Pubchem Bioassay Tools

Configuration File: pubchem_bioassay_tools.json Tool Type: Local Tools Count: 3

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

Available Tools

PubChemBioAssay_get_assay (Type: PubChemBioAssayTool)

Get detailed description of a PubChem BioAssay by its AID (Assay ID). PubChem BioAssay stores ove…

PubChemBioAssay_get_assay tool specification

Tool Information:

  • Name: PubChemBioAssay_get_assay

  • Type: PubChemBioAssayTool

  • Description: Get detailed description of a PubChem BioAssay by its AID (Assay ID). PubChem BioAssay stores over 1.3 million biological screening results from drug discovery, toxicology, and biological pathway research. Returns assay name, description, protocol, targets, and source information. 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_search_by_gene (Type: PubChemBioAssayTool)

Search for PubChem BioAssays that target a specific gene. Returns the list of assay IDs targeting…

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. Returns the list of assay IDs targeting the gene along with summaries for the top results. Useful for finding screening data, drug discovery efforts, and toxicology studies targeting a particular gene product. Example: searching for ‘TP53’ returns assays for p53 activation, p53-mediated apoptosis, and Tox21 genotoxicity screens; ‘TSHR’ returns thyroid stimulating hormone receptor assays.

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).

Example Usage:

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