Get Bioactivity
pubchem_get_bioactivityRead-onlyIdempotent
Retrieve a compound's bioactivity profile, including assays, outcomes, targets, quantitative values, and PubMed IDs. Filter by activity outcome, molecular target, or assay type to focus 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), quantitative values (IC50, EC50, Ki, etc.), each assay's type (confirmatory, screening, summary, other), and the PubMed IDs it cites. Filter by outcome, a specific molecular target (NCBI Gene ID or protein accession), and/or assay type to focus the profile — e.g. "is this compound active against target T in confirmatory assays?".
Tool call template
Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.
{
"id": 1,
"jsonrpc": "2.0",
"method": "tools/call",
"params": {
"arguments": {
"cid": "<cid>"
},
"name": "pubchem_get_bioactivity"
}
}Input 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. | |
| assayType | No | Keep only assays of these types: "confirmatory" (dose-response and other follow-up assays), "screening" (primary high-throughput screens), "summary" (records summarizing a project's assays), "other". Matched against PubChem's Assay Type regardless of case; an assay with no recorded type matches none. Combines with outcomeFilter and the target filters — an assay must pass all of them. Omit to keep every type. | |
| maxResults | No | Max assay results to return per page. The per-call cap is 100: a larger value (up to 1000) returns a page of 100 and is reported in cappedInputs. 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 (1 to 2147483647), including assays recorded only under a protein accession this compound's assay table pairs with the Gene ID (e.g. 5742 also reaches rows carrying only P23219 when another row pairs the two). Obtain Gene IDs from the GeneID:N in a pubchem_get_compound_interactions target entry's partner (kinds: ["target"]) or the targetGeneId field of a result here without a target filter (rows from untargeted screens carry none). Combine with outcomeFilter="active" to answer "is this compound active against target T?". | |
| outcomeFilter | No | Filter by activity outcome against each assay's reported target: the target a target filter matched, else the first target the assay lists. For a multi-target assay, outcomes against its other targets (in otherTargets) do not count. "active" keeps assays where that outcome is Active — most useful for understanding biological profile. Default: "all". | all |
| targetAccession | No | Filter to assays against this target protein accession (UniProt/RefSeq/GenBank/PDB chain), e.g. "P35354", including assays recorded only under a Gene ID or another accession this compound's assay table pairs with it. Uppercased before matching; a PDB chain ID (the "A" in "1ZHH_A") is kept as given. With targetGeneId, both must name the same target — when the table ties them to different targets, nothing matches. Obtain accessions from an assay's targets in pubchem_get_summary (entityType "assay"), the accession:X in a pubchem_get_compound_interactions target entry's partner, or the targetAccession field of a result here without a target filter. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| cap | No | The page size applied: maxResults, or the per-call cap when maxResults exceeds it. | |
| 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 whose outcome against their first listed target is "Active", across all assays and before any filter. A multi-target assay counts by its first target only. | |
| totalAssays | No | Total unique assays for this compound. | |
| 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. | |
| targetFilter | No | Target identifiers matched, when a target filter is set: those passed plus every Gene ID and accession the compound's assay table pairs with them. When the two inputs name different targets, only the two inputs. | |
| filteredCount | No | Exact number of assays matching the outcome, target, and assay-type filters, across all pages. | |
| inactiveCount | No | Assays whose outcome against their first listed target is "Inactive", across all assays and before any filter. A multi-target assay counts by its first target only. | |
| outcomeFilter | No | Outcome filter applied: active, inactive, or all. | |
| returnedCount | No | Assays returned on this page. | |
| assayTypeFilter | No | Assay types kept, comma-separated (e.g. "confirmatory, summary"), when assayType is set. |