent on success.
`shown`	No	AIDs returned on this page.
`notice`	No	Recovery guidance when no assays matched, when the offset runs past the result set, or when further pages remain. Absent when this page is complete and non-empty.
`offset`	No	Zero-based index of the first AID returned.
`truncated`	No	True when matching AIDs remain past this page.
`nextOffset`	No	Offset to pass on the next call to continue past this page. Omitted when no further AIDs match.
`targetType`	No	Target identifier type used: genesymbol, proteinname, geneid, or proteinaccession.
`totalFound`	No	Total AIDs found for this target, across all pages.
`targetQuery`	No	Target identifier searched.
`cappedInputs`	No	Inputs that asked for more than their per-call cap, with the value requested and the value served. An ID batch lists the IDs past the cap in unprocessed. Omitted when every input was within its cap.

Schema Changelog

Changes observed during successful MCP inspections.

Changed5 schema fields changedOct 15, 2026

changedInput schema / properties / maxResults / description

Previous value: -"Max AIDs to return per page (1-200). Popular targets may have thousands of assays; use offset to reach the ones past this page. Default: 50."New value: +"Max AIDs to return per page. The per-call cap is 200: a larger value (up to 1000) returns a page of 200 and is reported in cappedInputs. Popular targets may have thousands of assays; use offset to reach the ones past this page. Default: 50."

changedInput schema / properties / maxResults / maximum
```
Previous value: -200New value: +1000
```

changedInput schema / properties / targetQuery / description

Previous value: -"Target identifier. Examples: \"EGFR\" (genesymbol), \"Epidermal growth factor receptor\" (proteinname), \"1956\" (geneid), \"P00533\" (proteinaccession)."New value: +"Target identifier. Examples: \"EGFR\" (genesymbol), \"Epidermal growth factor receptor\" (proteinname), \"1956\" (geneid), \"P00533\" (proteinaccession; uppercased before lookup, except a PDB chain ID such as the \"A\" in \"1ZHH_A\", which is kept as given)."

changedOutput schema / properties / cap / description

Previous value: -"The maxResults cap that was applied."New value: +"The page size applied: maxResults, or the per-call cap when maxResults exceeds it."

addedOutput schema / properties / cappedInputs

Added value: +{
+  "description": "Inputs that asked for more than their per-call cap, with the value requested and the value served. An ID batch lists the IDs past the cap in unprocessed. Omitted when every input was within its cap.",
+  "items": {
+    "additionalProperties": false,
+    "description": "One input served at its per-call cap.",
+    "properties": {
+      "input": {
+        "description": "Input name, e.g. \"maxResults\" or \"cids\".",
+        "type": "string"
+      },
+      "requested": {
+        "description": "Value requested: the page size, or the number of IDs in the batch.",
+        "type": "number"
+      },
+      "served": {
+        "description": "Value served: the per-call cap.",
+        "type": "number"
+      },
+      "unprocessed": {
+        "description": "ID batches only: IDs past the cap, listed in unprocessed in input order.",
+        "type": "number"
+      }
+    },
+    "required": [
+      "input",
+      "requested",
+      "served"
+    ],
+    "type": "object"
+  },
+  "type": "array"
+}

Changed1 schema field changedOct 7, 2026

changedOutput schema / properties / error / properties / data / properties / reason / description

Previous value: -"Machine-readable failure mode. Declared by this tool: `blank_target_query`: targetQuery is empty or whitespace-only. `invalid_geneid_query`: targetType is \"geneid\" but targetQuery is not a positive integer. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `blank_target_query`: targetQuery is empty or whitespace-only. `invalid_geneid_query`: targetType is \"geneid\" but targetQuery contains characters other than digits. Other values are possible when a failure originates below the handler."

Changed1 schema field changedSep 19, 2026

changedOutput schema / properties / error / properties / data / properties / reason / description

Previous value: -"Machine-readable failure mode. Declared by this tool: `blank_target_query`: targetQuery is empty or whitespace-only `invalid_geneid_query`: targetType is \"geneid\" but targetQuery is not a positive integer Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `blank_target_query`: targetQuery is empty or whitespace-only. `invalid_geneid_query`: targetType is \"geneid\" but targetQuery is not a positive integer. Other values are possible when a failure originates below the handler."

Changed6 schema fields changedAug 21, 2026

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": [
+      "aids",
+      "targetType",
+      "targetQuery",
+      "totalFound",
+      "offset"
+    ]
+  },
+  {
+    "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. Declared by this tool: `blank_target_query`: targetQuery is empty or whitespace-only `invalid_geneid_query`: targetType is \"geneid\" but targetQuery is not a positive integer Other values are possible when a failure originates below the handler.",
+          "examples": [
+            "blank_target_query",
+            "invalid_geneid_query"
+          ],
+          "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: -[
-  "aids",
-  "targetType",
-  "targetQuery",
-  "totalFound",
-  "offset"
-]

Changed1 schema field changedJul 28, 2026
- changedInput schema / properties / maxResults / type
```
Previous value: -"number"New value: +"integer"
```

Changed9 schema fields changedJul 28, 2026

changedInput schema / properties / maxResults / description

Previous value: -"Max AIDs to return (1-200). Popular targets may have thousands of assays. Default: 50."New value: +"Max AIDs to return per page (1-200). Popular targets may have thousands of assays; use offset to reach the ones past this page. Default: 50."

addedInput schema / properties / offset

Added value: +{
+  "default": 0,
+  "description": "Zero-based index of the first AID to return. Pass the nextOffset from a previous call to read the following page. Default: 0.",
+  "maximum": 9007199254740991,
+  "minimum": 0,
+  "type": "integer"
+}

addedOutput schema / properties / nextOffset

Added value: +{
+  "description": "Offset to pass on the next call to continue past this page. Omitted when no further AIDs match.",
+  "type": "number"
+}

changedOutput schema / properties / notice / description

Previous value: -"Recovery guidance when no assays matched — echoes the target and suggests alternative search types. Absent when assays were returned."New value: +"Recovery guidance when no assays matched, when the offset runs past the result set, or when further pages remain. Absent when this page is complete and non-empty."

addedOutput schema / properties / offset

Added value: +{
+  "description": "Zero-based index of the first AID returned.",
+  "type": "number"
+}

changedOutput schema / properties / shown / description

Previous value: -"AIDs returned after the maxResults cap."New value: +"AIDs returned on this page."

changedOutput schema / properties / totalFound / description

Previous value: -"Total AIDs found before the maxResults cap."New value: +"Total AIDs found for this target, across all pages."

changedOutput schema / properties / truncated / description

Previous value: -"True when AIDs were capped at maxResults — more assays exist than returned."New value: +"True when matching AIDs remain past this page."

changedOutput schema / required

Previous value: -[
-  "aids",
-  "targetType",
-  "targetQuery",
-  "totalFound"
-]New value: +[
+  "aids",
+  "targetType",
+  "targetQuery",
+  "totalFound",
+  "offset"
+]

Changed3 schema fields changedJun 13, 2026

addedOutput schema / properties / cap

Added value: +{
+  "description": "The maxResults cap that was applied.",
+  "type": "number"
+}

addedOutput schema / properties / shown

Added value: +{
+  "description": "AIDs returned after the maxResults cap.",
+  "type": "number"
+}

addedOutput schema / properties / truncated

Added value: +{
+  "description": "True when AIDs were capped at maxResults — more assays exist than returned.",
+  "type": "boolean"
+}

Changed3 schema fields changedMay 30, 2026

addedOutput schema / properties / notice

Added value: +{
+  "description": "Recovery guidance when no assays matched — echoes the target and suggests alternative search types. Absent when assays were returned.",
+  "type": "string"
+}

changedOutput schema / properties / totalFound / description

Previous value: -"Total AIDs found."New value: +"Total AIDs found before the maxResults cap."

changedOutput schema / required

Previous value: -[
-  "targetType",
-  "targetQuery",
-  "totalFound",
-  "aids"
-]New value: +[
+  "aids",
+  "targetType",
+  "targetQuery",
+  "totalFound"
+]

Changed1 schema field changedMay 5, 2026

changedOutput schema / properties / targetType / description

Previous value: -"Target identifier type used."New value: +"Target identifier type used: genesymbol, proteinname, geneid, or proteinaccession."

First observedMar 28, 2026

TDQS

A4.1/5.0

Behavior3/5

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

Annotations already declare readOnlyHint, idempotentHint and openWorldHint, so the safety and repeatability profile is covered. The description adds the result granularity ('a page of assay IDs (AIDs)') and the pagination mental model, but that pagination detail is largely duplicated in the schema descriptions rather than adding new behavior such as rate limits or capping semantics.

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?

Three tight sentences: purpose first, accepted inputs second, output/pagination/next-step last. No filler, and the most decision-relevant information leads.

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

Completeness5/5

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

An output schema exists and annotations cover the safety profile, so the description only needs to establish search scope, input forms, and pagination behavior plus the downstream tool — all present. Nothing an agent needs to invoke this correctly is missing.

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%, so every parameter including targetType, targetQuery, offset and maxResults is already documented. The description's examples ('EGFR', '1956', 'P00533') mirror the schema's own examples, so it adds little semantic meaning beyond what the structured fields provide.

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 ('Find PubChem bioassays associated with a biological target') and immediately scopes the input domain (gene symbol, protein name, Gene ID, UniProt accession), which clearly separates it from pubchem_search_compounds. An agent can identify the tool's function without opening the schema.

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

Usage Guidelines4/5

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

Gives concrete accepted identifier forms with examples and names the natural follow-up tool ('explored further with pubchem_get_summary'), providing clear usage context. It stops short of explicit when-not-to-use guidance or naming the sibling that handles a different target type.

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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