Pubchem Bioassay Tools#

Configuration File: pubchem_bioassay_tools.json Tool Type: Local Tools Count: 4

This page contains all tools defined in the pubchem_bioassay_tools.json configuration file.

Available Tools#

PubChemBioAssay_get_assay (Type: PubChemBioAssayTool)#

Get the complete detailed description of a PubChem BioAssay by its AID (Assay ID), including ever…

PubChemBioAssay_get_assay tool specification

Tool Information:

  • Name: PubChemBioAssay_get_assay

  • Type: PubChemBioAssayTool

  • Description: Get the complete detailed description of a PubChem BioAssay by its AID (Assay ID), including every description, protocol, and comment paragraph plus explicit counts. PubChem BioAssay stores over 1.3 million biological screening results from drug discovery, toxicology, and biological pathway research. Example: AID 1234 returns ‘NIH Compound Library Profiling: Compound and DTT Dependent Redox Cycling H2O2 Generation’ from University of Pittsburgh MLSC.

Parameters:

  • aid (integer) (required) PubChem BioAssay ID (AID). Examples: 1234 (Redox Cycling H2O2 assay), 1259393 (TSHR counter screen), 504832 (Tox21 p53 activation).

Example Usage:

query = {
    "name": "PubChemBioAssay_get_assay",
    "arguments": {
        "aid": 10
    }
}
result = tu.run(query)

PubChemBioAssay_get_assay_summary (Type: PubChemBioAssayTool)#

Get summary and molecular target information for a PubChem BioAssay. Returns the assay name, sour…

PubChemBioAssay_get_assay_summary tool specification

Tool Information:

  • Name: PubChemBioAssay_get_assay_summary

  • Type: PubChemBioAssayTool

  • Description: Get summary and molecular target information for a PubChem BioAssay. Returns the assay name, source, method type, scoring information, and detailed target gene/protein data. More concise than get_assay but includes gene symbol and ID mapping for targets. Example: AID 1259393 returns target gene TSHR (Gene ID 7253), protein ‘thyroid stimulating hormone receptor’, method type ‘Summary’.

Parameters:

  • aid (integer) (required) PubChem BioAssay ID (AID). Examples: 1259393, 504832, 1234.

Example Usage:

query = {
    "name": "PubChemBioAssay_get_assay_summary",
    "arguments": {
        "aid": 10
    }
}
result = tu.run(query)

PubChemBioAssay_get_concise_activity_table (Type: PubChemBioAssayTool)#

Get the assay-wide concise bioactivity table for a PubChem BioAssay, one row per tested compound …

PubChemBioAssay_get_concise_activity_table tool specification

Tool Information:

  • Name: PubChemBioAssay_get_concise_activity_table

  • Type: PubChemBioAssayTool

  • Description: Get the assay-wide concise bioactivity table for a PubChem BioAssay, one row per tested compound with SID/CID, outcome, activity value/name, and target identifiers. Large assays can contain hundreds of thousands of rows; use max_rows/row_offset and continue with next_row_offset while has_more is true. total_rows is exact because PubChem returns the full table in one call.

Parameters:

  • aid (integer) (required) PubChem BioAssay ID (AID). Examples: 504832 (malaria qHTS, 305803 rows), 1259393 (TSHR counter screen).

  • max_rows ([‘integer’, ‘null’]) (optional) Maximum number of compound rows to return in the payload (default 1000, max 100000). total_rows always reports the true full count regardless of this cap.

  • row_offset (integer) (optional) Zero-based offset in the complete assay table. Continue with data.next_row_offset.

Example Usage:

query = {
    "name": "PubChemBioAssay_get_concise_activity_table",
    "arguments": {
        "aid": 10
    }
}
result = tu.run(query)

PubChemBioAssay_search_by_gene (Type: PubChemBioAssayTool)#

Search for PubChem BioAssays that target a specific gene with recoverable offset pagination. Retu…

PubChemBioAssay_search_by_gene tool specification

Tool Information:

  • Name: PubChemBioAssay_search_by_gene

  • Type: PubChemBioAssayTool

  • Description: Search for PubChem BioAssays that target a specific gene with recoverable offset pagination. Returns a summary for every assay on the requested page plus total_assays, has_more, and next_offset. Useful for finding screening data, drug discovery efforts, and toxicology studies targeting a particular gene product. Example: searching for ‘TP53’ returns hundreds of assays for p53 activation, apoptosis, and Tox21 genotoxicity screens.

Parameters:

  • gene_symbol (string) (required) Human gene symbol. Examples: ‘TP53’ (tumor protein p53), ‘EGFR’ (epidermal growth factor receptor), ‘TSHR’ (thyroid stimulating hormone receptor), ‘ESR1’ (estrogen receptor alpha).

  • limit (integer) (optional) Number of assay summaries per page (1-100; default 20).

  • offset (integer) (optional) Zero-based offset into all assay IDs for the gene. Continue with next_offset while has_more is true.

Example Usage:

query = {
    "name": "PubChemBioAssay_search_by_gene",
    "arguments": {
        "gene_symbol": "example_value"
    }
}
result = tu.run(query)