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)

Retrieve corresponding CID list (IdentifierList) by chemical compound name. Note: This tool only …

PubChem_get_CID_by_compound_name tool specification

Tool Information:

• Name: PubChem_get_CID_by_compound_name

• Type: PubChemRESTTool

• Description: Retrieve corresponding CID list (IdentifierList) by chemical compound name. Note: This tool only works with chemical compound names (e.g., drug names, molecules), not disease names or conditions.

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 no more than 10 CIDs (MaxRecords=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.

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 all CIDs in PubChem that contain the given substructure (SMILES).

PubChem_search_compounds_by_substructure tool specification

Tool Information:

• Name: PubChem_search_compounds_by_substructure

• Type: PubChemRESTTool

• Description: Search for all CIDs in PubChem that contain the given substructure (SMILES).

Parameters:

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

Example Usage:

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

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