pubchem-mcp-server

Get Bioactivity

pubchem_get_bioactivity

Read-onlyIdempotent

Get a compound's bioactivity profile: which assays tested it, activity outcomes (Active/Inactive/Inconclusive), target identifiers (NCBI Gene ID, UniProt/GenBank accession), and quantitative values (IC50, EC50, Ki, etc.). Filter by outcome and/or a specific molecular target (NCBI Gene ID or protein accession) to focus the profile — e.g. "is this compound active against target T?".

Input Schema

TableJSON Schema

Name	Required	Description	Default
`cid`	Yes	PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds.
`offset`	No	Zero-based index of the first assay to return, applied after the outcome and target filters. Pass the nextOffset from a previous call to read the following page. Default: 0.
`maxResults`	No	Max assay results to return per page (1-100). Well-studied compounds have thousands of records; use offset to reach the ones past this page. Default: 20.
`targetGeneId`	No	Filter to assays against this NCBI Gene ID. Obtain Gene IDs from pubchem_search_assays or the targetGeneId field of an unfiltered result here. Combine with outcomeFilter="active" to answer "is this compound active against target T?".
`outcomeFilter`	No	Filter by activity outcome. "active" shows only assays where the compound showed activity — most useful for understanding biological profile. Default: "all".	all
`targetAccession`	No	Filter to assays against this target protein accession (UniProt/GenBank), e.g. "P35354". Obtain accessions from pubchem_search_assays or the targetAccession field of an unfiltered result here.

Output Schema

TableJSON Schema

Name	Required	Description
`cap`	No	The maxResults cap that was applied.
`cid`	No	PubChem Compound ID.
`error`	No	Present when the call failed. Absent on success.
`shown`	No	Assays returned on this page.
`notice`	No	Recovery guidance when the filter yields no results or the compound has no bioactivity data.
`offset`	No	Zero-based index of the first assay returned.
`results`	No	Assay results matching the filter.
`truncated`	No	True when matching assays remain past this page.
`nextOffset`	No	Offset to pass on the next call to continue past this page. Omitted when no further assays match.
`activeCount`	No	Assays with "Active" outcome.
`totalAssays`	No	Total unique assays for this compound.
`targetFilter`	No	Target filter applied (gene ID and/or protein accession), when set.
`filteredCount`	No	Exact number of assays matching the outcome and target filters, across all pages.
`inactiveCount`	No	Assays with "Inactive" outcome.
`outcomeFilter`	No	Outcome filter applied: active, inactive, or all.
`returnedCount`	No	Assays returned on this page.

Schema Changelog

Changes observed during successful MCP inspections.

Changed4 schema fields changedSep 25, 2026
- removedInput schema / properties / cid / exclusiveMinimum
```
Removed value: -0
```
- addedInput schema / properties / cid / minimum
```
Added value: +1
```
- removedInput schema / properties / targetGeneId / exclusiveMinimum
```
Removed value: -0
```
- addedInput schema / properties / targetGeneId / minimum
```
Added value: +1
```

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": [
+      "cid",
+      "totalAssays",
+      "activeCount",
+      "inactiveCount",
+      "results",
+      "outcomeFilter",
+      "filteredCount",
+      "returnedCount",
+      "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.",
+          "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: -[
-  "cid",
-  "totalAssays",
-  "activeCount",
-  "inactiveCount",
-  "results",
-  "outcomeFilter",
-  "filteredCount",
-  "returnedCount",
-  "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 assay results to return (1-100). Well-studied compounds have thousands of records. Default: 20."New value: +"Max assay results to return per page (1-100). Well-studied compounds have thousands of records; use offset to reach the ones past this page. Default: 20."

addedInput schema / properties / offset

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

changedOutput schema / properties / filteredCount / description

Previous value: -"Assays matching the outcome and target filters, before the maxResults cap."New value: +"Exact number of assays matching the outcome and target filters, across all pages."

addedOutput schema / properties / nextOffset

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

addedOutput schema / properties / offset

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

changedOutput schema / properties / returnedCount / description

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

changedOutput schema / properties / shown / description

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

changedOutput schema / properties / truncated / description

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

changedOutput schema / required

Previous value: -[
-  "cid",
-  "totalAssays",
-  "activeCount",
-  "inactiveCount",
-  "results",
-  "outcomeFilter",
-  "filteredCount",
-  "returnedCount"
-]New value: +[
+  "cid",
+  "totalAssays",
+  "activeCount",
+  "inactiveCount",
+  "results",
+  "outcomeFilter",
+  "filteredCount",
+  "returnedCount",
+  "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": "Assays returned after the maxResults cap.",
+  "type": "number"
+}

addedOutput schema / properties / truncated

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

Changed8 schema fields changedJun 2, 2026

addedInput schema / properties / targetAccession

Added value: +{
+  "description": "Filter to assays against this target protein accession (UniProt/GenBank), e.g. \"P35354\". Obtain accessions from pubchem_search_assays or the targetAccession field of an unfiltered result here.",
+  "type": "string"
+}

addedInput schema / properties / targetGeneId

Added value: +{
+  "description": "Filter to assays against this NCBI Gene ID. Obtain Gene IDs from pubchem_search_assays or the targetGeneId field of an unfiltered result here. Combine with outcomeFilter=\"active\" to answer \"is this compound active against target T?\".",
+  "exclusiveMinimum": 0,
+  "maximum": 9007199254740991,
+  "type": "integer"
+}

addedOutput schema / properties / filteredCount

Added value: +{
+  "description": "Assays matching the outcome and target filters, before the maxResults cap.",
+  "type": "number"
+}

addedOutput schema / properties / notice

Added value: +{
+  "description": "Recovery guidance when the filter yields no results or the compound has no bioactivity data.",
+  "type": "string"
+}

addedOutput schema / properties / outcomeFilter

Added value: +{
+  "description": "Outcome filter applied: active, inactive, or all.",
+  "type": "string"
+}

addedOutput schema / properties / returnedCount

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

addedOutput schema / properties / targetFilter

Added value: +{
+  "description": "Target filter applied (gene ID and/or protein accession), when set.",
+  "type": "string"
+}

changedOutput schema / required

Previous value: -[
-  "cid",
-  "totalAssays",
-  "activeCount",
-  "inactiveCount",
-  "results"
-]New value: +[
+  "cid",
+  "totalAssays",
+  "activeCount",
+  "inactiveCount",
+  "results",
+  "outcomeFilter",
+  "filteredCount",
+  "returnedCount"
+]

Changed1 schema field changedMay 5, 2026

changedInput schema / properties / cid / description

Previous value: -"PubChem Compound ID."New value: +"PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds."

Changed2 schema fields changedApr 24, 2026
- addedOutput schema / properties / results / items / description
```
Added value: +"Assay result entry."
```
- addedOutput schema / properties / results / items / properties / activityValues / items / description
```
Added value: +"Quantitative activity measurement entry."
```
Changed3 schema fields changedApr 19, 2026
- changedOutput schema / properties / results / items / properties / activityValues / items / properties / name / description
```
Previous value: -"Measurement name (e.g. IC50, EC50, Ki)."New value: +"Measurement name (e.g. IC50, EC50, Ki). Omitted when not reported."
```
- changedOutput schema / properties / results / items / properties / activityValues / items / properties / unit / description
```
Previous value: -"Unit of measurement (e.g. uM, nM)."New value: +"Unit of measurement (e.g. uM, nM). Omitted when not reported."
```
- changedOutput schema / properties / results / items / properties / activityValues / items / required
```
Previous value: -[
-  "name",
-  "value",
-  "unit"
-]New value: +[
+  "value"
+]
```
First observedMar 28, 2026

TDQS

A4.3/5.0

Behavior4/5

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

Annotations already declare readOnlyHint, openWorldHint, and idempotentHint, so the safety profile is covered. The description adds meaningful behavioral context beyond annotations by specifying the composition of the bioactivity profile and the filtering behavior, without contradicting the annotations.

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?

The description is two dense, purposeful sentences. The main resource and result contents are front-loaded, and the filtering use case earns its place with a concrete example. There is no filler or redundancy.

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?

Given the rich input schema, output schema, and readOnly/openWorld/idempotent annotations, the description provides the missing orientation an agent needs: what a bioactivity profile contains and how to answer a target-specific question. Nothing essential to selecting and invoking the tool is absent.

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%, and the schema already documents every parameter in detail, including offset pagination and the targetGeneId/outcomeFilter combination. The description reinforces the intended query pattern but does not meaningfully add new parameter-level semantics, so the baseline 3 applies.

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 starts with a specific verb and resource ('Get a compound's bioactivity profile') and enumerates exactly what is returned: assays, activity outcomes, target identifiers, and quantitative values. The detail is specific enough to distinguish this from sibling tools like pubchem_get_compound_interactions and pubchem_get_compound_xrefs.

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?

The description gives clear context for when to use the tool, including a concrete example ('is this compound active against target T?') and how to focus results by outcome or target. It does not explicitly state when not to use it or name alternatives, so it falls just short of a 5.

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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