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Get Bioactivity

pubchem_get_bioactivity
Read-onlyIdempotent

Retrieve a compound's bioactivity profile including assays, activity outcomes, target IDs, and quantitative values. Filter by activity outcome or specific molecular target to focus the results.

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.
cidYesPubChem Compound ID.
shownNoAssays returned on this page.
noticeNoRecovery guidance when the filter yields no results or the compound has no bioactivity data.
offsetYesZero-based index of the first assay returned.
resultsYesAssay 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.
activeCountYesAssays with "Active" outcome.
totalAssaysYesTotal unique assays for this compound.
targetFilterNoTarget filter applied (gene ID and/or protein accession), when set.
filteredCountYesExact number of assays matching the outcome and target filters, across all pages.
inactiveCountYesAssays with "Inactive" outcome.
outcomeFilterYesOutcome filter applied: active, inactive, or all.
returnedCountYesAssays returned on this page.
Behavior5/5

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

The description discloses behavioral traits beyond annotations: it explains pagination (offset, maxResults) and the effect of filters on the result set. Annotations already indicate read-only and idempotent, which the description does not contradict. There is no destructive behavior, and the description adds useful context about what data is returned.

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 extremely concise with just two sentences. The first sentence defines the tool's purpose and outputs, and the second explains filtering with an example. Every word adds value; there is no redundancy or fluff.

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 tool has 6 parameters, rich annotations (readOnly, openWorld, idempotent), and an output schema (implied by context signals), the description is complete. It covers the primary functionality, filtering, pagination, and a use case. No gaps are evident.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 100%, so baseline is 3. The description adds value by explaining the purpose of filtering (e.g., 'focus the profile'), suggesting how to obtain the cid (using pubchem_search_compounds), and providing an example query. This goes beyond the schema's property descriptions.

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 clearly states the verb 'Get' and the resource 'bioactivity profile', specifying what data is returned: assays, outcomes, target identifiers, quantitative values. It distinguishes from sibling tools like pubchem_get_compound_details by focusing on bioactivity rather than general properties.

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 provides a concrete example ('is this compound active against target T?') and explains how to use filters to focus results. While it doesn't explicitly compare to sibling tools, the example gives clear guidance on when to use filtering. A slight improvement would be mentioning when this tool is preferred over others.

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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