Kegg Brite Tools

Configuration File: kegg_brite_tools.json Tool Type: Local Tools Count: 2

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

Available Tools

KEGG_get_brite_hierarchy (Type: KEGGExtTool)

Get the full hierarchical classification tree for a specific KEGG BRITE hierarchy in JSON format….

KEGG_get_brite_hierarchy tool specification

Tool Information:

  • Name: KEGG_get_brite_hierarchy

  • Type: KEGGExtTool

  • Description: Get the full hierarchical classification tree for a specific KEGG BRITE hierarchy in JSON format. Returns a nested tree structure where each node has a ‘name’ field and optionally a ‘children’ array of sub-nodes. This is extremely useful for functional classification of genes, proteins, enzymes, transporters, receptors, etc. Common hierarchies: ‘ko01000’ (Enzymes by EC number), ‘ko01001’ (Protein kinases), ‘ko01002’ (Peptidases and inhibitors), ‘ko02000’ (Transporters), ‘ko03000’ (Transcription factors), ‘ko04030’ (GPCRs), ‘ko04040’ (Ion channels), ‘ko04050’ (Cytokine receptors), ‘ko04090’ (CD molecules), ‘ko01504’ (Antimicrobial resistance genes), ‘ko03200’ (Viral proteins). The tree can be very large (e.g., ko00001 has thousands of entries).

Parameters:

  • hierarchy_id (string) (required) KEGG BRITE hierarchy ID. Examples: ‘ko01000’ (Enzymes), ‘ko01001’ (Protein kinases), ‘ko02000’ (Transporters), ‘ko03000’ (Transcription factors), ‘ko04030’ (GPCRs), ‘ko04040’ (Ion channels). Use KEGG_list_brite_hierarchies to see all available IDs.

Example Usage:

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

KEGG_list_brite_hierarchies (Type: KEGGExtTool)

List all available KEGG BRITE hierarchy classification files. KEGG BRITE is a collection of hiera…

KEGG_list_brite_hierarchies tool specification

Tool Information:

  • Name: KEGG_list_brite_hierarchies

  • Type: KEGGExtTool

  • Description: List all available KEGG BRITE hierarchy classification files. KEGG BRITE is a collection of hierarchical text (htext) files capturing functional hierarchies of various biological objects, especially those represented as KEGG objects. Returns hierarchy IDs and names including: ko00001 (KEGG Orthology), ko01000 (Enzymes), ko01001 (Protein kinases), ko01002 (Peptidases and inhibitors), ko02000 (Transporters), ko03000 (Transcription factors), ko04030 (G protein-coupled receptors), ko04040 (Ion channels), ko04050 (Cytokine receptors), ko04090 (CD molecules), br08001 (Compounds with biological roles), br08901 (KEGG pathway maps), and many more. Use the hierarchy ID with KEGG_get_brite_hierarchy to retrieve the full classification tree.

Parameters:

No parameters required.

Example Usage:

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