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Get Bioactivity

pubchem_get_bioactivity
Read-onlyIdempotent

Retrieve bioactivity profile for a PubChem compound, including assay outcomes, target identifiers, and quantitative values. Filter by activity outcome or specific molecular target.

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.
outcomeFilterNoFilter by activity outcome. "active" shows only assays where the compound showed activity — most useful for understanding biological profile. Default: "all".all
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?".
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.
maxResultsNoMax assay results to return (1-100). Well-studied compounds have thousands of records. Default: 20.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
cidYesPubChem Compound ID.
totalAssaysYesTotal unique assays for this compound.
activeCountYesAssays with "Active" outcome.
inactiveCountYesAssays with "Inactive" outcome.
resultsYesAssay results matching the filter.
outcomeFilterYesOutcome filter applied: active, inactive, or all.
targetFilterNoTarget filter applied (gene ID and/or protein accession), when set.
filteredCountYesAssays matching the outcome and target filters, before the maxResults cap.
returnedCountYesAssays returned after the maxResults cap.
truncatedNoTrue when results were capped at maxResults — more matching assays exist.
shownNoAssays returned after the maxResults cap.
capNoThe maxResults cap that was applied.
noticeNoRecovery guidance when the filter yields no results or the compound has no bioactivity data.
Behavior4/5

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

Annotations already declare readOnlyHint=true, idempotentHint=true, and openWorldHint=true. The description adds useful behavioral context: it notes that well-studied compounds have thousands of records (justifying the maxResults parameter) and explains how to obtain target identifiers. No contradictions with 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 sentences long, very concise. It front-loads the main purpose and efficiently conveys filtering options with an example. Every sentence adds value 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?

Given the presence of output schema (not shown but indicated) and full input schema coverage, the description is largely complete. It explains filtering, defaults, and cross-references to other tools. However, it does not address ordering of results or differentiate from sibling tools like pubchem_get_compound_interactions.

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 coverage is 100%, so the baseline is 3. The description adds a usage example and emphasizes the 'active' filter's utility, but does not provide significant new meaning beyond what is already in the parameter descriptions. The example helps but is not extensive.

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 it retrieves a compound's bioactivity profile, listing specific components (assays, outcomes, targets, quantitative values). The verb 'Get' and resource 'bioactivity' are unambiguous. It distinguishes from sibling tools like pubchem_get_compound_details by focusing specifically on bioactivity data.

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 clear usage context: it shows how to filter by outcome and target, and gives an example query ('is this compound active against target T?'). It also references resolving CIDs via another tool. However, it does not explicitly state when not to use this tool or compare it with alternatives like pubchem_get_compound_interactions.

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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