Pubchem Tools

Configuration File: pubchem_tools.json Tool Type: Local Tools Count: 18

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

Available Tools

PubChem_get_CID_by_SMILES (Type: PubChemRESTTool)

Retrieve corresponding CID list by SMILES string.

PubChem_get_CID_by_SMILES tool specification

Tool Information:

• Name: PubChem_get_CID_by_SMILES

• Type: PubChemRESTTool

• Description: Retrieve corresponding CID list by SMILES string.

Parameters:

• smiles (string) (required) SMILES expression (e.g., “CC(=O)OC1=CC=CC=C1C(=O)O” corresponds to aspirin).

Example Usage:

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

PubChem_get_CID_by_compound_name (Type: PubChemRESTTool)

Search PubChem by compound name to get CID(s). This is the PRIMARY tool for looking up a drug or …

PubChem_get_CID_by_compound_name tool specification

Tool Information:

• Name: PubChem_get_CID_by_compound_name

• Type: PubChemRESTTool

• Description: Search PubChem by compound name to get CID(s). This is the PRIMARY tool for looking up a drug or chemical by name (e.g., ‘cytarabine’, ‘aspirin’, ‘metformin’, ‘venetoclax’) to obtain PubChem Compound IDs. Use the returned CID with other PubChem tools for properties, patents, etc. Only works with chemical/drug names, not disease names.

Parameters:

• name (string) (required) Chemical compound name (e.g., “Aspirin”, “Acetaminophen”) or IUPAC name. Do not use disease names or medical conditions.

Example Usage:

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

PubChem_get_assay_active_compounds (Type: PubChemRESTTool)

Get CIDs of compounds that are ACTIVE in a bioassay. Returns compound IDs that passed the activit…

PubChem_get_assay_active_compounds tool specification

Tool Information:

• Name: PubChem_get_assay_active_compounds

• Type: PubChemRESTTool

• Description: Get CIDs of compounds that are ACTIVE in a bioassay. Returns compound IDs that passed the activity threshold. Use for hit identification from HTS screens.

Parameters:

• aid (integer) (required) PubChem BioAssay ID

Example Usage:

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

PubChem_get_assay_description (Type: PubChemRESTTool)

Get bioassay description and metadata by AID. Returns assay name, source, protocol, target inform…

PubChem_get_assay_description tool specification

Tool Information:

• Name: PubChem_get_assay_description

• Type: PubChemRESTTool

• Description: Get bioassay description and metadata by AID. Returns assay name, source, protocol, target information, activity outcomes, and data columns. Essential for understanding what an assay measures before retrieving results.

Parameters:

• aid (integer) (required) PubChem BioAssay ID (e.g., 1000, 504526)

Example Usage:

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

PubChem_get_assay_dose_response (Type: PubChemRESTTool)

Get dose-response data from a bioassay. Returns concentration-response curves for tested compound…

PubChem_get_assay_dose_response tool specification

Tool Information:

• Name: PubChem_get_assay_dose_response

• Type: PubChemRESTTool

• Description: Get dose-response data from a bioassay. Returns concentration-response curves for tested compounds. Essential for determining IC50/EC50 values. Limited to dose-response type assays.

Parameters:

• aid (integer) (required) PubChem BioAssay ID (must be a dose-response assay)

Example Usage:

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

PubChem_get_assay_summary (Type: PubChemRESTTool)

Get summary statistics for a bioassay by AID. Returns counts of active/inactive compounds, target…

PubChem_get_assay_summary tool specification

Tool Information:

• Name: PubChem_get_assay_summary

• Type: PubChemRESTTool

• Description: Get summary statistics for a bioassay by AID. Returns counts of active/inactive compounds, target information, and assay metadata. Useful for quick assessment of assay size and hit rate.

Parameters:

• aid (integer) (required) PubChem BioAssay ID

Example Usage:

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

PubChem_get_assay_targets (Type: PubChemRESTTool)

Get protein/gene targets for a bioassay. Returns GI numbers, protein names, gene IDs, and gene sy…

PubChem_get_assay_targets tool specification

Tool Information:

• Name: PubChem_get_assay_targets

• Type: PubChemRESTTool

• Description: Get protein/gene targets for a bioassay. Returns GI numbers, protein names, gene IDs, and gene symbols. Critical for understanding what molecular targets an assay screens against.

Parameters:

• aid (integer) (required) PubChem BioAssay ID

Example Usage:

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

PubChem_get_assays_for_compound_active (Type: PubChemRESTTool)

Get AIDs of assays where a compound is ACTIVE. Returns list of bioassay IDs where the compound sh…

PubChem_get_assays_for_compound_active tool specification

Tool Information:

• Name: PubChem_get_assays_for_compound_active

• Type: PubChemRESTTool

• Description: Get AIDs of assays where a compound is ACTIVE. Returns list of bioassay IDs where the compound showed activity. Use to understand a compound’s target profile.

Parameters:

• cid (integer) (required) PubChem Compound ID

Example Usage:

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

PubChem_get_associated_patents_by_CID (Type: PubChemRESTTool)

Get a list of patents associated with a specific compound CID.

PubChem_get_associated_patents_by_CID tool specification

Tool Information:

• Name: PubChem_get_associated_patents_by_CID

• Type: PubChemRESTTool

• Description: Get a list of patents associated with a specific compound CID.

Parameters:

• cid (integer) (required) PubChem compound ID to query, e.g., 2244 (Aspirin).

Example Usage:

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

PubChem_get_compound_2D_image_by_CID (Type: PubChemRESTTool)

Get 2D structure image (PNG format) of compound by CID.

PubChem_get_compound_2D_image_by_CID tool specification

Tool Information:

• Name: PubChem_get_compound_2D_image_by_CID

• Type: PubChemRESTTool

• Description: Get 2D structure image (PNG format) of compound by CID.

Parameters:

• cid (integer) (required) Compound ID to get image for, e.g., 2244.

• image_size (string) (required) Optional parameter, image size, like “200x200” (default).

Example Usage:

query = {
    "name": "PubChem_get_compound_2D_image_by_CID",
    "arguments": {
        "cid": 10,
        "image_size": "example_value"
    }
}
result = tu.run(query)

PubChem_get_compound_bioactivity (Type: PubChemRESTTool)

Get bioassay results summary for a compound by CID. Returns all assays the compound was tested in…

PubChem_get_compound_bioactivity tool specification

Tool Information:

• Name: PubChem_get_compound_bioactivity

• Type: PubChemRESTTool

• Description: Get bioassay results summary for a compound by CID. Returns all assays the compound was tested in, activity outcomes (active/inactive), and target information. Critical for understanding compound’s biological profile.

Parameters:

• cid (integer) (required) PubChem Compound ID

Example Usage:

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

PubChem_get_compound_properties_by_CID (Type: PubChemRESTTool)

Get a set of specified molecular properties through CID (Compound ID), such as molecular weight, …

PubChem_get_compound_properties_by_CID tool specification

Tool Information:

• Name: PubChem_get_compound_properties_by_CID

• Type: PubChemRESTTool

• Description: Get a set of specified molecular properties through CID (Compound ID), such as molecular weight, IUPAC name, Canonical SMILES.

Parameters:

• cid (integer) (required) PubChem compound ID to query, e.g., 2244 (Aspirin).

Example Usage:

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

PubChem_get_compound_synonyms_by_CID (Type: PubChemRESTTool)

Get complete list of synonyms for compound by CID.

PubChem_get_compound_synonyms_by_CID tool specification

Tool Information:

• Name: PubChem_get_compound_synonyms_by_CID

• Type: PubChemRESTTool

• Description: Get complete list of synonyms for compound by CID.

Parameters:

• cid (integer) (required) Compound ID to query synonyms for, e.g., 2244.

Example Usage:

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

PubChem_get_compound_xrefs_by_CID (Type: PubChemRESTTool)

Get external references (XRefs) for compound by CID, including links to ChEBI, DrugBank, KEGG, etc.

PubChem_get_compound_xrefs_by_CID tool specification

Tool Information:

• Name: PubChem_get_compound_xrefs_by_CID

• Type: PubChemRESTTool

• Description: Get external references (XRefs) for compound by CID, including links to ChEBI, DrugBank, KEGG, etc.

Parameters:

• cid (integer) (required) Compound ID to query external references for, e.g., 2244.

• xref_types (array) (required) List of external database types to query, e.g., [“RegistryID”, “RN”, “PubMedID”].

Example Usage:

query = {
    "name": "PubChem_get_compound_xrefs_by_CID",
    "arguments": {
        "cid": 10,
        "xref_types": ["item1", "item2"]
    }
}
result = tu.run(query)

PubChem_search_assays_by_target_gene (Type: PubChemRESTTool)

Search bioassays by target gene symbol. Returns AIDs of assays that screen against the specified …

PubChem_search_assays_by_target_gene tool specification

Tool Information:

• Name: PubChem_search_assays_by_target_gene

• Type: PubChemRESTTool

• Description: Search bioassays by target gene symbol. Returns AIDs of assays that screen against the specified gene. Example: USP2 returns assays targeting USP2 protease.

Parameters:

• gene_symbol (string) (required) Gene symbol to search (e.g., EGFR, USP2, TP53)

Example Usage:

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

PubChem_search_assays_by_type (Type: PubChemRESTTool)

Search bioassays by assay type. Types: screening (HTS), confirmatory, doseresponse, summary, cell…

PubChem_search_assays_by_type tool specification

Tool Information:

• Name: PubChem_search_assays_by_type

• Type: PubChemRESTTool

• Description: Search bioassays by assay type. Types: screening (HTS), confirmatory, doseresponse, summary, cellbased, biochemical, invivo, invitro. Returns list of matching AIDs.

Parameters:

• assay_type (string) (required) Type of assay to search for

Example Usage:

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

PubChem_search_compounds_by_similarity (Type: PubChemRESTTool)

Search by similarity (Tanimoto coefficient), returns CID list of compounds with similarity above …

PubChem_search_compounds_by_similarity tool specification

Tool Information:

• Name: PubChem_search_compounds_by_similarity

• Type: PubChemRESTTool

• Description: Search by similarity (Tanimoto coefficient), returns CID list of compounds with similarity above threshold to given SMILES molecule. Returns up to max_results CIDs (default 10).

Parameters:

• smiles (string) (required) SMILES expression of target molecule.

• threshold (number) (required) Similarity threshold (between 0 and 1), e.g., 0.9 means 90% similarity.

• max_results (integer) (optional) Maximum number of CIDs to return (default: 10, max: 10000).

Example Usage:

query = {
    "name": "PubChem_search_compounds_by_similarity",
    "arguments": {
        "smiles": "example_value",
        "threshold": "example_value"
    }
}
result = tu.run(query)

PubChem_search_compounds_by_substructure (Type: PubChemRESTTool)

Search for CIDs in PubChem that contain the given substructure (SMILES). Returns up to max_result…

PubChem_search_compounds_by_substructure tool specification

Tool Information:

• Name: PubChem_search_compounds_by_substructure

• Type: PubChemRESTTool

• Description: Search for CIDs in PubChem that contain the given substructure (SMILES). Returns up to max_results CIDs (default 10).

Parameters:

• smiles (string) (required) SMILES of substructure (e.g., “c1ccccc1” corresponds to benzene ring).

• max_results (integer) (optional) Maximum number of CIDs to return (default: 10, max: 10000).

Example Usage:

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

Navigation

• Available Tools - Back to Tools Overview

• Tool Loading Tutorial - Loading Local Tools