Sabiork Tools#

Configuration File: sabiork_tools.json Tool Type: Local Tools Count: 1

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

Available Tools#

SABIO_RK_search_reactions (Type: SABIORKTool)#

Search SABIO-RK for biochemical reaction kinetic laws. Returns exact total and offset pagination …

SABIO_RK_search_reactions tool specification

Tool Information:

  • Name: SABIO_RK_search_reactions

  • Type: SABIORKTool

  • Description: Search SABIO-RK for biochemical reaction kinetic laws. Returns exact total and offset pagination plus complete per-entry source JSON, kinetic parameter values and normalized units, experimental conditions, enzyme metadata, and publication evidence. Search by EC number, enzyme, substrate, organism, product, or parameter type. Use offset/next_offset to retrieve all results rather than silently stopping at the first page.

Parameters:

  • operation (string) (optional) Operation type (fixed: search_reactions)

  • ec_number (string) (optional) EC number (e.g., 1.1.1.1 for alcohol dehydrogenase, 2.7.1.1 for hexokinase)

  • enzyme_name (string) (optional) Enzyme common name (e.g., alcohol dehydrogenase, hexokinase, lactate dehydrogenase)

  • substrate (string) (optional) Substrate name (e.g., ethanol, glucose, ATP)

  • organism (string) (optional) Organism name (e.g., Homo sapiens, Escherichia coli, Saccharomyces cerevisiae)

  • product (string) (optional) Product name (e.g., acetaldehyde, pyruvate)

  • parameter_type (string) (optional) Filter by kinetic parameter type (e.g., Km, kcat, Vmax, Ki)

  • limit (integer) (optional) Maximum number of kinetic laws to return (default 20, max 100)

  • offset (integer) (optional) Zero-based result offset (default 0). When has_more is true, pass next_offset to retrieve the next disjoint page.

Example Usage:

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