Kegg Network Variant Tools

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

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

Available Tools

KEGG_get_network (Type: KEGGExtTool)

Get detailed KEGG network information including signaling pathway definition (e.g., EGF -> EGFR -…

KEGG_get_network tool specification

Tool Information:

  • Name: KEGG_get_network

  • Type: KEGGExtTool

  • Description: Get detailed KEGG network information including signaling pathway definition (e.g., EGF -> EGFR -> RAS -> RAF -> MEK -> ERK), associated disease classes, linked diseases, drug targets, and pathway elements. KEGG networks model specific molecular interaction cascades perturbed in disease. Example: N00001 returns EGF-EGFR-RAS-ERK signaling pathway linked to colorectal cancer, melanoma, breast cancer, and 7+ other cancer types.

Parameters:

  • network_id (string) (required) KEGG network ID in N##### format (e.g., ‘N00001’ for EGF-EGFR-RAS-ERK, ‘N00010’ for WNT signaling).

Example Usage:

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

KEGG_get_variant (Type: KEGGExtTool)

Get detailed KEGG variant information including gene name, mutation type (gain/loss of function),…

KEGG_get_variant tool specification

Tool Information:

  • Name: KEGG_get_variant

  • Type: KEGGExtTool

  • Description: Get detailed KEGG variant information including gene name, mutation type (gain/loss of function), specific mutations with ClinVar/dbSNP/COSMIC cross-references, associated signaling networks, diseases, and targeted drugs. Example: hsa_var:673v1 (BRAF) returns V600E and V600K mutations with ClinVar:13961, dbSNP:rs113488022, COSM:476, linked to melanoma and thyroid cancer, targeted by dabrafenib and encorafenib.

Parameters:

  • variant_id (string) (required) KEGG variant ID. Can be with prefix ‘hsa_var:673v1’ or without ‘673v1’. Get IDs from KEGG_search_variant. Format: {entrez_gene_id}v{variant_number}.

Example Usage:

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

KEGG_search_network (Type: KEGGExtTool)

Search the KEGG NETWORK database for signaling pathway networks by gene or keyword. KEGG NETWORK …

KEGG_search_network tool specification

Tool Information:

  • Name: KEGG_search_network

  • Type: KEGGExtTool

  • Description: Search the KEGG NETWORK database for signaling pathway networks by gene or keyword. KEGG NETWORK contains 800+ disease/drug-associated molecular interaction networks representing signal transduction pathways perturbed in cancer, infection, and other diseases. Returns network IDs (N#####) and pathway names. Example: searching ‘EGFR’ returns N00001 EGF-EGFR-RAS-ERK signaling pathway, N00006 Amplified EGFR, etc.

Parameters:

  • keyword (string) (required) Search keyword for network/pathway name or gene (e.g., ‘EGFR’, ‘RAS’, ‘p53’, ‘WNT’, ‘NOTCH’). Case-insensitive.

  • max_results (integer) (optional) Maximum number of results (default: 25).

Example Usage:

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

KEGG_search_variant (Type: KEGGExtTool)

Search the KEGG VARIANT database for human gene variants associated with disease. KEGG VARIANT ca…

KEGG_search_variant tool specification

Tool Information:

  • Name: KEGG_search_variant

  • Type: KEGGExtTool

  • Description: Search the KEGG VARIANT database for human gene variants associated with disease. KEGG VARIANT catalogs gain-of-function mutations, loss-of-function mutations, and other variants in human genes linked to cancer and other diseases. Returns variant IDs and descriptions. Example: searching ‘BRAF’ returns 673v1 (BRAF mutation) and 673v2 (BRAF mutation). Use KEGG_get_variant for mutation details, ClinVar/dbSNP cross-references, and associated diseases/drugs.

Parameters:

  • keyword (string) (required) Gene name to search (e.g., ‘BRAF’, ‘TP53’, ‘EGFR’, ‘KRAS’, ‘PIK3CA’). Case-insensitive.

  • max_results (integer) (optional) Maximum number of results (default: 25).

Example Usage:

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