Synergxdb Tools

Configuration File: synergxdb_tools.json Tool Type: Local Tools Count: 7

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

Available Tools

SYNERGxDB_get_combo_matrix (Type: SYNERGxDBTool)

Get the dose-response matrix data for a specific drug combination experiment in SYNERGxDB. Return…

SYNERGxDB_get_combo_matrix tool specification

Tool Information:

  • Name: SYNERGxDB_get_combo_matrix

  • Type: SYNERGxDBTool

  • Description: Get the dose-response matrix data for a specific drug combination experiment in SYNERGxDB. Returns concentration pairs and raw viability plus synergy matrices (Bliss, Loewe, HSA, ZIP). The combo_id and source_id can be obtained from SYNERGxDB_search_combos results.

Parameters:

  • operation (string) (optional) Operation type

  • combo_id (integer) (required) Combination design ID from search_combos results (comboId field)

  • source_id (integer) (required) Dataset source ID (idSource field from search_combos or list_datasets)

Example Usage:

query = {
    "name": "SYNERGxDB_get_combo_matrix",
    "arguments": {
        "combo_id": 10,
        "source_id": 10
    }
}
result = tu.run(query)

SYNERGxDB_get_combo_stats (Type: SYNERGxDBTool)

Get per-dataset combination statistics from SYNERGxDB. Returns the number of unique drug combinat…

SYNERGxDB_get_combo_stats tool specification

Tool Information:

  • Name: SYNERGxDB_get_combo_stats

  • Type: SYNERGxDBTool

  • Description: Get per-dataset combination statistics from SYNERGxDB. Returns the number of unique drug combinations, total experiments, and data points for each screening study. Useful for understanding the scale and coverage of each integrated dataset.

Parameters:

  • operation (string) (optional) Operation type

Example Usage:

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

SYNERGxDB_get_drug (Type: SYNERGxDBTool)

Get detailed information about a specific drug in SYNERGxDB by its database ID. Returns drug name…

SYNERGxDB_get_drug tool specification

Tool Information:

  • Name: SYNERGxDB_get_drug

  • Type: SYNERGxDBTool

  • Description: Get detailed information about a specific drug in SYNERGxDB by its database ID. Returns drug name, ATC code, PubChem ID, and DrugBank ID. Known drug IDs: 11 (Bortezomib), 24 (Dasatinib), 34 (Erlotinib), 41 (Fluorouracil), 48 (Imatinib), 52 (Lapatinib), 97 (Topotecan), 106 (Vorinostat).

Parameters:

  • operation (string) (optional) Operation type

  • drug_id (integer) (required) SYNERGxDB drug ID (e.g., 11 for Bortezomib)

Example Usage:

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

SYNERGxDB_list_cell_lines (Type: SYNERGxDBTool)

List all cancer cell lines in the SYNERGxDB database. Returns cell line names, tissue types, dise…

SYNERGxDB_list_cell_lines tool specification

Tool Information:

  • Name: SYNERGxDB_list_cell_lines

  • Type: SYNERGxDBTool

  • Description: List all cancer cell lines in the SYNERGxDB database. Returns cell line names, tissue types, disease annotations, Cellosaurus IDs, and demographic data. Contains 151 cancer cell lines. Tissue types include blood, breast, lung, colon, CNS, ovary, prostate, kidney, skin.

Parameters:

  • operation (string) (optional) Operation type

Example Usage:

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

SYNERGxDB_list_datasets (Type: SYNERGxDBTool)

List all drug combination screening datasets integrated in SYNERGxDB. Returns dataset names, numb…

SYNERGxDB_list_datasets tool specification

Tool Information:

  • Name: SYNERGxDB_list_datasets

  • Type: SYNERGxDBTool

  • Description: List all drug combination screening datasets integrated in SYNERGxDB. Returns dataset names, number of drugs, cell lines, and publication references. Key datasets: NCI-ALMANAC (101 drugs, 60 cell lines), MERCK (38 drugs, 39 cell lines), STANFORD, YALE-PDAC, YALE-TNBC, MIT-MELANOMA, CLOUD, ASTRAZENECA.

Parameters:

  • operation (string) (optional) Operation type

Example Usage:

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

SYNERGxDB_list_drugs (Type: SYNERGxDBTool)

List drugs in the SYNERGxDB database with their identifiers. Returns drug names, IDs, PubChem CID…

SYNERGxDB_list_drugs tool specification

Tool Information:

  • Name: SYNERGxDB_list_drugs

  • Type: SYNERGxDBTool

  • Description: List drugs in the SYNERGxDB database with their identifiers. Returns drug names, IDs, PubChem CIDs, DrugBank IDs, SMILES, InChIKey, and associated datasets. Contains 1977 unique compounds. Use ‘query’ or ‘name’ to filter by drug name (e.g., ‘imatinib’). Use drug IDs from this list in SYNERGxDB_search_combos queries.

Parameters:

  • operation (string) (optional) Operation type

  • query (string) (optional) Filter by drug name (case-insensitive substring match, e.g., ‘imatinib’, ‘taxol’). Alias: name.

  • name (string) (optional) Alias for query. Filter by drug name.

Example Usage:

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

SYNERGxDB_search_combos (Type: SYNERGxDBTool)

Search drug combination synergy scores in SYNERGxDB. Returns synergy metrics (Bliss, Loewe, HSA, …

SYNERGxDB_search_combos tool specification

Tool Information:

  • Name: SYNERGxDB_search_combos

  • Type: SYNERGxDBTool

  • Description: Search drug combination synergy scores in SYNERGxDB. Returns synergy metrics (Bliss, Loewe, HSA, ZIP) for drug pairs across cancer cell lines. Filter by drug IDs, cell line/tissue, and dataset. The database integrates 22,507 unique drug combinations from 9 major studies (NCI-ALMANAC, MERCK, MIT-MELANOMA, VISAGE, DECREASE, YALE-TNBC, YALE-PDAC, STANFORD, CLOUD). Positive ZIP scores indicate synergy. Use list_drugs first to find drug IDs. NOTE: SYNERGxDB covers pairwise in vitro cytotoxicity screening; standard-of-care clinical regimens (FOLFOX, FOLFIRI, CAPOX, R-CHOP) and most targeted therapies/biologics (BRAF/MEK/KRAS inhibitors, immune checkpoint inhibitors, monoclonal antibodies) are not represented.

Parameters:

  • operation (string) (optional) Operation type

  • drug_id_1 ([‘integer’, ‘null’]) (optional) SYNERGxDB drug ID for drug A. Use SYNERGxDB_list_drugs to find IDs. Examples: 11 (Bortezomib), 48 (Imatinib), 52 (Lapatinib). Alternatively, use drug_name_1 for automatic ID lookup.

  • drug_name_1 ([‘string’, ‘null’]) (optional) Drug name for drug A — triggers automatic SYNERGxDB ID lookup (e.g., ‘gemcitabine’, ‘imatinib’, ‘paclitaxel’). Aliases: drug1. Use instead of drug_id_1 when you don’t know the integer ID.

  • drug_id_2 ([‘integer’, ‘null’]) (optional) SYNERGxDB drug ID for drug B. Examples: 97 (Topotecan), 34 (Erlotinib), 24 (Dasatinib). Alternatively, use drug_name_2 for automatic ID lookup.

  • drug_name_2 ([‘string’, ‘null’]) (optional) Drug name for drug B — triggers automatic SYNERGxDB ID lookup (e.g., ‘erlotinib’, ‘topotecan’, ‘oxaliplatin’). Aliases: drug2. Use instead of drug_id_2 when you don’t know the integer ID.

  • sample ([‘string’, ‘null’]) (optional) Cell line ID (integer as string) or tissue name. Valid tissue names: ‘colorectal’ (NOT ‘colon’), ‘blood’, ‘breast’, ‘lung’, ‘ovary’, ‘skin’, ‘CNS’, ‘prostate’, ‘kidney’, ‘pancreas’, ‘gastric’, ‘melanoma’. Use SYNERGxDB_list_cell_lines to find valid values. Aliases: tissue_name, tissue. Common alias ‘colon’ is auto-mapped to ‘colorectal’.

  • dataset ([‘integer’, ‘string’, ‘null’]) (optional) Dataset source ID (integer) or name (string). Examples: 2 or ‘NCI-ALMANAC’, 1 or ‘MERCK’, 10 or ‘VISAGE’, 7 or ‘MIT-MELANOMA’. Use SYNERGxDB_list_datasets to see all available datasets and their IDs.

  • page (integer) (optional) Page number for paginated results (default: 1)

  • per_page (integer) (optional) Results per page (default: 20, max: 500)

Example Usage:

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