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pubchem-mcp-server

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Get Bioactivity

pubchem_get_bioactivity
Read-onlyIdempotent

Retrieve a compound's bioactivity profile: assays, activity outcomes, targets, and quantitative values. Filter by outcome or specific target to check activity against a protein.

Instructions

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
NameRequiredDescriptionDefault
cidYesPubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds.
offsetNoZero-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.
maxResultsNoMax 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.
targetGeneIdNoFilter 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?".
outcomeFilterNoFilter by activity outcome. "active" shows only assays where the compound showed activity — most useful for understanding biological profile. Default: "all".all
targetAccessionNoFilter 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
NameRequiredDescriptionDefault
capNoThe maxResults cap that was applied.
cidNoPubChem Compound ID.
errorNoPresent when the call failed. Absent on success.
shownNoAssays returned on this page.
noticeNoRecovery guidance when the filter yields no results or the compound has no bioactivity data.
offsetNoZero-based index of the first assay returned.
resultsNoAssay results matching the filter.
truncatedNoTrue when matching assays remain past this page.
nextOffsetNoOffset to pass on the next call to continue past this page. Omitted when no further assays match.
activeCountNoAssays with "Active" outcome.
totalAssaysNoTotal unique assays for this compound.
targetFilterNoTarget filter applied (gene ID and/or protein accession), when set.
filteredCountNoExact number of assays matching the outcome and target filters, across all pages.
inactiveCountNoAssays with "Inactive" outcome.
outcomeFilterNoOutcome filter applied: active, inactive, or all.
returnedCountNoAssays returned on this page.

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": [
+      "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"
-]
  2. Changed10 schema fields changedv0.6.0
    • 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."
    • changedInput schema / properties / maxResults / type
      Previous value: -"number"New value: +"integer"
    • 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"
+]
  3. Changed3 schema fields changedv0.2.4
    • 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"
+}
  4. Changed8 schema fields changedv0.2.2
    • 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"
+]
  5. Changed6 schema fields changedv0.1.22
    • changedInput schema / properties / cid / description
      Previous value: -"PubChem Compound ID."New value: +"PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds."
    • 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."
    • 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"
+]
  6. First observedv0.1.11

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 useful behavioral context about the type of data returned and the filtering workflow. Pagination and result-shape details are not in the description, but the schema and output schema carry that burden.

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 a clear front-loaded purpose, followed by a compact enumeration of outputs and a practical example. Every clause earns its place, and there is no redundant restating of parameter names or schema content.

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 a rich input schema, output schema, and annotations, the description provides all essential context: what the tool returns, what filters exist, and how to frame a target-specific question. Nothing critical is missing for an agent to select and invoke it correctly.

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 the baseline is 3. The description adds a meaningful use case for combining targetGeneId and outcomeFilter, but it does not materially improve on the already-detailed parameter descriptions in the schema.

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 names a specific verb and resource: 'Get a compound's bioactivity profile', then enumerates the concrete contents (assays, outcomes, target identifiers, quantitative values). This clearly distinguishes it from sibling tools such as get_compound_details or get_compound_interactions without needing to open 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?

The description gives clear usage context: retrieve a bioactivity profile and optionally filter by outcome or molecular target. The concrete example 'is this compound active against target T?' makes the intended use immediately actionable. It does not explicitly name exclusions or alternative sibling tools, but for a read-only profile query the context is clear.

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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